diff --git a/README.md b/README.md
index 763b337046f7587faa334d723e749ca43420532e..64a1c16ba3f21e5348be4f4c1c4556f159a8f19b 100755
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-Převod html dokumentace do md formátu (version 0.51) - BETA
+Převod html dokumentace do md formátu (version 0.52) - BETA
===========================================================
VĂ˝sledkem projektu by mÄ›l bĂ˝t skript pro staĹľenĂ a pĹ™evod stávajĂcĂ dokumentace na docs.it4i.cz do md formátu
@@ -28,8 +28,7 @@ Pro svou práci si naklonujete Gitem repozitář do svĂ©ho pracovnĂho adresář
|0.45|7m56s|optimalizace|
|0.47|11m7s|přidánà filtrů pro opravu a nahrazenà tabulek, vylepšenà filtrace, ...|
|0.51|16m37s|export do pdf, export do epub, filtry, ...|
-
-
+|0.52|16m37s|oprava exportu do pdf, nový filtr pro poslednà opravu formátovánà a chyb, ...|
>**Problémy**
> * internĂ a externĂ odkazy
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.epub
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md
index aa9b5ccae231a958aa72b62a3140d6b1fb5dcd17..f43ed041f1efad27eea824b186d9e3f200856675 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md
@@ -9,12 +9,12 @@ Connection restrictions
Outgoing connections, from Anselm Cluster login nodes to the outside
world, are restricted to following ports:
- Port Protocol
- ------ ----------
- 22 ssh
- 80 http
- 443 https
- 9418 git
+ |Port|Protocol|
+ |---|---|
+ |22|ssh|
+ |80|http|
+ |443|https|
+ |9418|git|
Please use **ssh port forwarding** and proxy servers to connect from
Anselm to all other remote ports.
@@ -37,9 +37,9 @@ workstation and forwarding from the workstation to the remote host.
Pick some unused port on Anselm login node (for example 6000) and
establish the port forwarding:
-```
+`
local $ ssh -R 6000:remote.host.com:1234 anselm.it4i.cz
-```
+`
In this example, we establish port forwarding between port 6000 on
Anselm and port 1234 on the remote.host.com. By accessing
@@ -55,9 +55,9 @@ remote.host.com:1234. Click Add button, then Open.
Port forwarding may be established directly to the remote host. However,
this requires that user has ssh access to remote.host.com
-```
+`
$ ssh -L 6000:localhost:1234 remote.host.com
-```
+`
Note: Port number 6000 is chosen as an example only. Pick any free port.
@@ -73,9 +73,9 @@ above](outgoing-connections.html#port-forwarding-from-login-nodes).
Second, invoke port forwarding from the compute node to the login node.
Insert following line into your jobscript or interactive shell
-```
+`
$ ssh -TN -f -L 6000:localhost:6000 login1
-```
+`
In this example, we assume that port forwarding from login1:6000 to
remote.host.com:1234 has been established beforehand. By accessing
@@ -96,9 +96,9 @@ SOCKS proxy server software. On Linux, sshd demon provides the
functionality. To establish SOCKS proxy server listening on port 1080
run:
-```
+`
local $ ssh -D 1080 localhost
-```
+`
On Windows, install and run the free, open source [Sock
Puppet](http://sockspuppet.com/) server.
@@ -107,9 +107,9 @@ Once the proxy server is running, establish ssh port forwarding from
Anselm to the proxy server, port 1080, exactly as [described
above](outgoing-connections.html#port-forwarding-from-login-nodes).
-```
+`
local $ ssh -R 6000:localhost:1080 anselm.it4i.cz
-```
+`
Now, configure the applications proxy settings to **localhost:6000**.
Use port forwarding to access the [proxy server from compute
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.epub
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
index 54153190f57c7671d3ff56670844550dcd615e8a..7fb3a55a6994bc2a357e6d8f214af6f426c5ae25 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
@@ -10,11 +10,11 @@ The Anselm cluster is accessed by SSH protocol via login nodes login1
and login2 at address anselm.it4i.cz. The login nodes may be addressed
specifically, by prepending the login node name to the address.
- Login address Port Protocol Login node
- ----------------------- ------ ---------- ----------------------------------------------
- anselm.it4i.cz 22 ssh round-robin DNS record for login1 and login2
- login1.anselm.it4i.cz 22 ssh login1
- login2.anselm.it4i.cz 22 ssh login2
+ Login address |Port|Protocol| Login node
+ ----------------------- |---|---| ----------------------------------------------
+ anselm.it4i.cz |22|ssh| round-robin DNS record for login1 and login2
+ login1.anselm.it4i.cz |22|ssh| login1
+ login2.anselm.it4i.cz |22|ssh| login2
The authentication is by the [private
key](../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
@@ -26,20 +26,20 @@ d4:6f:5c:18:f4:3f:70:ef:bc:fc:cc:2b:fd:13:36:b7Â (RSA)
Â
-Private keys authentication:
+Private key (`id_rsa/id_rsa.ppk` ): `600 (-rw-------)`s authentication:
On **Linux** or **Mac**, use
-```
+`
local $ ssh -i /path/to/id_rsa username@anselm.it4i.cz
-```
+`
If you see warning message "UNPROTECTED PRIVATE KEY FILE!", use this
command to set lower permissions to private key file.
-```
+`
local $ chmod 600 /path/to/id_rsa
-```
+`
On **Windows**, use [PuTTY ssh
client](../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html).
@@ -66,22 +66,22 @@ Data Transfer
Data in and out of the system may be transferred by the
[scp](http://en.wikipedia.org/wiki/Secure_copy) and sftp
-protocols. class="discreet">(Not available yet.) In case large
+protocols. (Not available yet.) In case large
volumes of data are transferred, use dedicated data mover node
dm1.anselm.it4i.cz for increased performance.
- Address Port Protocol
- -------------------------------------------------- ---------------------------------- -----------------------------------------
- anselm.it4i.cz 22 scp, sftp
- login1.anselm.it4i.cz 22 scp, sftp
- login2.anselm.it4i.cz 22 scp, sftp
- class="discreet">dm1.anselm.it4i.cz 22 class="discreet">scp, sftp</span>
+ |Address|Port|Protocol|
+ -------------------- |---|---|- -----------------------------------------
+ |anselm.it4i.cz|22|scp, sftp|
+ |login1.anselm.it4i.cz|22|scp, sftp|
+ |login2.anselm.it4i.cz|22|scp, sftp|
+ |dm1.anselm.it4i.cz|22|scp, sftp|
 The authentication is by the [private
key](../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
Data transfer rates up to **160MB/s** can be achieved with scp or sftp.
-1TB may be transferred in 1:50h.
+ may be transferred in 1:50h.
To achieve 160MB/s transfer rates, the end user must be connected by 10G
line all the way to IT4Innovations and use computer with fast processor
@@ -93,38 +93,38 @@ network provider.
On linux or Mac, use scp or sftp client to transfer the data to Anselm:
-```
+`
local $ scp -i /path/to/id_rsa my-local-file username@anselm.it4i.cz:directory/file
-```
+`
-```
+`
local $ scp -i /path/to/id_rsa -r my-local-dir username@anselm.it4i.cz:directory
-```
+`
-> or
+ or
-```
+`
local $ sftp -o IdentityFile=/path/to/id_rsa username@anselm.it4i.cz
-```
+`
Very convenient way to transfer files in and out of the Anselm computer
is via the fuse filesystem
[sshfs](http://linux.die.net/man/1/sshfs)
-```
+`
local $ sshfs -o IdentityFile=/path/to/id_rsa username@anselm.it4i.cz:. mountpoint
-```
+`
Using sshfs, the users Anselm home directory will be mounted on your
local computer, just like an external disk.
Learn more on ssh, scp and sshfs by reading the manpages
-```
+`
$ man ssh
$ man scp
$ man sshfs
-```
+`
On Windows, use [WinSCP
client](http://winscp.net/eng/download.php) to transfer
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md
index c9658ea20320bea1399068cb30bd80c23baaec26..2b4f237033d2eb02b9e8a405fc8d8a7f71831c14 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md
@@ -6,7 +6,7 @@ VPN Access
Accessing IT4Innovations internal resources via VPN
---------------------------------------------------
-Failed to initialize connection subsystem Win 8.1 - 02-10-15 MS
+**Failed to initialize connection subsystem Win 8.1 - 02-10-15 MS
patch**
Workaround can be found at
[https://docs.it4i.cz/vpn-connection-fail-in-win-8.1](../../vpn-connection-fail-in-win-8.1.html)
@@ -27,7 +27,7 @@ the following operating systems:
It is impossible to connect to VPN from other operating systems.
->VPN client installation
+VPN client installation
------------------------------------
You can install VPN client from web interface after successful login
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.epub
index bb59c0b13d6af03e8b845151686fe0baa7258258..a236f7be1816a15a627c24a3876df35a3ef95dca 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.md b/converted/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.md
index 69f7661afb1b28ec75e64f6b7a2b811ca3559307..18ff5199a3a32582e6c25ce3acac1eae7d303e31 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.md
@@ -245,9 +245,9 @@ Nodes equipped with Intel Xeon E5-2665 CPU have set PBS resource
attribute cpu_freq = 24, nodes equipped with Intel Xeon E5-2470 CPU
have set PBS resource attribute cpu_freq = 23.
-```
+`
$ qsub -A OPEN-0-0 -q qprod -l select=4:ncpus=16:cpu_freq=24 -I
-```
+`
In this example, we allocate 4 nodes, 16 cores at 2.4GHhz per node.
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.md b/converted/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.md
index 552b4504dd5266be1556fb2164e25c8ef0ca66a8..80ac34c467c727502fa3aff1eadafcf0098ee80b 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.md
@@ -9,7 +9,7 @@ After logging in, you may want to configure the environment. Write your
preferred path definitions, aliases, functions and module loads in the
.bashrc file
-```
+`
# ./bashrc
# Source global definitions
@@ -26,13 +26,13 @@ if [ -n "$SSH_TTY" ]
then
module list # Display loaded modules
fi
-```
+`
Do not run commands outputing to standard output (echo, module list,
etc) in .bashrc for non-interactive SSH sessions. It breaks fundamental
functionality (scp, PBS) of your account! Take care for SSH session
-interactivity for such commands as id="result_box"
- class="hps alt-edited">stated
+interactivity for such commands as
+ stated in the previous example.
in the previous example.
### Application Modules
@@ -55,36 +55,36 @@ needs.
To check available modules use
-```
+`
$ module avail
-```
+`
To load a module, for example the octave module use
-```
+`
$ module load octave
-```
+`
loading the octave module will set up paths and environment variables of
your active shell such that you are ready to run the octave software
To check loaded modules use
-```
+`
$ module list
-```
+`
 To unload a module, for example the octave module use
-```
+`
$ module unload octave
-```
+`
Learn more on modules by reading the module man page
-```
+`
$ man module
-```
+`
Following modules set up the development environment
@@ -103,9 +103,9 @@ In case that you want to use some applications that are build by
EasyBuild already, you have to modify your MODULEPATH environment
variable.
-```
+`
export MODULEPATH=$MODULEPATH:/apps/easybuild/modules/all/
-```
+`
This command expands your searched paths to modules. You can also add
this command to the .bashrc file to expand paths permanently. After this
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.pdf
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index 4a09c7799b99a49095fc1977ce6c01cd9184a8d5..e70624ac373dd777964cb9144416af656f6bd55a 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/hardware-overview.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/hardware-overview.md
@@ -35,10 +35,10 @@ Management infrastructure
Rack 01, Switch isw5
- -------------- -------------- -------------- -------------- --------------
+ -------- |---|---|---- -------------- -------------- --------------
cn186 cn187 cn188 cn189
cn181 cn182 cn183 cn184 cn185
- -------------- -------------- -------------- -------------- --------------
+ -------- |---|---|---- -------------- -------------- --------------
Rack 01, Switch isw4
@@ -269,10 +269,10 @@ cn135
cn136
Rack 05, Switch isw21
- -------------- -------------- -------------- -------------- --------------
+ -------- |---|---|---- -------------- -------------- --------------
cn201 cn202 cn203 cn204
cn196 cn197 cn198 cn199 cn200
- -------------- -------------- -------------- -------------- --------------
+ -------- |---|---|---- -------------- -------------- --------------
----------------
Fat node cn208
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index bc1478be186b8a99c6919f4deb03c67c87678884..b897039fe15a2ddc1374459f610af810a773f42a 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/network.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/network.md
@@ -40,18 +40,18 @@ The network provides **114MB/s** transfer rates via the TCP connection.
Example
-------
-```
+`
$ qsub -q qexp -l select=4:ncpus=16 -N Name0 ./myjob
$ qstat -n -u username
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
---------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
+--------------- -------- -- |---|---| ------ --- --- ------ ----- - -----
15209.srv11 username qexp Name0 5530 4 64 -- 01:00 R 00:00
cn17/0*16+cn108/0*16+cn109/0*16+cn110/0*16
$ ssh 10.2.1.110
$ ssh 10.1.1.108
-```
+`
In this example, we access the node cn110 by Infiniband network via the
ib0 interface, then from cn110 to cn108 by Ethernet network.
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/network.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/network.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/prace.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/prace.epub
index aecc78c317970d83a38fd86c5e91145429b2b0b7..32aca172b1417a01a47d16c43c221fcc51fb5d45 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/prace.md b/converted/docs.it4i.cz/anselm-cluster-documentation/prace.md
index 6d73d1df1e8648f90931510304af893ae598fef9..9d29c080f0a885c9022254e5024020f52f0304ba 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/prace.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/prace.md
@@ -97,15 +97,15 @@ To access Anselm cluster, two login nodes running GSI SSH service are
available. The service is available from public Internet as well as from
the internal PRACE network (accessible only from other PRACE partners).
-Access from PRACE network:**
+***Access from PRACE network:**
It is recommended to use the single DNS name
anselm-prace.it4i.cz which is distributed
between the two login nodes. If needed, user can login directly to one
of the login nodes. The addresses are:
- Login address Port Protocol Login node
- ----------------------------- ------ ---------- ------------------
+ Login address |Port|Protocol| Login node
+ ----------------------------- |---|---| ------------------
anselm-prace.it4i.cz 2222 gsissh login1 or login2
login1-prace.anselm.it4i.cz 2222 gsissh login1
login2-prace.anselm.it4i.cz 2222 gsissh login2
@@ -121,15 +121,15 @@ used:
Â
-Access from public Internet:**
+***Access from public Internet:**
It is recommended to use the single DNS name
anselm.it4i.cz which is distributed between the
two login nodes. If needed, user can login directly to one of the login
nodes. The addresses are:
- Login address Port Protocol Login node
- ----------------------- ------ ---------- ------------------
+ Login address |Port|Protocol| Login node
+ ----------------------- |---|---| ------------------
anselm.it4i.cz 2222 gsissh login1 or login2
login1.anselm.it4i.cz 2222 gsissh login1
login2.anselm.it4i.cz 2222 gsissh login2
@@ -196,10 +196,10 @@ PRACE partners).
There's one control server and three backend servers for striping and/or
backup in case one of them would fail.
-Access from PRACE network:**
+***Access from PRACE network:**
Login address Port Node role
- ------------------------------ ------ -----------------------------
+ ----- |---|---|
gridftp-prace.anselm.it4i.cz 2812 Front end /control server
login1-prace.anselm.it4i.cz 2813 Backend / data mover server
login2-prace.anselm.it4i.cz 2813 Backend / data mover server
@@ -224,10 +224,10 @@ Or by using prace_service script:
Â
-Access from public Internet:**
+***Access from public Internet:**
Login address Port Node role
- ------------------------ ------ -----------------------------
+ ------------------------ |---|---|-------------------
gridftp.anselm.it4i.cz 2812 Front end /control server
login1.anselm.it4i.cz 2813 Backend / data mover server
login2.anselm.it4i.cz 2813 Backend / data mover server
@@ -254,10 +254,10 @@ Or by using prace_service script:
Generally both shared file systems are available through GridFTP:
- File system mount point Filesystem Comment
- ------------------------- ------------ ----------------------------------------------------------------
- /home Lustre Default HOME directories of users in format /home/prace/login/
- /scratch Lustre Shared SCRATCH mounted on the whole cluster
+ |File system mount point|Filesystem|Comment|
+ |---|---|
+ |/home|Lustre|Default HOME directories of users in format /home/prace/login/|
+ |/scratch|Lustre|Shared SCRATCH mounted on the whole cluster|
More information about the shared file systems is available
[here](storage.html).
@@ -303,20 +303,20 @@ users can also use two other queues "qexp" and "qfree".
-------------------------------------------------------------------------------------------------------------------------
queue Active project Project resources Nodes priority authorization walltime
- default/max
- --------------------- -|---|---|---|- ---------- --------------- -------------
+
+ --------------------- -|---|---|---|- ---- |---|---|----- -------------
**qexp** no none required 2 reserved, high no 1 / 1h
- Express queue 8 total
+ \ 8 total
- **qprace** yes > 0 178 w/o accelerator medium no 24 / 48h
- Production queue
+ gt; 0 >1006 nodes, max 86 per job 0 no 24 / 48h> 0 178 w/o accelerator medium no 24 / 48h
+ \
**qfree** yes none required 178 w/o accelerator very low no 12 / 12h
- Free resource queue
+ \
-------------------------------------------------------------------------------------------------------------------------
-qprace**, the PRACE Production queue****: This queue is intended for
+qprace**, the PRACE \***: This queue is intended for
normal production runs. It is required that active project with nonzero
remaining resources is specified to enter the qprace. The queue runs
with medium priority and no special authorization is required to use it.
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/prace.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/prace.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.epub
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md b/converted/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md
index 9c992325d431d7bf5774b50a5db61889eee8e142..e0c1e9600beca6a880c140b4c4193607c3b04f74 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md
@@ -67,7 +67,7 @@ Otherwise only the geometry (desktop size) definition is needed.
This example defines desktop with dimensions 1200x700 pixels and 24 bit
color depth.
-```
+`
$ module load turbovnc/1.2.2
$ vncserver -geometry 1200x700 -depth 24
@@ -75,27 +75,27 @@ Desktop 'TurboVNC: login2:1 (username)' started on display login2:1
Starting applications specified in /home/username/.vnc/xstartup.turbovnc
Log file is /home/username/.vnc/login2:1.log
-```
+`
#### 3. Remember which display number your VNC server runs (you will need it in the future to stop the server). {#3-remember-which-display-number-your-vnc-server-runs-you-will-need-it-in-the-future-to-stop-the-server}
-```
+`
$ vncserver -list
TurboVNC server sessions:
X DISPLAY # PROCESS ID
:1 23269
-```
+`
In this example the VNC server runs on display **:1**.
#### 4. Remember the exact login node, where your VNC server runs. {#4-remember-the-exact-login-node-where-your-vnc-server-runs}
-```
+`
$ uname -n
login2
-```
+`
In this example the VNC server runs on **login2**.
@@ -103,10 +103,10 @@ In this example the VNC server runs on **login2**.
To get the port you have to look to the log file of your VNC server.
-```
+`
$ grep -E "VNC.*port" /home/username/.vnc/login2:1.log
20/02/2015 14:46:41 Listening for VNC connections on TCP port 5901
-```
+`
In this example the VNC server listens on TCP port **5901**.
@@ -114,9 +114,9 @@ In this example the VNC server listens on TCP port **5901**.
Tunnel the TCP port on which your VNC server is listenning.
-```
+`
$ ssh login2.anselm.it4i.cz -L 5901:localhost:5901
-```
+`
*If you use Windows and Putty, please refer to port forwarding setup
in the documentation:*
@@ -131,9 +131,9 @@ Get it from: <http://sourceforge.net/projects/turbovnc/>
Mind that you should connect through the SSH tunneled port. In this
example it is 5901 on your workstation (localhost).
-```
+`
$ vncviewer localhost:5901
-```
+`
*If you use Windows version of TurboVNC Viewer, just run the Viewer and
use address **localhost:5901**.*
@@ -148,9 +148,9 @@ workstation.*
*Don't forget to correctly shutdown your own VNC server on the login
node!*
-```
+`
$ vncserver -kill :1
-```
+`
Access the visualization node
-----------------------------
@@ -158,15 +158,7 @@ Access the visualization node
To access the node use a dedicated PBS Professional scheduler queue
qviz**. The queue has following properties:
-<col width="12%" />
-<col width="12%" />
-<col width="12%" />
-<col width="12%" />
-<col width="12%" />
-<col width="12%" />
-<col width="12%" />
-<col width="12%" />
- |queue |active project |project resources<th align="left">nodes<th align="left">min ncpus*<th align="left">priority<th align="left">authorization<th align="left">walltimedefault/max |
+ |queue |active project |project resources |nodes<th align="left">min ncpus*<th align="left">priority<th align="left">authorization<th align="left">walltime |
| --- | --- |
|<strong>qviz              </strong> Visualization queue\ |yes |none required |2 |4 |><em>150</em> |no |1 hour / 2 hours |
@@ -184,16 +176,16 @@ To access the visualization node, follow these steps:
*This step is necessary to allow you to proceed with next steps.*
-```
+`
$ qsub -I -q qviz -A PROJECT_ID
-```
+`
In this example the default values for CPU cores and usage time are
used.
-```
+`
$ qsub -I -q qviz -A PROJECT_ID -l select=1:ncpus=16 -l walltime=02:00:00
-```
+`
*Substitute **PROJECT_ID** with the assigned project identification
string.*
@@ -203,10 +195,10 @@ In this example a whole node for 2 hours is requested.
If there are free resources for your request, you will have a shell
running on an assigned node. Please remember the name of the node.
-```
+`
$ uname -n
srv8
-```
+`
In this example the visualization session was assigned to node **srv8**.
@@ -215,34 +207,34 @@ In this example the visualization session was assigned to node **srv8**.
Setup the VirtualGL connection to the node, which PBSPro allocated for
your job.
-```
+`
$ vglconnect srv8
-```
+`
You will be connected with created VirtualGL tunnel to the visualization
node, where you will have a shell.
#### 3. Load the VirtualGL module. {#3-load-the-virtualgl-module}
-```
+`
$ module load virtualgl/2.4
-```
+`
#### 4. Run your desired OpenGL accelerated application using VirtualGL script "vglrun". {#4-run-your-desired-opengl-accelerated-application-using-virtualgl-script-vglrun}
-```
+`
$ vglrun glxgears
-```
+`
Please note, that if you want to run an OpenGL application which is
available through modules, you need at first load the respective module.
E. g. to run the **Mentat** OpenGL application from **MARC** software
package use:
-```
+`
$ module load marc/2013.1
$ vglrun mentat
-```
+`
#### 5. After you end your work with the OpenGL application. {#5-after-you-end-your-work-with-the-opengl-application}
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md
index 32786d7e74cbc1a239ef90004175f15ea4290dd7..e05f7ce6eb1e7c1bf9a5d62e77271668435ea368 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md
@@ -73,13 +73,13 @@ files with program executable myprog.x, each as a separate job.
First, we create a tasklist file (or subjobs list), listing all tasks
(subjobs) - all input files in our example:
-```
+`
$ find . -name 'file*' > tasklist
-```
+`
Then we create jobscript:
-```
+`
#!/bin/bash
#PBS -A PROJECT_ID
#PBS -q qprod
@@ -100,7 +100,7 @@ cp $PBS_O_WORKDIR/$TASK input ; cp $PBS_O_WORKDIR/myprog.x .
# copy output file to submit directory
cp output $PBS_O_WORKDIR/$TASK.out
-```
+`
In this example, the submit directory holds the 900 input files,
executable myprog.x and the jobscript file. As input for each run, we
@@ -127,10 +127,10 @@ To submit the job array, use the qsub -J command. The 900 jobs of the
[example above](capacity-computing.html#array_example) may
be submitted like this:
-```
+`
$ qsub -N JOBNAME -J 1-900 jobscript
12345[].dm2
-```
+`
In this example, we submit a job array of 900 subjobs. Each subjob will
run on full node and is assumed to take less than 2 hours (please note
@@ -140,9 +140,9 @@ forget to set your valid PROJECT_ID and desired queue).
Sometimes for testing purposes, you may need to submit only one-element
array. This is not allowed by PBSPro, but there's a workaround:
-```
+`
$ qsub -N JOBNAME -J 9-10:2 jobscript
-```
+`
This will only choose the lower index (9 in this example) for
submitting/running your job.
@@ -151,27 +151,27 @@ submitting/running your job.
Check status of the job array by the qstat command.
-```
+`
$ qstat -a 12345[].dm2
dm2:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
---------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
+--------------- -------- -- |---|---| ------ --- --- ------ ----- - -----
12345[].dm2 user2 qprod xx 13516 1 16 -- 00:50 B 00:02
-```
+`
The status B means that some subjobs are already running.
Check status of the first 100 subjobs by the qstat command.
-```
+`
$ qstat -a 12345[1-100].dm2
dm2:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
---------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
+--------------- -------- -- |---|---| ------ --- --- ------ ----- - -----
12345[1].dm2 user2 qprod xx 13516 1 16 -- 00:50 R 00:02
12345[2].dm2 user2 qprod xx 13516 1 16 -- 00:50 R 00:02
12345[3].dm2 user2 qprod xx 13516 1 16 -- 00:50 R 00:01
@@ -179,28 +179,28 @@ Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
. . . . . . . . . . .
, . . . . . . . . . .
12345[100].dm2 user2 qprod xx 13516 1 16 -- 00:50 Q --
-```
+`
Delete the entire job array. Running subjobs will be killed, queueing
subjobs will be deleted.
-```
+`
$ qdel 12345[].dm2
-```
+`
Deleting large job arrays may take a while.
Display status information for all user's jobs, job arrays, and subjobs.
-```
+`
$ qstat -u $USER -t
-```
+`
Display status information for all user's subjobs.
-```
+`
$ qstat -u $USER -tJ
-```
+`
Read more on job arrays in the [PBSPro Users
guide](../../pbspro-documentation.html).
@@ -217,10 +217,10 @@ useful in running single core jobs via the queue system on Anselm.
For more information and examples see the parallel man page:
-```
+`
$ module add parallel
$ man parallel
-```
+`
### GNU parallel jobscript
@@ -238,13 +238,13 @@ job. We call these single core jobs tasks.
First, we create a tasklist file, listing all tasks - all input files in
our example:
-```
+`
$ find . -name 'file*' > tasklist
-```
+`
Then we create jobscript:
-```
+`
#!/bin/bash
#PBS -A PROJECT_ID
#PBS -q qprod
@@ -268,7 +268,7 @@ cat input > output
# copy output file to submit directory
cp output $PBS_O_WORKDIR/$TASK.out
-```
+`
In this example, tasks from tasklist are executed via the GNU
parallel. The jobscript executes multiple instances of itself in
@@ -286,10 +286,10 @@ To submit the job, use the qsub command. The 101 tasks' job of the
[example above](capacity-computing.html#gp_example) may be
submitted like this:
-```
+`
$ qsub -N JOBNAME jobscript
12345.dm2
-```
+`
In this example, we submit a job of 101 tasks. 16 input files will be
processed in parallel. The 101 tasks on 16 cores are assumed to
@@ -330,20 +330,20 @@ job. We call these single core jobs tasks.
First, we create a tasklist file, listing all tasks - all input files in
our example:
-```
+`
$ find . -name 'file*' > tasklist
-```
+`
Next we create a file, controlling how many tasks will be executed in
one subjob
-```
+`
$ seq 32 > numtasks
-```
+`
Then we create jobscript:
-```
+`
#!/bin/bash
#PBS -A PROJECT_ID
#PBS -q qprod
@@ -369,7 +369,7 @@ cat input > output
# copy output file to submit directory
cp output $PBS_O_WORKDIR/$TASK.out
-```
+`
In this example, the jobscript executes in multiple instances in
parallel, on all cores of a computing node. Variable $TASK expands to
@@ -398,10 +398,10 @@ the [example
above](capacity-computing.html#combined_example) may be
submitted like this:
-```
+`
$ qsub -N JOBNAME -J 1-992:32 jobscript
12345[].dm2
-```
+`
In this example, we submit a job array of 31 subjobs. Note the -J
1-992:**32**, this must be the same as the number sent to numtasks file.
@@ -424,10 +424,10 @@ production jobs.
Unzip the archive in an empty directory on Anselm and follow the
instructions in the README file
-```
+`
$ unzip capacity.zip
$ cat README
-```
+`
Â
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.md b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.md
index dcd7d9c93cf7eb47eb0d5ad34f2ca849ca4c8b2e..e42b4037ca0dbbcb978d985a69a1548c71ef1fdc 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.md
@@ -25,8 +25,8 @@ queueing the jobs. The queues provide prioritized and exclusive access
to the computational resources. Following queues are available to Anselm
users:
-- **qexp**, the Express queue
-- **qprod**, the Production queue****
+- **qexp**, the \
+- **qprod**, the \***
- **qlong**, the Long queue, regula
- **qnvidia, qmic, qfat**, the Dedicated queues
- **qfree,** the Free resource utilization queue
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.epub
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md
index 3af84893fd6ec4b9ecea190f2974a9c9128eecb4..2ef433187bd002e6ac28e8f8303c4864bc76602b 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md
@@ -48,25 +48,24 @@ Usage counts allocated corehours (ncpus*walltime). Usage is decayed, or
cut in half periodically, at the interval 168 hours (one week).
Jobs queued in queue qexp are not calculated to project's usage.
->Calculated usage and fairshare priority can be seen at
+Calculated usage and fairshare priority can be seen at
<https://extranet.it4i.cz/anselm/projects>.
->
->Calculated fairshare priority can be also seen as
+Calculated fairshare priority can be also seen as
Resource_List.fairshare attribute of a job.
-### >Eligible time
+###Eligible time
Eligible time is amount (in seconds) of eligible time job accrued while
waiting to run. Jobs with higher eligible time gains higher
-pri>>ority.
+priority.
Eligible time has the least impact on execution priority. Eligible time
is used for sorting jobs with equal queue priority and fairshare
priority. It is very, very difficult for >eligible time to
compete with fairshare priority.
->>Eligible time can be seen as eligible_time attribute of
+Eligible time can be seen as eligible_time attribute of
job.
### Formula
@@ -77,7 +76,7 @@ Job execution priority (job sort formula) is calculated as:
### Job backfilling
->Anselm cluster uses job backfilling.
+Anselm cluster uses job backfilling.
Backfilling means fitting smaller jobs around the higher-priority jobs
that the scheduler is going to run next, in such a way that the
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.pdf
index ad5a6adcd0e14ebaa965f0a39f1bff4b5f3135a2..f462f2397e70ae234b3cbba1ee952648d140f983 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.epub
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md
index 638d6eed264a7fd758f9733c62366694578525f8..599e0563344a9a675daae7c8adaa83a8956aabf9 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md
@@ -21,9 +21,9 @@ the computational resources.
Submit the job using the qsub command:
-```
+`
$ qsub -A Project_ID -q queue -l select=x:ncpus=y,walltime=[[hh:]mm:]ss[.ms] jobscript
-```
+`
The qsub submits the job into the queue, in another words the qsub
command creates a request to the PBS Job manager for allocation of
@@ -34,9 +34,9 @@ on first of the allocated nodes.**
### Job Submission Examples
-```
+`
$ qsub -A OPEN-0-0 -q qprod -l select=64:ncpus=16,walltime=03:00:00 ./myjob
-```
+`
In this example, we allocate 64 nodes, 16 cores per node, for 3 hours.
We allocate these resources via the qprod queue, consumed resources will
@@ -45,9 +45,9 @@ myjob will be executed on the first node in the allocation.
Â
-```
+`
$ qsub -q qexp -l select=4:ncpus=16 -I
-```
+`
In this example, we allocate 4 nodes, 16 cores per node, for 1 hour. We
allocate these resources via the qexp queue. The resources will be
@@ -55,9 +55,9 @@ available interactively
Â
-```
+`
$ qsub -A OPEN-0-0 -q qnvidia -l select=10:ncpus=16 ./myjob
-```
+`
In this example, we allocate 10 nvidia accelerated nodes, 16 cores per
node, for 24 hours. We allocate these resources via the qnvidia queue.
@@ -65,9 +65,9 @@ Jobscript myjob will be executed on the first node in the allocation.
Â
-```
+`
$ qsub -A OPEN-0-0 -q qfree -l select=10:ncpus=16 ./myjob
-```
+`
In this example, we allocate 10Â nodes, 16 cores per node, for 12 hours.
We allocate these resources via the qfree queue. It is not required that
@@ -81,18 +81,18 @@ All qsub options may be [saved directly into the
jobscript](job-submission-and-execution.html#PBSsaved). In
such a case, no options to qsub are needed.
-```
+`
$ qsub ./myjob
-```
+`
Â
By default, the PBS batch system sends an e-mail only when the job is
aborted. Disabling mail events completely can be done like this:
-```
+`
$ qsub -m n
-```
+`
Advanced job placement
----------------------
@@ -101,9 +101,9 @@ Advanced job placement
Specific nodes may be allocated via the PBS
-```
+`
qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=16:host=cn171+1:ncpus=16:host=cn172 -I
-```
+`
In this example, we allocate nodes cn171 and cn172, all 16 cores per
node, for 24 hours. Consumed resources will be accounted to the Project
@@ -119,15 +119,15 @@ via the PBS resource attribute
cpu_freq .
CPU Type base freq. Nodes cpu_freq attribute
- -------------------- ------------ ---------------------------- ---------------------
+ -------------- |---|---|-- ---------------------------- ---------------------
Intel Xeon E5-2665 2.4GHz cn[1-180], cn[208-209] 24
Intel Xeon E5-2470 2.3GHz cn[181-207] 23
Â
-```
+`
$ qsub -A OPEN-0-0 -q qprod -l select=4:ncpus=16:cpu_freq=24 -I
-```
+`
In this example, we allocate 4 nodes, 16 cores, selecting only the nodes
with Intel Xeon E5-2665 CPU.
@@ -198,26 +198,26 @@ Job Management
Check status of your jobs using the **qstat** and **check-pbs-jobs**
commands
-```
+`
$ qstat -a
$ qstat -a -u username
$ qstat -an -u username
$ qstat -f 12345.srv11
-```
+`
Example:
-```
+`
$ qstat -a
srv11:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
---------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
+--------------- -------- -- |---|---| ------ --- --- ------ ----- - -----
16287.srv11 user1 qlong job1 6183 4 64 -- 144:0 R 38:25
16468.srv11 user1 qlong job2 8060 4 64 -- 144:0 R 17:44
16547.srv11 user2 qprod job3x 13516 2 32 -- 48:00 R 00:58
-```
+`
In this example user1 and user2 are running jobs named job1, job2 and
job3x. The jobs job1 and job2 are using 4 nodes, 16 cores per node each.
@@ -232,7 +232,7 @@ of user's PBS jobs' processes on execution hosts. Display load,
processes. Display job standard and error output. Continuously display
(tail -f) job standard or error output.
-```
+`
$ check-pbs-jobs --check-all
$ check-pbs-jobs --print-load --print-processes
$ check-pbs-jobs --print-job-out --print-job-err
@@ -240,23 +240,23 @@ $ check-pbs-jobs --print-job-out --print-job-err
$ check-pbs-jobs --jobid JOBID --check-all --print-all
$ check-pbs-jobs --jobid JOBID --tailf-job-out
-```
+`
Examples:
-```
+`
$ check-pbs-jobs --check-all
JOB 35141.dm2, session_id 71995, user user2, nodes cn164,cn165
Check session id: OK
Check processes
cn164: OK
cn165: No process
-```
+`
In this example we see that job 35141.dm2 currently runs no process on
allocated node cn165, which may indicate an execution error.
-```
+`
$ check-pbs-jobs --print-load --print-processes
JOB 35141.dm2, session_id 71995, user user2, nodes cn164,cn165
Print load
@@ -268,13 +268,13 @@ cn164: 0.0 -bash
cn164: 0.0 /bin/bash /var/spool/PBS/mom_priv/jobs/35141.dm2.SC
cn164: 99.7 run-task
...
-```
+`
In this example we see that job 35141.dm2 currently runs process
run-task on node cn164, using one thread only, while node cn165 is
empty, which may indicate an execution error.
-```
+`
$ check-pbs-jobs --jobid 35141.dm2 --print-job-out
JOB 35141.dm2, session_id 71995, user user2, nodes cn164,cn165
Print job standard output:
@@ -284,7 +284,7 @@ Script name  : script
Run loop 1
Run loop 2
Run loop 3
-```
+`
In this example, we see actual output (some iteration loops) of the job
35141.dm2
@@ -294,21 +294,21 @@ qdel,** **qsig** or **qalter** commands
You may release your allocation at any time, using qdel command
-```
+`
$ qdel 12345.srv11
-```
+`
You may kill a running job by force, using qsig command
-```
+`
$ qsig -s 9 12345.srv11
-```
+`
Learn more by reading the pbs man page
-```
+`
$ man pbs_professional
-```
+`
Job Execution
-------------
@@ -326,17 +326,17 @@ manager.
The jobscript or interactive shell is executed on first of the allocated
nodes.
-```
+`
$ qsub -q qexp -l select=4:ncpus=16 -N Name0 ./myjob
$ qstat -n -u username
srv11:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
---------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
+--------------- -------- -- |---|---| ------ --- --- ------ ----- - -----
15209.srv11 username qexp Name0 5530 4 64 -- 01:00 R 00:00
cn17/0*16+cn108/0*16+cn109/0*16+cn110/0*16
-```
+`
 In this example, the nodes cn17, cn108, cn109 and cn110 were allocated
for 1 hour via the qexp queue. The jobscript myjob will be executed on
@@ -346,14 +346,14 @@ use as well.
The jobscript or interactive shell is by default executed in home
directory
-```
+`
$ qsub -q qexp -l select=4:ncpus=16 -I
qsub: waiting for job 15210.srv11 to start
qsub: job 15210.srv11 ready
$ pwd
/home/username
-```
+`
In this example, 4 nodes were allocated interactively for 1 hour via the
qexp queue. The interactive shell is executed in the home directory.
@@ -368,7 +368,7 @@ Calculations on allocated nodes may be executed remotely via the MPI,
ssh, pdsh or clush. You may find out which nodes belong to the
allocation by reading the $PBS_NODEFILE file
-```
+`
qsub -q qexp -l select=4:ncpus=16 -I
qsub: waiting for job 15210.srv11 to start
qsub: job 15210.srv11 ready
@@ -387,7 +387,7 @@ cn17: cn17
cn108: cn108
cn109: cn109
cn110: cn110
-```
+`
In this example, the hostname program is executed via pdsh from the
interactive shell. The execution runs on all four allocated nodes. The
@@ -402,7 +402,7 @@ The recommended way to run production jobs is to change to /scratch
directory early in the jobscript, copy all inputs to /scratch, execute
the calculations and copy outputs to home directory.
-```
+`
#!/bin/bash
# change to scratch directory, exit on failure
@@ -425,7 +425,7 @@ cp output $PBS_O_WORKDIR/.
#exit
exit
-```
+`
In this example, some directory on the /home holds the input file input
and executable mympiprog.x . We create a directory myjob on the /scratch
@@ -452,7 +452,7 @@ execution.
Example jobscript for an MPI job with preloaded inputs and executables,
options for qsub are stored within the script :
-```
+`
#!/bin/bash
#PBS -q qprod
#PBS -N MYJOB
@@ -471,7 +471,7 @@ mpiexec ./mympiprog.x
#exit
exit
-```
+`
In this example, input and executable files are assumed preloaded
manually in /scratch/$USER/myjob directory. Note the **mpiprocs** and
@@ -493,7 +493,7 @@ scratch will be deleted immediately after the job ends.
Example jobscript for single node calculation, using [local
scratch](../storage.html) on the node:
-```
+`
#!/bin/bash
# change to local scratch directory
@@ -511,7 +511,7 @@ cp output $PBS_O_WORKDIR/.
#exit
exit
-```
+`
In this example, some directory on the home holds the input file input
and executable myprog.x . We copy input and executable files from the
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.epub
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
index 34cab0ac07e1507dc797235af541a56c5939ed4d..58da4ca5bc6e08cd916173b5a71a0cfe291999d6 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
@@ -16,21 +16,13 @@ queues provide prioritized and exclusive access to the computational
resources. Following table provides the queue partitioning overview:Â Â
Â
-<col width="12%" />
-<col width="12%" />
-<col width="12%" />
-<col width="12%" />
-<col width="12%" />
-<col width="12%" />
-<col width="12%" />
-<col width="12%" />
- |queue |active project |project resources<th align="left">nodes<th align="left">min ncpus*<th align="left">priority<th align="left">authorization<th align="left">walltimedefault/max |
+ |queue |active project |project resources |nodes<th align="left">min ncpus*<th align="left">priority<th align="left">authorization<th align="left">walltime |
| --- | --- |
- |<strong>qexp</strong>Express queue |no |none required |2 reserved, 31 totalincluding MIC, GPU and FAT nodes |1 |><em>150</em> |no |1h |
- |<strong>qprod</strong>Production queue |yes |> 0 |><em>178 nodes w/o accelerator</em>\ |16 |0 |no |24/48h |
+ |<strong>qexp</strong>\ |no |none required |2 reserved, 31 totalincluding MIC, GPU and FAT nodes |1 |><em>150</em> |no |1h |
+ |<strong>qprod</strong>\ |yes |> 0 |><em>178 nodes w/o accelerator</em>\ |16 |0 |no |24/48h |
|<strong>qlong</strong>Long queue\ |yes |> 0 |60 nodes w/o accelerator |16 |0 |no |72/144h |
|<strong>qnvidia, qmic, qfat</strong>Dedicated queues\ |yes |<p>> 0\ |23 total qnvidia4 total qmic2 total qfat |16 |><em>200</em> |yes |24/48h |
- |<strong>qfree</strong>Free resource queue |yes |none required |178 w/o accelerator |16 |-1024 |no |12h |
+ |<strong>qfree</strong>\ |yes |none required |178 w/o accelerator |16 |-1024 |no |12h |
The qfree queue is not free of charge**. [Normal
accounting](resources-allocation-policy.html#resources-accounting-policy)
@@ -45,7 +37,7 @@ clock speed.** Should you need the very same CPU speed, you have to
select the proper nodes during the PSB job submission.
**
-- **qexp**, the Express queue: This queue is dedicated for testing and
+- **qexp**, the \: This queue is dedicated for testing and
running very small jobs. It is not required to specify a project to
enter the qexp. >*>There are 2 nodes always reserved for
this queue (w/o accelerator), maximum 8 nodes are available via the
@@ -56,7 +48,7 @@ select the proper nodes during the PSB job submission.
RAM requirements.* The nodes may be allocated on per
core basis. No special authorization is required to use it. The
maximum runtime in qexp is 1 hour.
-- **qprod**, the Production queue****: This queue is intended for
+- **qprod**, the \***: This queue is intended for
normal production runs. It is required that active project with
nonzero remaining resources is specified to enter the qprod. All
nodes may be accessed via the qprod queue, except the reserved ones.
@@ -65,7 +57,7 @@ select the proper nodes during the PSB job submission.
are allocated. The queue runs with medium priority and no special
authorization is required to use it. The maximum runtime in qprod is
48 hours.
-- **qlong**, the Long queue****: This queue is intended for long
+- **qlong**, the Long queue***: This queue is intended for long
production runs. It is required that active project with nonzero
remaining resources is specified to enter the qlong. Only 60 nodes
without acceleration may be accessed via the qlong queue. Full
@@ -73,7 +65,7 @@ select the proper nodes during the PSB job submission.
priority and no special authorization is required to use it.>
*The maximum runtime in qlong is 144 hours (three times of the
standard qprod time - 3 * 48 h).*
-- **qnvidia, qmic, qfat**, the Dedicated queues****: The queue qnvidia
+- **qnvidia, qmic, qfat**, the Dedicated queues***: The queue qnvidia
is dedicated to access the Nvidia accelerated nodes, the qmic to
access MIC nodes and qfat the Fat nodes. It is required that active
project with nonzero remaining resources is specified to enter
@@ -85,7 +77,7 @@ select the proper nodes during the PSB job submission.
[support](https://support.it4i.cz/rt/) for
authorization to enter the dedicated queues for all users associated
to her/his Project.
-- **qfree**, The Free resource queue****: The queue qfree is intended
+- **qfree**, The \***: The queue qfree is intended
for utilization of free resources, after a Project exhausted all its
allocated computational resources (Does not apply to DD projects
by default. DD projects have to request for persmission on qfree
@@ -120,14 +112,14 @@ Check the status of jobs, queues and compute nodes at
Display the queue status on Anselm:
-```
+`
$ qstat -q
-```
+`
The PBS allocation overview may be obtained also using the rspbs
command.
-```
+`
$ rspbs
Usage: rspbs [options]
@@ -181,7 +173,7 @@ Options:
                       Only for given node state (affects only --get-node*
                       --get-qlist-* --get-ibswitch-* actions)
 --incl-finished      Include finished jobs
-```
+`
Resources Accounting Policy
-------------------------------
@@ -208,14 +200,14 @@ User may check at any time, how many core-hours have been consumed by
himself/herself and his/her projects. The command is available on
clusters' login nodes.
-```
+`
$ it4ifree
Password:
    PID  Total Used ...by me Free
  -------- ------- ------ -------- -------
  OPEN-0-0 1500000 400644  225265 1099356
  DD-13-1   10000 2606 2606 7394
-```
+`
Â
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys.epub
index b81f5410198477da9de96506252b35d790c83584..6b1596683e68fd8b138f6ccbe6696fc30ed74258 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys.md
index 2dfb705ee4fd1e80527df74b726b7652c24424c4..e5130c0709a9ea0b0dccb4808bcf53472da91af8 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys.md
@@ -1,8 +1,8 @@
Overview of ANSYS Products
==========================
-[SVS FEM](http://www.svsfem.cz/)** as ***[ANSYS
-Channel partner](http://www.ansys.com/)***Â for Czech
+[SVS FEM](http://www.svsfem.cz/)** as **[ANSYS
+Channel partner](http://www.ansys.com/)**Â for Czech
Republic provided all ANSYS licenses for ANSELM cluster and supports of
all ANSYS Products (Multiphysics, Mechanical, MAPDL, CFX, Fluent,
Maxwell, LS-DYNA...) to IT staff and ANSYS users. If you are challenging
@@ -13,7 +13,7 @@ Anselm provides as commercial as academic variants. Academic variants
are distinguished by "**Academic...**" word in the name of  license or
by two letter preposition "**aa_**" in the license feature name. Change
of license is realized on command line respectively directly in user's
-pbs file (see individual products). [ id="result_box"
+pbs file (see individual products). [
More about
licensing
here](ansys/licensing.html)
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.epub
index 54f05f601fe8e97e9634ac1283fff0aa694c523f..39f257413fd6ae91a5bcbc5c688296574c2e6011 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.md
index f9d31703a36344a6b81ed356c585f6aac8a6cd14..5d50cda135ee04d574eb928dbb7b2aedf1a87013 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.md
@@ -15,10 +15,10 @@ environment, with extensive capabilities for customization and
automation using session files, scripting and a powerful expression
language.
->To run ANSYS CFX in batch mode you can utilize/modify the default
+To run ANSYS CFX in batch mode you can utilize/modify the default
cfx.pbs script and execute it via the qsub command.
-```
+`
#!/bin/bash
#PBS -l nodes=2:ppn=16
#PBS -q qprod
@@ -59,7 +59,7 @@ echo Machines: $hl
#-dev input.def includes the input of CFX analysis in DEF format
#-P the name of prefered license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial))
/ansys_inc/v145/CFX/bin/cfx5solve -def input.def -size 4 -size-ni 4x -part-large -start-method "Platform MPI Distributed Parallel" -par-dist $hl -P aa_r
-```
+`
Header of the pbs file (above) is common and description can be find
on [this
@@ -77,9 +77,9 @@ CFX def file which is attached to the cfx solver via parameter
License**Â should be selected by parameter -P (Big letter **P**).
Licensed products are the following: aa_r
-(ANSYSÂ **Academic**Â Research), ane3fl (ANSYS
-Multiphysics)-**Commercial.**
-[ id="result_box" More
+(ANSYS **Academic Research), ane3fl (ANSYS
+Multiphysics)-**Commercial.
+[ More
about licensing
here](licensing.html)
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.pdf
index 99ca79cfd2e132c063280f34b658e4b5bd03d608..fc4b652916fba772511253b97690b64cb23040c1 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.epub
index 426e0efb933ed8c6c47d29d5f1a71420719a94d3..2e8e0c43eaf03e899ca34319777b0cb3563f8ba7 100644
Binary files a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.epub and b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.epub differ
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.md
index e6ee9de61d5fad509934dc6785d9b51cd7bf7144..ab675d3381dc6377e63df7b7a5db21ff7db72aff 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.md
@@ -12,13 +12,13 @@ treatment plants. Special models that give the software the ability to
model in-cylinder combustion, aeroacoustics, turbomachinery, and
multiphase systems have served to broaden its reach.
->1. Common way to run Fluent over pbs file
+1. Common way to run Fluent over pbs file
------------------------------------------------------
->To run ANSYS Fluent in batch mode you can utilize/modify the
+To run ANSYS Fluent in batch mode you can utilize/modify the
default fluent.pbs script and execute it via the qsub command.
-```
+`
#!/bin/bash
#PBS -S /bin/bash
#PBS -l nodes=2:ppn=16
@@ -47,7 +47,7 @@ module load ansys
NCORES=`wc -l $PBS_NODEFILE |awk '{print $1}'`
/ansys_inc/v145/fluent/bin/fluent 3d -t$NCORES -cnf=$PBS_NODEFILE -g -i fluent.jou
-```
+`
Header of the pbs file (above) is common and description can be find
on [this
@@ -76,15 +76,15 @@ structure:
/file/write-case-dat aircraft_2m-solution
/exit yes
->The appropriate dimension of the problem has to be set by
+The appropriate dimension of the problem has to be set by
parameter (2d/3d).Â
->2. Fast way to run Fluent from command line
+2. Fast way to run Fluent from command line
--------------------------------------------------------
-```
+`
fluent solver_version [FLUENT_options] -i journal_file -pbs
-```
+`
This syntax will start the ANSYS FLUENT job under PBS Professional using
the qsub command in a batch manner. When
@@ -108,17 +108,17 @@ from which the jobs are submitted (which is also the directory in which
the jobs are executed). The following is an example of what the content
of pbs_fluent.conf can be:
-```
+`
input="example_small.flin"
case="Small-1.65m.cas"
fluent_args="3d -pmyrinet"
outfile="fluent_test.out"
mpp="true"
-```
+`
The following is an explanation of the parameters:
-> input is the name of the input
+ input is the name of the input
file.
case is the name of the
@@ -141,11 +141,11 @@ the standard output will be sent.
mpp="true" will tell the job script to
execute the job across multiple processors. Â Â Â Â Â Â Â Â
->To run ANSYS Fluent in batch mode with user's config file you can
+To run ANSYS Fluent in batch mode with user's config file you can
utilize/modify the following script and execute it via the qsub
command.
-```
+`
#!/bin/sh
#PBS -l nodes=2:ppn=4
#PBS -1 qprod
@@ -192,9 +192,9 @@ command.
#run the solver
/ansys_inc/v145/fluent/bin/fluent $fluent_args > $outfile
-```
+`
->It runs the jobs out of the directory from which they are
+It runs the jobs out of the directory from which they are
submitted (PBS_O_WORKDIR).
4. Running Fluent in parralel
@@ -205,9 +205,9 @@ do so this ANSYS Academic Research license must be placed before ANSYS
CFD license in user preferences. To make this change anslic_admin
utility should be run
-```
+`
/ansys_inc/shared_les/licensing/lic_admin/anslic_admin
-```
+`
ANSLIC_ADMIN Utility will be run
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.pdf
index e93c63bae3fc2fb2b14ad2e4d5f9428876fd7b80..a8cb414d10d2ec67660ccd3e515fd55d66a5b301 100644
Binary files a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.pdf and b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.pdf differ
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.epub
index 0cb0105d2730f8e47a18075eee183bc792813fae..cf958993e36e7c6814b7de36e59800b9b1cac772 100644
Binary files a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.epub and b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.epub differ
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md
index 0da653d747fa1cafdba6f1f0b0f2c0369cdd65b6..397aa94adba08eb00f01dec704c3031739e8d110 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md
@@ -19,10 +19,10 @@ result visualization and comprehensive report generation are all
available within a single fully interactive modern graphical user
environment.
->To run ANSYS LS-DYNA in batch mode you can utilize/modify the
+To run ANSYS LS-DYNA in batch mode you can utilize/modify the
default ansysdyna.pbs script and execute it via the qsub command.
-```
+`
#!/bin/bash
#PBS -l nodes=2:ppn=16
#PBS -q qprod
@@ -66,9 +66,9 @@ done
echo Machines: $hl
/ansys_inc/v145/ansys/bin/ansys145 -dis -lsdynampp i=input.k -machines $hl
-```
+`
->Header of the pbs file (above) is common and description can be
+Header of the pbs file (above) is common and description can be
find on [this
site](../../resource-allocation-and-job-execution/job-submission-and-execution.html)>.
[SVS FEM](http://www.svsfem.cz) recommends to utilize
@@ -82,5 +82,5 @@ queue. Input file should be in working directory or full path to input
file has to be specified. Input file has to be defined by common LS-DYNA
.**k** file which is attached to the ansys solver via parameter i=
->>Â
+Â
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.pdf
index 046ff0f7b12d042b12ad4af524a9ba8e14f612fc..f397f5c2e18babcac4fb0a3088d3554ab432222d 100644
Binary files a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.pdf and b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.pdf differ
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.epub
index 889aa7ef2b6d39a60e4799cb2274d6c261cb69c2..bd0064616c42f7ea4cc0947150959c1cb79177cc 100644
Binary files a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.epub and b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.epub differ
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
index 35aa73d291763dab28aa7a2d8a5580c0f5a423e8..ac6357c2f9a6df62253546816739944985f0270e 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
@@ -1,7 +1,7 @@
ANSYS MAPDL
===========
->**[ANSYS
+**[ANSYS
Multiphysics](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/ANSYS+Multiphysics)**
software offers a comprehensive product solution for both multiphysics
and single-physics analysis. The product includes structural, thermal,
@@ -10,10 +10,10 @@ product also contains solutions for both direct and sequentially coupled
physics problems including direct coupled-field elements and the ANSYS
multi-field solver.
->To run ANSYS MAPDL in batch mode you can utilize/modify the
+To run ANSYS MAPDL in batch mode you can utilize/modify the
default mapdl.pbs script and execute it via the qsub command.
-```
+`
#!/bin/bash
#PBS -l nodes=2:ppn=16
#PBS -q qprod
@@ -55,7 +55,7 @@ echo Machines: $hl
#-o file.out is output file from ansys where all text outputs will be redirected
#-p the name of license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial), aa_r_dy=Academic AUTODYN)
/ansys_inc/v145/ansys/bin/ansys145 -b -dis -p aa_r -i input.dat -o file.out -machines $hl -dir $WORK_DIR
-```
+`
Header of the pbs file (above) is common and description can be find on
[this
@@ -72,10 +72,10 @@ file has to be specified. Input file has to be defined by common APDL
file which is attached to the ansys solver via parameter -i
License** should be selected by parameter -p. Licensed products are
-the following: aa_r (ANSYS **Academic** Research), ane3fl (ANSYS
-Multiphysics)-**Commercial**, aa_r_dy (ANSYS **Academic**
+the following: aa_r (ANSYS **Academic Research), ane3fl (ANSYS
+Multiphysics)-**Commercial**, aa_r_dy (ANSYS **Academic
AUTODYN)>
-[ id="result_box" More
+[ More
about licensing
here](licensing.html)
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.pdf
index 80a86d0324a2956d8e84b0b8b5159d8500f9d556..e92ebe21782842e6da0b45445145b3e2f6dc7927 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.epub
index 3f46fb0d21843e399d969d85a496947a07347f22..1c9dfd8dad800f72ab601592311ce89e0cf8395d 100644
Binary files a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.epub and b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.epub differ
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.md
index 1e3d5ca76544b5aed7dca0b9868590c702f98cec..c2a86aa8574d0e7491af73766adce0e82c56bcd5 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.md
@@ -18,14 +18,14 @@ materials like composites, ceramics, concrete, or wood. Moreover, it is
used in biomechanics, human modelling, molecular structures, casting,
forging, or virtual testing.
->Anselm provides **1 commercial license of LS-DYNA without HPC**
+Anselm provides **1 commercial license of LS-DYNA without HPC**
support now.Â
->>To run LS-DYNA in batch mode you can utilize/modify the
+To run LS-DYNA in batch mode you can utilize/modify the
default lsdyna.pbs script and execute it via the qsub
command.
-```
+`
#!/bin/bash
#PBS -l nodes=1:ppn=16
#PBS -q qprod
@@ -47,7 +47,7 @@ echo Directory is `pwd`
module load lsdyna
/apps/engineering/lsdyna/lsdyna700s i=input.k
-```
+`
Header of the pbs file (above) is common and description can be find
on [this
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.pdf
index ac2011d0582e5abf7b357402ee61170ff6cbf555..d68a4fe9c5d207799c1ba4b204aa6fe341006557 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.epub
index e79a36a84b2250a4b50610259e8c924104e31f79..adf0c0de69caa1b25ad81303c16743945fe291ee 100644
Binary files a/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.epub and b/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.epub differ
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.md
index 47b17a5f279052db6db9968c5c53eba410912f12..ff0be71faecd1c1b6374e9b2d92fbf44bece4eda 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.md
@@ -19,7 +19,7 @@ license. Please contact support to enable access to Molpro if you have a
valid license appropriate for running on our cluster (eg. >academic
research group licence, parallel execution).
->To run Molpro, you need to have a valid license token present in
+To run Molpro, you need to have a valid license token present in
" $HOME/.molpro/token". You can
download the token from [Molpro
website](https://www.molpro.net/licensee/?portal=licensee).
@@ -32,15 +32,15 @@ parallel version compiled with Intel compilers and Intel MPI.
Compilation parameters are default :
- Parameter Value
- ------------------------------------------------- -----------------------------
- >max number of atoms 200
- >max number of valence orbitals 300
- >max number of basis functions 4095
- >max number of states per symmmetry 20
- >max number of state symmetries 16
- >max number of records 200
- >max number of primitives >maxbfn x [2]
+ |Parameter|Value|
+ ------------------------------------------- |---|---|-------------------
+ |max number of atoms|200|
+ |max number of valence orbitals|300|
+ |max number of basis functions|4095|
+ |max number of states per symmmetry|20|
+ |max number of state symmetries|16|
+ |max number of records|200|
+ |max number of primitives|maxbfn x [2]|
Â
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.pdf
index 81db48ece31b2d610061effbc3fa74db4f8d2b59..0e6a1e387ceab9ac6a7780be00f304075bab0444 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.epub
index 24a8a033dfd4d740e5baea60dc70cdc322d3a7cf..d6aa11d333ed7f1c567d93dc18e8ed0e3fbe8310 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.md
index 2484c2c1176f6184aec65a3c7d2ab9a12f349f6d..d52644e00840ab4ec5be1f3d856e2e2b82a83d45 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.md
@@ -3,10 +3,10 @@ NWChem
High-Performance Computational Chemistry
->Introduction
+Introduction
-------------------------
->NWChem aims to provide its users with computational chemistry
+NWChem aims to provide its users with computational chemistry
tools that are scalable both in their ability to treat large scientific
computational chemistry problems efficiently, and in their use of
available parallel computing resources from high-performance parallel
@@ -50,7 +50,7 @@ jobs applies. Sample jobscript :
module add nwchem/6.3-rev2-patch1
mpirun -np 16 nwchem h2o.nw
->Options
+Options
--------------------
Please refer to [the
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.pdf
index ad84898954f69e163a44244cec49a4355aa5c659..9f093c187795b1570b8dbc576065c8626226e100 100644
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index 7d9b278ba3126eb91d13c54ddc13a35fce7e89e9..402512f3c3462d1ee3e8abc69cff085458113174 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.epub
index 6c066efc336cee7e1c2254f7ded3919210361ef2..077443c5cb958f2f75cd1b5b1b29bf0558906cca 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.md
index d1c7bcd308f3df8e497e699c7051c3b63223ea83..25f1c4d0fd1cf538124f230a2297a279820118ce 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.md
@@ -3,11 +3,11 @@ COMSOL Multiphysics®
->>Introduction
+Introduction
-------------------------
->>[COMSOL](http://www.comsol.com)
+[COMSOL](http://www.comsol.com)
is a powerful environment for modelling and solving various engineering
and scientific problems based on partial differential equations. COMSOL
is designed to solve coupled or multiphysics phenomena. For many
@@ -15,89 +15,89 @@ standard engineering problems COMSOL provides add-on products such as
electrical, mechanical, fluid flow, and chemical
applications.
-- >>[Structural Mechanics
+- >[Structural Mechanics
Module](http://www.comsol.com/structural-mechanics-module),
-- >>[Heat Transfer
+- >[Heat Transfer
Module](http://www.comsol.com/heat-transfer-module),
-- >>[CFD
+- >[CFD
Module](http://www.comsol.com/cfd-module),
-- >>[Acoustics
+- >[Acoustics
Module](http://www.comsol.com/acoustics-module),
-- >>and [many
+- >and [many
others](http://www.comsol.com/products)
->>COMSOL also allows an
->>interface support for
+COMSOL also allows an
+interface support for
equation-based modelling of
->>partial differential
+partial differential
equations.
->>Execution
+Execution
----------------------
->>On the Anselm cluster COMSOL is available in the latest
+On the Anselm cluster COMSOL is available in the latest
stable version. There are two variants of the release:
-- >>**Non commercial** or so
- called >>**EDU
- variant**>>, which can be used for research
+- >**Non commercial** or so
+ called >**EDU
+ variant**>, which can be used for research
and educational purposes.
-- >>**Commercial** or so called
- >>**COM variant**,
+- >**Commercial** or so called
+ >**COM variant**,
which can used also for commercial activities.
- >>**COM variant**
+ >**COM variant**
has only subset of features compared to the
- >>**EDU
- variant**>> available. <span
- id="result_box"
+ >**EDU
+ variant**> available.
+
More about
licensing will be posted here
- soon.</span>
+ soon.
->>To load the of COMSOL load the module
+To load the of COMSOL load the module
-```
+`
$ module load comsol
-```
+`
->>By default the **EDU
-variant**>> will be loaded. If user needs other
+By default the **EDU
+variant**> will be loaded. If user needs other
version or variant, load the particular version. To obtain the list of
available versions use
-```
+`
$ module avail comsol
-```
+`
->>If user needs to prepare COMSOL jobs in the interactive mode
+If user needs to prepare COMSOL jobs in the interactive mode
it is recommend to use COMSOL on the compute nodes via PBS Pro
scheduler. In order run the COMSOL Desktop GUI on Windows is recommended
to use the [Virtual Network Computing
(VNC)](https://docs.it4i.cz/anselm-cluster-documentation/software/comsol/resolveuid/11e53ad0d2fd4c5187537f4baeedff33).
-```
+`
$ xhost +
$ qsub -I -X -A PROJECT_ID -q qprod -l select=1:ncpus=16
$ module load comsol
$ comsol
-```
+`
->>To run COMSOL in batch mode, without the COMSOL Desktop GUI
+To run COMSOL in batch mode, without the COMSOL Desktop GUI
environment, user can utilized the default (comsol.pbs) job script and
execute it via the qsub command.
-```
+`
#!/bin/bash
#PBS -l select=3:ncpus=16
#PBS -q qprod
@@ -108,9 +108,9 @@ cd /scratch/$USER/ || exit
echo Time is `date`
echo Directory is `pwd`
-echo '***PBS_NODEFILE***START*******'
+echo '**PBS_NODEFILE***START*******'
cat $PBS_NODEFILE
-echo '***PBS_NODEFILE***END*********'
+echo '**PBS_NODEFILE***END*********'
text_nodes < cat $PBS_NODEFILE
@@ -120,9 +120,9 @@ module load comsol
ntask=$(wc -l $PBS_NODEFILE)
comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/$USER/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log
-```
+`
->>Working directory has to be created before sending the
+Working directory has to be created before sending the
(comsol.pbs) job script into the queue. Input file (name_input_f.mph)
has to be in working directory or full path to input file has to be
specified. The appropriate path to the temp directory of the job has to
@@ -131,43 +131,43 @@ be set by command option (-tmpdir).
LiveLink™* *for MATLAB®^
-------------------------
->>COMSOL is the software package for the numerical solution of
+COMSOL is the software package for the numerical solution of
the partial differential equations. LiveLink for MATLAB allows
connection to the
-COMSOL>><span><span><span><span><span>**®**</span></span></span>^
+COMSOL>><span><span><span><span>**®**</span>^
API (Application Programming Interface) with the benefits of the
programming language and computing environment of the MATLAB.
->>LiveLink for MATLAB is available in both
->>**EDU** and
->>**COM**
->>**variant** of the
+LiveLink for MATLAB is available in both
+**EDU** and
+**COM**
+**variant** of the
COMSOL release. On Anselm 1 commercial
-(>>**COM**) license
+(>**COM**) license
and the 5 educational
-(>>**EDU**) licenses
+(>**EDU**) licenses
of LiveLink for MATLAB (please see the [ISV
Licenses](../isv_licenses.html)) are available.
Following example shows how to start COMSOL model from MATLAB via
LiveLink in the interactive mode.
-```
+`
$ xhost +
$ qsub -I -X -A PROJECT_ID -q qexp -l select=1:ncpus=16
$ module load matlab
$ module load comsol
$ comsol server matlab
-```
+`
->>At the first time to launch the LiveLink for MATLAB
+At the first time to launch the LiveLink for MATLAB
(client-MATLAB/server-COMSOL connection) the login and password is
requested and this information is not requested again.
->>To run LiveLink for MATLAB in batch mode with
+To run LiveLink for MATLAB in batch mode with
(comsol_matlab.pbs) job script you can utilize/modify the following
script and execute it via the qsub command.
-```
+`
#!/bin/bash
#PBS -l select=3:ncpus=16
#PBS -q qprod
@@ -178,9 +178,9 @@ cd /scratch/$USER || exit
echo Time is `date`
echo Directory is `pwd`
-echo '***PBS_NODEFILE***START*******'
+echo '**PBS_NODEFILE***START*******'
cat $PBS_NODEFILE
-echo '***PBS_NODEFILE***END*********'
+echo '**PBS_NODEFILE***END*********'
text_nodes < cat $PBS_NODEFILE
@@ -192,7 +192,7 @@ ntask=$(wc -l $PBS_NODEFILE)
comsol -nn ${ntask} server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/$USER &
cd /apps/engineering/comsol/comsol43b/mli
matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/$USER; test_job"
-```
+`
This example shows how to run Livelink for MATLAB with following
configuration: 3 nodes and 16 cores per node. Working directory has to
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.epub
index 4cfac9fa48723301ebe16ce11144466d1291fc01..4aa30432a79d7ee60ff9f0c8a7d17f22ee1794b8 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
index 405d8c41da3be215557fab61f362d76bb0aa83aa..237f66e9b50348ea499370f53427860f0c779afb 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
@@ -47,11 +47,11 @@ Load the Allinea DDT module:
Compile the code:
-```
+`
$ mpicc -g -O0 -o test_debug test.c
$ mpif90 -g -O0 -o test_debug test.f
-```
+`
Â
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.pdf
index da732ca19fce110fbcaf9e3abda2c5dc27191b79..1f17e922b98920bce479e1c762aa4cd40117e256 100644
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index 18c7f4bd55aab2d78d41196bd485dc0986ee99d1..692f3bdb9d45b4aabc4e53e7cd3a860feae24c32 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md
index 147678cb0cc7b29919e28bd1759732cc43b327d9..eeb8206b2c86d2cc09b8ae5f1e84409b700a597b 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md
@@ -11,7 +11,7 @@ is that PCM supports only Intel hardware, but PCM can monitor also
uncore metrics, like memory controllers and >QuickPath Interconnect
links.
->Installed version
+Installed version
------------------------------
Currently installed version 2.6. To load the
@@ -85,7 +85,7 @@ Usage:Â >Â pcm-power.x <delay> |
### pcm
This command provides an overview of performance counters and memory
-usage. >Usage: > <span pcm.x
+usage. >Usage: > pcm.x
<delay> | <external program>
Sample output :
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.pdf
index c9c9569808cb0dc10bb0ba42606b773ee69f608b..0fe2b2c4c703872da44a3bfb0acc95e123efb5ea 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.epub
index 187a2fd157645f94d876adc7a567be94782a7d32..3654997e7bd2d4b1e185261b25701f52f86a0876 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md
index 4171d30eeb08c935c1b1450f09cd004e06ffaed9..b22b73f2b336d267a0279892d251d20b30381838 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md
@@ -30,13 +30,13 @@ To launch the GUI, first load the module:
$Â amplxe-gui
->To profile an application with VTune Amplifier, special kernel
+To profile an application with VTune Amplifier, special kernel
modules need to be loaded. The modules are not loaded on Anselm login
nodes, thus direct profiling on login nodes is not possible. Use VTune
on compute nodes and refer to the documentation on [using GUI
applications](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/resolveuid/11e53ad0d2fd4c5187537f4baeedff33).
->The GUI will open in new window. Click on "*New Project...*" to
+The GUI will open in new window. Click on "*New Project...*" to
create a new project. After clicking *OK*, a new window with project
properties will appear. Â At "*Application:*", select the bath to your
binary you want to profile (the binary should be compiled with -g flag).
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.epub
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.md
index eaeac4a5cebe1cbe4888e032120647dd6492907d..df34e4232f4b6059c4522aa033e9e8bf0fc5c08f 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.md
@@ -13,10 +13,10 @@ misses) found in most modern architectures. With the new component
framework, PAPI is not limited only to CPU counters, but offers also
components for CUDA, network, Infiniband etc.
->PAPI provides two levels of interface - a simpler, high level
+PAPI provides two levels of interface - a simpler, high level
interface and more detailed low level interface.
->PAPI can be used with parallel as well as serial programs.
+PAPI can be used with parallel as well as serial programs.
Usage
-----
@@ -78,16 +78,16 @@ CPU.
### papi_native_avail
->Prints which native events are available on the current
+Prints which native events are available on the current
CPU.
### class="s1">papi_cost
->Measures the cost (in cycles) of basic PAPI operations.
+Measures the cost (in cycles) of basic PAPI operations.
-### >papi_mem_info
+###papi_mem_info
->Prints information about the memory architecture of the current
+Prints information about the memory architecture of the current
CPU.
PAPI API
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.md
index 69192c14894413b185b5824b2ce6fd62d453d4cb..df942821880a9b653310e3d01b1489cf13665e76 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.md
@@ -1,7 +1,7 @@
Scalasca
========
->Introduction
+Introduction
-------------------------
[Scalasca](http://www.scalasca.org/) is a software tool
@@ -69,7 +69,6 @@ collected.
By default, Scalasca saves the data to a directory with
prefix >scorep_, followed by name of the executable and launch
configuration.
->
Scalasca can generate a huge amount of data, especially if tracing is
enabled. Please consider saving the data to a [scratch
@@ -84,15 +83,15 @@ tool is launched.
To launch the analysis, run :
-```
+`
scalasca -examine [options] <experiment_directory>
-```
+`
If you do not wish to launch the GUI tool, use the "-s" option :
-```
+`
scalasca -examine -s <experiment_directory>
-```
+`
Alternatively you can open CUBE and load the data directly from here.
Keep in mind that in that case the preprocessing is not done and not all
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.pdf
index 22acb68130f026f0399b2aba83b74766787a0a2d..2ae6d8ff1fe3c9d0d04d60c6249bbf7ef2f1d9a7 100644
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index 5e50e48517af6ad2d7afd65e71438b8d50d593de..83cd10a67728b96eae8b4ff19bbe616b31ecbbaf 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.md
index 03e5d0f928bbbb3968cea189987059c7a8197be9..0462b82ff2e97f3e2c0078740dc241bae80272e2 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.md
@@ -21,7 +21,7 @@ on Anselm :
- class="s1">scorep/1.2.3-gcc-openmpi>, for usage
with [GNU
- Compiler](../compilers.html)> and [OpenMPI](../mpi-1/Running_OpenMPI.html){.internal>,</span>
+ Compiler](../compilers.html)> and [OpenMPI](../mpi-1/Running_OpenMPI.html){.internal>,
- class="s1">scorep/1.2.3-icc-impi>, for usage
with [Intel
@@ -31,7 +31,7 @@ on Anselm :
Instrumentation
---------------
->There are three ways to instrument your parallel applications in
+There are three ways to instrument your parallel applications in
order to enable performance data collection :
1. >Automated instrumentation using compiler
@@ -49,19 +49,19 @@ To use automated instrumentation, simply prepend
scorep to your compilation command. For
example, replace :Â
-```
+`
$ mpif90 -c foo.f90
$ mpif90 -c bar.f90
$ mpif90 -o myapp foo.o bar.o
-```
+`
with :
-```
+`
$ scorep mpif90 -c foo.f90
$ scorep mpif90 -c bar.f90
$ scorep mpif90 -o myapp foo.o bar.o
-```
+`
Usually your program is compiled using a Makefile or similar script, so
it advisable to add the scorep command to
@@ -72,7 +72,7 @@ It is important that scorep is prepended
also to the linking command, in order to link with Score-P
instrumentation libraries.
-### >Manual instrumentation using API calls
+###Manual instrumentation using API calls
To use this kind of instrumentation, use
scorep with switch
@@ -105,7 +105,7 @@ An example in C/C++ :
Please refer to the [documentation for description of the
API](https://silc.zih.tu-dresden.de/scorep-current/pdf/scorep.pdf).
-### >Manual instrumentation using directives
+###Manual instrumentation using directives
This method uses POMP2 directives to mark regions to be instrumented. To
use this method, use command scorep
@@ -127,7 +127,7 @@ Example directives in C/C++ :
#pragma pomp inst end(foo)
}
->and in Fortran :
+and in Fortran :
subroutine foo(...)
!declarations
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index d2d7f59ee61351a144bce1ade3d34fefcd4fcad8..80f33804620da30a6a75a8ffbaa3dca219f865ae 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.md
index 5effda9bfc7d4dc6c5454fa750415fc736c299d9..6299f5b9f8fcb19bc5381389b708af21b4b94ff3 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.md
@@ -99,9 +99,9 @@ you have to add the following function to your **~/.tvdrc** file:
   set file_component [file tail $executable_name]
   if {[lsearch -exact $starter_programs $file_component] != -1} {
- Â Â Â Â Â Â Â puts "**************************************"
+ Â Â Â Â Â Â Â puts "*************************************"
       puts "Automatically starting $file_component"
- Â Â Â Â Â Â Â puts "**************************************"
+ Â Â Â Â Â Â Â puts "*************************************"
       dgo
   }
}
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.pdf
index 149b1c2580ad991e346ef3e46c2a5912285d3d1e..fedeef3322d9c2519a335ef64c9063b272ee05da 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.epub
index 37dfbfb006bb8c33fd4b892d08d6c6a675141206..435e364b582963e474b924d1684d8ec37a59b6e0 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.md
index a80314cb944abd867212e1ace0b3e5dde9c8db7e..615b26a1fe671bd05d586143f70f955b30f09b93 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.md
@@ -42,7 +42,7 @@ There are two versions of Valgrind available on Anselm.
>This version is available by default, without the need
to load any module. This version however does not provide additional
MPI support.
-- >>Version 3.9.0 with support for Intel MPI, available in
+- >Version 3.9.0 with support for Intel MPI, available in
[module](../../environment-and-modules.html)Â
valgrind/3.9.0-impi. After loading the
module, this version replaces the default valgrind.
@@ -158,7 +158,7 @@ with --leak-check=full option :
Now we can see that the memory leak is due to the
malloc() at line 6.
->Usage with MPI
+Usage with MPI
---------------------------
Although Valgrind is not primarily a parallel debugger, it can be used
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.pdf
index 84e25e6ec048f136f0b071b9195927f089bad757..534ecaf3e3c2467079fe4d29f2282093d39a4bf0 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.epub
index f469263229f9ea9cd08e02c67addefa6ad57f08a..95449dbf7febc0516e57224013cf19ae7a681428 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.md
index d1dd206c9b05bf47317efffe0817487205845b29..25fb484c6bf776ca15594007823269357514b8d3 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.md
@@ -9,7 +9,7 @@ as [Score-P](../../../salomon/software/debuggers/score-p.html))
first to collect the traces.
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+-------------------------------------
Installed versions
------------------
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.pdf
index cc6a0b948613f8765ecac52dc58c1d931ba82759..138928acfdd979c6d36ddf3164d4720738d47069 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.epub
index 710370537de27c6072ac38bf6f3dd54568c77480..d7da3ccac5d7ea38565bb9e03179e6d146f37213 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.md
index d8972caa08f54e74930f370dc3b2a8bf5fe019fd..79cf34786cbae1912747eb9dc563d189cc9c8df7 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.md
@@ -18,7 +18,7 @@ The GPI-2 library
implements the GASPI specification (Global Address Space Programming
Interface,
[www.gaspi.de](http://www.gaspi.de/en/project.html)).
->GASPI is a Partitioned Global Address Space (PGAS) API. It aims at
+GASPI is a Partitioned Global Address Space (PGAS) API. It aims at
scalable, flexible and failure tolerant computing in massively parallel
environments.
@@ -38,7 +38,7 @@ Linking
Link with -lGPI2 -libverbs
-Load the gpi2 module. Link using **-lGPI2** and **** **-libverbs**
+Load the gpi2 module. Link using **-lGPI2** and *** **-libverbs**
switches to link your code against GPI-2. The GPI-2 requires the OFED
infinband communication library ibverbs.
@@ -57,7 +57,7 @@ infinband communication library ibverbs.
Running the GPI-2 codes
-----------------------
->gaspi_run
+gaspi_run
gaspi_run starts the GPI-2 application
@@ -66,7 +66,7 @@ The gaspi_run utility is used to start and run GPI-2 applications:
$ gaspi_run -m machinefile ./myprog.x
A machine file (**machinefile**) with the hostnames of nodes where the
-application will run, must be provided. The**** machinefile lists all
+application will run, must be provided. The*** machinefile lists all
nodes on which to run, one entry per node per process. This file may be
hand created or obtained from standard $PBS_NODEFILE:
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.epub
index 01c353c4c88e50628a36187e22454da11666d718..1f8301053ddc1c113c741cf19367220ecf2512da 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md
index 107926c7ca511eb82a3f62c59d69d6470cf43d1d..5cef1f8f67d5d7759953e5579300adeff1c21af1 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md
@@ -46,20 +46,20 @@ IPP example
//Get CPU features enabled with selected library level
fm=ippGetEnabledCpuFeatures();
- printf("SSE :%cn",(fm>>1)&1?'Y':'N');
- printf("SSE2 :%cn",(fm>>2)&1?'Y':'N');
- printf("SSE3 :%cn",(fm>>3)&1?'Y':'N');
- printf("SSSE3 :%cn",(fm>>4)&1?'Y':'N');
- printf("SSE41 :%cn",(fm>>6)&1?'Y':'N');
- printf("SSE42 :%cn",(fm>>7)&1?'Y':'N');
- printf("AVX :%cn",(fm>>8)&1 ?'Y':'N');
- printf("AVX2 :%cn", (fm>>15)&1 ?'Y':'N' );
+ printf("SSE :%cn",(fm>1)&1?'Y':'N');
+ printf("SSE2 :%cn",(fm>2)&1?'Y':'N');
+ printf("SSE3 :%cn",(fm>3)&1?'Y':'N');
+ printf("SSSE3 :%cn",(fm>4)&1?'Y':'N');
+ printf("SSE41 :%cn",(fm>6)&1?'Y':'N');
+ printf("SSE42 :%cn",(fm>7)&1?'Y':'N');
+ printf("AVX :%cn",(fm>8)&1 ?'Y':'N');
+ printf("AVX2 :%cn", (fm>15)&1 ?'Y':'N' );
printf("----------n");
- printf("OS Enabled AVX :%cn", (fm>>9)&1 ?'Y':'N');
- printf("AES :%cn", (fm>>10)&1?'Y':'N');
- printf("CLMUL :%cn", (fm>>11)&1?'Y':'N');
- printf("RDRAND :%cn", (fm>>13)&1?'Y':'N');
- printf("F16C :%cn", (fm>>14)&1?'Y':'N');
+ printf("OS Enabled AVX :%cn", (fm>9)&1 ?'Y':'N');
+ printf("AES :%cn", (fm>10)&1?'Y':'N');
+ printf("CLMUL :%cn", (fm>11)&1?'Y':'N');
+ printf("RDRAND :%cn", (fm>13)&1?'Y':'N');
+ printf("F16C :%cn", (fm>14)&1?'Y':'N');
return 0;
}
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.epub
index a3af9d4e2f983326120b5ba81815f77b78f632af..1729c95241ae08c9d724ac1f608905a851a8a903 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.md
index ead5eae8f8e2dfb7d59ec64ca1dc9e651a4f4fdd..935f78fcce4c90447fcd259318490f69f03fced7 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.md
@@ -85,9 +85,9 @@ type (necessary for indexing large arrays, with more than 231^-1
elements), whereas the LP64 libraries index arrays with the 32-bit
integer type.
- Interface Integer type
- ----------- -----------------------------------------------
- LP64 32-bit, int, integer(kind=4), MPI_INT
+ |Interface|Integer type|
+ ----- |---|---|-------------------------------------
+ |LP64|32-bit, int, integer(kind=4), MPI_INT|
ILP64 64-bit, long int, integer(kind=8), MPI_INT64
### Linking
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.pdf
index 1cd23c8367c24ae97e5e37fd8e68258ef77edc1b..76038148c6b66456fdd66e43c27d571e17af3d67 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.epub
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.epub
index 11609bb9b19229df5346c671be1544717d119a07..97ab1f7e82719223a45791fe572be0bdd518009b 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.md
index ada902709a44ebe6b652fbecfcc18c11c365a28e..aba81d0dd10865fbf1eae0bcc866efa394615fe4 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.md
@@ -428,7 +428,7 @@ was used to compile the code on the host computer.
For your information the list of libraries and their location required
for execution of an OpenMP parallel code on Intel Xeon Phi is:
->/apps/intel/composer_xe_2013.5.192/compiler/lib/mic
+/apps/intel/composer_xe_2013.5.192/compiler/lib/mic
libiomp5.so
libimf.so
@@ -436,14 +436,14 @@ libsvml.so
libirng.so
libintlc.so.5
->Finally, to run the compiled code use:
+Finally, to run the compiled code use:
$ ~/path_to_binary/vect-add-mic
->OpenCL
+OpenCL
-------------------
->OpenCL (Open Computing Language) is an open standard for
+OpenCL (Open Computing Language) is an open standard for
general-purpose parallel programming for diverse mix of multi-core CPUs,
GPU coprocessors, and other parallel processors. OpenCL provides a
flexible execution model and uniform programming environment for
@@ -451,27 +451,27 @@ software developers to write portable code for systems running on both
the CPU and graphics processors or accelerators like the Intel® Xeon
Phi.
->On Anselm OpenCL is installed only on compute nodes with MIC
+On Anselm OpenCL is installed only on compute nodes with MIC
accelerator, therefore OpenCL code can be compiled only on these nodes.
module load opencl-sdk opencl-rt
->Always load "opencl-sdk" (providing devel files like headers) and
+Always load "opencl-sdk" (providing devel files like headers) and
"opencl-rt" (providing dynamic library libOpenCL.so) modules to compile
and link OpenCL code. Load "opencl-rt" for running your compiled code.
->There are two basic examples of OpenCL code in the following
+There are two basic examples of OpenCL code in the following
directory:
/apps/intel/opencl-examples/
->First example "CapsBasic" detects OpenCL compatible hardware, here
+First example "CapsBasic" detects OpenCL compatible hardware, here
CPU and MIC, and prints basic information about the capabilities of
it.Â
/apps/intel/opencl-examples/CapsBasic/capsbasic
->To compile and run the example copy it to your home directory, get
+To compile and run the example copy it to your home directory, get
a PBS interactive session on of the nodes with MIC and run make for
compilation. Make files are very basic and shows how the OpenCL code can
be compiled on Anselm.
@@ -480,11 +480,11 @@ be compiled on Anselm.
$ qsub -I -q qmic -A NONE-0-0
$ make
->The compilation command for this example is:
+The compilation command for this example is:
$ g++ capsbasic.cpp -lOpenCL -o capsbasic -I/apps/intel/opencl/include/
->After executing the complied binary file, following output should
+After executing the complied binary file, following output should
be displayed.
./capsbasic
@@ -497,7 +497,7 @@ be displayed.
   CL_DEVICE_TYPE_GPU: 0
   CL_DEVICE_TYPE_ACCELERATOR: 1
- *** Detailed information for each device ***
+ ** Detailed information for each device ***
CL_DEVICE_TYPE_CPU[0]
   CL_DEVICE_NAME:       Intel(R) Xeon(R) CPU E5-2470 0 @ 2.30GHz
@@ -511,10 +511,10 @@ be displayed.
...
->More information about this example can be found on Intel website:
+More information about this example can be found on Intel website:
<http://software.intel.com/en-us/vcsource/samples/caps-basic/>
->The second example that can be found in
+The second example that can be found in
"/apps/intel/opencl-examples" >directory is General Matrix
Multiply. You can follow the the same procedure to download the example
to your directory and compile it.Â
@@ -524,11 +524,11 @@ to your directory and compile it.Â
$ cd GEMM
$ make
->The compilation command for this example is:
+The compilation command for this example is:
$ g++ cmdoptions.cpp gemm.cpp ../common/basic.cpp ../common/cmdparser.cpp ../common/oclobject.cpp -I../common -lOpenCL -o gemm -I/apps/intel/opencl/include/
->To see the performance of Intel Xeon Phi performing the DGEMM run
+To see the performance of Intel Xeon Phi performing the DGEMM run
the example as follows:
./gemm -d 1
@@ -549,10 +549,10 @@ the example as follows:
Host perf: 426.081 GFLOPS
...
->Please note: GNU compiler is used to compile the OpenCL codes for
+Please note: GNU compiler is used to compile the OpenCL codes for
Intel MIC. You do not need to load Intel compiler module.
->MPIÂ
+MPIÂ
-----------------
### Environment setup and compilation
@@ -607,7 +607,7 @@ and pasted to a .c file)
### MPI programming models
->Intel MPI for the Xeon Phi coprocessors offers different MPI
+Intel MPI for the Xeon Phi coprocessors offers different MPI
programming models:
Host-only model** - all MPI ranks reside on the host. The coprocessors
@@ -620,9 +620,9 @@ coprocessors.
Symmetric model** - the MPI ranks reside on both the host and the
coprocessor. Most general MPI case.
-### >Host-only model
+###Host-only model
->In this case all environment variables are set by modules,
+In this case all environment variables are set by modules,
so to execute the compiled MPI program on a single node, use:
$ mpirun -np 4 ./mpi-test
@@ -636,7 +636,7 @@ The output should be similar to:
### Coprocessor-only model
->There are two ways how to execute an MPI code on a single
+There are two ways how to execute an MPI code on a single
coprocessor: 1.) lunch the program using "**mpirun**" from the
coprocessor; or 2.) lunch the task using "**mpiexec.hydra**" from a
host.
@@ -690,7 +690,7 @@ The output should be similar to:
Hello world from process 3 of 4 on host cn207-mic0
Hello world from process 0 of 4 on host cn207-mic0
-Execution on host**
+**Execution on host**
If the MPI program is launched from host instead of the coprocessor, the
environmental variables are not set using the ".profile" file. Therefore
@@ -732,10 +732,10 @@ execute:
  $ ssh mic0 ls /bin/pmi_proxy
 /bin/pmi_proxy
-Execution on host - MPI processes distributed over multiple
+**Execution on host - MPI processes distributed over multiple
accelerators on multiple nodes**
->To get access to multiple nodes with MIC accelerator, user has to
+To get access to multiple nodes with MIC accelerator, user has to
use PBS to allocate the resources. To start interactive session, that
allocates 2 compute nodes = 2 MIC accelerators run qsub command with
following parameters:
@@ -744,38 +744,38 @@ following parameters:
$ module load intel/13.5.192 impi/4.1.1.036
->This command connects user through ssh to one of the nodes
+This command connects user through ssh to one of the nodes
immediately. To see the other nodes that have been allocated use:
$ cat $PBS_NODEFILE
->For example:
+For example:
cn204.bullx
cn205.bullx
->This output means that the PBS allocated nodes cn204 and cn205,
+This output means that the PBS allocated nodes cn204 and cn205,
which means that user has direct access to "**cn204-mic0**" and
"**cn-205-mic0**" accelerators.
->Please note: At this point user can connect to any of the
+Please note: At this point user can connect to any of the
allocated nodes or any of the allocated MIC accelerators using ssh:
- to connect to the second node : ** $ ssh
cn205**
->- to connect to the accelerator on the first node from the first
+- to connect to the accelerator on the first node from the first
node: **$ ssh cn204-mic0** or
$ ssh mic0**
-** to connect to the accelerator on the second node from the first
node: **$ ssh cn205-mic0**
->At this point we expect that correct modules are loaded and binary
+At this point we expect that correct modules are loaded and binary
is compiled. For parallel execution the mpiexec.hydra is used.
Again the first step is to tell mpiexec that the MPI can be executed on
MIC accelerators by setting up the environmental variable "I_MPI_MIC"
$ export I_MPI_MIC=1
->The launch the MPI program use:
+The launch the MPI program use:
$ mpiexec.hydra -genv LD_LIBRARY_PATH /apps/intel/impi/4.1.1.036/mic/lib/
-genv I_MPI_FABRICS_LIST tcp
@@ -817,15 +817,15 @@ The same way MPI program can be executed on multiple hosts:Â
-host cn204 -n 4 ~/mpi-test
: -host cn205 -n 6 ~/mpi-test
-### >Symmetric model
+###Symmetric model
->In a symmetric mode MPI programs are executed on both host
+In a symmetric mode MPI programs are executed on both host
computer(s) and MIC accelerator(s). Since MIC has a different
architecture and requires different binary file produced by the Intel
compiler two different files has to be compiled before MPI program is
executed.
->In the previous section we have compiled two binary files, one for
+In the previous section we have compiled two binary files, one for
hosts "**mpi-test**" and one for MIC accelerators "**mpi-test-mic**".
These two binaries can be executed at once using mpiexec.hydra:
@@ -842,18 +842,18 @@ environment variables for execution. The third line specifies binary
that is executed on host (here cn205) and the last line specifies the
binary that is execute on the accelerator (here cn205-mic0).
->The output of the program is:
+The output of the program is:
Hello world from process 0 of 4 on host cn205
Hello world from process 1 of 4 on host cn205
Hello world from process 2 of 4 on host cn205-mic0
Hello world from process 3 of 4 on host cn205-mic0
->The execution procedure can be simplified by using the mpirun
+The execution procedure can be simplified by using the mpirun
command with the machine file a a parameter. Machine file contains list
of all nodes and accelerators that should used to execute MPI processes.
->An example of a machine file that uses 2 >hosts (**cn205**
+An example of a machine file that uses 2 >hosts (**cn205**
and **cn206**) and 2 accelerators **(cn205-mic0** and **cn206-mic0**) to
run 2 MPI processes on each of them:
@@ -863,7 +863,7 @@ run 2 MPI processes on each of them:
cn206:2
cn206-mic0:2
->In addition if a naming convention is set in a way that the name
+In addition if a naming convention is set in a way that the name
of the binary for host is **"bin_name"**Â and the name of the binary
for the accelerator is **"bin_name-mic"** then by setting up the
environment variable **I_MPI_MIC_POSTFIX** to **"-mic"** user do not
@@ -886,7 +886,7 @@ suffix to get a name of the binary for accelerator (i..e.
-machinefile hosts_file_mix
~/mpi-test
->A possible output of the MPI "hello-world" example executed on two
+A possible output of the MPI "hello-world" example executed on two
hosts and two accelerators is:
Hello world from process 0 of 8 on host cn204
@@ -906,11 +906,11 @@ Using the PBS automatically generated node-files
PBS also generates a set of node-files that can be used instead of
manually creating a new one every time. Three node-files are genereated:
-Host only node-file:**
+**Host only node-file:**
 - /lscratch/${PBS_JOBID}/nodefile-cn
-MIC only node-file**:
+MIC only node-file:
 - /lscratch/${PBS_JOBID}/nodefile-mic
-Host and MIC node-file**:
+Host and MIC node-file:
 - /lscratch/${PBS_JOBID}/nodefile-mix
Please note each host or accelerator is listed only per files. User has
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.epub
index c354a709c95a0b286d31338b68fd534e79ea35bb..ca15e4bad15763a47673c42ef712c960eefcd70c 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md
index a2a1335bc2d7a4c89fbec1a364ed6ef08c20ac1f..719fa3fd918379f0dd6564387b74270fdc5be2bd 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md
@@ -42,7 +42,7 @@ number of used and number of free license features. The text files are
accessible from the Anselm command prompt.
Product File with license state Note
- ------------ ----------------------------------------------------- ---------------------
+ ------ |---|---|------------------------------------------- ---------------------
ansys /apps/user/licenses/ansys_features_state.txt Commercial
comsol /apps/user/licenses/comsol_features_state.txt Commercial
comsol-edu /apps/user/licenses/comsol-edu_features_state.txt Non-commercial only
@@ -78,7 +78,7 @@ License tracking in PBS Pro scheduler and users usage
Each feature of each license is accounted and checked by the scheduler
of PBS Pro. If you ask for certain licences, the scheduler won't start
the job until the asked licenses are free (available). This prevents to
-crash batch jobs, just because of id="result_box"
+crash batch jobs, just because of
unavailability of the
needed licenses.
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/java.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/java.epub
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/kvirtualization.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/kvirtualization.epub
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/kvirtualization.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/kvirtualization.md
index 106d6dfeb8d432a4645c5dc086b14867bc74636e..803b896d1f2dc44638431b0e9c4d24efd4699d7e 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/kvirtualization.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/kvirtualization.md
@@ -66,7 +66,7 @@ Licensing
---------
IT4Innovations does not provide any licenses for operating systems and
-software of virtual machines. Users are ( id="result_box">
+software of virtual machines. Users are ( >
in accordance with [Acceptable use policy
document](http://www.it4i.cz/acceptable-use-policy.pdf))
fully responsible for licensing all software running in virtual machines
@@ -141,15 +141,15 @@ information see [Virtio
Linux](http://www.linux-kvm.org/page/Virtio) and [Virtio
Windows](http://www.linux-kvm.org/page/WindowsGuestDrivers/Download_Drivers).
-Disable all id="result_box"
+Disable all
unnecessary services
and tasks. Restrict all unnecessary operating system operations.
-Remove all id="result_box"
+Remove all
unnecessary software and
files.
- id="result_box"
+
Remove all paging
space, swap files, partitions, etc.
@@ -186,31 +186,31 @@ Example startup script for Windows virtual machine:
echo %DATE% %TIME% Running startup script>%LOG%
rem Mount share
- echo %DATE% %TIME% Mounting shared drive>>%LOG%
- net use z: 10.0.2.4qemu >>%LOG% 2>&1
- dir z: >>%LOG% 2>&1
- echo. >>%LOG%
+ echo %DATE% %TIME% Mounting shared drive>%LOG%
+ net use z: 10.0.2.4qemu >%LOG% 2>&1
+ dir z: >%LOG% 2>&1
+ echo. >%LOG%
if exist %MAPDRIVE% (
- Â echo %DATE% %TIME% The drive "%MAPDRIVE%" exists>>%LOG%
+ Â echo %DATE% %TIME% The drive "%MAPDRIVE%" exists>%LOG%
 if exist %SCRIPT% (
- Â Â Â echo %DATE% %TIME% The script file "%SCRIPT%"exists>>%LOG%
- Â Â Â echo %DATE% %TIME% Running script %SCRIPT%>>%LOG%
+ Â Â Â echo %DATE% %TIME% The script file "%SCRIPT%"exists>%LOG%
+ Â Â Â echo %DATE% %TIME% Running script %SCRIPT%>%LOG%
   set TIMEOUT=0
   call %SCRIPT%
 ) else (
- Â Â Â echo %DATE% %TIME% The script file "%SCRIPT%"does not exist>>%LOG%
+ Â Â Â echo %DATE% %TIME% The script file "%SCRIPT%"does not exist>%LOG%
 )
) else (
- Â echo %DATE% %TIME% The drive "%MAPDRIVE%" does not exist>>%LOG%
+ Â echo %DATE% %TIME% The drive "%MAPDRIVE%" does not exist>%LOG%
)
- echo. >>%LOG%
+ echo. >%LOG%
timeout /T %TIMEOUT%
- echo %DATE% %TIME% Shut down>>%LOG%
+ echo %DATE% %TIME% Shut down>%LOG%
shutdown /s /t 0
Example startup script maps shared job script as drive z: and looks for
@@ -219,7 +219,7 @@ for 5 minutes, then shutdown virtual machine.
### Create job script for executing virtual machine
-Create job script according recommended id="result_box"
+Create job script according recommended
[Virtual Machine Job
Workflow](virtualization.html#virtual-machine-job-workflow).
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/kvirtualization.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/kvirtualization.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md
index 1e6126a2fd6294c4972b6b84e737c4b3638316a4..03477ba6e3b3ecd0b61b5086adb72f431dfc91b1 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md
@@ -137,7 +137,7 @@ later) the following variables may be used for Intel or GCC:
$ export OMP_PROC_BIND=true
$ export OMP_PLACES=coresÂ
->OpenMPI Process Mapping and Binding
+OpenMPI Process Mapping and Binding
------------------------------------------------
The mpiexec allows for precise selection of how the MPI processes will
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.md
index d865beb6b5792af8b52f974d2de0b83b53bec853..fb348bb0091106d09774641c992a2f6ecca9cd56 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.md
@@ -37,7 +37,7 @@ used in conjunction with any compiler.
The defaults are selected via the modules in following way
Module MPI Compiler suite
- -------------- ------------------ --------------------------------------------------------------------------------
+ -------- |---|---|-------- --------------------------------------------------------------------------------
PrgEnv-gnu bullxmpi-1.2.4.1 bullx GNU 4.4.6
PrgEnv-intel Intel MPI 4.1.1 Intel 13.1.1
bullxmpi bullxmpi-1.2.4.1 none, select via module
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.md
index 49ce677e23df78b03aeb717fac60226b6729ab6a..e79ef4b1f0d649557a23691f3cc9e03070193127 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.md
@@ -45,7 +45,7 @@ to run
$ mpiexec python <script>.py
->For example
+For example
$ mpiexec python hello_world.py
@@ -62,7 +62,7 @@ Examples
comm.Barrier() Â # wait for everybody to synchronize
-### >Collective Communication with NumPy arrays
+###Collective Communication with NumPy arrays
from mpi4py import MPI
from __future__ import division
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.pdf
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index ef0a8ddfa8fd73cde55a9c4b70ef45359ce1be5a..eec66a690a4eb80bcb53fe398bfe0fe6d514147d 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.md
@@ -70,7 +70,7 @@ To use Distributed Computing, you first need to setup a parallel
profile. We have provided the profile for you, you can either import it
in MATLAB command line:
- >> parallel.importProfile('/apps/all/MATLAB/2015a-EDU/SalomonPBSPro.settings')
+ > parallel.importProfile('/apps/all/MATLAB/2015a-EDU/SalomonPBSPro.settings')
ans =
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave.md
index 59336da59a237700a123821c28bf747cf32a5053..6db86f6251cf7ff58eda6530eddab0dae8ab4de9 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave.md
@@ -14,12 +14,12 @@ for data visualization and manipulation. Octave is normally used through
its interactive command line interface, but it can also be used to write
non-interactive programs. The Octave language is quite similar to Matlab
so that most programs are easily portable. Read more on
-<http://www.gnu.org/software/octave/>****
+<http://www.gnu.org/software/octave/>***
Two versions of octave are available on Anselm, via module
Version module
- ----------------------------------------------------------- ---------------------------
+ ----------------------------------------------------- |---|---|-----------------
Octave 3.8.2, compiled with GCC and Multithreaded MKL Octave/3.8.2-gimkl-2.11.5
Octave 4.0.1, compiled with GCC and Multithreaded MKL Octave/4.0.1-gimkl-2.11.5
Octave 4.0.0, compiled with >GCC and OpenBLAS Octave/4.0.0-foss-2015g
@@ -138,11 +138,11 @@ function, [parallel
package](http://octave.sourceforge.net/parallel/) or
other mechanism) will actually run slower than on host CPU.
->To use Octave on a node with Xeon Phi:
+To use Octave on a node with Xeon Phi:
$ ssh mic0 # login to the MIC card
$ source /apps/tools/octave/3.8.2-mic/bin/octave-env.sh # set up environment variables
$ octave -q /apps/tools/octave/3.8.2-mic/example/test0.m # run an exampleÂ
->Â
+Â
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.epub
index 036d51700951f1d06b7974b31a3a66252dbde4bf..5829e13d11a96d061c8101e07c320b16d39749ce 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.md
index 5c4a03897fa28dd1476ab104d215ae447aa9fea1..694a9d570eb57a6c8a23934110518d13bca2ae08 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.md
@@ -32,10 +32,10 @@ Modules
**The R version 3.0.1 is available on Anselm, along with GUI interface
Rstudio
- Application Version module
- ------------- -------------- ---------
+ |Application|Version|module|
+ ------- |---|---|---- ---------
**R** R 3.0.1 R
- **Rstudio** Rstudio 0.97 Rstudio
+ |**Rstudio**|Rstudio 0.97|Rstudio|
$ module load R
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.md
index b36e1df414473cb2252b5d22842b0b6314d914e1..dc843fe8be9b69939bcbdbb202714a220d4cfdfd 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.md
@@ -22,7 +22,7 @@ gnu** compilers. These are available via modules:
<col width="25%" />
<col width="25%" />
<col width="25%" />
- |Version |Parallelization |module<th align="left">linker options |
+ |Version |Parallelization |module |linker options |
| --- | --- |
|FFTW3 gcc3.3.3 |pthread, OpenMP |fftw3/3.3.3-gcc |-lfftw3, -lfftw3_threads-lfftw3_omp |
|FFTW3 icc3.3.3\ |pthread, OpenMP |fftw3 |-lfftw3, -lfftw3_threads-lfftw3_omp |
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl.md
index 4852c3514728f5c82d659910f1b9945c57144071..35894dad44cd6d9d3990a456db65894d75c7961e 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl.md
@@ -19,7 +19,7 @@ wrappers to be written for very high level languages.
The library covers a wide range of topics in numerical computing.
Routines are available for the following areas:
- ------------------------ ------------------------ ------------------------
+ ------------------ |---|---|-------------- ------------------------
Complex Numbers Roots of Polynomials
Special Functions Vectors and Matrices
@@ -55,7 +55,7 @@ Routines are available for the following areas:
IEEE Floating-Point Physical Constants
Basis Splines Wavelets
- ------------------------ ------------------------ ------------------------
+ ------------------ |---|---|-------------- ------------------------
Modules
-------
@@ -64,7 +64,7 @@ The GSL 1.16 is available on Anselm, compiled for GNU and Intel
compiler. These variants are available via modules:
Module Compiler
- ----------------------- -----------
+ ----------------- |---|---|-
gsl/1.16-gcc gcc 4.8.6
gsl/1.16-icc(default) icc
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index 9192829dccfd2511d25b006010ceeb9794d5ef65..de3e37ad1154a0c4ff92221b5968d58deb24206f 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
index fe336aa4fb107845ec1e35c9af485b5be160ea27..7c6d9def6a429dcfb1695f4872af6cab1c8bc091 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
@@ -19,7 +19,7 @@ Versions **1.8.11** and **1.8.13** of HDF5 library are available on
Anselm, compiled for **Intel MPI** and **OpenMPI** using **intel** and
gnu** compilers. These are available via modules:
- |Version |Parallelization |module<th align="left">C linker options<th align="left">C++ linker options<th align="left">Fortran linker options |
+ |Version |Parallelization |module |C linker options<th align="left">C++ linker options<th align="left">Fortran linker options |
| --- | --- |
|HDF5 icc serial |pthread |hdf5/1.8.11 |$HDF5_INC $HDF5_SHLIB |$HDF5_INC $HDF5_CPP_LIB |$HDF5_INC $HDF5_F90_LIB |
|HDF5 icc parallel MPI\ |pthread, IntelMPI |hdf5-parallel/1.8.11 |$HDF5_INC $HDF5_SHLIB |Not supported |$HDF5_INC $HDF5_F90_LIB |
@@ -116,5 +116,5 @@ For further informations, please see the website:
class="smarterwiki-popup-bubble-tip">
-btnI=I'm+Feeling+Lucky&btnI=I'm+Feeling+Lucky&q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB+wikipedia "Search Wikipedia"){.smarterwiki-popup-bubble</span>
+btnI=I'm+Feeling+Lucky&btnI=I'm+Feeling+Lucky&q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB+wikipedia "Search Wikipedia"){.smarterwiki-popup-bubble
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.md
index 3c3baa148e0a03f923f93305a5339bd06aa4f12a..01168124d53b6b2006bb10669c056b33eb97b2c5 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.md
@@ -26,7 +26,7 @@ compile a CUDA source code, use nvcc compiler.
$ nvcc --version
->CUDA Toolkit comes with large number of examples, that can be
+CUDA Toolkit comes with large number of examples, that can be
helpful to start with. To compile and test these examples user should
copy them to its home directoryÂ
@@ -158,7 +158,7 @@ example. You can directly copy and paste the code to test it.Â
 cudaMemcpy( dev_b, b, size, cudaMemcpyHostToDevice );
 // launch add_gpu() kernel with blocks and threads
- Â add_gpu<<< N/THREADS_PER_BLOCK, THREADS_PER_BLOCK >>>( dev_a, dev_b, dev_c, N );
+ Â add_gpu<<< N/THREADS_PER_BLOCK, THREADS_PER_BLOCK >>( dev_a, dev_b, dev_c, N );
 // copy device result back to host copy of c
 cudaMemcpy( c, dev_c, size, cudaMemcpyDeviceToHost );
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.pdf
index 0a7766caef13063a79e617fe116a4056d652b2c4..68ecd5acc01a5cc47b7abcd8ad14c102028a3d44 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.epub
index c2521e95e7dfeb906eb08f6ad81a98b7cf9640be..f9c50bfb3eddb2035956e110d085bf6b827c783e 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md
index 1d64ec161c43715dafac51e30c7b5d4aff3b902d..3a6927548f74855361b39ee291a0ccf95aac8046 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md
@@ -38,7 +38,7 @@ increases.](fig5.png)
Â
-*Figure 5. ****Interface of the application. Panels for defining
+*Figure 5. ***Interface of the application. Panels for defining
targeted regions of interest can be set up by just drag and drop known
disease genes or disease definitions from the lists. Thus, virtual
panels can be interactively improved as the knowledge of the disease
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.pdf
index a504d54c24de83f1a1ded039af661887cc62333d..633a4fe4e1814998ff3aa0c980f71a3a6169e18d 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.epub b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.epub
index 66498d624bc1fd627fa424702274c4dd018e9561..46da8844d17db94c2f478c7dfa3ed088f7caf1a7 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md
index aa82e9852509460a0a5b4b533696c67a8f64acae..0382b6936197e3ccd09774224ddd043c277b8135 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md
@@ -29,7 +29,7 @@ component where they can be analysed directly by the user that produced
them, depending of the experimental design carried
out.](fig1.png)
-*Figure 1.*** *OMICS MASTER solution overview. Data is produced in the
+*Figure 1.** *OMICS MASTER solution overview. Data is produced in the
external labs and comes to IT4I (represented by the blue dashed line).
The data pre-processor converts raw data into a list of variants and
annotations for each sequenced patient. These lists files together with
@@ -89,7 +89,7 @@ Output: FASTQ file plus an HTML file containing statistics on the
data.Â
FASTQ formatÂ
->It represents the nucleotide sequence and its corresponding
+It represents the nucleotide sequence and its corresponding
quality scores.
@@ -112,24 +112,24 @@ number of mismatches or indels.
Input: FASTQ file.
-Output:** Aligned file in BAM format.****
+Output:** Aligned file in BAM format.***
Sequence Alignment/Map (SAM)**
->It is a human readable tab-delimited format in which each read and
+It is a human readable tab-delimited format in which each read and
its alignment is represented on a single line. The format can represent
unmapped reads, reads that are mapped to unique locations, and reads
that are mapped to multiple locations.
->The SAM format (1)^> consists of one header
+The SAM format (1)^> consists of one header
section and one alignment section. The lines in the header section start
with character â€@’, and lines in the alignment section do not. All lines
are TAB delimited.
->In SAM, each alignment line has 11 mandatory fields and a variable
+In SAM, each alignment line has 11 mandatory fields and a variable
number of optional fields. The mandatory fields are briefly described in
Table 1. They must be present but their value can be a
-â€*’>> or a zero (depending on the field) if the
+â€*’> or a zero (depending on the field) if the
corresponding information is unavailable. Â
<col width="33%" />
@@ -148,10 +148,8 @@ corresponding information is unavailable. Â
|10\ |<p>SEQÂ \ |<p>Query SEQuence on the same strand as the reference</p> |
|11\ |<p>QUALÂ \ |<p>Query QUALity (ASCII-33=Phred base quality)</p> |
->
+*Table 1.** *Mandatory fields in the SAM format.
-*Table 1.*** *Mandatory fields in the SAM format.
->
The standard CIGAR description of pairwise alignment defines three
operations: â€M’ for match/mismatch, â€I’ for insertion compared with the
reference and â€D’ for deletion. The extended CIGAR proposed in SAM added
@@ -176,7 +174,7 @@ present in the sequence field. The NM tag gives the number of
mismatches. Read r004 is aligned across an intron, indicated by the N
operation.](fig3.png)
*
-Figure 3.*** *SAM format file. The â€@SQ’ line in the header section
+Figure 3.** *SAM format file. The â€@SQ’ line in the header section
gives the order of reference sequences. Notably, r001 is the name of a
read pair. According to FLAG 163 (=1+2+32+128), the read mapped to
position 7 is the second read in the pair (128) and regarded as properly
@@ -194,7 +192,7 @@ by the N operation.**
Binary Alignment/Map (BAM)**
->BAM is the binary representation of SAM and keeps exactly the same
+BAM is the binary representation of SAM and keeps exactly the same
information as SAM. BAM uses lossless compression to reduce the size of
the data by about 75% and provides an indexing system that allows reads
that overlap a region of the genome to be retrieved and rapidly
@@ -230,7 +228,7 @@ Output:** VCF**
**Variant Call Format (VCF)**
->VCF (3)^> is a standardized format for storing the
+VCF (3)^> is a standardized format for storing the
most prevalent types of sequence variation, including SNPs, indels and
larger structural variants, together with rich annotations. The format
was developed with the primary intention to represent human genetic
@@ -310,7 +308,7 @@ coordinate refers to the first reference base. (g) Users are advised to
use simplest representation possible and lowest coordinate in cases
where the position is ambiguous.
-### >Annotating
+###Annotating
Component:** HPG-Variant
@@ -407,7 +405,7 @@ module and all the required modules (
hpg-aligner,
gatk, etc)
-> If we launch ngsPipeline with â€-h’, we will get the usage
+ If we launch ngsPipeline with â€-h’, we will get the usage
help:Â
$ ngsPipeline -h
@@ -468,23 +466,23 @@ end the pipeline in a specific stage we must use -e.
     *--log*. Using log argument NGSpipeline will prompt all the logs
to this file.
->Â Â Â Â *--project*>. Project ID of your supercomputer
+Â Â Â Â *--project*>. Project ID of your supercomputer
allocation.Â
->Â Â Â Â *--queue*.
+Â Â Â Â *--queue*.
[Queue](../../resource-allocation-and-job-execution/introduction.html)
to run the jobs in.
 >Input, output and ped arguments are mandatory. If the output
folder does not exist, the pipeline will create it.
->Examples
+Examples
---------------------
This is an example usage of NGSpipeline:
We have a folder with the following structure in >
-/apps/bio/omics/1.0/sample_data/Â >:</span>
+/apps/bio/omics/1.0/sample_data/Â >:
/apps/bio/omics/1.0/sample_data
└── data
@@ -523,10 +521,10 @@ should use the next command:
$ ngsPipeline -i /scratch/$USER/omics/sample_data/data -o /scratch/$USER/omics/results -p /scratch/$USER/omics/sample_data/data/file.ped -s 4 -e 20 --project OPEN-0-0 --queue qprod
->Details on the pipeline
+Details on the pipeline
------------------------------------
->The pipeline calls the following tools:
+The pipeline calls the following tools:
- >[fastqc](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/),
a>Â quality control tool for high throughput
@@ -550,23 +548,23 @@ should use the next command:
- >[hpg-fastq](http://docs.bioinfo.cipf.es/projects/fastqhpc/wiki), > a
quality control tool for high throughput
sequence data.
-- >>[hpg-variant](http://wiki.opencb.org/projects/hpg/doku.php?id=variant:downloads), <span>The
+- >[hpg-variant](http://wiki.opencb.org/projects/hpg/doku.php?id=variant:downloads), >The
HPG Variant suite is an ambitious project aimed to provide a
complete suite of tools to work with genomic variation data, from
VCF tools to variant profiling or genomic statistics. It is being
implemented using High Performance Computing technologies to provide
- the best performance possible.</span>
-- >>[picard](http://picard.sourceforge.net/), <span>Picard
+ the best performance possible.
+- >[picard](http://picard.sourceforge.net/), >Picard
comprises Java-based command-line utilities that manipulate SAM
files, and a Java API (HTSJDK) for creating new programs that read
and write SAM files. Both SAM text format and SAM binary (BAM)
- format are supported.</span>
-- >>[samtools](http://samtools.sourceforge.net/samtools-c.shtml), <span>SAM
+ format are supported.
+- >[samtools](http://samtools.sourceforge.net/samtools-c.shtml), >SAM
Tools provide various utilities for manipulating alignments in the
SAM format, including sorting, merging, indexing and generating
alignments in a
- per-position format.</span>
-- >><span>[snpEff](http://snpeff.sourceforge.net/), <span>Genetic
+ per-position format.
+- >>[snpEff](http://snpeff.sourceforge.net/), <span>Genetic
variant annotation and effect
prediction toolbox.
@@ -602,7 +600,7 @@ This listing show which tools are used in each step of the pipeline :
- >stage-27: snpEff
- >stage-28: hpg-variant
->Interpretation
+Interpretation
---------------------------
The output folder contains all the subfolders with the intermediate
@@ -613,13 +611,13 @@ file button. It is important to note here that the entire management of
the VCF file is local: no patient’s sequence data is sent over the
Internet thus avoiding any problem of data privacy or confidentiality.
->
-*Figure 7***. *TEAM upload panel.* *Once the file has been uploaded, a
-panel must be chosen from the Panel **** list. Then, pressing the Run
+*Figure 7**. *TEAM upload panel.* *Once the file has been uploaded, a
+panel must be chosen from the Panel *** list. Then, pressing the Run
button the diagnostic process starts.*
Once the file has been uploaded, a panel must be chosen from the Panel
@@ -642,7 +640,7 @@ associated to an already existing disease term (action E). Disease terms
can be removed by simply dragging themback (action
H).](fig7x.png)
-*Figure 7.*** *The panel manager. The elements used to define a panel
+*Figure 7.** *The panel manager. The elements used to define a panel
are (**A**) disease terms, (**B**) diagnostic mutations and (**C**)
genes. Arrows represent actions that can be taken in the panel manager.
Panels can be defined by using the known mutations and genes of a
@@ -662,7 +660,7 @@ BierApp by using the following form:
job as well as a description.
](fig8.png)*
-**Figure 8.*** *BierApp VCF upload panel. It is recommended to choose
+**Figure 8.** *BierApp VCF upload panel. It is recommended to choose
a name for the job as well as a description.**
Each prioritization (â€job’) has three associated screens that facilitate
@@ -681,135 +679,133 @@ column. In this case, the variant 7:132481242 C>T is associated to
the phenotype: large intestine
tumor.](fig9.png)
-***Figure 9.*** *This picture shows all the information associated to
+**Figure 9.*** *This picture shows all the information associated to
the variants. If a variant has an associated phenotype we could see it
in the last column. In this case, the variant 7:132481242 C>T is
-associated to the phenotype: large intestine tumor.***
+associated to the phenotype: large intestine tumor.**
*
*
->
-
->References
+References
-----------------------
-1. class="discreet">Heng Li, Bob Handsaker, Alec Wysoker, Tim
+1. Heng Li, Bob Handsaker, Alec Wysoker, Tim
Fennell, Jue Ruan, Nils Homer, Gabor Marth5, Goncalo Abecasis6,
Richard Durbin and 1000 Genome Project Data Processing Subgroup: The
Sequence Alignment/Map format and SAMtools. Bioinformatics 2009,
25: 2078-2079.
-2. class="discreet">>McKenna A, Hanna M, Banks E, Sivachenko
+2. >McKenna A, Hanna M, Banks E, Sivachenko
A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S,
Daly M, DePristo MA: The Genome Analysis Toolkit: a MapReduce
framework for analyzing next-generation DNA sequencing data.
- *Genome Res* >2010, 20:1297-1303.</span>
-3. class="discreet">Petr Danecek, Adam Auton, Goncalo Abecasis,
+ *Genome Res* >2010, 20:1297-1303.
+3. Petr Danecek, Adam Auton, Goncalo Abecasis,
Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert E.
Handsaker, Gerton Lunter, Gabor T. Marth, Stephen T. Sherry, Gilean
McVean, Richard Durbin, and 1000 Genomes Project Analysis Group. The
variant call format and VCFtools. Bioinformatics 2011,
27: 2156-2158.
-4. class="discreet">Medina I, De Maria A, Bleda M, Salavert F,
+4. Medina I, De Maria A, Bleda M, Salavert F,
Alonso R, Gonzalez CY, Dopazo J: VARIANT: Command Line, Web service
and Web interface for fast and accurate functional characterization
of variants found by Next-Generation Sequencing. Nucleic Acids Res
2012, 40:W54-58.
-5. class="discreet">Bleda M, Tarraga J, de Maria A, Salavert F,
+5. Bleda M, Tarraga J, de Maria A, Salavert F,
Garcia-Alonso L, Celma M, Martin A, Dopazo J, Medina I: CellBase, a
comprehensive collection of RESTful web services for retrieving
relevant biological information from heterogeneous sources. Nucleic
Acids Res 2012, 40:W609-614.
-6. class="discreet">Flicek,P., Amode,M.R., Barrell,D., Beal,K.,
+6. Flicek,P., Amode,M.R., Barrell,D., Beal,K.,
Brent,S., Carvalho-Silva,D., Clapham,P., Coates,G.,
Fairley,S., Fitzgerald,S. et al. (2012) Ensembl 2012. Nucleic Acids
Res., 40, D84–D90.
-7. class="discreet">UniProt Consortium. (2012) Reorganizing the
+7. UniProt Consortium. (2012) Reorganizing the
protein space at the Universal Protein Resource (UniProt). Nucleic
Acids Res., 40, D71–D75.
-8. class="discreet">Kozomara,A. and Griffiths-Jones,S. (2011)
+8. Kozomara,A. and Griffiths-Jones,S. (2011)
miRBase: integrating microRNA annotation and deep-sequencing data.
Nucleic Acids Res., 39, D152–D157.
-9. class="discreet">Xiao,F., Zuo,Z., Cai,G., Kang,S., Gao,X.
+9. Xiao,F., Zuo,Z., Cai,G., Kang,S., Gao,X.
and Li,T. (2009) miRecords: an integrated resource for
microRNA-target interactions. Nucleic Acids Res.,
37, D105–D110.
-10. class="discreet">Hsu,S.D., Lin,F.M., Wu,W.Y., Liang,C.,
+10. Hsu,S.D., Lin,F.M., Wu,W.Y., Liang,C.,
Huang,W.C., Chan,W.L., Tsai,W.T., Chen,G.Z., Lee,C.J., Chiu,C.M.
et al. (2011) miRTarBase: a database curates experimentally
validated microRNA-target interactions. Nucleic Acids Res.,
39, D163–D169.
-11. class="discreet">Friedman,R.C., Farh,K.K., Burge,C.B.
+11. Friedman,R.C., Farh,K.K., Burge,C.B.
and Bartel,D.P. (2009) Most mammalian mRNAs are conserved targets
of microRNAs. Genome Res., 19, 92–105.
-12. class="discreet">Betel,D., Wilson,M., Gabow,A., Marks,D.S.
+12. Betel,D., Wilson,M., Gabow,A., Marks,D.S.
and Sander,C. (2008) The microRNA.org resource: targets
and expression. Nucleic Acids Res., 36, D149–D153.
-13. class="discreet">Dreszer,T.R., Karolchik,D., Zweig,A.S.,
+13. Dreszer,T.R., Karolchik,D., Zweig,A.S.,
Hinrichs,A.S., Raney,B.J., Kuhn,R.M., Meyer,L.R., Wong,M.,
Sloan,C.A., Rosenbloom,K.R. et al. (2012) The UCSC genome browser
database: extensions and updates 2011. Nucleic Acids Res.,
40, D918–D923.
-14. class="discreet">Smith,B., Ashburner,M., Rosse,C., Bard,J.,
+14. Smith,B., Ashburner,M., Rosse,C., Bard,J.,
Bug,W., Ceusters,W., Goldberg,L.J., Eilbeck,K.,
Ireland,A., Mungall,C.J. et al. (2007) The OBO Foundry: coordinated
evolution of ontologies to support biomedical data integration. Nat.
Biotechnol., 25, 1251–1255.
-15. class="discreet">Hunter,S., Jones,P., Mitchell,A.,
+15. Hunter,S., Jones,P., Mitchell,A.,
Apweiler,R., Attwood,T.K.,Bateman,A., Bernard,T., Binns,D.,
Bork,P., Burge,S. et al. (2012) InterPro in 2011: new developments
in the family and domain prediction database. Nucleic Acids Res.,
40, D306–D312.
-16. class="discreet">Sherry,S.T., Ward,M.H., Kholodov,M.,
+16. Sherry,S.T., Ward,M.H., Kholodov,M.,
Baker,J., Phan,L., Smigielski,E.M. and Sirotkin,K. (2001) dbSNP: the
NCBI database of genetic variation. Nucleic Acids Res.,
29, 308–311.
-17. class="discreet">Altshuler,D.M., Gibbs,R.A., Peltonen,L.,
+17. Altshuler,D.M., Gibbs,R.A., Peltonen,L.,
Dermitzakis,E., Schaffner,S.F., Yu,F., Bonnen,P.E., de Bakker,P.I.,
Deloukas,P., Gabriel,S.B. et al. (2010) Integrating common and rare
genetic variation in diverse human populations. Nature,
467, 52–58.
-18. class="discreet">1000 Genomes Project Consortium. (2010) A map
+18. 1000 Genomes Project Consortium. (2010) A map
of human genome variation from population-scale sequencing. Nature,
467, 1061–1073.
-19. class="discreet">Hindorff,L.A., Sethupathy,P., Junkins,H.A.,
+19. Hindorff,L.A., Sethupathy,P., Junkins,H.A.,
Ramos,E.M., Mehta,J.P., Collins,F.S. and Manolio,T.A. (2009)
Potential etiologic and functional implications of genome-wide
association loci for human diseases and traits. Proc. Natl Acad.
Sci. USA, 106, 9362–9367.
-20. class="discreet">Stenson,P.D., Ball,E.V., Mort,M.,
+20. Stenson,P.D., Ball,E.V., Mort,M.,
Phillips,A.D., Shiel,J.A., Thomas,N.S., Abeysinghe,S., Krawczak,M.
and Cooper,D.N. (2003) Human gene mutation database (HGMD):
2003 update. Hum. Mutat., 21, 577–581.
-21. class="discreet">Johnson,A.D. and O’Donnell,C.J. (2009) An
+21. Johnson,A.D. and O’Donnell,C.J. (2009) An
open access database of genome-wide association results. BMC Med.
Genet, 10, 6.
-22. class="discreet">McKusick,V. (1998) A Catalog of Human Genes
+22. McKusick,V. (1998) A Catalog of Human Genes
and Genetic Disorders, 12th edn. John Hopkins University
Press,Baltimore, MD.
-23. class="discreet">Forbes,S.A., Bindal,N., Bamford,S., Cole,C.,
+23. Forbes,S.A., Bindal,N., Bamford,S., Cole,C.,
Kok,C.Y., Beare,D., Jia,M., Shepherd,R., Leung,K., Menzies,A. et al.
(2011) COSMIC: mining complete cancer genomes in the catalogue of
somatic mutations in cancer. Nucleic Acids Res.,
39, D945–D950.
-24. class="discreet">Kerrien,S., Aranda,B., Breuza,L., Bridge,A.,
+24. Kerrien,S., Aranda,B., Breuza,L., Bridge,A.,
Broackes-Carter,F., Chen,C., Duesbury,M., Dumousseau,M.,
Feuermann,M., Hinz,U. et al. (2012) The Intact molecular interaction
database in 2012. Nucleic Acids Res., 40, D841–D846.
-25. class="discreet">Croft,D., O’Kelly,G., Wu,G., Haw,R.,
+25. Croft,D., O’Kelly,G., Wu,G., Haw,R.,
Gillespie,M., Matthews,L., Caudy,M., Garapati,P.,
Gopinath,G., Jassal,B. et al. (2011) Reactome: a database of
reactions, pathways and biological processes. Nucleic Acids Res.,
39, D691–D697.
-26. class="discreet">Demir,E., Cary,M.P., Paley,S., Fukuda,K.,
+26. Demir,E., Cary,M.P., Paley,S., Fukuda,K.,
Lemer,C., Vastrik,I.,Wu,G., D’Eustachio,P., Schaefer,C., Luciano,J.
et al. (2010) The BioPAX community standard for pathway
data sharing. Nature Biotechnol., 28, 935–942.
-27. class="discreet">Alemán Z, GarcĂa-GarcĂa F, Medina I, Dopazo J
+27. Alemán Z, GarcĂa-GarcĂa F, Medina I, Dopazo J
(2014): A web tool for the design and management of panels of genes
for targeted enrichment and massive sequencing for
clinical applications. Nucleic Acids Res 42: W83-7.
-28. class="discreet">[Alemán
+28. [Alemán
A](http://www.ncbi.nlm.nih.gov/pubmed?term=Alem%C3%A1n%20A%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Garcia-Garcia
F](http://www.ncbi.nlm.nih.gov/pubmed?term=Garcia-Garcia%20F%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Salavert
F](http://www.ncbi.nlm.nih.gov/pubmed?term=Salavert%20F%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Medina
@@ -819,15 +815,13 @@ associated to the phenotype: large intestine tumor.***
disease candidate genes in whole-exome sequencing studies.
[Nucleic
Acids Res.](http://www.ncbi.nlm.nih.gov/pubmed/?term=BiERapp "Nucleic acids research.")>42 :W88-93.
-29. class="discreet">Landrum,M.J., Lee,J.M., Riley,G.R., Jang,W.,
+29. Landrum,M.J., Lee,J.M., Riley,G.R., Jang,W.,
Rubinstein,W.S., Church,D.M. and Maglott,D.R. (2014) ClinVar: public
archive of relationships among sequence variation and
human phenotype. Nucleic Acids Res., 42, D980–D985.
-30. class="discreet">Medina I, Salavert F, Sanchez R, de Maria A,
+30. Medina I, Salavert F, Sanchez R, de Maria A,
Alonso R, Escobar P, Bleda M, Dopazo J: Genome Maps, a new
generation genome browser. Nucleic Acids Res 2013, 41:W41-46.
Â
->
-
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.pdf
index 8724944dd6bc51910b1447a0eaca894b48df8432..cc4db0a896fec9ef06944c0999ab5f90f00ebb67 100644
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.md
index 945ab2969b1f5d89b1270f49bfafddb1dc08057f..a6cd22b5866bbbb95035359d3f1ffddf1c4772cf 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.md
@@ -9,9 +9,9 @@ BiERApp is available at the following address
The address is accessible only
via [VPN. ](../../accessing-the-cluster/vpn-access.html)
-### >BiERApp
+###BiERApp
-### >This tool is aimed to discover new disease genes or variants by studying affected families or cases and controls. It carries out a filtering process to sequentially remove:Â (i) variants which are not no compatible with the disease because are not expected to have impact on the protein function; (ii) variants that exist at frequencies incompatible with the disease; (iii) variants that do not segregate with the disease. The result is a reduced set of disease gene candidates that should be further validated experimentally.
+###This tool is aimed to discover new disease genes or variants by studying affected families or cases and controls. It carries out a filtering process to sequentially remove:Â (i) variants which are not no compatible with the disease because are not expected to have impact on the protein function; (ii) variants that exist at frequencies incompatible with the disease; (iii) variants that do not segregate with the disease. The result is a reduced set of disease gene candidates that should be further validated experimentally.
BiERapp >(28) efficiently helps in the identification of
causative variants in family and sporadic genetic diseases. The program
@@ -34,7 +34,7 @@ filters available. The tool includes a genomic viewer (Genome Maps 30)
that enables the representation of the variants in the corresponding
genomic coordinates.](fig6.png)
-*Figure 6***. *Web interface to the prioritization tool.* *This
+*Figure 6**. *Web interface to the prioritization tool.* *This
figure*Â *shows the interface of the web tool for candidate gene
prioritization with the filters available. The tool includes a genomic
viewer (Genome Maps >30) that enables the representation of
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.pdf b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.pdf
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.md
index 7c99083bd251ba4addecf9fa2f0d8fb9bd5d6d76..f5579ca1e525599353caf270ff971a04d4c23d58 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.md
@@ -25,24 +25,24 @@ Anselm.
For example syntax of available OpenFOAM module is:
->< openfoam/2.2.1-icc-openmpi1.6.5-DP >
+< openfoam/2.2.1-icc-openmpi1.6.5-DP >
this means openfoam version >2.2.1 compiled by
->ICC compiler with >openmpi1.6.5 in<span> double
+ICC compiler with >openmpi1.6.5 in> double
precision.
Naming convection of the installed versions is following:
->Â Â
-openfoam/<>VERSION>>-<</span><span>COMPILER</span><span>>-<</span><span>openmpiVERSION</span><span>>-<</span><span>PRECISION</span><span>></span>
+Â Â
+openfoam/<>VERSION>>-<>COMPILER<span>>-<</span><span>openmpiVERSION</span><span>>-<</span><span>PRECISION</span><span>></span>
-- ><>VERSION<span>> - version of
+- ><>VERSION>> - version of
openfoam
- ><>COMPILER> - version of used
compiler
- ><>openmpiVERSION> - version of used
openmpi/impi
-- ><>PRECISION> - DP/<span>SP –
+- ><>PRECISION> - DP/>SP –
double/single precision
###Available OpenFOAM modules**
@@ -102,11 +102,9 @@ in a cavity.
Running Serial Applications**
-------------------------------
->Create a Bash script >test.shÂ
+Create a Bash script >test.shÂ
->
-
->
+
#!/bin/bash
module load openfoam/2.2.1-icc-openmpi1.6.5-DP
source $FOAM_BASHRC
@@ -119,34 +117,32 @@ Running Serial Applications**
runApplication blockMesh
runApplication icoFoam
->
+
->
+
->Job submission
+Job submission
->
+
$ qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=16,walltime=03:00:00 test.sh
->
+
-> For information about job submission please [look
+ For information about job submission please [look
here](../resource-allocation-and-job-execution/job-submission-and-execution.html "Job submission").
->Running applications in parallel**
+Running applications in parallel**
-------------------------------------------------
->Run the second case for example external incompressible turbulent
+Run the second case for example external incompressible turbulent
flow - case - motorBike.
->First we must run serial application bockMesh and decomposePar for
+First we must run serial application bockMesh and decomposePar for
preparation of parallel computation.
->
-
->Create a Bash scrip test.sh:
+Create a Bash scrip test.sh:
->
+
#!/bin/bash
module load openfoam/2.2.1-icc-openmpi1.6.5-DP
source $FOAM_BASHRC
@@ -159,24 +155,22 @@ preparation of parallel computation.
runApplication blockMesh
runApplication decomposePar
->
+
->
+Job submission
->Job submission
-
->
+
$ qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=16,walltime=03:00:00 test.sh
->
+
->>This job create simple block mesh and domain decomposition.
+This job create simple block mesh and domain decomposition.
Check your decomposition, and submit parallel computation:
->>Create a PBS script<span>
-testParallel.pbs:</span>
+Create a PBS script>
+testParallel.pbs:
->
+
#!/bin/bash
#PBS -N motorBike
#PBS -l select=2:ncpus=16
@@ -197,64 +191,62 @@ testParallel.pbs:</span>
mpirun -hostfile ${PBS_NODEFILE} -np $nproc simpleFoam -parallel | tee simpleFoam.log
->
+
->nproc – number of subdomains
+nproc – number of subdomains
->Job submission
+Job submission
->
+
$ qsub testParallel.pbs
->
+
->Compile your own solver**
+Compile your own solver**
----------------------------------------
->Initialize OpenFOAM environment before compiling your solver
+Initialize OpenFOAM environment before compiling your solver
->
+
$ module load openfoam/2.2.1-icc-openmpi1.6.5-DP
$ source $FOAM_BASHRC
$ cd $FOAM_RUN/
->Create directory applications/solvers in user directory
+Create directory applications/solvers in user directory
->
+
$ mkdir -p applications/solvers
$ cd applications/solvers
->
+
->Copy icoFoam solver’s source files
+Copy icoFoam solver’s source files
->
+
$ cp -r $FOAM_SOLVERS/incompressible/icoFoam/ My_icoFoam
$ cd My_icoFoam
->Rename icoFoam.C to My_icoFOAM.C
+Rename icoFoam.C to My_icoFOAM.C
->
+
$ mv icoFoam.C My_icoFoam.C
->
+
->Edit >*files* file in *Make* directory:
+Edit >*files* file in *Make* directory:
->
+
icoFoam.C
EXE = $(FOAM_APPBIN)/icoFoam
->and change to:
+and change to:
My_icoFoam.C
EXE = $(FOAM_USER_APPBIN)/My_icoFoam
->
-
->In directory My_icoFoam give the compilation command:
+In directory My_icoFoam give the compilation command:
->
+
$ wmake
------------------------------------------------------------------------
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diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.md b/converted/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.md
index ce8989c5b0c71722750299e4a1417c8fb0de6228..2a58b726d505798696080198c159d55dbc9138f9 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.md
@@ -81,14 +81,14 @@ setstripe command for setting the stripe parameters to get optimal I/O
performance The correct stripe setting depends on your needs and file
access patterns.Â
-```
+`
$ lfs getstripe dir|filename
$ lfs setstripe -s stripe_size -c stripe_count -o stripe_offset dir|filename
-```
+`
Example:
-```
+`
$ lfs getstripe /scratch/username/
/scratch/username/
stripe_count: 1 stripe_size: 1048576 stripe_offset: -1
@@ -97,7 +97,7 @@ $ lfs setstripe -c -1 /scratch/username/
$ lfs getstripe /scratch/username/
/scratch/username/
stripe_count: 10 stripe_size: 1048576 stripe_offset: -1
-```
+`
In this example, we view current stripe setting of the
/scratch/username/ directory. The stripe count is changed to all OSTs,
@@ -107,10 +107,10 @@ and verified. All files written to this directory will be striped over
Use lfs check OSTs to see the number and status of active OSTs for each
filesystem on Anselm. Learn more by reading the man page
-```
+`
$ lfs check osts
$ man lfs
-```
+`
### Hints on Lustre Stripping
@@ -278,18 +278,18 @@ Default stripe count
1
Number of OSTs
10
-### >Disk usage and quota commands
+### Disk usage and quota commands
->User quotas on the file systems can be checked and reviewed using
+User quotas on the file systems can be checked and reviewed using
following command:
-```
+`
$ lfs quota dir
-```
+`
Example for Lustre HOME directory:
-```
+`
$ lfs quota /home
Disk quotas for user user001 (uid 1234):
Filesystem kbytes quota limit grace files quota limit grace
@@ -297,14 +297,14 @@ Disk quotas for user user001 (uid 1234):
Disk quotas for group user001 (gid 1234):
Filesystem kbytes quota limit grace files quota limit grace
/home 300096 0 0 - 2102 0 0 -
-```
+`
In this example, we view current quota size limit of 250GB and 300MB
currently used by user001.
Example for Lustre SCRATCH directory:
-```
+`
$ lfs quota /scratch
Disk quotas for user user001 (uid 1234):
Filesystem kbytes quota limit grace files quota limit grace
@@ -312,7 +312,7 @@ Disk quotas for user user001 (uid 1234):
Disk quotas for group user001 (gid 1234):
Filesystem kbytes quota limit grace files quota limit grace
/scratch    8    0    0    -    3    0    0    -
-```
+`
In this example, we view current quota size limit of 100TB and 8KB
currently used by user001.
@@ -322,13 +322,13 @@ currently used by user001.
To have a better understanding of where the space is exactly used, you
can use following command to find out.
-```
+`
$ du -hs dir
-```
+`
Example for your HOME directory:
-```
+`
$ cd /home
$ du -hs * .[a-zA-z0-9]* | grep -E "[0-9]*G|[0-9]*M" | sort -hr
258M cuda-samples
@@ -336,23 +336,23 @@ $ du -hs * .[a-zA-z0-9]* | grep -E "[0-9]*G|[0-9]*M" | sort -hr
13M .mozilla
5,5M .eclipse
2,7M .idb_13.0_linux_intel64_app
-```
+`
This will list all directories which are having MegaBytes or GigaBytes
of consumed space in your actual (in this example HOME) directory. List
is sorted in descending order from largest to smallest
files/directories.
->To have a better understanding of previous commands, you can read
+To have a better understanding of previous commands, you can read
manpages.
-```
+`
$ man lfs
-```
+`
-```
+`
$ man du
-```
+`
### Extended ACLs
@@ -366,7 +366,7 @@ ACLs on a Lustre file system work exactly like ACLs on any Linux file
system. They are manipulated with the standard tools in the standard
manner. Below, we create a directory and allow a specific user access.
-```
+`
[vop999@login1.anselm ~]$ umask 027
[vop999@login1.anselm ~]$ mkdir test
[vop999@login1.anselm ~]$ ls -ld test
@@ -391,7 +391,7 @@ user:johnsm:rwx
group::r-x
mask::rwx
other::---
-```
+`
Default ACL mechanism can be used to replace setuid/setgid permissions
on directories. Setting a default ACL on a directory (-d flag to
@@ -491,7 +491,7 @@ Summary
----------
Mountpoint Usage Protocol Net Capacity Throughput Limitations Access Services
- ------------------------------------------ --------------------------- ---------- ---------------- ------------ ------------- ------------------------- -----------------------------
+ ------------------------------------ |---|---|----------------- ---------- ---------------- ------------ ------------- ---------- |**Version**|**Module**|------
/home home directory Lustre 320 TiB 2 GB/s Quota 250GB Compute and login nodes backed up
/scratch cluster shared jobs' data Lustre 146 TiB 6 GB/s Quota 100TB Compute and login nodes files older 90 days removed
/lscratch node local jobs' data local 330 GB 100 MB/s none Compute nodes purged after job ends
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index b8c1a2f6f2e5088dcc568dcbd7edd2579ac24ded..3631336e742b5e38f1a6853c98a420f578604d57 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md
@@ -3,14 +3,14 @@ Cygwin and X11 forwarding
### If no able to forward X11 using PuTTY to CygwinX
-```
+`
[usename@login1.anselm ~]$ gnome-session &
[1] 23691
[usename@login1.anselm ~]$ PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused
PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused
- (gnome-session:23691): WARNING **: Cannot open display:
-```
+ (gnome-session:23691): WARNING **: Cannot open display:**
+`
Â
@@ -23,7 +23,7 @@ PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connect
change it
- to</span>
+ to
C:*cygwin64binXWin.exe -listen tcp*
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diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md
index fa671a00ce2053203073a88faafae83ba7db2182..c5a12afddbfa6c971301e937485c404bed4e8457 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md
@@ -29,11 +29,11 @@ Create VNC password
Local VNC password should be set before the first login. Do use a strong
password.
-```
+`
[username@login2 ~]$ vncpasswd
Password:
Verify:
-```
+`
Start vncserver
---------------
@@ -47,42 +47,42 @@ You can find ports which are already occupied. Here you can see that
ports " /usr/bin/Xvnc :79" and "
/usr/bin/Xvnc :60" are occupied.
-```
+`
[username@login2 ~]$ ps aux | grep Xvnc
username   5971 0.0 0.0 201072 92564 ?       SN  Sep22  4:19 /usr/bin/Xvnc :79 -desktop login2:79 (username) -auth /home/gre196/.Xauthority -geometry 1024x768 -rfbwait 30000 -rfbauth /home/username/.vnc/passwd -rfbport 5979 -fp catalogue:/etc/X11/fontpath.d -pn
username   10296 0.0 0.0 131772 21076 pts/29  SN  13:01  0:01 /usr/bin/Xvnc :60 -desktop login2:61 (username) -auth /home/username/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/jir13/.vnc/passwd -rfbport 5960 -fp catalogue:/etc/X11/fontpath.d -pn
.....
-```
+`
Choose free port e.g. 61 and start your VNC server:
-```
+`
[username@login2 ~]$ vncserver :61 -geometry 1600x900 -depth 16
New 'login2:1 (username)' desktop is login2:1
Starting applications specified in /home/username/.vnc/xstartup
Log file is /home/username/.vnc/login2:1.log
-```
+`
Check if VNC server is started on the port (in this example 61):
-```
+`
[username@login2 .vnc]$ vncserver -list
TigerVNC server sessions:
X DISPLAY #Â Â Â Â PROCESS ID
:61Â Â Â Â Â Â Â Â Â Â Â Â Â 18437
-```
+`
Another command:
-```
+`
[username@login2 .vnc]$ Â ps aux | grep Xvnc
username   10296 0.0 0.0 131772 21076 pts/29  SN  13:01  0:01 /usr/bin/Xvnc :61 -desktop login2:61 (username) -auth /home/jir13/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/username/.vnc/passwd -rfbport 5961 -fp catalogue:/etc/X11/fontpath.d -pn
-```
+`
To access the VNC server you have to create a tunnel between the login
node using TCP **port 5961** and your machine using a free TCP port (for
@@ -96,34 +96,34 @@ might point to a different node due to DNS round robin.
At your machine, create the tunnel:
-```
+`
local $Â ssh -TN -f username@login2.cluster-name.it4i.cz -L 5961:localhost:5961
-```
+`
Issue the following command to check the tunnel is established (please
note the PID 2022 in the last column, you'll need it for closing the
tunnel):
-```
+`
local $ netstat -natp | grep 5961
(Not all processes could be identified, non-owned process info
 will not be shown, you would have to be root to see it all.)
tcp       0     0 127.0.0.1:5961         0.0.0.0:*              LISTEN     2022/ssh      Â
tcp6Â Â Â Â Â Â 0Â Â Â Â Â 0 ::1:5961Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â :::*Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â LISTENÂ Â Â Â Â 2022/ssh
-```
+`
Or on Mac OS use this command:
-```
+`
local-mac $ lsof -n -i4TCP:5961 | grep LISTEN
ssh 75890 sta545 7u IPv4 0xfb062b5c15a56a3b 0t0 TCP 127.0.0.1:5961 (LISTEN)
-```
+`
Connect with the VNC client:
-```
+`
local $ vncviewer 127.0.0.1:5961
-```
+`
In this example, we connect to VNC server on port 5961, via the ssh
tunnel. The connection is encrypted and secured. The VNC server
@@ -133,9 +133,9 @@ You have to destroy the SSH tunnel which is still running at the
background after you finish the work. Use the following command (PID
2022 in this case, see the netstat command above):
-```
+`
kill 2022
-```
+`
### Windows example of creating a tunnel
@@ -143,15 +143,15 @@ Use PuTTY to log in on cluster.
Start vncserver using command vncserver described above.
-Search for the localhost and port number (in this case
+**Search for the localhost and port number (in this case
127.0.0.1:5961).**
-```
+`
[username@login2 .vnc]$ netstat -tanp | grep Xvnc
(Not all processes could be identified, non-owned process info
 will not be shown, you would have to be root to see it all.)
tcp       0     0 127.0.0.1:5961             0.0.0.0:*                  LISTEN     24031/Xvnc
-```
+`
On the PuTTY Configuration screen go to Connection->SSH->Tunnels
to set up the tunnel.
@@ -191,7 +191,7 @@ You should see after the successful login.
Open Screensaver preferences dialog:
-Preferences](gdmscreensaver.png/@@images/8e80a92f-f691-4d92-8e62-344128dcc00b.png "Screensaver Preferences")](../../../../salomon/gnome_screen.jpg.1)
+
Uncheck both options below the slider:
@@ -202,29 +202,29 @@ Uncheck both options below the slider:
If the screen gets locked you have to kill the screensaver. Do not to
forget to disable the screensaver then.
-```
+`
[username@login2 .vnc]$ ps aux | grep screen
username    1503 0.0 0.0 103244  892 pts/4   S+  14:37  0:00 grep screen
username    24316 0.0 0.0 270564 3528 ?       Ss  14:12  0:00 gnome-screensaver
[username@login2 .vnc]$ kill 24316
-```
+`
### Kill vncserver after finished work
You should kill your VNC server using command:
-```
+`
[username@login2 .vnc]$ vncserver -kill :61
Killing Xvnc process ID 7074
Xvnc process ID 7074 already killed
-```
+`
Or this way:
-```
+`
[username@login2 .vnc]$Â pkill vnc
-```
+`
GUI applications on compute nodes over VNC
------------------------------------------
@@ -232,7 +232,7 @@ GUI applications on compute nodes over VNC
The very [same methods as described
above](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-and-vnc#gui-applications-on-compute-nodes),
may be used to run the GUI applications on compute nodes. However, for
-maximum performance**, proceed following these steps:
+maximum performance, proceed following these steps:
Open a Terminal (Applications -> System Tools -> Terminal). Run
all the next commands in the terminal.
@@ -241,9 +241,9 @@ all the next commands in the terminal.
Allow incoming X11 graphics from the compute nodes at the login node:
-```
+`
$ xhost +
-```
+`
Get an interactive session on a compute node (for more detailed info
[look
@@ -252,16 +252,16 @@ Use the **-v DISPLAY** option to propagate the DISPLAY on the compute
node. In this example, we want a complete node (24 cores in this
example) from the production queue:
-```
+`
$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A PROJECT_ID -q qprod -l select=1:ncpus=24
-```
+`
Test that the DISPLAY redirection into your VNC session works, by
running a X11 application (e. g. XTerm) on the assigned compute node:
-```
+`
$ xterm
-```
+`
Example described above:
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.pdf b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.pdf
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diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md
index 74ff25da710bc3d2087efc856b1845cf7e6a9d9d..9f9415f98911d88fa4de72b3e10a931b48702c54 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md
@@ -23,9 +23,9 @@ In order to display graphical user interface GUI of various software
tools, you need to enable the X display forwarding. On Linux and Mac,
log in using the -X option tho ssh client:
-```
+`
local $ ssh -X username@cluster-name.it4i.cz
-```
+`
### X Display Forwarding on Windows
@@ -35,15 +35,15 @@ checkbox before logging in. Then log in as usual.
To verify the forwarding, type
-```
+`
$ echo $DISPLAY
-```
+`
if you receive something like
-```
+`
localhost:10.0
-```
+`
then the X11 forwarding is enabled.
@@ -84,14 +84,14 @@ Make sure that X forwarding is activated and the X server is running.
Then launch the application as usual. Use the & to run the application
in background.
-```
+`
$ module load intel (idb and gvim not installed yet)
$ gvim &
-```
+`
-```
+`
$ xterm
-```
+`
In this example, we activate the intel programing environment tools,
then start the graphical gvim editor.
@@ -100,20 +100,20 @@ then start the graphical gvim editor.
Allocate the compute nodes using -X option on the qsub command
-```
+`
$ qsub -q qexp -l select=2:ncpus=24 -X -I
-```
+`
In this example, we allocate 2 nodes via qexp queue, interactively. We
request X11 forwarding with the -X option. It will be possible to run
the GUI enabled applications directly on the first compute node.
-Better performance** is obtained by logging on the allocated compute
+**Better performance** is obtained by logging on the allocated compute
node via ssh, using the -X option.
-```
+`
$ ssh -X r24u35n680
-```
+`
In this example, we log in on the r24u35n680 compute node, with the X11
forwarding enabled.
@@ -134,9 +134,9 @@ xserver-xephyr, on OS X it is part of
[XQuartz](http://xquartz.macosforge.org/landing/).
First, launch Xephyr on local machine:
-```
+`
local $ Xephyr -ac -screen 1024x768 -br -reset -terminate :1 &
-```
+`
This will open a new X window with size 1024x768 at DISPLAY :1. Next,
ssh to the cluster with DISPLAY environment variable set and launch
@@ -150,9 +150,9 @@ On older systems where Xephyr is not available, you may also try Xnest
instead of Xephyr. Another option is to launch a new X server in a
separate console, via:
-```
+`
xinit /usr/bin/ssh -XT -i .ssh/path_to_your_key yourname@cluster-namen.it4i.cz gnome-session -- :1 vt12
-```
+`
However this method does not seem to work with recent Linux
distributions and you will need to manually source
@@ -167,9 +167,9 @@ Use Xlaunch to start the Xming server or run the XWin.exe. Select the
Log in to the cluster, using PuTTY. On the cluster, run the
gnome-session command.
-```
+`
$ gnome-session &
-```
+`
In this way, we run remote gnome session on the cluster, displaying it
in the local X server
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.pdf b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.pdf
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index 84366f60e281d2ed5a6a8cf163e97a73d05d6bc0..b3e8ac55e8c717c08cb7af7294514312ababac88 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md
@@ -9,16 +9,16 @@ PuTTY - before we start SSH connection
### Windows PuTTY Installer
We recommned you to download "**A Windows installer for everything
-except PuTTYtel**" with ***Pageant*** (SSH authentication agent) and
-PuTTYgen** (PuTTY key generator) which is available
+except PuTTYtel**" with **Pageant*** (SSH authentication agent) and
+**PuTTYgen** (PuTTY key generator) which is available
[here](http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html).
After installation you can proceed directly
to private keys authentication using
["Putty"](putty.html#putty).
"Change Password for Existing Private Key" is optional.
-"Generate a New Public/Private key pair" is intended for users without
-Public/Private key in the initial email containing login credentials.
+"Generate a New Public/Private key (`id_rsa/id_rsa.ppk` ): `600 (-rw-------)` pair" is intended for users without
+Public/Private key (`id_rsa/id_rsa.ppk` ): `600 (-rw-------)` in the initial email containing login credentials.
"Pageant" is optional.
### PuTTYgen
@@ -72,8 +72,8 @@ PuTTY - how to connect to the IT4Innovations cluster
"username@salomon.it4i.cz".
- Enter passphrase for selected [private
- key](../ssh-keys.html) file if Pageant ****SSH
- authentication agent is not used.
+ key](../ssh-keys.html) file if Pageant **SSH
+ authentication agent is not used.**
Another PuTTY Settings
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diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.md
index 174363130d244e4e52c6d9a12b929fa3445d321a..33228da49215e9b2a979d6f1480a2df4868a69e8 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.md
@@ -23,11 +23,11 @@ Make sure to backup the key.
Â
-### Generate a New Public/Private key pair
+### Generate a New Public/Private key (`id_rsa/id_rsa.ppk` ): `600 (-rw-------)` pair
You can generate an additional public/private key pair and insert public
key into authorized_keys file for authentication with your own private
->key.
+key.
- Start with *Generate* button.
@@ -62,7 +62,7 @@ key into authorized_keys file for authentication with your own private
- Now you can insert additional public key into authorized_keys file
- for authentication with your own private >key.
+ for authentication with your own private key.
You must log in using ssh key received after registration. Then
proceed to [How to add your own
key](../ssh-keys.html).
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.pdf b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.pdf
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diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.epub b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.epub
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diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
index b6ab094e1c23af5689fb6872d48e602b532953e4..e6055adb455bae6e89c944a8d73325730ff74072 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
@@ -25,15 +25,15 @@ the cluster.
### Access privileges on .ssh folder
-- `.ssh`
+- `.ssh` Â directory: 700 (drwx------)
 directory:
700 (drwx------)
-
- Authorized_keys,Â
+ Authorized_keys, known_hosts and public key (`.pub` file): `644 (-rw-r--r--)`Â
- known_hosts</span> and
+ known_hosts and
public keyÂ
(`.pub`
@@ -43,7 +43,7 @@ the cluster.
-
``
- Private key
+ Private key (`id_rsa/id_rsa.ppk` ): `600 (-rw-------)`
(`id_rsa/id_rsa.ppk`
):
`600 (-rw-------)`
@@ -58,14 +58,14 @@ the cluster.
chmod 600 .ssh/id_rsa
chmod 600Â .ssh/id_rsa.ppk
-Private key
+Private key (`id_rsa/id_rsa.ppk` ): `600 (-rw-------)`
-----------
The path to a private key is usually /home/username/.ssh/
-Private key file in "id_rsa" or `"*.ppk" `format is used to
+Private key (`id_rsa/id_rsa.ppk` ): `600 (-rw-------)` file in "id_rsa" or `"*.ppk" `format is used to
authenticate with the servers.
-Private key is present locally
+Private key (`id_rsa/id_rsa.ppk` ): `600 (-rw-------)` is present locally
on local side and used for example in SSH agent [Pageant (for Windows
users)](putty/PageantV.png). The private key should
always be kept in a safe place.
@@ -126,13 +126,13 @@ First, generate a new keypair of your public and private key:
Please, enter **strong** **passphrase** for securing your private key.
You can insert additional public key into authorized_keys file for
-authentication with your own private >key. Additional records in
+authentication with your own private key. Additional records in
authorized_keys file must be delimited by new line. Users are
not advised to remove the default public key from authorized_keys file.
Example:
- $ cat additional_key.pub >> ~/.ssh/authorized_keys
+ $ cat additional_key.pub > ~/.ssh/authorized_keys
In this example, we add an additional public key, stored in file
additional_key.pub into the authorized_keys. Next time we log in, we
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.pdf b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.pdf
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diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.epub b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.epub
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diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.md
index f0a9413a92bbfb8afa34ad7df960c381ee714e53..22f2e4bca3f27cebef3b76f66211257f09c66c9e 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.md
@@ -1,7 +1,7 @@
VPN - Connection fail in Win 8.1
================================
-Failed to initialize connection subsystem Win 8.1 - 02-10-15 MS patch
+**Failed to initialize connection subsystem Win 8.1 - 02-10-15 MS patch
AnyConnect users on Windows 8.1 will receive a "Failed to initialize
connection subsystem" error after installing the Windows 8.1 02/10/15
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.pdf b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.pdf
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diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.epub b/converted/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.epub
index d20ece2103adc5778983b663917fb0fcd4d2beb9..b62ad8293b02af2fc23b67d9a40d867da811dacb 100644
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diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.md b/converted/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.md
index 85b976e2d155ac67e25dceb9c9a173d5c0210783..165ccc7ba2823473be622c1b500b9069a5734cb6 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.md
@@ -23,11 +23,11 @@ In all cases, IT4Innovations’ access mechanisms are aimed at
distributing computational resources while taking into account the
development and application of supercomputing methods and their benefits
and usefulness for society. The applicants are expected to submit a
-proposal. In the proposal, the applicants ***apply for a particular
-amount of core-hours*** of computational resources. The requested
+proposal. In the proposal, the applicants **apply for a particular
+amount of core-hours** of computational resources. The requested
core-hours should be substantiated by scientific excellence of the
proposal, its computational maturity and expected impacts.
->Proposals do undergo a scientific, technical and economic
+Proposals do undergo a scientific, technical and economic
evaluation. The allocation decisions are based on this
evaluation. More information at [Computing resources
allocation](http://www.it4i.cz/computing-resources-allocation/?lang=en)
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.pdf b/converted/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.pdf
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diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.epub b/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.epub
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diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md b/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
index f62dc9bec1109fe8bce7bc3baa55735a9bba80cd..524ef4e374c26f87276e276c851df14e1675b927 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
@@ -26,7 +26,7 @@ of use. We mention here:
Â
-However, users need only manage User and CA certificates. Note that your
+**However, users need only manage User and CA certificates. Note that your
user certificate is protected by an associated private key, and this
private key must never be disclosed**.
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.pdf b/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.pdf
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diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md b/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
index bdde412f84e088da3525e44a5c1112a567c9f3da..3cbe8e759f76b67c6eabb4c69281a50d0b436915 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
@@ -144,7 +144,7 @@ We accept certificates issued by any widely respected certification
authority.
For various reasons we do not accept PGP keys.** Please, use only
-X.509 PKI certificates for communication with us.
+X.509 PKI certificates for communication with us.**
You will receive your personal login credentials by protected e-mail.
The login credentials include:
@@ -163,9 +163,9 @@ listed on <http://support.it4i.cz/>.
On Linux, use
-```
+`
local $ ssh-keygen -f id_rsa -p
-```
+`
On Windows, use [PuTTY Key
Generator](../accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.html).
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.pdf b/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.pdf
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diff --git a/converted/docs.it4i.cz/index.epub b/converted/docs.it4i.cz/index.epub
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diff --git a/converted/docs.it4i.cz/index.md b/converted/docs.it4i.cz/index.md
index 1276398b4a7d67a4992011aeb9170bca400d8830..f99c494d9c204a5832fe1c55d520658ef12b5a1c 100644
--- a/converted/docs.it4i.cz/index.md
+++ b/converted/docs.it4i.cz/index.md
@@ -119,15 +119,15 @@ examples. We use the following conventions:
 Cluster command prompt
-```
+`
$
-```
+`
Your local linux host command prompt
-```
+`
local $
-```
+`
 Errata
-------
diff --git a/converted/docs.it4i.cz/index.pdf b/converted/docs.it4i.cz/index.pdf
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diff --git a/converted/docs.it4i.cz/salomon/accessing-the-cluster.md b/converted/docs.it4i.cz/salomon/accessing-the-cluster.md
index a2208dfc3b371417789cb2db916964356fd83041..88e1d77ab3ecadc0bfd0c16ea3124c142f0632f2 100644
--- a/converted/docs.it4i.cz/salomon/accessing-the-cluster.md
+++ b/converted/docs.it4i.cz/salomon/accessing-the-cluster.md
@@ -15,7 +15,7 @@ The alias >salomon.it4i.cz is currently not available through VPN
connection. Please use loginX.salomon.it4i.cz when connected to
VPN.
- |Login address|Port|Protocol|Login node|
+ |Login address|Port|Protocol|Login node|
|---|---|---|---|
|salomon.it4i.cz|22|ssh|round-robin DNS record for login[1-4]|
|login1.salomon.it4i.cz|22|ssh|login1|
@@ -33,20 +33,20 @@ f6:28:98:e4:f9:b2:a6:8f:f2:f4:2d:0a:09:67:69:80Â (DSA)
Â
-Private keys authentication:
+Private key (`id_rsa/id_rsa.ppk` ): `600 (-rw-------)`s authentication:
On **Linux** or **Mac**, use
-```
+`
local $ ssh -i /path/to/id_rsa username@salomon.it4i.cz
-```
+`
If you see warning message "UNPROTECTED PRIVATE KEY FILE!", use this
command to set lower permissions to private key file.
-```
+`
local $ chmod 600 /path/to/id_rsa
-```
+`
On **Windows**, use [PuTTY ssh
client](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html).
@@ -83,12 +83,12 @@ nodes cedge[1-3].salomon.it4i.cz for increased performance.
HTML commented section #1 (removed cedge servers from the table)
- Address Port Protocol
- ------------------------------------------------------ ------ -----------------------------------------
+ Address |Port|Protocol|
+ ----------------------- |---|---|------------
salomon.it4i.cz 22 scp, sftp
login1.salomon.it4i.cz 22 scp, sftp
login2.salomon.it4i.cz 22 scp, sftp
- class="discreet">login3.salomon.it4i.cz 22 scp, sftp
+ login3.salomon.it4i.cz 22 scp, sftp
login4.salomon.it4i.cz 22 scp, sftp
 The authentication is by the [private
@@ -99,40 +99,40 @@ verified)
On linux or Mac, use scp or sftp client to transfer the data to Salomon:
-```
+`
local $ scp -i /path/to/id_rsa my-local-file username@salomon.it4i.cz:directory/file
-```
+`
-```
+`
local $ scp -i /path/to/id_rsa -r my-local-dir username@salomon.it4i.cz:directory
-```
+`
-> or
+ or
-```
+`
local $ sftp -o IdentityFile=/path/to/id_rsa username@salomon.it4i.cz
-```
+`
Very convenient way to transfer files in and out of the Salomon computer
is via the fuse filesystem
[sshfs](http://linux.die.net/man/1/sshfs)
-```
+`
local $ sshfs -o IdentityFile=/path/to/id_rsa username@salomon.it4i.cz:. mountpoint
-```
+`
Using sshfs, the users Salomon home directory will be mounted on your
local computer, just like an external disk.
Learn more on ssh, scp and sshfs by reading the manpages
-```
+`
$ man ssh
$ man scp
$ man sshfs
-```
+`
->On Windows, use [WinSCP
+On Windows, use [WinSCP
client](http://winscp.net/eng/download.php) to transfer
the data. The [win-sshfs
client](http://code.google.com/p/win-sshfs/) provides a
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diff --git a/converted/docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.md b/converted/docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.md
index b476020bee4143f2c49fd354036ddbccdb592277..252d36b8f957e110b01c4094bd9bacbe8eca5cc7 100644
--- a/converted/docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.md
+++ b/converted/docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.md
@@ -9,12 +9,12 @@ Connection restrictions
Outgoing connections, from Salomon Cluster login nodes to the outside
world, are restricted to following ports:
- Port Protocol
- ------ ----------
- 22 ssh
- 80 http
- 443 https
- 9418 git
+ |Port|Protocol|
+ |---|---|
+ |22|ssh|
+ |80|http|
+ |443|https|
+ |9418|git|
Please use **ssh port forwarding** and proxy servers to connect from
Salomon to all other remote ports.
@@ -37,9 +37,9 @@ workstation and forwarding from the workstation to the remote host.
Pick some unused port on Salomon login node (for example 6000) and
establish the port forwarding:
-```
+`
local $ ssh -R 6000:remote.host.com:1234 salomon.it4i.cz
-```
+`
In this example, we establish port forwarding between port 6000 on
Salomon and port 1234 on the remote.host.com. By accessing
@@ -55,9 +55,9 @@ remote.host.com:1234. Click Add button, then Open.
Port forwarding may be established directly to the remote host. However,
this requires that user has ssh access to remote.host.com
-```
+`
$ ssh -L 6000:localhost:1234 remote.host.com
-```
+`
Note: Port number 6000 is chosen as an example only. Pick any free port.
@@ -73,9 +73,9 @@ above](outgoing-connections.html#port-forwarding-from-login-nodes).
Second, invoke port forwarding from the compute node to the login node.
Insert following line into your jobscript or interactive shell
-```
+`
$ ssh -TN -f -L 6000:localhost:6000 login1
-```
+`
In this example, we assume that port forwarding from login1:6000 to
remote.host.com:1234 has been established beforehand. By accessing
@@ -96,9 +96,9 @@ SOCKS proxy server software. On Linux, sshd demon provides the
functionality. To establish SOCKS proxy server listening on port 1080
run:
-```
+`
local $ ssh -D 1080 localhost
-```
+`
On Windows, install and run the free, open source [Sock
Puppet](http://sockspuppet.com/) server.
@@ -107,9 +107,9 @@ Once the proxy server is running, establish ssh port forwarding from
Salomon to the proxy server, port 1080, exactly as [described
above](outgoing-connections.html#port-forwarding-from-login-nodes).
-```
+`
local $ ssh -R 6000:localhost:1080 salomon.it4i.cz
-```
+`
Now, configure the applications proxy settings to **localhost:6000**.
Use port forwarding to access the [proxy server from compute
diff --git a/converted/docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.pdf b/converted/docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.pdf
index b245a152268762ffcdd0367a1aa81b9189ce1238..202da1c0eeadf65f344756ce769f951857e49768 100644
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diff --git a/converted/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.epub b/converted/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.epub
index 0b7f0f5d94bc68709c7b02c8be5cce05b4ddbb27..7e426f8a977e36bf88c67986eb3be0a2e8e85ad6 100644
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diff --git a/converted/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.md b/converted/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.md
index 3606f72d16c0de393dd1fa75a0da4779d90a7ad9..7ac87bb0cfa7c952517362d712bfdacad650d468 100644
--- a/converted/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.md
+++ b/converted/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.md
@@ -20,7 +20,7 @@ the following operating systems:
It is impossible to connect to VPN from other operating systems.
->VPN client installation
+VPN client installation
------------------------------------
You can install VPN client from web interface after successful login
@@ -35,7 +35,7 @@ for automatic installation.
-Install](https://docs.it4i.cz/salomon/vpn_web_install_2.png/@@images/c2baba93-824b-418d-b548-a73af8030320.png "VPN Install")](../vpn_web_install_2.png)
+
After successful installation, VPN connection will be established and
diff --git a/converted/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.pdf b/converted/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.pdf
index 5f74b4cdc263804d76d6f76031af26e5802ed3e7..b0a7d009cfbfb8b2f4d9ed54ddf859c27c02c2d9 100644
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diff --git a/converted/docs.it4i.cz/salomon/environment-and-modules.epub b/converted/docs.it4i.cz/salomon/environment-and-modules.epub
index 895f1fef1b4599f061961b2099dc46eab9816d8d..0b2378dd2c06af91e74bc1e204d7fe2487ac85f4 100644
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diff --git a/converted/docs.it4i.cz/salomon/environment-and-modules.md b/converted/docs.it4i.cz/salomon/environment-and-modules.md
index 402ca97891738c2ad8822bbafd6a9ab16b481a60..e9da01143447365624c102d1cb9ba090afe59d95 100644
--- a/converted/docs.it4i.cz/salomon/environment-and-modules.md
+++ b/converted/docs.it4i.cz/salomon/environment-and-modules.md
@@ -9,7 +9,7 @@ After logging in, you may want to configure the environment. Write your
preferred path definitions, aliases, functions and module loads in the
.bashrc file
-```
+`
# ./bashrc
# Source global definitions
@@ -26,13 +26,13 @@ if [ -n "$SSH_TTY" ]
then
module list # Display loaded modules
fi
-```
+`
Do not run commands outputing to standard output (echo, module list,
etc) in .bashrc for non-interactive SSH sessions. It breaks fundamental
functionality (scp, PBS) of your account! Take care for SSH session
-interactivity for such commands as id="result_box"
- class="hps alt-edited">stated
+interactivity for such commands as
+ stated in the previous example.
in the previous example.
### Application Modules
@@ -44,7 +44,7 @@ Application modules on Salomon cluster are built using
[EasyBuild](http://hpcugent.github.io/easybuild/ "EasyBuild"). The
modules are divided into the following structure:
-```
+`
base: Default module class
bio: Bioinformatics, biology and biomedical
cae: Computer Aided Engineering (incl. CFD)
@@ -66,7 +66,7 @@ modules are divided into the following structure:
toolchain: EasyBuild toolchains
tools: General purpose tools
vis: Visualization, plotting, documentation and typesetting
-```
+`
The modules set up the application paths, library paths and environment
variables for running particular application.
@@ -76,36 +76,36 @@ needs.
To check available modules use
-```
+`
$ module avail
-```
+`
To load a module, for example the OpenMPI module use
-```
+`
$ module load OpenMPI
-```
+`
loading the OpenMPI module will set up paths and environment variables
of your active shell such that you are ready to run the OpenMPI software
To check loaded modules use
-```
+`
$ module list
-```
+`
 To unload a module, for example the OpenMPI module use
-```
+`
$ module unload OpenMPI
-```
+`
Learn more on modules by reading the module man page
-```
+`
$ man module
-```
+`
### EasyBuild Toolchains
diff --git a/converted/docs.it4i.cz/salomon/environment-and-modules.pdf b/converted/docs.it4i.cz/salomon/environment-and-modules.pdf
index d72b295e64592a397db9b251544eef0d6a25c1e2..58c0b257fc6482aaf480eff37380e24d97bfab1f 100644
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diff --git a/converted/docs.it4i.cz/salomon/hardware-overview-1/hardware-overview.epub b/converted/docs.it4i.cz/salomon/hardware-overview-1/hardware-overview.epub
index de8542622df72ef12a9b62dfbae1ff690ef98e68..57b6e5c2eedeb97b3f92db1ef67ca0b93c6b7264 100644
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diff --git a/converted/docs.it4i.cz/salomon/hardware-overview-1/hardware-overview.md b/converted/docs.it4i.cz/salomon/hardware-overview-1/hardware-overview.md
index 54540b576db50fe005e96f231228c2cab8f7ee27..58d4f81c6fc3a45654ba30fb51e6e43da6f4f8a7 100644
--- a/converted/docs.it4i.cz/salomon/hardware-overview-1/hardware-overview.md
+++ b/converted/docs.it4i.cz/salomon/hardware-overview-1/hardware-overview.md
@@ -53,14 +53,14 @@ In total**
Total theoretical peak performance (Rpeak)
2011 Tflop/s
Total amount of RAM
->129.024 TB
+129.024 TB
Compute nodes
-------------
- Node Count Processor Cores Memory Accelerator
- ----------------- ------- ---------------------------------- ------- -------- --------------------------------------------
- w/o accelerator 576 2x Intel Xeon E5-2680v3, 2.5GHz 24 128GB -
- MIC accelerated 432 2x Intel Xeon E5-2680v3, 2.5GHz 24 128GB 2x Intel Xeon Phi 7120P, 61cores, 16GB RAM
+ |Node|Count|Processor|Cores|Memory|Accelerator|
+ ----------------- - |---|---|------------------------ ------- -------- --------------------------------------------
+ |w/o accelerator|576|2x Intel Xeon E5-2680v3, 2.5GHz|24|128GB|-|
+ |MIC accelerated|432|2x Intel Xeon E5-2680v3, 2.5GHz|24|128GB|2x Intel Xeon Phi 7120P, 61cores, 16GB RAM|
For more details please refer to the [Compute
nodes](../compute-nodes.html).
@@ -71,9 +71,9 @@ Remote visualization nodes
For remote visualization two nodes with NICE DCV software are available
each configured:
- Node Count Processor Cores Memory GPU Accelerator
- --------------- ------- --------------------------------- ------- -------- ------------------------------
- visualization 2 2x Intel Xeon E5-2695v3, 2.3GHz 28 512GB NVIDIA QUADRO K5000, 4GB RAM
+ |Node|Count|Processor|Cores|Memory|GPU Accelerator|
+ --------------- - |---|---|----------------------- ------- -------- ------------------------------
+ |visualization|2|2x Intel Xeon E5-2695v3, 2.3GHz|28|512GB|NVIDIA QUADRO K5000, 4GB RAM|
SGI UV 2000
-----------
@@ -81,7 +81,7 @@ SGI UV 2000
For large memory computations a special SMP/NUMA SGI UV 2000 server is
available:
- |Node |Count |Processor<th align="left">Cores<th align="left">Memory<th align="left">Extra HW |
+ |Node |Count |Processor |Cores<th align="left">Memory<th align="left">Extra HW |
| --- | --- |
|UV2000 |1 |14x Intel Xeon E5-4627v2, 3.3GHz, 8cores |112 |3328GB DDR3@1866MHz |2x 400GB local SSD1x NVIDIA GM200(GeForce GTX TITAN X),12GB RAM\ |
diff --git a/converted/docs.it4i.cz/salomon/hardware-overview-1/hardware-overview.pdf b/converted/docs.it4i.cz/salomon/hardware-overview-1/hardware-overview.pdf
index 8846a3522711dfc6648184c8a0aa3e47570079af..0fc4209f5367df313907f3daf38a2eb252e1cedf 100644
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diff --git a/converted/docs.it4i.cz/salomon/introduction.epub b/converted/docs.it4i.cz/salomon/introduction.epub
index ef47066de63e1eca4e23872fa423b722397fabbb..d64ab1f11da949d911088083f28b1bf13723cdb4 100644
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diff --git a/converted/docs.it4i.cz/salomon/introduction.md b/converted/docs.it4i.cz/salomon/introduction.md
index 471506fbc31baa871c6ec14059936488aa75b76b..7996d06642a9fb087c549727b1e0a05e224569e3 100644
--- a/converted/docs.it4i.cz/salomon/introduction.md
+++ b/converted/docs.it4i.cz/salomon/introduction.md
@@ -19,7 +19,7 @@ the RedHat [
Linux
family.](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)
-Water-cooled Compute Nodes With MIC Accelerator**
+**Water-cooled Compute Nodes With MIC Accelerator**
diff --git a/converted/docs.it4i.cz/salomon/introduction.pdf b/converted/docs.it4i.cz/salomon/introduction.pdf
index 9ce2e43f57ed95ddb5ec7e1c17c0d9e38c1f9cf2..33182423e7576889b1010af10ad5843d6adfa1f1 100644
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diff --git a/converted/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.epub b/converted/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.epub
index 504ade5dbde38d70d04aee55c575866feee9d74c..a5fe18cfe1cbe4c59e172016d86878c74e8205ea 100644
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diff --git a/converted/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.md b/converted/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.md
index d02fc5b19ec4545dd2731f37d2fb8e9034036918..633115bd68cf9f0dcf0da9beefdc8c1d55a97ee4 100644
--- a/converted/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.md
+++ b/converted/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.md
@@ -6,15 +6,15 @@ dimension.](../resource-allocation-and-job-execution/job-submission-and-executio
Nodes may be selected via the PBS resource attribute ehc_[1-7]d .
- Hypercube dimension
- --------------------- -------------------------------------------
- 1D ehc_1d
- 2D ehc_2d
- 3D ehc_3d
- 4D ehc_4d
- 5D ehc_5d
- 6D ehc_6d
- 7D ehc_7d
+ |Hypercube|dimension|
+ --------------- |---|---|---------------------------------
+ |1D|ehc_1d|
+ |2D|ehc_2d|
+ |3D|ehc_3d|
+ |4D|ehc_4d|
+ |5D|ehc_5d|
+ |6D|ehc_6d|
+ |7D|ehc_7d|
[Schematic representation of the Salomon cluster IB single-plain
topology represents hypercube
@@ -26,13 +26,12 @@ dimension 0](ib-single-plane-topology.html).
Â
- Node type Count Short name Long name Rack
- -------------------------------------- ------- ------------------ -------------------------- -------
- M-Cell compute nodes w/o accelerator 576 cns1 -cns576 r1i0n0 - r4i7n17 1-4
- compute nodes MIC accelerated 432 cns577 - cns1008 r21u01n577 - r37u31n1008 21-38
+ |Node type|Count|Short name|Long name|Rack|
+ -------------------------------------- - |---|---|-------- -------------------------- -------
+ |M-Cell compute nodes w/o accelerator|576|cns1 -cns576|r1i0n0 - r4i7n17|1-4|
+ |compute nodes MIC accelerated|432|cns577 - cns1008|r21u01n577 - r37u31n1008|21-38|
### Â IB Topology
-Â [](Salomon_IB_topology.png)
+
diff --git a/converted/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.pdf b/converted/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.pdf
index 8075ea92674db4679c015c3f43705d2fe9fb17e3..5af1129d138c3eba8c9a18ca68d96865cf033463 100644
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diff --git a/converted/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.epub b/converted/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.epub
index 37f95ba4795533f1804f728a5f41c421d4d6936a..5444e4743a358ea87a9f5958bb903c3b542617bb 100644
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diff --git a/converted/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.md b/converted/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.md
index 6d58629127deb1585f1b87529ed96fbdca442907..70bd60ea10df3857aea3e4b8e7295e0aa3f8cf5f 100644
--- a/converted/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.md
+++ b/converted/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.md
@@ -18,7 +18,7 @@ with connections as follows:
- 24 ports from each switch chip connect to the external bulkhead, for
a total of 48
-###IB single-plane topology - ICEX Mcell**
+###IB single-plane topology - ICEX Mcell
Each colour in each physical IRU represents one dual-switch ASIC switch.
@@ -33,7 +33,7 @@ Mcell rack. 18x D rack with MIC accelerated nodes [r21-r38] are
equivalent to 3 Mcell racks as shown in a diagram [7D Enhanced
Hypercube](7d-enhanced-hypercube.html).
-As shown in a diagram [IB
+As shown in a diagram :
- Racks 21, 22, 23, 24, 25, 26 are equivalent to one Mcell rack.
diff --git a/converted/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.pdf b/converted/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.pdf
index 6de30aba8e6a002ff866582f48e597499f965e7e..354593ab49e03d86715dde69968b3d7c86e2ccbe 100644
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diff --git a/converted/docs.it4i.cz/salomon/network-1/network.epub b/converted/docs.it4i.cz/salomon/network-1/network.epub
index a380348ca31f6c15b1f2df8576e27e5a83bb0f13..956f83b21b8ca2c0d484c341927b668bfef67303 100644
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diff --git a/converted/docs.it4i.cz/salomon/network-1/network.md b/converted/docs.it4i.cz/salomon/network-1/network.md
index 87a52d529cafd9a44dc27dd0ef9b501590371b1b..79187d02c3c1a7c5905fd4d4fb4e2939f6e19c09 100644
--- a/converted/docs.it4i.cz/salomon/network-1/network.md
+++ b/converted/docs.it4i.cz/salomon/network-1/network.md
@@ -24,10 +24,7 @@ hypercube](7d-enhanced-hypercube.html).
Read more about schematic representation of the Salomon cluster [IB
single-plain topology](ib-single-plane-topology.html)
([hypercube dimension](7d-enhanced-hypercube.html)
-0).[>](IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf/view.html){.state-missing-value
-.contenttype-file}
-
-- -
+0).[>](IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf/view.html)
The compute nodes may be accessed via the Infiniband network using ib0
network interface, in address range 10.17.0.0 (mask 255.255.224.0). The
@@ -42,27 +39,27 @@ The network provides **2170MB/s** transfer rates via the TCP connection
Example
-------
-```
+`
$ qsub -q qexp -l select=4:ncpus=16 -N Name0 ./myjob
$ qstat -n -u username
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
---------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
+--------------- -------- -- |---|---| ------ --- --- ------ ----- - -----
15209.isrv5 username qexp Name0 5530 4 96 -- 01:00 R 00:00
r4i1n0/0*24+r4i1n1/0*24+r4i1n2/0*24+r4i1n3/0*24
-```
+`
In this example, we access the node r4i1n0 by Infiniband network via the
ib0 interface.
-```
+`
$ ssh 10.17.35.19
-```
+`
In this example, we get
information of the Infiniband network.
-```
+`
$ ifconfig
....
inet addr:10.17.35.19....
@@ -73,5 +70,5 @@ $ ip addr show ib0
....
inet 10.17.35.19....
....
-```
+`
diff --git a/converted/docs.it4i.cz/salomon/network-1/network.pdf b/converted/docs.it4i.cz/salomon/network-1/network.pdf
index 20b99d7f9df8e17c8fce7d3dca66d4068c433fae..7093d52d1e60e571bce683a46024876d37fc81c3 100644
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diff --git a/converted/docs.it4i.cz/salomon/prace.epub b/converted/docs.it4i.cz/salomon/prace.epub
index 209ee4e4e49979ca6b85dec3aca8c4018fe9033b..f4e5c2dc57393244aa2027fc92a9b623b49a2591 100644
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diff --git a/converted/docs.it4i.cz/salomon/prace.md b/converted/docs.it4i.cz/salomon/prace.md
index ec73ce655fee201653259ad722cecc692b138c72..daee862130cdbcfc236bfec42e8ae7eab7bbb0bf 100644
--- a/converted/docs.it4i.cz/salomon/prace.md
+++ b/converted/docs.it4i.cz/salomon/prace.md
@@ -97,20 +97,20 @@ To access Salomon cluster, two login nodes running GSI SSH service are
available. The service is available from public Internet as well as from
the internal PRACE network (accessible only from other PRACE partners).
-Access from PRACE network:**
+***Access from PRACE network:**
It is recommended to use the single DNS name
salomon-prace.it4i.cz which is distributed
between the two login nodes. If needed, user can login directly to one
of the login nodes. The addresses are:
- Login address Port Protocol Login node
- ------------------------------ ------ ---------- ----------------------------------
- salomon-prace.it4i.cz 2222 gsissh login1, login2, login3 or login4
- login1-prace.salomon.it4i.cz 2222 gsissh login1
- login2-prace.salomon.it4i.cz 2222 gsissh login2
- login3-prace.salomon.it4i.cz 2222 gsissh login3
- login4-prace.salomon.it4i.cz 2222 gsissh login4
+ |Login address|Port|Protocol|Login node|
+ |---|---|
+ |salomon-prace.it4i.cz|2222|gsissh|login1, login2, login3 or login4|
+ |login1-prace.salomon.it4i.cz|2222|gsissh|login1|
+ |login2-prace.salomon.it4i.cz|2222|gsissh|login2|
+ |login3-prace.salomon.it4i.cz|2222|gsissh|login3|
+ |login4-prace.salomon.it4i.cz|2222|gsissh|login4|
Â
@@ -123,20 +123,20 @@ used:
Â
-Access from public Internet:**
+***Access from public Internet:**
It is recommended to use the single DNS name
salomon.it4i.cz which is distributed between
the two login nodes. If needed, user can login directly to one of the
login nodes. The addresses are:
- |Login address|Port|Protocol|Login node|
- ------------------------ ------ ---------- ----------------------------------
- salomon.it4i.cz 2222 gsissh login1, login2, login3 or login4
- login1.salomon.it4i.cz 2222 gsissh login1
- login2.salomon.it4i.cz 2222 gsissh login2
- login3.salomon.it4i.cz 2222 gsissh login3
- login4.salomon.it4i.cz 2222 gsissh login4
+ |Login address|Port|Protocol|Login node|
+ |---|---|
+ |salomon.it4i.cz|2222|gsissh|login1, login2, login3 or login4|
+ |login1.salomon.it4i.cz|2222|gsissh|login1|
+ |login2-prace.salomon.it4i.cz|2222|gsissh|login2|
+ |login3-prace.salomon.it4i.cz|2222|gsissh|login3|
+ |login4-prace.salomon.it4i.cz|2222|gsissh|login4|
$ gsissh -p 2222 salomon.it4i.cz
@@ -200,14 +200,14 @@ PRACE partners).
There's one control server and three backend servers for striping and/or
backup in case one of them would fail.
-Access from PRACE network:**
+***Access from PRACE network:**
- Login address Port Node role
- ------------------------------- ------ -----------------------------
- gridftp-prace.salomon.it4i.cz 2812 Front end /control server
- lgw1-prace.salomon.it4i.cz 2813 Backend / data mover server
- lgw2-prace.salomon.it4i.cz 2813 Backend / data mover server
- lgw3-prace.salomon.it4i.cz 2813 Backend / data mover server
+ |Login address|Port|Node role|
+ |---|---|
+ |gridftp-prace.salomon.it4i.cz|2812|Front end /control server|
+ |lgw1-prace.salomon.it4i.cz|2813|Backend / data mover server|
+ |lgw2-prace.salomon.it4i.cz|2813|Backend / data mover server|
+ |lgw3-prace.salomon.it4i.cz|2813|Backend / data mover server|
Copy files **to** Salomon by running the following commands on your
local machine:
@@ -228,14 +228,14 @@ Or by using prace_service script:
Â
-Access from public Internet:**
+***Access from public Internet:**
- Login address Port Node role
- ------------------------- ------ -----------------------------
- gridftp.salomon.it4i.cz 2812 Front end /control server
- lgw1.salomon.it4i.cz 2813 Backend / data mover server
- lgw2.salomon.it4i.cz 2813 Backend / data mover server
- lgw3.salomon.it4i.cz 2813 Backend / data mover server
+ |Login address|Port|Node role|
+ |---|---|
+ |gridftp.salomon.it4i.cz|2812|Front end /control server|
+ |lgw1.salomon.it4i.cz|2813|Backend / data mover server|
+ |lgw2.salomon.it4i.cz|2813|Backend / data mover server|
+ |lgw3.salomon.it4i.cz|2813|Backend / data mover server|
Copy files **to** Salomon by running the following commands on your
local machine:
@@ -258,10 +258,10 @@ Or by using prace_service script:
Generally both shared file systems are available through GridFTP:
- File system mount point Filesystem Comment
- ------------------------- ------------ ----------------------------------------------------------------
- /home Lustre Default HOME directories of users in format /home/prace/login/
- /scratch Lustre Shared SCRATCH mounted on the whole cluster
+ |File system mount point|Filesystem|Comment|
+ |---|---|
+ |/home|Lustre|Default HOME directories of users in format /home/prace/login/|
+ |/scratch|Lustre|Shared SCRATCH mounted on the whole cluster|
More information about the shared file systems is available
[here](storage.html).
@@ -269,10 +269,10 @@ More information about the shared file systems is available
Please note, that for PRACE users a "prace" directory is used also on
the SCRATCH file system.
- Data type Default path
- ------------------------------ ---------------------------------
- large project files /scratch/work/user/prace/login/
- large scratch/temporary data /scratch/temp/
+ |Data type|Default path|
+ |---|---|
+ |large project files|/scratch/work/user/prace/login/|
+ |large scratch/temporary data|/scratch/temp/|
Usage of the cluster
--------------------
@@ -312,22 +312,22 @@ documentation](resource-allocation-and-job-execution/introduction.html).
For PRACE users, the default production run queue is "qprace". PRACE
users can also use two other queues "qexp" and "qfree".
- ---------------------------------------------------------------------------------------------------------------------------------------------
- queue Active project Project resources Nodes priority authorization walltime
- default/max
- --------------------- -|---|---|---|--------------------- ---------- --------------- -------------
- **qexp** no none required 32 nodes, max 8 per user 150 no 1 / 1h
- Express queue
+
+ |queue|Active project|Project resources|Nodes|priority|authorization|walltime |
+
+ |---|---|
+ |**qexp** \|no|none required|32 nodes, max 8 per user|150|no|1 / 1h|
+ \
- **qprace** yes > 0 >1006 nodes, max 86 per job 0 no 24 / 48h
- Production queue
+ gt; 0 >1006 nodes, max 86 per job 0 no 24 / 48h> 0 >1006 nodes, max 86 per job 0 no 24 / 48h
+ \
- **qfree** yes none required 752 nodes, max 86 per job -1024 no 12 / 12h
- Free resource queue
- ---------------------------------------------------------------------------------------------------------------------------------------------
+ |**qfree** \|yes|none required|752 nodes, max 86 per job|-1024|no|12 / 12h|
+ \
+
-qprace**, the PRACE Production queue****: This queue is intended for
+qprace**, the PRACE \***: This queue is intended for
normal production runs. It is required that active project with nonzero
remaining resources is specified to enter the qprace. The queue runs
with medium priority and no special authorization is required to use it.
diff --git a/converted/docs.it4i.cz/salomon/prace.pdf b/converted/docs.it4i.cz/salomon/prace.pdf
index 4ed614046921ccfcc2be200293b9185aec9413ce..644409062ae379def08a203669a13e9bd4fedfb5 100644
Binary files a/converted/docs.it4i.cz/salomon/prace.pdf and b/converted/docs.it4i.cz/salomon/prace.pdf differ
diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.epub b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.epub
index ffce25a37533a4a9866a9ba24f4de2950ec386ec..37ac51ad1af99e5885abef4f87f8c7d38ae54e8f 100644
Binary files a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.epub and b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.epub differ
diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.md b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.md
index d70fb34345ee7f39d4e56e930a04aa98ae0c6e9b..1282e33dae3f896100f05b4046a6c45f404ae549 100644
--- a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.md
+++ b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.md
@@ -73,13 +73,13 @@ files with program executable myprog.x, each as a separate job.
First, we create a tasklist file (or subjobs list), listing all tasks
(subjobs) - all input files in our example:
-```
+`
$ find . -name 'file*' > tasklist
-```
+`
Then we create jobscript:
-```
+`
#!/bin/bash
#PBS -A PROJECT_ID
#PBS -q qprod
@@ -100,7 +100,7 @@ cp $PBS_O_WORKDIR/$TASK input ; cp $PBS_O_WORKDIR/myprog.x .
# copy output file to submit directory
cp output $PBS_O_WORKDIR/$TASK.out
-```
+`
In this example, the submit directory holds the 900 input files,
executable myprog.x and the jobscript file. As input for each run, we
@@ -127,10 +127,10 @@ To submit the job array, use the qsub -J command. The 900 jobs of the
[example above](capacity-computing.html#array_example) may
be submitted like this:
-```
+`
$ qsub -N JOBNAME -J 1-900 jobscript
506493[].isrv5
-```
+`
In this example, we submit a job array of 900 subjobs. Each subjob will
run on full node and is assumed to take less than 2 hours (please note
@@ -140,9 +140,9 @@ forget to set your valid PROJECT_ID and desired queue).
Sometimes for testing purposes, you may need to submit only one-element
array. This is not allowed by PBSPro, but there's a workaround:
-```
+`
$ qsub -N JOBNAME -J 9-10:2 jobscript
-```
+`
This will only choose the lower index (9 in this example) for
submitting/running your job.
@@ -151,27 +151,27 @@ submitting/running your job.
Check status of the job array by the qstat command.
-```
+`
$ qstat -a 506493[].isrv5
isrv5:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
---------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
+--------------- -------- -- |---|---| ------ --- --- ------ ----- - -----
12345[].dm2 user2 qprod xx 13516 1 24 -- 00:50 B 00:02
-```
+`
The status B means that some subjobs are already running.
Check status of the first 100 subjobs by the qstat command.
-```
+`
$ qstat -a 12345[1-100].isrv5
isrv5:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
---------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
+--------------- -------- -- |---|---| ------ --- --- ------ ----- - -----
12345[1].isrv5 user2 qprod xx 13516 1 24 -- 00:50 R 00:02
12345[2].isrv5 user2 qprod xx 13516 1 24 -- 00:50 R 00:02
12345[3].isrv5 user2 qprod xx 13516 1 24 -- 00:50 R 00:01
@@ -179,28 +179,28 @@ Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
. . . . . . . . . . .
, . . . . . . . . . .
12345[100].isrv5 user2 qprod xx 13516 1 24 -- 00:50 Q --
-```
+`
Delete the entire job array. Running subjobs will be killed, queueing
subjobs will be deleted.
-```
+`
$ qdel 12345[].isrv5
-```
+`
Deleting large job arrays may take a while.
Display status information for all user's jobs, job arrays, and subjobs.
-```
+`
$ qstat -u $USER -t
-```
+`
Display status information for all user's subjobs.
-```
+`
$ qstat -u $USER -tJ
-```
+`
Read more on job arrays in the [PBSPro Users
guide](../../pbspro-documentation.html).
@@ -217,10 +217,10 @@ useful in running single core jobs via the queue system on Anselm.
For more information and examples see the parallel man page:
-```
+`
$ module add parallel
$ man parallel
-```
+`
### GNU parallel jobscript
@@ -238,13 +238,13 @@ job. We call these single core jobs tasks.
First, we create a tasklist file, listing all tasks - all input files in
our example:
-```
+`
$ find . -name 'file*' > tasklist
-```
+`
Then we create jobscript:
-```
+`
#!/bin/bash
#PBS -A PROJECT_ID
#PBS -q qprod
@@ -268,7 +268,7 @@ cat input > output
# copy output file to submit directory
cp output $PBS_O_WORKDIR/$TASK.out
-```
+`
In this example, tasks from tasklist are executed via the GNU
parallel. The jobscript executes multiple instances of itself in
@@ -286,10 +286,10 @@ To submit the job, use the qsub command. The 101 tasks' job of the
[example above](capacity-computing.html#gp_example) may be
submitted like this:
-```
+`
$ qsub -N JOBNAME jobscript
12345.dm2
-```
+`
In this example, we submit a job of 101 tasks. 24 input files will be
processed in parallel. The 101 tasks on 24 cores are assumed to
@@ -330,20 +330,20 @@ job. We call these single core jobs tasks.
First, we create a tasklist file, listing all tasks - all input files in
our example:
-```
+`
$ find . -name 'file*' > tasklist
-```
+`
Next we create a file, controlling how many tasks will be executed in
one subjob
-```
+`
$ seq 32 > numtasks
-```
+`
Then we create jobscript:
-```
+`
#!/bin/bash
#PBS -A PROJECT_ID
#PBS -q qprod
@@ -369,7 +369,7 @@ cat input > output
# copy output file to submit directory
cp output $PBS_O_WORKDIR/$TASK.out
-```
+`
In this example, the jobscript executes in multiple instances in
parallel, on all cores of a computing node. Variable $TASK expands to
@@ -398,10 +398,10 @@ the [example
above](capacity-computing.html#combined_example) may be
submitted like this:
-```
+`
$ qsub -N JOBNAME -J 1-992:32 jobscript
12345[].dm2
-```
+`
In this example, we submit a job array of 31 subjobs. Note the -J
1-992:**48**, this must be the same as the number sent to numtasks file.
@@ -424,11 +424,11 @@ production jobs.
Unzip the archive in an empty directory on Anselm and follow the
instructions in the README file
-```
+`
$ unzip capacity.zip
$ cd capacity
$ cat README
-```
+`
Â
diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.pdf b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.pdf
index 495d3b1917382569e5675d862489dd7bba677eab..90d894b275908ffb1bbf654c415c0801d1361a87 100644
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diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.epub b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.epub
index fdbb4da25e760995e5b340f79a54756372038561..5e4b4d7c72e7fb9f78f3acacc024d517f12bc7d1 100644
Binary files a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.epub and b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.epub differ
diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.md b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.md
index e89875d5d7c57156ad6119ea0070fc7c725f5c22..6ef6f4cfabb1db6af5bb44a227aa167f223246c0 100644
--- a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.md
+++ b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.md
@@ -26,8 +26,8 @@ queueing the jobs. The queues provide prioritized and exclusive access
to the computational resources. Following queues are available to Anselm
users:
-- **qexp**, the Express queue
-- **qprod**, the Production queue****
+- **qexp**, the \
+- **qprod**, the \***
- **qlong**, the Long queue
- **qmpp**, the Massively parallel queue
- **qfat**, the queue to access SMP UV2000 machine
@@ -54,6 +54,3 @@ on first of the allocated nodes.**
Read more on the [Job submission and
execution](job-submission-and-execution.html) page.
-HTML commented section #1 (removed Capacity computing section, this
-will be optimized for Salomon)
-
diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.pdf b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.pdf
index 3325d30cb4927cfc231d9aa3ad0079259ce66137..ef7ea9f124c31695cdb674a013abc7b3eeeb4ee9 100644
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diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.epub b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.epub
index 0c6ec0a7fcbc6374e511311752c4faaafb2902fe..4ac3a4ed17e64aa9ae72ac20137a4a09ceea5052 100644
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diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.md b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.md
index 5754dc8ea62c9f6564692b9cbb4a45f8be5a05ad..43919cced0890a66a683f0a02c26d8aed8aa75ef 100644
--- a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.md
+++ b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.md
@@ -49,25 +49,24 @@ Usage counts allocated corehours (ncpus*walltime). Usage is decayed, or
cut in half periodically, at the interval 168 hours (one week).
Jobs queued in queue qexp are not calculated to project's usage.
->Calculated usage and fairshare priority can be seen at
+Calculated usage and fairshare priority can be seen at
<https://extranet.it4i.cz/rsweb/salomon/projects>.
->
->Calculated fairshare priority can be also seen as
+Calculated fairshare priority can be also seen as
Resource_List.fairshare attribute of a job.
-### >Eligible time
+###Eligible time
Eligible time is amount (in seconds) of eligible time job accrued while
waiting to run. Jobs with higher eligible time gains higher
-pri>>ority.
+priority.
Eligible time has the least impact on execution priority. Eligible time
is used for sorting jobs with equal queue priority and fairshare
priority. It is very, very difficult for >eligible time to
compete with fairshare priority.
->>Eligible time can be seen as eligible_time attribute of
+Eligible time can be seen as eligible_time attribute of
job.
### Formula
@@ -78,7 +77,7 @@ Job execution priority (job sort formula) is calculated as:
### Job backfilling
->The scheduler uses job backfilling.
+The scheduler uses job backfilling.
Backfilling means fitting smaller jobs around the higher-priority jobs
that the scheduler is going to run next, in such a way that the
diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.pdf b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.pdf
index 14804dfa4b7c6cb30c5e028d2e46866c84012f15..2c68a8d741e053c928e558203c32cbd9727f4327 100644
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diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.epub b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.epub
index 2c8f641317de2504e309fd7aa2e969e4395edb4a..3a21831030fab66b7baa5da6bdeedd6bccc16317 100644
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diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md
index 5fe712b4cb1ccb7435108e1f5b6882f053bbc26d..e0499050b26d8c4e6f9e56c36bc9acf7f3811ebb 100644
--- a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md
+++ b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md
@@ -21,9 +21,9 @@ the computational resources.
Submit the job using the qsub command:
-```
+`
$ qsub -A Project_ID -q queue -l select=x:ncpus=y,walltime=[[hh:]mm:]ss[.ms] jobscript
-```
+`
The qsub submits the job into the queue, in another words the qsub
command creates a request to the PBS Job manager for allocation of
@@ -37,9 +37,9 @@ cluster.**
### Job Submission Examples
-```
+`
$ qsub -A OPEN-0-0 -q qprod -l select=64:ncpus=24,walltime=03:00:00 ./myjob
-```
+`
In this example, we allocate 64 nodes, 24 cores per node, for 3 hours.
We allocate these resources via the qprod queue, consumed resources will
@@ -48,9 +48,9 @@ myjob will be executed on the first node in the allocation.
Â
-```
+`
$ qsub -q qexp -l select=4:ncpus=24 -I
-```
+`
In this example, we allocate 4 nodes, 24 cores per node, for 1 hour. We
allocate these resources via the qexp queue. The resources will be
@@ -58,9 +58,9 @@ available interactively
Â
-```
+`
$ qsub -A OPEN-0-0 -q qlong -l select=10:ncpus=24 ./myjob
-```
+`
In this example, we allocate 10 nodes, 24 cores per node, for 72 hours.
We allocate these resources via the qlong queue. Jobscript myjob will be
@@ -68,9 +68,9 @@ executed on the first node in the allocation.
Â
-```
+`
$ qsub -A OPEN-0-0 -q qfree -l select=10:ncpus=24 ./myjob
-```
+`
In this example, we allocate 10Â nodes, 24 cores per node, for 12 hours.
We allocate these resources via the qfree queue. It is not required that
@@ -94,17 +94,17 @@ resources have been spent, etc. The Phi cards are thus also available to
PRACE users. There's no need to ask for permission to utilize the Phi
cards in project proposals.
-```
+`
$ qsub -A OPEN-0-0 -I -q qprod -l select=1:ncpus=24:accelerator=True:naccelerators=2:accelerator_model=phi7120 ./myjob
-```
+`
In this example, we allocate 1 node, with 24 cores, with 2 Xeon Phi
7120p cards, running batch job ./myjob. The default time for qprod is
used, e. g. 24 hours.
-```
+`
$ qsub -A OPEN-0-0 -I -q qlong -l select=4:ncpus=24:accelerator=True:naccelerators=2 -l walltime=56:00:00 -I
-```
+`
In this example, we allocate 4 nodes, with 24 cores per node (totalling
96 cores), with 2 Xeon Phi 7120p cards per node (totalling 8 Phi cards),
@@ -127,17 +127,17 @@ user may not utilize CPU or memory allocated to a job by other user.
Always, full chunks are allocated, a job may only use resources of the
NUMA nodes allocated to itself.
-```
+`
 $ qsub -A OPEN-0-0 -q qfat -l select=14 ./myjob
-```
+`
In this example, we allocate all 14 NUMA nodes (corresponds to 14
chunks), 112 cores of the SGI UV2000 node for 72 hours. Jobscript myjob
will be executed on the node uv1.
-```
+`
$ qsub -A OPEN-0-0 -q qfat -l select=1:mem=2000GB ./myjob
-```
+`
In this example, we allocate 2000GB of memory on the UV2000 for 72
hours. By requesting 2000GB of memory, 10 chunks are allocated.
@@ -149,18 +149,18 @@ All qsub options may be [saved directly into the
jobscript](job-submission-and-execution.html#PBSsaved). In
such a case, no options to qsub are needed.
-```
+`
$ qsub ./myjob
-```
+`
Â
By default, the PBS batch system sends an e-mail only when the job is
aborted. Disabling mail events completely can be done like this:
-```
+`
$ qsub -m n
-```
+`
Advanced job placement
--------------------------
@@ -169,40 +169,40 @@ Advanced job placement
Specific nodes may be allocated via the PBS
-```
+`
qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=24:host=r24u35n680+1:ncpus=24:host=r24u36n681 -I
-```
+`
Or using short names
-```
+`
qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=24:host=cns680+1:ncpus=24:host=cns681 -I
-```
+`
In this example, we allocate nodes r24u35n680 and r24u36n681, all 24
cores per node, for 24 hours. Consumed resources will be accounted to
the Project identified by Project ID OPEN-0-0. The resources will be
available interactively.
-### Placement by Hypercube dimension
+### Placement by |Hypercube|dimension|
Nodes may be selected via the PBS resource attribute ehc_[1-7]d .
- Hypercube dimension
- --------------------- -------------------------------------------
- 1D ehc_1d
- 2D ehc_2d
- 3D ehc_3d
- 4D ehc_4d
- 5D ehc_5d
- 6D ehc_6d
- 7D ehc_7d
+ |Hypercube|dimension|
+ --------------- |---|---|---------------------------------
+ |1D|ehc_1d|
+ |2D|ehc_2d|
+ |3D|ehc_3d|
+ |4D|ehc_4d|
+ |5D|ehc_5d|
+ |6D|ehc_6d|
+ |7D|ehc_7d|
Â
-```
+`
$ qsub -A OPEN-0-0 -q qprod -l select=4:ncpus=24 -l place=group=ehc_1d -I
-```
+`
In this example, we allocate 4 nodes, 24 cores, selecting only the nodes
with [hypercube
@@ -221,17 +221,17 @@ There are at most 9 nodes sharing the same Infiniband switch.
Infiniband switch list:
-```
+`
$ qmgr -c "print node @a" | grep switch
set node r4i1n11 resources_available.switch = r4i1s0sw1
set node r2i0n0 resources_available.switch = r2i0s0sw1
set node r2i0n1 resources_available.switch = r2i0s0sw1
...
-```
+`
List of all nodes per Infiniband switch:
-```
+`
$ qmgr -c "print node @a" | grep r36sw3
set node r36u31n964 resources_available.switch = r36sw3
set node r36u32n965 resources_available.switch = r36sw3
@@ -242,7 +242,7 @@ set node r36u36n969 resources_available.switch = r36sw3
set node r37u32n970 resources_available.switch = r36sw3
set node r37u33n971 resources_available.switch = r36sw3
set node r37u34n972 resources_available.switch = r36sw3
-```
+`
Nodes sharing the same switch may be selected via the PBS resource
attribute switch.
@@ -251,16 +251,16 @@ We recommend allocating compute nodes of a single switch when best
possible computational network performance is required to run the job
efficiently:
-```
+`
$ qsub -A OPEN-0-0 -q qprod -l select=9:ncpus=24:switch=r4i1s0sw1 ./myjob
-```
+`
In this example, we request all the 9 nodes sharing the r4i1s0sw1 switch
for 24 hours.
-```
+`
$ qsub -A OPEN-0-0 -q qprod -l select=9:ncpus=24 -l place=group=switch ./myjob
-```
+`
In this example, we request 9 nodes placed on the same switch using node
grouping placement for 24 hours.
@@ -273,26 +273,26 @@ Job Management
Check status of your jobs using the **qstat** and **check-pbs-jobs**
commands
-```
+`
$ qstat -a
$ qstat -a -u username
$ qstat -an -u username
$ qstat -f 12345.isrv5
-```
+`
Example:
-```
+`
$ qstat -a
srv11:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
---------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
+--------------- -------- -- |---|---| ------ --- --- ------ ----- - -----
16287.isrv5 user1 qlong job1 6183 4 64 -- 144:0 R 38:25
16468.isrv5 user1 qlong job2 8060 4 64 -- 144:0 R 17:44
16547.isrv5 user2 qprod job3x 13516 2 32 -- 48:00 R 00:58
-```
+`
In this example user1 and user2 are running jobs named job1, job2 and
job3x. The jobs job1 and job2 are using 4 nodes, 16 cores per node each.
@@ -307,29 +307,29 @@ of user's PBS jobs' processes on execution hosts. Display load,
processes. Display job standard and error output. Continuously display
(tail -f) job standard or error output.
-```
+`
$ check-pbs-jobs --check-all
$ check-pbs-jobs --print-load --print-processes
$ check-pbs-jobs --print-job-out --print-job-err
$ check-pbs-jobs --jobid JOBID --check-all --print-all
$ check-pbs-jobs --jobid JOBID --tailf-job-out
-```
+`
Examples:
-```
+`
$ check-pbs-jobs --check-all
JOB 35141.dm2, session_id 71995, user user2, nodes r3i6n2,r3i6n3
Check session id: OK
Check processes
r3i6n2: OK
r3i6n3: No process
-```
+`
In this example we see that job 35141.dm2 currently runs no process on
allocated node r3i6n2, which may indicate an execution error.
-```
+`
$ check-pbs-jobs --print-load --print-processes
JOB 35141.dm2, session_id 71995, user user2, nodes r3i6n2,r3i6n3
Print load
@@ -341,13 +341,13 @@ r3i6n2: 0.0 -bash
r3i6n2: 0.0 /bin/bash /var/spool/PBS/mom_priv/jobs/35141.dm2.SC
r3i6n2: 99.7 run-task
...
-```
+`
In this example we see that job 35141.dm2 currently runs process
run-task on node r3i6n2, using one thread only, while node r3i6n3 is
empty, which may indicate an execution error.
-```
+`
$ check-pbs-jobs --jobid 35141.dm2 --print-job-out
JOB 35141.dm2, session_id 71995, user user2, nodes r3i6n2,r3i6n3
Print job standard output:
@@ -357,7 +357,7 @@ Script name  : script
Run loop 1
Run loop 2
Run loop 3
-```
+`
In this example, we see actual output (some iteration loops) of the job
35141.dm2
@@ -367,21 +367,21 @@ qdel,** **qsig** or **qalter** commands
You may release your allocation at any time, using qdel command
-```
+`
$ qdel 12345.isrv5
-```
+`
You may kill a running job by force, using qsig command
-```
+`
$ qsig -s 9 12345.isrv5
-```
+`
Learn more by reading the pbs man page
-```
+`
$ man pbs_professional
-```
+`
Job Execution
-------------
@@ -399,17 +399,17 @@ manager.
The jobscript or interactive shell is executed on first of the allocated
nodes.
-```
+`
$ qsub -q qexp -l select=4:ncpus=24 -N Name0 ./myjob
$ qstat -n -u username
isrv5:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
---------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
+--------------- -------- -- |---|---| ------ --- --- ------ ----- - -----
15209.isrv5 username qexp Name0 5530 4 96 -- 01:00 R 00:00
r21u01n577/0*24+r21u02n578/0*24+r21u03n579/0*24+r21u04n580/0*24
-```
+`
 In this example, the nodes r21u01n577, r21u02n578, r21u03n579,
r21u04n580 were allocated for 1 hour via the qexp queue. The jobscript
@@ -419,14 +419,14 @@ nodes r21u02n578, r21u03n579, r21u04n580 are available for use as well.
The jobscript or interactive shell is by default executed in home
directory
-```
+`
$ qsub -q qexp -l select=4:ncpus=24 -I
qsub: waiting for job 15210.isrv5 to start
qsub: job 15210.isrv5 ready
$ pwd
/home/username
-```
+`
In this example, 4 nodes were allocated interactively for 1 hour via the
qexp queue. The interactive shell is executed in the home directory.
@@ -441,7 +441,7 @@ Calculations on allocated nodes may be executed remotely via the MPI,
ssh, pdsh or clush. You may find out which nodes belong to the
allocation by reading the $PBS_NODEFILE file
-```
+`
qsub -q qexp -l select=2:ncpus=24 -I
qsub: waiting for job 15210.isrv5 to start
qsub: job 15210.isrv5 ready
@@ -461,7 +461,7 @@ r4i6n13: r4i6n13
r2i5n6: r2i5n6
r4i7n2: r4i7n2
r4i7n0: r4i7n0
-```
+`
In this example, the hostname program is executed via pdsh from the
interactive shell. The execution runs on all four allocated nodes. The
@@ -476,7 +476,7 @@ The recommended way to run production jobs is to change to /scratch
directory early in the jobscript, copy all inputs to /scratch, execute
the calculations and copy outputs to home directory.
-```
+`
#!/bin/bash
# change to scratch directory, exit on failure
@@ -499,7 +499,7 @@ cp output $PBS_O_WORKDIR/.
#exit
exit
-```
+`
In this example, some directory on the /home holds the input file input
and executable mympiprog.x . We create a directory myjob on the /scratch
@@ -526,7 +526,7 @@ execution.
Example jobscript for an MPI job with preloaded inputs and executables,
options for qsub are stored within the script :
-```
+`
#!/bin/bash
#PBS -q qprod
#PBS -N MYJOB
@@ -545,7 +545,7 @@ mpiexec ./mympiprog.x
#exit
exit
-```
+`
In this example, input and executable files are assumed preloaded
manually in /scratch/$USER/myjob directory. Note the **mpiprocs** and
@@ -566,7 +566,7 @@ operational memory.
Example jobscript for single node calculation, using [local
scratch](../storage.html) on the node:
-```
+`
#!/bin/bash
# change to local scratch directory
@@ -584,7 +584,7 @@ cp output $PBS_O_WORKDIR/.
#exit
exit
-```
+`
In this example, some directory on the home holds the input file input
and executable myprog.x . We copy input and executable files from the
@@ -593,5 +593,3 @@ scratch /lscratch/$PBS_JOBID, execute the myprog.x and copy the output
file back to the /home directory. The myprog.x runs on one node only and
may use threads.
-HTML commented section #3 (Capacity computing need to be reworked)
-
diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.pdf b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.pdf
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diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.epub b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.epub
index 64f1949871d08f5f1865097d0c592515de16a51b..f09c536c3b73e84cdcd50bd5f3016aa88f7e3224 100644
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diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
index 9453f57ebf292c984fc155cfa6fdd62d4e1acff1..3395d6f7301eb6413d10d9be1c1faea632cf2a47 100644
--- a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
+++ b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
@@ -17,22 +17,14 @@ resources. Following table provides the queue partitioning overview:
Â
-<col width="12%" />
-<col width="12%" />
-<col width="12%" />
-<col width="12%" />
-<col width="12%" />
-<col width="12%" />
-<col width="12%" />
-<col width="12%" />
- |queue |active project |project resources<th align="left">nodes<th align="left">min ncpus*<th align="left">priority<th align="left">authorization<th align="left">walltimedefault/max |
+ |queue |active project |project resources |nodes<th align="left">min ncpus*<th align="left">priority<th align="left">authorization<th align="left">walltime |
| --- | --- |
- |<strong>qexp</strong>Express queue |no |none required |32 nodes, max 8 per user |24 |>150 |no |1 / 1h |
- |<strong>qprod</strong>Production queue |yes |> 0 |>1006 nodes, max 86 per job\ |24 |0 |no |24 / 48h |
+ |<strong>qexp</strong>\ |no |none required |32 nodes, max 8 per user |24 |>150 |no |1 / 1h |
+ |<strong>qprod</strong>\ |yes |> 0 |>1006 nodes, max 86 per job\ |24 |0 |no |24 / 48h |
|<strong>qlong</strong>Long queue |yes |> 0 |256 nodes, max 40 per job, only non-accelerated nodes allowed |24 |0 |no |72 / 144h |
|<strong>qmpp</strong>Massive parallel queue |yes |> 0 |1006 nodes |24 |0 |yes |2 / 4h |
|<strong>qfat</strong>UV2000 queue |yes |> 0\ |1 (uv1) |8 |0 |yes |24 / 48h |
- |<strong>qfree</strong>Free resource queue |yes |none required |752 nodes, max 86 per job |24 |-1024 |no |12 / 12h |
+ |<strong>qfree</strong>\ |yes |none required |752 nodes, max 86 per job |24 |-1024 |no |12 / 12h |
|<strong><strong>qviz</strong></strong>Visualization queue |yes |none required |2 (with NVIDIA Quadro K5000) |4 |150 |no |1 / 2h |
Â
@@ -47,21 +39,21 @@ is allowed after request for this queue.
Â
-- **qexp**, the Express queue: This queue is dedicated for testing and
+- **qexp**, the \: This queue is dedicated for testing and
running very small jobs. It is not required to specify a project to
enter the qexp. >*>There are 2 nodes always reserved for
this queue (w/o accelerator), maximum 8 nodes are available via the
qexp for a particular user. *The nodes may be
allocated on per core basis. No special authorization is required to
use it. The maximum runtime in qexp is 1 hour.
-- **qprod**, the Production queue****: This queue is intended for
+- **qprod**, the \***: This queue is intended for
normal production runs. It is required that active project with
nonzero remaining resources is specified to enter the qprod. All
nodes may be accessed via the qprod queue, however only 86 per job.
** Full nodes, 24 cores per node are allocated. The queue runs with
medium priority and no special authorization is required to use it.
The maximum runtime in qprod is 48 hours.
-- **qlong**, the Long queue****: This queue is intended for long
+- **qlong**, the Long queue***: This queue is intended for long
production runs. It is required that active project with nonzero
remaining resources is specified to enter the qlong. Only 336 nodes
without acceleration may be accessed via the qlong queue. Full
@@ -69,7 +61,7 @@ is allowed after request for this queue.
priority and no special authorization is required to use it.>
*The maximum runtime in qlong is 144 hours (three times of the
standard qprod time - 3 * 48 h)*
-- >****qmpp**, the massively parallel queue. This queue is
+- >***qmpp**, the massively parallel queue. This queue is
intended for massively parallel runs. It is required that active
project with nonzero remaining resources is specified to enter
the qmpp. All nodes may be accessed via the qmpp queue. ** Full
@@ -80,14 +72,14 @@ is allowed after request for this queue.
for authorization to enter the queue for all users associated to
her/his Project.
-- >****qfat**, the UV2000 queue. This queue is dedicated
+- >***qfat**, the UV2000 queue. This queue is dedicated
to access the fat SGI UV2000 SMP machine. The machine (uv1) has 112
Intel IvyBridge cores at 3.3GHz and 3.25TB RAM. An PI> *needs
explicitly* ask
[support](https://support.it4i.cz/rt/) for
authorization to enter the queue for all users associated to her/his
- Project.****
-- **qfree**, the Free resource queue****: The queue qfree is intended
+ Project.***
+- **qfree**, the \***: The queue qfree is intended
for utilization of free resources, after a Project exhausted all its
allocated computational resources (Does not apply to DD projects
by default. DD projects have to request for persmission on qfree
@@ -98,7 +90,7 @@ is allowed after request for this queue.
this queue. Full nodes, 24 cores per node are allocated. The queue
runs with very low priority and no special authorization is required
to use it. The maximum runtime in qfree is 12 hours.
-- **qviz**, the Visualization queue****: Intended for
+- **qviz**, the Visualization queue***: Intended for
pre-/post-processing using OpenGL accelerated graphics. Currently
when accessing the node, each user gets 4 cores of a CPU allocated,
thus approximately 73 GB of RAM and 1/7 of the GPU capacity
@@ -115,7 +107,7 @@ To access node with Xeon Phi co-processor user needs to specify that in
[job submission select
statement](job-submission-and-execution.html).
-### Notes**
+### Notes
The job wall clock time defaults to **half the maximum time**, see table
above. Longer wall time limits can be [set manually, see
@@ -142,14 +134,14 @@ Check the status of jobs, queues and compute nodes at
Display the queue status on Salomon:
-```
+`
$ qstat -q
-```
+`
The PBS allocation overview may be obtained also using the rspbs
command.
-```
+`
$ rspbs
Usage: rspbs [options]
@@ -204,7 +196,7 @@ Options:
                       Only for given node state (affects only --get-node*
                       --get-qlist-* --get-ibswitch-* actions)
 --incl-finished      Include finished jobs
-```
+`
Resources Accounting Policy
-------------------------------
@@ -231,14 +223,14 @@ User may check at any time, how many core-hours have been consumed by
himself/herself and his/her projects. The command is available on
clusters' login nodes.
-```
+`
$ it4ifree
Password:
    PID  Total Used ...by me Free
  -------- ------- ------ -------- -------
  OPEN-0-0 1500000 400644  225265 1099356
  DD-13-1   10000 2606 2606 7394
-```
+`
Â
diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.pdf b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.pdf
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diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-cfx.epub b/converted/docs.it4i.cz/salomon/software/ansys/ansys-cfx.epub
index 496e45899ef3966e7684d6a577748655b0989d76..d4fb57c12229c5b4d4457f1af87ac2f795c4dc17 100644
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diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-cfx.md b/converted/docs.it4i.cz/salomon/software/ansys/ansys-cfx.md
index 467fa0d56d6788051ba7511e33b82c897e31349c..39777fa74cf823baa4e4d062eff1d37394b24d4b 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/ansys-cfx.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/ansys-cfx.md
@@ -15,7 +15,7 @@ environment, with extensive capabilities for customization and
automation using session files, scripting and a powerful expression
language.
->To run ANSYS CFX in batch mode you can utilize/modify the default
+To run ANSYS CFX in batch mode you can utilize/modify the default
cfx.pbs script and execute it via the qsub command.
#!/bin/bash
@@ -77,9 +77,9 @@ CFX def file which is attached to the cfx solver via parameter
License**Â should be selected by parameter -P (Big letter **P**).
Licensed products are the following: aa_r
-(ANSYSÂ **Academic**Â Research), ane3fl (ANSYS
-Multiphysics)-**Commercial.**
->[More about licensing here](licensing.html)
+(ANSYS **Academic Research), ane3fl (ANSYS
+Multiphysics)-**Commercial.
+[More about licensing here](licensing.html)
 We have observed that the -P settings does not always work. Please set
your [license
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-cfx.pdf b/converted/docs.it4i.cz/salomon/software/ansys/ansys-cfx.pdf
index c429ee8fd4dab9d1c95c4710abc0ba0d5699048a..4bca308237e3b1ecf62fd699687a41cf842e8da9 100644
Binary files a/converted/docs.it4i.cz/salomon/software/ansys/ansys-cfx.pdf and b/converted/docs.it4i.cz/salomon/software/ansys/ansys-cfx.pdf differ
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-fluent.epub b/converted/docs.it4i.cz/salomon/software/ansys/ansys-fluent.epub
index 610401a862bb2805bf459febaf601108d72f97d2..a9e9f704d63f6f26382211a4d4249ef3bcebbcd5 100644
Binary files a/converted/docs.it4i.cz/salomon/software/ansys/ansys-fluent.epub and b/converted/docs.it4i.cz/salomon/software/ansys/ansys-fluent.epub differ
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-fluent.md b/converted/docs.it4i.cz/salomon/software/ansys/ansys-fluent.md
index 7830ed906dae31170141493690b2621174d76e59..bbacf3ea538d8b030f0c1504601ab9869e6dd166 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/ansys-fluent.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/ansys-fluent.md
@@ -12,10 +12,10 @@ treatment plants. Special models that give the software the ability to
model in-cylinder combustion, aeroacoustics, turbomachinery, and
multiphase systems have served to broaden its reach.
->1. Common way to run Fluent over pbs file
+1. Common way to run Fluent over pbs file
------------------------------------------------------
->To run ANSYS Fluent in batch mode you can utilize/modify the
+To run ANSYS Fluent in batch mode you can utilize/modify the
default fluent.pbs script and execute it via the qsub command.
#!/bin/bash
@@ -74,10 +74,10 @@ structure:
/file/write-case-dat aircraft_2m-solution
/exit yes
->The appropriate dimension of the problem has to be set by
+The appropriate dimension of the problem has to be set by
parameter (2d/3d).Â
->2. Fast way to run Fluent from command line
+2. Fast way to run Fluent from command line
--------------------------------------------------------
fluent solver_version [FLUENT_options] -i journal_file -pbs
@@ -104,17 +104,17 @@ from which the jobs are submitted (which is also the directory in which
the jobs are executed). The following is an example of what the content
of pbs_fluent.conf can be:
-```
+`
input="example_small.flin"
case="Small-1.65m.cas"
fluent_args="3d -pmyrinet"
outfile="fluent_test.out"
mpp="true"
-```
+`
The following is an explanation of the parameters:
-> input is the name of the input
+ input is the name of the input
file.
case is the name of the
@@ -137,11 +137,11 @@ the standard output will be sent.
mpp="true" will tell the job script to
execute the job across multiple processors. Â Â Â Â Â Â Â Â
->To run ANSYS Fluent in batch mode with user's config file you can
+To run ANSYS Fluent in batch mode with user's config file you can
utilize/modify the following script and execute it via the qsub
command.
-```
+`
#!/bin/sh
#PBS -l nodes=2:ppn=24
#PBS -1 qprod
@@ -188,9 +188,9 @@ command.
#run the solver
/apps/cae/ANSYS/16.1/v161/fluent/bin/fluent $fluent_args > $outfile
-```
+`
->It runs the jobs out of the directory from which they are
+It runs the jobs out of the directory from which they are
submitted (PBS_O_WORKDIR).
4. Running Fluent in parralel
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-fluent.pdf b/converted/docs.it4i.cz/salomon/software/ansys/ansys-fluent.pdf
index 8ead0271ab5ed69921187c071f096d4a9e62d68e..c2f576abc888dc0eb4ccd8de7cdda7d7cdf6a673 100644
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diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.epub b/converted/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.epub
index 47e7a2620f5b8afcc27c49403ebe2793bc332bcf..e89a94d2dffa5aa55721fd52040cd6c27612b020 100644
Binary files a/converted/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.epub and b/converted/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.epub differ
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.md b/converted/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.md
index 35dfd4a0a2c6c4f967c2b8de36950229d66a3fd5..6120f49e88e3dd9187c4459573cf1f83f9053228 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.md
@@ -19,7 +19,7 @@ result visualization and comprehensive report generation are all
available within a single fully interactive modern graphical user
environment.
->To run ANSYS LS-DYNA in batch mode you can utilize/modify the
+To run ANSYS LS-DYNA in batch mode you can utilize/modify the
default ansysdyna.pbs script and execute it via the qsub command.
#!/bin/bash
@@ -63,7 +63,7 @@ default ansysdyna.pbs script and execute it via the qsub command.
lsdyna161 -dis -usessh -machines "$hl" i=input.k
->Header of the pbs file (above) is common and description can be
+Header of the pbs file (above) is common and description can be
find > on [this
site](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
[SVS FEM](http://www.svsfem.cz) recommends to utilize
@@ -82,5 +82,3 @@ fail to run on nodes with Xeon Phi accelerator (it will use the virtual
interface of Phi cards instead of the real InfiniBand interface and MPI
will fail.
->>
-
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.pdf b/converted/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.pdf
index d5b9d4763e86f25566258a7dcd7742bbf23e99c5..ab307abf74981849cb4144586ed55df0b7b88ed0 100644
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diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.epub b/converted/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.epub
index ca84e6b4c00d60d4d35e43d983f9c3ccfebeaee8..3488b53efa4245bd83996f93415b78fcd7ee166e 100644
Binary files a/converted/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.epub and b/converted/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.epub differ
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.md b/converted/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.md
index e54cdf2753dc2ed7ca13e0b6e7b1395885312511..a33a8bf916a7290a08343efecbb3dd2f663a5f32 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.md
@@ -1,7 +1,7 @@
ANSYS MAPDL
===========
->**[ANSYS
+**[ANSYS
Multiphysics](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/ANSYS+Multiphysics)**
software offers a comprehensive product solution for both multiphysics
and single-physics analysis. The product includes structural, thermal,
@@ -10,7 +10,7 @@ product also contains solutions for both direct and sequentially coupled
physics problems including direct coupled-field elements and the ANSYS
multi-field solver.
->To run ANSYS MAPDL in batch mode you can utilize/modify the
+To run ANSYS MAPDL in batch mode you can utilize/modify the
default mapdl.pbs script and execute it via the qsub command.
#!/bin/bash
@@ -72,8 +72,8 @@ file has to be specified. Input file has to be defined by common APDL
file which is attached to the ansys solver via parameter -i
License** should be selected by parameter -p. Licensed products are
-the following: aa_r (ANSYS **Academic** Research), ane3fl (ANSYS
-Multiphysics)-**Commercial**, aa_r_dy (ANSYS **Academic**
+the following: aa_r (ANSYS **Academic Research), ane3fl (ANSYS
+Multiphysics)-**Commercial**, aa_r_dy (ANSYS **Academic
AUTODYN)>
[More about licensing here](licensing.html)
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.pdf b/converted/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.pdf
index 58ce4e4421c6a02587276482c20b63a25de37d52..5fd949d4122a04443f5e39bc267ab4a8c5277e5b 100644
Binary files a/converted/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.pdf and b/converted/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.pdf differ
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.epub b/converted/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.epub
index 0ee59c9f721fc06b7f769a8e0554ba732ebd1d80..ed14dce891db395d945ba9de55c9960fe6c27f20 100644
Binary files a/converted/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.epub and b/converted/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.epub differ
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md b/converted/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md
index 0a8d958dc4eb1e3cdef9fe2a4e2687de7230a3df..43dffc3a14231d9bb0e2e31dcfc09d6e3bd5f759 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md
@@ -1,8 +1,8 @@
Overview of ANSYS Products
==========================
-[SVS FEM](http://www.svsfem.cz/)** as ***[ANSYS
-Channel partner](http://www.ansys.com/)***Â for Czech
+[SVS FEM](http://www.svsfem.cz/)** as **[ANSYS
+Channel partner](http://www.ansys.com/)**Â for Czech
Republic provided all ANSYS licenses for all clusters and supports of
all ANSYS Products (Multiphysics, Mechanical, MAPDL, CFX, Fluent,
Maxwell, LS-DYNA...) to IT staff and ANSYS users. If you are challenging
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.pdf b/converted/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.pdf
index 7834d9359ac8d336db5f9b520ac018124bd83055..a4ae171ac87942ae788dd2064041d3de568de3d3 100644
Binary files a/converted/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.pdf and b/converted/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.pdf differ
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys.epub b/converted/docs.it4i.cz/salomon/software/ansys/ansys.epub
index 67f3e0c037a71eabe472906e82637185e9ccec03..d68a8eb9d6f1813df605fcc6e8fc16731dd036b2 100644
Binary files a/converted/docs.it4i.cz/salomon/software/ansys/ansys.epub and b/converted/docs.it4i.cz/salomon/software/ansys/ansys.epub differ
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys.md b/converted/docs.it4i.cz/salomon/software/ansys/ansys.md
index 9cacfcf54143558e160d71ff51bfe834fa1f0547..93f9c151da204a8a03bf3d4696f63f151ec898da 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/ansys.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/ansys.md
@@ -1,8 +1,8 @@
Overview of ANSYS Products
==========================
-[SVS FEM](http://www.svsfem.cz/)** as ***[ANSYS
-Channel partner](http://www.ansys.com/)***Â for Czech
+[SVS FEM](http://www.svsfem.cz/)** as **[ANSYS
+Channel partner](http://www.ansys.com/)**Â for Czech
Republic provided all ANSYS licenses for all clusters and supports of
all ANSYS Products (Multiphysics, Mechanical, MAPDL, CFX, Fluent,
Maxwell, LS-DYNA...) to IT staff and ANSYS users. If you are challenging
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys.pdf b/converted/docs.it4i.cz/salomon/software/ansys/ansys.pdf
index d439e2086186e4c6e2092045e1178c1eba5da906..f864f7886d115ed795fc8f29b1b17e73023ad8f4 100644
Binary files a/converted/docs.it4i.cz/salomon/software/ansys/ansys.pdf and b/converted/docs.it4i.cz/salomon/software/ansys/ansys.pdf differ
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/licensing.epub b/converted/docs.it4i.cz/salomon/software/ansys/licensing.epub
index 9762e8c53317d2a55c682473f6ffe9d036df6812..6fe1223199c10d72a2b63a40b450c7ac642ee221 100644
Binary files a/converted/docs.it4i.cz/salomon/software/ansys/licensing.epub and b/converted/docs.it4i.cz/salomon/software/ansys/licensing.epub differ
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/licensing.md b/converted/docs.it4i.cz/salomon/software/ansys/licensing.md
index 7e4f1d755e0fd5f4cd4b4ff0706ad0aef2d7f8f1..8ee4bc1c61dc30f9579e90c4c646752c25513f3d 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/licensing.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/licensing.md
@@ -10,11 +10,11 @@ ANSYS licence can be used by:
CE IT4Innovations project partners, particularly the University of
Ostrava, the Brno University of Technology - Faculty of Informatics,
the Silesian University in Opava, Institute of Geonics AS CR.)
-- id="result_box" all
+- all
persons who have a valid
license
-- id="result_box" students
- of the Technical University</span>
+- students
+ of the Technical University
ANSYS Academic Research
-----------------------
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/licensing.pdf b/converted/docs.it4i.cz/salomon/software/ansys/licensing.pdf
index f57922d5e2308d4115172e6adfd74caa0fe11234..71a0515f46caff06c1c4e437781345a44c3b4e19 100644
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diff --git a/converted/docs.it4i.cz/salomon/software/ansys/setting-license-preferences.epub b/converted/docs.it4i.cz/salomon/software/ansys/setting-license-preferences.epub
index 9bd33b7b2f9114d579610b8321d5d35afcf7c7ce..768ed3f0d2f7fa11364c336acfe6c7af6c6e7458 100644
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diff --git a/converted/docs.it4i.cz/salomon/software/ansys/setting-license-preferences.md b/converted/docs.it4i.cz/salomon/software/ansys/setting-license-preferences.md
index 9152432b475f63db8b68233c75f3d9ae259501d3..5c6d63842d2d5b6e76f056815beebba89e8e8989 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/setting-license-preferences.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/setting-license-preferences.md
@@ -19,7 +19,7 @@ ANSLIC_ADMIN Utility will be run
-[](Fluent_Licence_2.jpg)
+
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/setting-license-preferences.pdf b/converted/docs.it4i.cz/salomon/software/ansys/setting-license-preferences.pdf
index a2ab966620011a2aceb4e86f5c55e1f083d1da87..51b049c041e7af366b425bbd9645b1a5eda7494b 100644
Binary files a/converted/docs.it4i.cz/salomon/software/ansys/setting-license-preferences.pdf and b/converted/docs.it4i.cz/salomon/software/ansys/setting-license-preferences.pdf differ
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/workbench.epub b/converted/docs.it4i.cz/salomon/software/ansys/workbench.epub
index 59c2b68615ef2538921f75ba341d4154e5dfdcd9..083b277c9d325bb8d8de15811e6e2a2df3dfd76e 100644
Binary files a/converted/docs.it4i.cz/salomon/software/ansys/workbench.epub and b/converted/docs.it4i.cz/salomon/software/ansys/workbench.epub differ
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/workbench.md b/converted/docs.it4i.cz/salomon/software/ansys/workbench.md
index 250c7765bf1581322b4cde87a809e7cad7c99377..78ec8caa5d83c589a2542035fac57d0cd997b75a 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/workbench.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/workbench.md
@@ -54,7 +54,7 @@ launch the job:
echo -n "" > mpifile.txt
for host in `cat $PBS_NODEFILE`
do
- echo "-h $host -np $procs_per_host $ANSYS160_DIR/bin/ansysdis161 -dis" >> mpifile.txt
+ echo "-h $host -np $procs_per_host $ANSYS160_DIR/bin/ansysdis161 -dis" > mpifile.txt
done
#-i input.dat includes the input of analysis in APDL format
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/workbench.pdf b/converted/docs.it4i.cz/salomon/software/ansys/workbench.pdf
index dc4b1709a777eb82b9173fb2729e2f5689deb431..8495d4281d1ba9a8d2a22682ba53f023e2d53432 100644
Binary files a/converted/docs.it4i.cz/salomon/software/ansys/workbench.pdf and b/converted/docs.it4i.cz/salomon/software/ansys/workbench.pdf differ
diff --git a/converted/docs.it4i.cz/salomon/software/chemistry/molpro.epub b/converted/docs.it4i.cz/salomon/software/chemistry/molpro.epub
index bf9e776e3a2e530c20d7c0ef97e4cd2805260674..ab6faa3beeeaa11ad50acbb5fca10684c463b9e5 100644
Binary files a/converted/docs.it4i.cz/salomon/software/chemistry/molpro.epub and b/converted/docs.it4i.cz/salomon/software/chemistry/molpro.epub differ
diff --git a/converted/docs.it4i.cz/salomon/software/chemistry/molpro.md b/converted/docs.it4i.cz/salomon/software/chemistry/molpro.md
index c01f1cc7b8ff6a50b37f7f2859e987463082b433..44f8d92337f0c4f4ae4b4dd0d4e90cab4d53ce28 100644
--- a/converted/docs.it4i.cz/salomon/software/chemistry/molpro.md
+++ b/converted/docs.it4i.cz/salomon/software/chemistry/molpro.md
@@ -19,7 +19,7 @@ license. Please contact support to enable access to Molpro if you have a
valid license appropriate for running on our cluster (eg. >academic
research group licence, parallel execution).
->To run Molpro, you need to have a valid license token present in
+To run Molpro, you need to have a valid license token present in
" $HOME/.molpro/token". You can
download the token from [Molpro
website](https://www.molpro.net/licensee/?portal=licensee).
@@ -32,15 +32,15 @@ parallel version compiled with Intel compilers and Intel MPI.
Compilation parameters are default :
- Parameter Value
- ------------------------------------------------- -----------------------------
- >max number of atoms 200
- >max number of valence orbitals 300
- >max number of basis functions 4095
- >max number of states per symmmetry 20
- >max number of state symmetries 16
- >max number of records 200
- >max number of primitives >maxbfn x [2]
+ |Parameter|Value|
+ ------------------------------------------- |---|---|-------------------
+ |max number of atoms|200|
+ |max number of valence orbitals|300|
+ |max number of basis functions|4095|
+ |max number of states per symmmetry|20|
+ |max number of state symmetries|16|
+ |max number of records|200|
+ |max number of primitives|maxbfn x [2]|
Â
diff --git a/converted/docs.it4i.cz/salomon/software/chemistry/molpro.pdf b/converted/docs.it4i.cz/salomon/software/chemistry/molpro.pdf
index 495378a8b8fe0f854e3ad4875842fe2a51313375..88478a4c09563a1e1f09d91b882a4b4a26218819 100644
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diff --git a/converted/docs.it4i.cz/salomon/software/chemistry/nwchem.epub b/converted/docs.it4i.cz/salomon/software/chemistry/nwchem.epub
index 4c9e1bbc327d25951e5b2eb4c3abd8bdf7b4f533..7fd07bcc2aa85f6f86194284d2eb75ebb4e8609b 100644
Binary files a/converted/docs.it4i.cz/salomon/software/chemistry/nwchem.epub and b/converted/docs.it4i.cz/salomon/software/chemistry/nwchem.epub differ
diff --git a/converted/docs.it4i.cz/salomon/software/chemistry/nwchem.md b/converted/docs.it4i.cz/salomon/software/chemistry/nwchem.md
index 2f7c34118bba74a8338ba236a14f38278837a691..b37cb96e6ff2cfcabcfcf4e78a741e1a86e8eaf8 100644
--- a/converted/docs.it4i.cz/salomon/software/chemistry/nwchem.md
+++ b/converted/docs.it4i.cz/salomon/software/chemistry/nwchem.md
@@ -3,10 +3,10 @@ NWChem
High-Performance Computational Chemistry
->Introduction
+Introduction
-------------------------
->NWChem aims to provide its users with computational chemistry
+NWChem aims to provide its users with computational chemistry
tools that are scalable both in their ability to treat large scientific
computational chemistry problems efficiently, and in their use of
available parallel computing resources from high-performance parallel
@@ -50,7 +50,7 @@ jobs applies. Sample jobscript :
module add NWChem/6.5.revision26243-intel-2015b-2014-09-10-Python-2.7.8
mpirun nwchem h2o.nw
->Options
+Options
--------------------
Please refer to [the
diff --git a/converted/docs.it4i.cz/salomon/software/chemistry/nwchem.pdf b/converted/docs.it4i.cz/salomon/software/chemistry/nwchem.pdf
index 5c2bc1b317cb7340ab936e4fa4744b04b8feb16b..32dc498934c944f399596aaec5f6990118e60250 100644
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diff --git a/converted/docs.it4i.cz/salomon/software/chemistry/phono3py.epub b/converted/docs.it4i.cz/salomon/software/chemistry/phono3py.epub
index 172022e2ccb3d6c50368c0f848c99a8a07506daa..af83faf7539d57dabfebc002c394bff4a9130334 100644
Binary files a/converted/docs.it4i.cz/salomon/software/chemistry/phono3py.epub and b/converted/docs.it4i.cz/salomon/software/chemistry/phono3py.epub differ
diff --git a/converted/docs.it4i.cz/salomon/software/chemistry/phono3py.md b/converted/docs.it4i.cz/salomon/software/chemistry/phono3py.md
index 363372116dba57feed4dc43bedc210348936557a..14148e5a9e3f53cf593765a7b697a35fc5ab2be7 100644
--- a/converted/docs.it4i.cz/salomon/software/chemistry/phono3py.md
+++ b/converted/docs.it4i.cz/salomon/software/chemistry/phono3py.md
@@ -15,9 +15,9 @@ http://atztogo.github.io/phono3py/index.html
Load the phono3py/0.9.14-ictce-7.3.5-Python-2.7.9 module
-```
+`
$ module load phono3py/0.9.14-ictce-7.3.5-Python-2.7.9
-```
+`
Example of calculating thermal conductivity of Si using VASP code.
------------------------------------------------------------------
@@ -29,7 +29,7 @@ using the diamond structure of silicon stored in
[POSCAR](phono3py-input/poscar-si)Â (the same form as in
VASP) using single displacement calculations within supercell.
-```
+`
$ cat POSCAR
 Si
  1.0
@@ -47,19 +47,19 @@ Direct
  0.1250000000000000 0.6250000000000000 0.6250000000000000
  0.6250000000000000 0.1250000000000000 0.6250000000000000
  0.6250000000000000 0.6250000000000000 0.1250000000000000
-```
+`
### Generating displacement using 2x2x2 supercell for both second and third order force constants
-```
+`
$ phono3py -d --dim="2 2 2" -c POSCAR
-```
+`
111 displacements is created stored in
disp_fc3.yaml, and the structure input files with this
displacements are POSCAR-00XXX, where the XXX=111.
-```
+`
disp_fc3.yaml POSCAR-00008 POSCAR-00017 POSCAR-00026 POSCAR-00035 POSCAR-00044 POSCAR-00053 POSCAR-00062 POSCAR-00071 POSCAR-00080 POSCAR-00089 POSCAR-00098 POSCAR-00107
POSCARÂ Â Â Â Â Â Â Â POSCAR-00009Â POSCAR-00018Â POSCAR-00027Â POSCAR-00036Â POSCAR-00045Â POSCAR-00054Â POSCAR-00063Â POSCAR-00072Â POSCAR-00081Â POSCAR-00090Â POSCAR-00099Â POSCAR-00108
POSCAR-00001Â Â POSCAR-00010Â POSCAR-00019Â POSCAR-00028Â POSCAR-00037Â POSCAR-00046Â POSCAR-00055Â POSCAR-00064Â POSCAR-00073Â POSCAR-00082Â POSCAR-00091Â POSCAR-00100Â POSCAR-00109
@@ -69,7 +69,7 @@ POSCAR-00004Â Â POSCAR-00013Â POSCAR-00022Â POSCAR-00031Â POSCAR-00040Â POS
POSCAR-00005Â Â POSCAR-00014Â POSCAR-00023Â POSCAR-00032Â POSCAR-00041Â POSCAR-00050Â POSCAR-00059Â POSCAR-00068Â POSCAR-00077Â POSCAR-00086Â POSCAR-00095Â POSCAR-00104
POSCAR-00006Â Â POSCAR-00015Â POSCAR-00024Â POSCAR-00033Â POSCAR-00042Â POSCAR-00051Â POSCAR-00060Â POSCAR-00069Â POSCAR-00078Â POSCAR-00087Â POSCAR-00096Â POSCAR-00105
POSCAR-00007Â Â POSCAR-00016Â POSCAR-00025Â POSCAR-00034Â POSCAR-00043Â POSCAR-00052Â POSCAR-00061Â POSCAR-00070Â POSCAR-00079Â POSCAR-00088Â POSCAR-00097Â POSCAR-00106
-```
+`
For each displacement the forces needs to be
calculated, i.e. in form of the output file of VASP (vasprun.xml). For a
@@ -83,7 +83,7 @@ script. Then each of the single 111 calculations is submitted
[run.sh](phono3py-input/run.sh) by
[submit.sh](phono3py-input/submit.sh).
-```
+`
$./prepare.sh
$ls
disp-00001Â disp-00009Â disp-00017Â disp-00025Â disp-00033Â disp-00041Â disp-00049Â disp-00057Â disp-00065Â disp-00073Â disp-00081Â disp-00089Â disp-00097Â disp-00105Â Â Â Â INCAR
@@ -94,15 +94,15 @@ disp-00005Â disp-00013Â disp-00021Â disp-00029Â disp-00037Â disp-00045Â di
disp-00006Â disp-00014Â disp-00022Â disp-00030Â disp-00038Â disp-00046Â disp-00054Â disp-00062Â disp-00070Â disp-00078Â disp-00086Â disp-00094Â disp-00102Â disp-00110Â Â Â Â run.sh
disp-00007Â disp-00015Â disp-00023Â disp-00031Â disp-00039Â disp-00047Â disp-00055Â disp-00063Â disp-00071Â disp-00079Â disp-00087Â disp-00095Â disp-00103Â disp-00111Â Â Â Â submit.sh
disp-00008Â disp-00016Â disp-00024Â disp-00032Â disp-00040Â disp-00048Â disp-00056Â disp-00064Â disp-00072Â disp-00080Â disp-00088Â disp-00096Â disp-00104Â disp_fc3.yaml
-```
+`
Taylor your run.sh script to fit into your project and
other needs and submit all 111 calculations using submit.sh
script
-```
+`
$ ./submit.sh
-```
+`
Collecting results and post-processing with phono3py
---------------------------------------------------------------------------
@@ -110,18 +110,18 @@ $ ./submit.sh
Once all jobs are finished and vasprun.xml is created in
each disp-XXXXX directory the collection is done by
-```
+`
$ phono3py --cf3 disp-{00001..00111}/vasprun.xml
-```
+`
and
`disp_fc2.yaml, FORCES_FC2`, `FORCES_FC3`{.docutils
.literal} and disp_fc3.yaml should appear and put into the hdf
format by
-```
+`
$ phono3py --dim="2 2 2" -c POSCAR
-```
+`
resulting in `fc2.hdf5` and `fc3.hdf5`{.docutils
.literal}
@@ -131,13 +131,13 @@ resulting in `fc2.hdf5` and `fc3.hdf5`{.docutils
The phonon lifetime calculations takes some time,
however is independent on grid points, so could be splitted:
-```
+`
$ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" --sigma 0.1 --wgp
-```
+`
### Inspecting ir_grid_points.yaml
-```
+`
$ grep grid_point ir_grid_points.yaml
num_reduced_ir_grid_points: 35
ir_grid_points:Â # [address, weight]
@@ -176,27 +176,27 @@ ir_grid_points:Â # [address, weight]
- grid_point: 274
- grid_point: 283
- grid_point: 364
-```
+`
one finds which grid points needed to be calculated, for instance using
following
-```
+`
$ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCARÂ --sigma 0.1 --br --write-gamma --gp="0 1 2
-```
+`
one calculates grid points 0, 1, 2. To automize one can
use for instance scripts to submit 5 points in series, see
[gofree-cond1.sh](phono3py-input/gofree-cond1.sh)
-```
+`
$ qsub gofree-cond1.sh
-```
+`
Finally the thermal conductivity result is produced by
grouping single conductivity per grid calculations usingÂ
-```
+`
$ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" --br --read_gamma
-```
+`
diff --git a/converted/docs.it4i.cz/salomon/software/chemistry/phono3py.pdf b/converted/docs.it4i.cz/salomon/software/chemistry/phono3py.pdf
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index 86b406b4fe0e52535241c6537ea28962f54c4fd1..0a16f173541bebb89c95ccd32e22768e1cc7b461 100644
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diff --git a/converted/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.md b/converted/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.md
index 4ecb213eee8e00cf0cbccd3672f4d3a8a0b4a615..5948a933f5fc8c928e5c34e481359a1fa446601f 100644
--- a/converted/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.md
+++ b/converted/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.md
@@ -3,11 +3,11 @@ COMSOL Multiphysics®
->>Introduction
+Introduction
-------------------------
->>[COMSOL](http://www.comsol.com)
+[COMSOL](http://www.comsol.com)
is a powerful environment for modelling and solving various engineering
and scientific problems based on partial differential equations. COMSOL
is designed to solve coupled or multiphysics phenomena. For many
@@ -15,89 +15,89 @@ standard engineering problems COMSOL provides add-on products such as
electrical, mechanical, fluid flow, and chemical
applications.
-- >>[Structural Mechanics
+- >[Structural Mechanics
Module](http://www.comsol.com/structural-mechanics-module),
-- >>[Heat Transfer
+- >[Heat Transfer
Module](http://www.comsol.com/heat-transfer-module),
-- >>[CFD
+- >[CFD
Module](http://www.comsol.com/cfd-module),
-- >>[Acoustics
+- >[Acoustics
Module](http://www.comsol.com/acoustics-module),
-- >>and [many
+- >and [many
others](http://www.comsol.com/products)
->>COMSOL also allows an
->>interface support for
+COMSOL also allows an
+interface support for
equation-based modelling of
->>partial differential
+partial differential
equations.
->>Execution
+Execution
----------------------
->>On the clusters COMSOL is available in the latest stable
+On the clusters COMSOL is available in the latest stable
version. There are two variants of the release:
-- >>**Non commercial** or so
- called >>**EDU
- variant**>>, which can be used for research
+- >**Non commercial** or so
+ called >**EDU
+ variant**>, which can be used for research
and educational purposes.
-- >>**Commercial** or so called
- >>**COM variant**,
+- >**Commercial** or so called
+ >**COM variant**,
which can used also for commercial activities.
- >>**COM variant**
+ >**COM variant**
has only subset of features compared to the
- >>**EDU
- variant**>> available. <span
- id="result_box"
+ >**EDU
+ variant**> available.
+
More about
licensing will be posted here
- soon.</span>
+ soon.
->>To load the of COMSOL load the module
+To load the of COMSOL load the module
-```
+`
$ module load COMSOL/51-EDU
-```
+`
->>By default the **EDU
-variant**>> will be loaded. If user needs other
+By default the **EDU
+variant**> will be loaded. If user needs other
version or variant, load the particular version. To obtain the list of
available versions use
-```
+`
$ module avail COMSOL
-```
+`
->>If user needs to prepare COMSOL jobs in the interactive mode
+If user needs to prepare COMSOL jobs in the interactive mode
it is recommend to use COMSOL on the compute nodes via PBS Pro
scheduler. In order run the COMSOL Desktop GUI on Windows is recommended
to use the [Virtual Network Computing
(VNC)](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
-```
+`
$ xhost +
$ qsub -I -X -A PROJECT_ID -q qprod -l select=1:ppn=24
$ module load COMSOL
$ comsol
-```
+`
->>To run COMSOL in batch mode, without the COMSOL Desktop GUI
+To run COMSOL in batch mode, without the COMSOL Desktop GUI
environment, user can utilized the default (comsol.pbs) job script and
execute it via the qsub command.
-```
+`
#!/bin/bash
#PBS -l select=3:ppn=24
#PBS -q qprod
@@ -108,9 +108,9 @@ cd /scratch/work/user/$USER/ || exit
echo Time is `date`
echo Directory is `pwd`
-echo '***PBS_NODEFILE***START*******'
+echo '**PBS_NODEFILE***START*******'
cat $PBS_NODEFILE
-echo '***PBS_NODEFILE***END*********'
+echo '**PBS_NODEFILE***END*********'
text_nodes < cat $PBS_NODEFILE
@@ -120,9 +120,9 @@ module load COMSOL
ntask=$(wc -l $PBS_NODEFILE)
comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/$USER/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log
-```
+`
->>Working directory has to be created before sending the
+Working directory has to be created before sending the
(comsol.pbs) job script into the queue. Input file (name_input_f.mph)
has to be in working directory or full path to input file has to be
specified. The appropriate path to the temp directory of the job has to
@@ -131,43 +131,43 @@ be set by command option (-tmpdir).
LiveLink™* *for MATLAB®^
-------------------------
->>COMSOL is the software package for the numerical solution of
+COMSOL is the software package for the numerical solution of
the partial differential equations. LiveLink for MATLAB allows
connection to the
-COMSOL>><span><span><span><span><span>**®**</span></span></span>^
+COMSOL>><span><span><span><span>**®**</span>^
API (Application Programming Interface) with the benefits of the
programming language and computing environment of the MATLAB.
->>LiveLink for MATLAB is available in both
->>**EDU** and
->>**COM**
->>**variant** of the
+LiveLink for MATLAB is available in both
+**EDU** and
+**COM**
+**variant** of the
COMSOL release. On the clusters 1 commercial
-(>>**COM**) license
+(>**COM**) license
and the 5 educational
-(>>**EDU**) licenses
+(>**EDU**) licenses
of LiveLink for MATLAB (please see the [ISV
Licenses](../isv_licenses.html)) are available.
Following example shows how to start COMSOL model from MATLAB via
LiveLink in the interactive mode.
-```
+`
$ xhost +
$ qsub -I -X -A PROJECT_ID -q qexp -l select=1:ppn=24
$ module load MATLAB
$ module load COMSOL
$ comsol server MATLAB
-```
+`
->>At the first time to launch the LiveLink for MATLAB
+At the first time to launch the LiveLink for MATLAB
(client-MATLAB/server-COMSOL connection) the login and password is
requested and this information is not requested again.
->>To run LiveLink for MATLAB in batch mode with
+To run LiveLink for MATLAB in batch mode with
(comsol_matlab.pbs) job script you can utilize/modify the following
script and execute it via the qsub command.
-```
+`
#!/bin/bash
#PBS -l select=3:ppn=24
#PBS -q qprod
@@ -178,9 +178,9 @@ cd /scratch/work/user/$USER || exit
echo Time is `date`
echo Directory is `pwd`
-echo '***PBS_NODEFILE***START*******'
+echo '**PBS_NODEFILE***START*******'
cat $PBS_NODEFILE
-echo '***PBS_NODEFILE***END*********'
+echo '**PBS_NODEFILE***END*********'
text_nodes < cat $PBS_NODEFILE
@@ -192,7 +192,7 @@ ntask=$(wc -l $PBS_NODEFILE)
comsol -nn ${ntask} server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/work/user/$USER/work &
cd /apps/cae/COMSOL/51/mli
matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/work/user/$USER/work; test_job"
-```
+`
This example shows how to run Livelink for MATLAB with following
configuration: 3 nodes and 16 cores per node. Working directory has to
diff --git a/converted/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.pdf b/converted/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.pdf
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index 7271d8ffcb0494bb002a73dc90988cc6dfa7574f..5a3997590d2c5c5846228cc559698faa56cecf3d 100644
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diff --git a/converted/docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions.md b/converted/docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions.md
index 3438f6ef61aca8c965573d47c34365efc8fa111c..ffafbd5d118af4ba88750cfc5ac284e0a536d501 100644
--- a/converted/docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions.md
+++ b/converted/docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions.md
@@ -10,11 +10,11 @@ Comsol licence can be used by:
CE IT4Innovations project partners, particularly the University of
Ostrava, the Brno University of Technology - Faculty of Informatics,
the Silesian University in Opava, Institute of Geonics AS CR.)
-- id="result_box" all
+- all
persons who have a valid
license
-- id="result_box" students
- of the Technical University</span>
+- students
+ of the Technical University
Comsol EDU Network Licence
--------------------------
@@ -27,7 +27,7 @@ Comsol COM Network Licence
The licence intended to be used for science and research, publications,
students’ projects, commercial research with no commercial use
-restrictions. id="result_box"> E<span
+restrictions. > E
nables the solution
of at least one job
by one user in one
diff --git a/converted/docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions.pdf b/converted/docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions.pdf
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index f78132f9afc69fcb26f29583155eb10ae0d24b62..ca9d44c11ee2289d3d1dc69e9612a863fa32d191 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers/aislinn.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers/aislinn.md
@@ -22,7 +22,7 @@ problems, please contact the author: <stanislav.bohm@vsb.cz>.
Let us have the following program that contains a bug that is not
manifested in all runs:
-```
+`
#include <mpi.h>
#include <stdlib.h>
@@ -53,7 +53,7 @@ int main(int argc, char **argv) {
MPI_Finalize();
return 0;
}
-```
+`
The program does the following: process 0 receives two messages from
anyone and processes 1 and 2 send a message to process 0. If a message
@@ -63,9 +63,9 @@ memory write occurs at line 16.
To verify this program by Aislinn, we first load Aislinn itself:
-```
+`
$ module load aislinn
-```
+`
Now we compile the program by Aislinn implementation of MPI. There are
`mpicc` for C programs and `mpicxx`{.docutils
@@ -73,9 +73,9 @@ Now we compile the program by Aislinn implementation of MPI. There are
has to be recompiled; non-MPI parts may remain untouched. Let us assume
that our program is in `test.cpp`.
-```
+`
$ mpicc -g test.cpp -o test
-```
+`
The `-g` flag is not necessary, but it puts more
debugging information into the program, hence Aislinn may provide more
@@ -86,18 +86,18 @@ Now we run the Aislinn itself. The argument `-p 3`
specifies that we want to verify our program for the case of three MPI
processes
-```
+`
$ aislinn -p 3 ./test
==AN== INFO: Aislinn v0.3.0
==AN== INFO: Found error 'Invalid write'
==AN== INFO: 1 error(s) found
==AN== INFO: Report written into 'report.html'
-```
+`
Aislinn found an error and produced HTML report. To view it, we can use
any browser, e.g.:
-> $ firefox report.html
+ $ firefox report.html
At the beginning of the report there are some basic summaries of the
verification. In the second part (depicted in the following picture),
@@ -106,12 +106,12 @@ the error is described.
It shows us:
-> - Error occurs in process 0 in test.cpp on line 16.
-> - Stdout and stderr streams are empty. (The program does not
-> write anything).
-> - The last part shows MPI calls for each process that occurs in the
-> invalid run. The more detailed information about each call can be
-> obtained by mouse cursor.
+ - Error occurs in process 0 in test.cpp on line 16.
+ - Stdout and stderr streams are empty. (The program does not
+ write anything).
+ - The last part shows MPI calls for each process that occurs in the
+ invalid run. The more detailed information about each call can be
+ obtained by mouse cursor.
### Limitations
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/aislinn.pdf b/converted/docs.it4i.cz/salomon/software/debuggers/aislinn.pdf
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index f352f152e30831d17de4e0e2be584c3660c1889e..9e813674d24bfe1a955da35324c1da0e6fdf65ae 100644
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index fd7e93e932834b94d60340cbdcc5ba5b03e9e1a3..e84881fc28688701accedcbd6f91a6d057b83f08 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers/allinea-ddt.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers/allinea-ddt.md
@@ -47,11 +47,11 @@ Load the Allinea DDT module:
Compile the code:
-```
+`
$ mpicc -g -O0 -o test_debug test.c
$ mpif90 -g -O0 -o test_debug test.f
-```
+`
### Compiler flags
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/allinea-ddt.pdf b/converted/docs.it4i.cz/salomon/software/debuggers/allinea-ddt.pdf
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diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.epub b/converted/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.epub
index 992f6013687964515ed0947016d91fc42d9119cb..2658e7ea1f434a3a2587e76eac3fe77e396955db 100644
Binary files a/converted/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.epub and b/converted/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.epub differ
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.md b/converted/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.md
index 672cb18b876accbcfabcad69477db2bac878c788..efb8cd82bcadf7f0d3acc92c19803b5c0713d346 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.md
@@ -22,7 +22,7 @@ highlight of the features:
Usage
-----
->To profile an application with VTune Amplifier, special kernel
+To profile an application with VTune Amplifier, special kernel
modules need to be loaded. The modules are not loaded on the login
nodes, thus direct profiling on login nodes is not possible. By default,
the kernel modules ale not loaded on compute nodes neither. In order to
@@ -49,7 +49,7 @@ To launch the GUI, first load the module:
$Â amplxe-gui
->The GUI will open in new window. Click on "*New Project...*" to
+The GUI will open in new window. Click on "*New Project...*" to
create a new project. After clicking *OK*, a new window with project
properties will appear. Â At "*Application:*", select the bath to your
binary you want to profile (the binary should be compiled with -g flag).
@@ -132,6 +132,6 @@ References
Tuning for Intel® Xeon Phi™ Coprocessors
2. ><https://software.intel.com/en-us/intel-vtune-amplifier-xe-support/documentation> >Intel®
VTune™ Amplifier Support
-3. >><https://software.intel.com/en-us/amplifier_help_linux>Â Linux
+3. ><https://software.intel.com/en-us/amplifier_help_linux>Â Linux
user guide
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.pdf b/converted/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.pdf
index 8b51181a185e6374493f16712090fb34a72819ac..99d469aef4ffb5a73eff1bbea2d1f0bdb10f5700 100644
Binary files a/converted/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.pdf and b/converted/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.pdf differ
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/summary.epub b/converted/docs.it4i.cz/salomon/software/debuggers/summary.epub
index 61d0d2f7f589f3539333eb4e71804fcbc724fe2f..bc74c576373a7571ed7f2fb85c2da5fcb0d66c1b 100644
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diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/summary.pdf b/converted/docs.it4i.cz/salomon/software/debuggers/summary.pdf
index f23f85a39eded79213b12912ccc5da8ec48197b0..58f0e7032860accd6f02db19925eaa8a6623e90e 100644
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diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/total-view.epub b/converted/docs.it4i.cz/salomon/software/debuggers/total-view.epub
index 98d7bce770ca95830c2006c87ccff032065115c5..65aed7e2ab8ffc3deb5fb3665bc85e0e36e270b9 100644
Binary files a/converted/docs.it4i.cz/salomon/software/debuggers/total-view.epub and b/converted/docs.it4i.cz/salomon/software/debuggers/total-view.epub differ
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/total-view.md b/converted/docs.it4i.cz/salomon/software/debuggers/total-view.md
index 350a3e0472c30ea13a2e6f15a93f05cb30d22499..9a7166c437444f5245d4d70baad456a4469e85c5 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers/total-view.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers/total-view.md
@@ -90,9 +90,9 @@ you have to add the following function to your **~/.tvdrc** file:
   set file_component [file tail $executable_name]
   if {[lsearch -exact $starter_programs $file_component] != -1} {
- Â Â Â Â Â Â Â puts "**************************************"
+ Â Â Â Â Â Â Â puts "*************************************"
       puts "Automatically starting $file_component"
- Â Â Â Â Â Â Â puts "**************************************"
+ Â Â Â Â Â Â Â puts "*************************************"
       dgo
   }
}
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/total-view.pdf b/converted/docs.it4i.cz/salomon/software/debuggers/total-view.pdf
index 549df6f7c4239c7eb76af5246ddfb35cd2d93dd4..44d9ec2b519cbeb2bb30c80ed644fe921517a830 100644
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diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/valgrind.epub b/converted/docs.it4i.cz/salomon/software/debuggers/valgrind.epub
index d8c08be85fa3df8b1d3f996c9b68ab4b94877cc0..52c799ec49c85f02d9aba465491dbec2927d74cd 100644
Binary files a/converted/docs.it4i.cz/salomon/software/debuggers/valgrind.epub and b/converted/docs.it4i.cz/salomon/software/debuggers/valgrind.epub differ
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/valgrind.md b/converted/docs.it4i.cz/salomon/software/debuggers/valgrind.md
index 099c02e1fbee2586f4adf8f18152b88bd9f20bcd..1cd426c1d28c0d13acb0208e7f071cd062f547d9 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers/valgrind.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers/valgrind.md
@@ -44,7 +44,7 @@ There are two versions of Valgrind available on the cluster.
MPI support. Also, it does not support AVX2 instructions,
**debugging of an AVX2-enabled executable with this version will
fail**
-- >>Version 3.11.0 built by ICC with support for Intel MPI,
+- >Version 3.11.0 built by ICC with support for Intel MPI,
available in
[module](../../environment-and-modules.html)Â
Valgrind/3.11.0-intel-2015b. After loading
@@ -163,7 +163,7 @@ with --leak-check=full option :
Now we can see that the memory leak is due to the
malloc() at line 6.
->Usage with MPI
+Usage with MPI
---------------------------
Although Valgrind is not primarily a parallel debugger, it can be used
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/valgrind.pdf b/converted/docs.it4i.cz/salomon/software/debuggers/valgrind.pdf
index 75d531f9d48038295a1d7172f98987cde5b3dff6..7a1654469562401fc2eefd6a54dd6d3d5519120e 100644
Binary files a/converted/docs.it4i.cz/salomon/software/debuggers/valgrind.pdf and b/converted/docs.it4i.cz/salomon/software/debuggers/valgrind.pdf differ
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/vampir.epub b/converted/docs.it4i.cz/salomon/software/debuggers/vampir.epub
index 255ca3b3224a95869dd93c8558e180a65e2fb2a7..190f2aaaff4e963b798f1267f8ef9db7e2d3d60a 100644
Binary files a/converted/docs.it4i.cz/salomon/software/debuggers/vampir.epub and b/converted/docs.it4i.cz/salomon/software/debuggers/vampir.epub differ
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/vampir.md b/converted/docs.it4i.cz/salomon/software/debuggers/vampir.md
index c193f8b6453ae551b4427b47163c6866209f3b1e..9d213a4212613538afaf684b13c9a01e59f6eaad 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers/vampir.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers/vampir.md
@@ -8,7 +8,7 @@ functionality to collect traces, you need to use a trace collection tool
traces.
-----------------------------------------------------------------------------------------------------------------------------------------------
+-
Installed versions
------------------
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/vampir.pdf b/converted/docs.it4i.cz/salomon/software/debuggers/vampir.pdf
index 5d6324bde14d7d91a29e33427363eff8dbb3e918..21c10fbf7093425f82b3b922ed3f9f4e8a8ad545 100644
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diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.epub b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.epub
index 9858e66f764390f5050d539444de705e9d52dda1..7f81e286997dd9fdd95fd746b233269f50c685b6 100644
Binary files a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.epub and b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.epub differ
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.md b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.md
index 4ffe726097f9bef9fc7aaf296e0f56810ee7730d..805e7d905e3995fbc824d02091d6cefc569f374d 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.md
@@ -11,10 +11,10 @@ Installed versions
The following versions are currently available on Salomon as modules:
- --------------- -----------------------
- **Version** **Module**
- 2016 Update 2 Advisor/2016_update2
- --------------- -----------------------
+ --------- |---|---|-------------
+ |---|---|
+ |2016 Update 2|Advisor/2016_update2|
+ --------- |---|---|-------------
Usage
-----
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.pdf b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.pdf
index 8e52b28b94fb98990fcdf083cbc53f5acce18c15..372b7462f24bfd9b1cca9cd92d5bce9033023417 100644
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diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.epub b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.epub
index 7d81986dbdbdf4727685438546ef8a132bf7b3a7..2b20fbaa47b45d372652e6f2b8858915c013818c 100644
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diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.pdf b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.pdf
index 3ffea9d77b9d8b42cb3940ab154f1edee1d58c98..526e82384df59a94dfca476d49d1391179acc140 100644
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diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.epub b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.epub
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diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.pdf b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.pdf
index 7dd2d3e3b8bd39ae88b67f442e9e5e6daa629669..def98618d29f42b6171f19e3805ab79d273f24f5 100644
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diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.epub b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.epub
index 291370f0c90e1d90bc15d3bf22904cfbc8b2fc87..e681a823d266b03fa577d0a2f655bb7aad61c9e4 100644
Binary files a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.epub and b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.epub differ
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.md b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.md
index c9de50dd4ffa2aa3d1c50aa8906bf57cd1e31a46..cfbde48083ddaa8cc5cc60a481e0278375177302 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.md
@@ -11,10 +11,10 @@ Installed versions
The following versions are currently available on Salomon as modules:
- --------------- -------------------------
- **Version** **Module**
- 2016 Update 1 Inspector/2016_update1
- --------------- -------------------------
+ --------- |---|---|---------------
+ |---|---|
+ |2016 Update 1|Inspector/2016_update1|
+ --------- |---|---|---------------
Usage
-----
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.pdf b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.pdf
index 1a91e2a8db2e9aaf8865f284d3a52ca95e29f350..2ea8c386469e2db68f8ea42e879e6af40309fa97 100644
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diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives.epub b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives.epub
index d3b13883fb9171dc2e7c7976c816f2b40ebd5c0b..ac5276f878a5fd997c8216f547b4fd7b6dbe6620 100644
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diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives.md b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives.md
index cbfa598d9652baf1efc638939232b2eb3447b210..5ec3bf70b64bf35c2fdf3382bc0c354afe340941 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives.md
@@ -46,20 +46,20 @@ IPP example
//Get CPU features enabled with selected library level
fm=ippGetEnabledCpuFeatures();
- printf("SSE :%cn",(fm>>1)&1?'Y':'N');
- printf("SSE2 :%cn",(fm>>2)&1?'Y':'N');
- printf("SSE3 :%cn",(fm>>3)&1?'Y':'N');
- printf("SSSE3 :%cn",(fm>>4)&1?'Y':'N');
- printf("SSE41 :%cn",(fm>>6)&1?'Y':'N');
- printf("SSE42 :%cn",(fm>>7)&1?'Y':'N');
- printf("AVX :%cn",(fm>>8)&1 ?'Y':'N');
- printf("AVX2 :%cn", (fm>>15)&1 ?'Y':'N' );
+ printf("SSE :%cn",(fm>1)&1?'Y':'N');
+ printf("SSE2 :%cn",(fm>2)&1?'Y':'N');
+ printf("SSE3 :%cn",(fm>3)&1?'Y':'N');
+ printf("SSSE3 :%cn",(fm>4)&1?'Y':'N');
+ printf("SSE41 :%cn",(fm>6)&1?'Y':'N');
+ printf("SSE42 :%cn",(fm>7)&1?'Y':'N');
+ printf("AVX :%cn",(fm>8)&1 ?'Y':'N');
+ printf("AVX2 :%cn", (fm>15)&1 ?'Y':'N' );
printf("----------n");
- printf("OS Enabled AVX :%cn", (fm>>9)&1 ?'Y':'N');
- printf("AES :%cn", (fm>>10)&1?'Y':'N');
- printf("CLMUL :%cn", (fm>>11)&1?'Y':'N');
- printf("RDRAND :%cn", (fm>>13)&1?'Y':'N');
- printf("F16C :%cn", (fm>>14)&1?'Y':'N');
+ printf("OS Enabled AVX :%cn", (fm>9)&1 ?'Y':'N');
+ printf("AES :%cn", (fm>10)&1?'Y':'N');
+ printf("CLMUL :%cn", (fm>11)&1?'Y':'N');
+ printf("RDRAND :%cn", (fm>13)&1?'Y':'N');
+ printf("F16C :%cn", (fm>14)&1?'Y':'N');
return 0;
}
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives.pdf b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives.pdf
index e13b97e74a4772c9d5207332a753e6bd42918cfc..999a01506ffa2ea8fe209fa1837379dd06010c1d 100644
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diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.epub b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.epub
index 815c1298b0682d47834ea1dabe41c84b2837ec78..7c178c840ec887ee12002c3b5dbedc811a1a4b60 100644
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diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.md b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.md
index f9cfe5aa6717850fde13c061dd53b81eb42b217b..57711b34ae2797e4040aa04a62ce81c096be5d6e 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.md
@@ -85,9 +85,9 @@ integer type (necessary for indexing large arrays, with more than
231^-1 elements), whereas the LP64 libraries index arrays with the
32-bit integer type.
- Interface Integer type
- ----------- -----------------------------------------------
- LP64 32-bit, int, integer(kind=4), MPI_INT
+ |Interface|Integer type|
+ ----- |---|---|-------------------------------------
+ |LP64|32-bit, int, integer(kind=4), MPI_INT|
ILP64 64-bit, long int, integer(kind=8), MPI_INT64
### Linking
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.pdf b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.pdf
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diff --git a/converted/docs.it4i.cz/salomon/software/intel-xeon-phi.md b/converted/docs.it4i.cz/salomon/software/intel-xeon-phi.md
index 96c36b75a50776f7c9b35bc8cacf7057882e5f65..55e70e7577678526a8a1fb197ac915527ff85895 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-xeon-phi.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-xeon-phi.md
@@ -333,7 +333,7 @@ modification.Â
$ vim sgemm-ao-short.c
-```
+`
#include <stdio.h>
#include <stdlib.h>
#include <malloc.h>
@@ -386,7 +386,7 @@ int main(int argc, char **argv)
   return 0;
}
-```
+`
Please note: This example is simplified version of an example from MKL.
The expanded version can be found here:
@@ -540,7 +540,7 @@ compiler module that was used to compile the code on the host computer.
For your information the list of libraries and their location required
for execution of an OpenMP parallel code on Intel Xeon Phi is:
->/apps/all/icc/2015.3.187-GNU-5.1.0-2.25/composer_xe_2015.3.187/compiler/lib/mic
+/apps/all/icc/2015.3.187-GNU-5.1.0-2.25/composer_xe_2015.3.187/compiler/lib/mic
libiomp5.so
libimf.so
@@ -548,14 +548,14 @@ libsvml.so
libirng.so
libintlc.so.5
->Finally, to run the compiled code use:
+Finally, to run the compiled code use:
$ ~/path_to_binary/vect-add-mic
->OpenCL
+OpenCL
-------------------
->OpenCL (Open Computing Language) is an open standard for
+OpenCL (Open Computing Language) is an open standard for
general-purpose parallel programming for diverse mix of multi-core CPUs,
GPU coprocessors, and other parallel processors. OpenCL provides a
flexible execution model and uniform programming environment for
@@ -563,27 +563,27 @@ software developers to write portable code for systems running on both
the CPU and graphics processors or accelerators like the Intel® Xeon
Phi.
->On Anselm OpenCL is installed only on compute nodes with MIC
+On Anselm OpenCL is installed only on compute nodes with MIC
accelerator, therefore OpenCL code can be compiled only on these nodes.
module load opencl-sdk opencl-rt
->Always load "opencl-sdk" (providing devel files like headers) and
+Always load "opencl-sdk" (providing devel files like headers) and
"opencl-rt" (providing dynamic library libOpenCL.so) modules to compile
and link OpenCL code. Load "opencl-rt" for running your compiled code.
->There are two basic examples of OpenCL code in the following
+There are two basic examples of OpenCL code in the following
directory:
/apps/intel/opencl-examples/
->First example "CapsBasic" detects OpenCL compatible hardware, here
+First example "CapsBasic" detects OpenCL compatible hardware, here
CPU and MIC, and prints basic information about the capabilities of
it.Â
/apps/intel/opencl-examples/CapsBasic/capsbasic
->To compile and run the example copy it to your home directory, get
+To compile and run the example copy it to your home directory, get
a PBS interactive session on of the nodes with MIC and run make for
compilation. Make files are very basic and shows how the OpenCL code can
be compiled on Anselm.
@@ -592,11 +592,11 @@ be compiled on Anselm.
$ qsub -I -q qprod -l select=1:ncpus=24:accelerator=True:naccelerators=2:accelerator_model=phi7120 -A NONE-0-0
$ make
->The compilation command for this example is:
+The compilation command for this example is:
$ g++ capsbasic.cpp -lOpenCL -o capsbasic -I/apps/intel/opencl/include/
->After executing the complied binary file, following output should
+After executing the complied binary file, following output should
be displayed.
./capsbasic
@@ -609,7 +609,7 @@ be displayed.
   CL_DEVICE_TYPE_GPU: 0
   CL_DEVICE_TYPE_ACCELERATOR: 1
- *** Detailed information for each device ***
+ ** Detailed information for each device ***
CL_DEVICE_TYPE_CPU[0]
   CL_DEVICE_NAME:       Intel(R) Xeon(R) CPU E5-2470 0 @ 2.30GHz
@@ -623,10 +623,10 @@ be displayed.
...
->More information about this example can be found on Intel website:
+More information about this example can be found on Intel website:
<http://software.intel.com/en-us/vcsource/samples/caps-basic/>
->The second example that can be found in
+The second example that can be found in
"/apps/intel/opencl-examples" >directory is General Matrix
Multiply. You can follow the the same procedure to download the example
to your directory and compile it.Â
@@ -636,11 +636,11 @@ to your directory and compile it.Â
$ cd GEMM
$ make
->The compilation command for this example is:
+The compilation command for this example is:
$ g++ cmdoptions.cpp gemm.cpp ../common/basic.cpp ../common/cmdparser.cpp ../common/oclobject.cpp -I../common -lOpenCL -o gemm -I/apps/intel/opencl/include/
->To see the performance of Intel Xeon Phi performing the DGEMM run
+To see the performance of Intel Xeon Phi performing the DGEMM run
the example as follows:
./gemm -d 1
@@ -661,10 +661,10 @@ the example as follows:
Host perf: 426.081 GFLOPS
...
->Please note: GNU compiler is used to compile the OpenCL codes for
+Please note: GNU compiler is used to compile the OpenCL codes for
Intel MIC. You do not need to load Intel compiler module.
->MPI
+MPI
----------------
### Environment setup and compilation
@@ -717,7 +717,7 @@ An example of basic MPI version of "hello-world" example in C language,
that can be executed on both host and Xeon Phi is (can be directly copy
and pasted to a .c file)
-```
+`
#include <stdio.h>
#include <mpi.h>
@@ -740,11 +740,11 @@ int main (argc, argv)
 MPI_Finalize();
 return 0;
}
-```
+`
### MPI programming models
->Intel MPI for the Xeon Phi coprocessors offers different MPI
+Intel MPI for the Xeon Phi coprocessors offers different MPI
programming models:
Host-only model** - all MPI ranks reside on the host. The coprocessors
@@ -757,9 +757,9 @@ coprocessors.
Symmetric model** - the MPI ranks reside on both the host and the
coprocessor. Most general MPI case.
-### >Host-only model
+###Host-only model
->In this case all environment variables are set by modules,
+In this case all environment variables are set by modules,
so to execute the compiled MPI program on a single node, use:
$ mpirun -np 4 ./mpi-test
@@ -773,7 +773,7 @@ The output should be similar to:
### Coprocessor-only model
->There are two ways how to execute an MPI code on a single
+There are two ways how to execute an MPI code on a single
coprocessor: 1.) lunch the program using "**mpirun**" from the
coprocessor; or 2.) lunch the task using "**mpiexec.hydra**" from a
host.
@@ -836,7 +836,7 @@ The output should be similar to:
 **
-Execution on host**
+**Execution on host**
If the MPI program is launched from host instead of the coprocessor, the
environmental variables are not set using the ".profile" file. Therefore
@@ -880,10 +880,10 @@ execute:
 **
-Execution on host - MPI processes distributed over multiple
+**Execution on host - MPI processes distributed over multiple
accelerators on multiple nodes**
->To get access to multiple nodes with MIC accelerator, user has to
+To get access to multiple nodes with MIC accelerator, user has to
use PBS to allocate the resources. To start interactive session, that
allocates 2 compute nodes = 2 MIC accelerators run qsub command with
following parameters:
@@ -892,34 +892,34 @@ following parameters:
$ module load intel impi
->This command connects user through ssh to one of the nodes
+This command connects user through ssh to one of the nodes
immediately. To see the other nodes that have been allocated use:
$ cat $PBS_NODEFILE
->For example:
+For example:
r38u31n1000.bullx
r38u32n1001.bullx
->This output means that the PBS allocated nodes r38u31n1000 and
+This output means that the PBS allocated nodes r38u31n1000 and
r38u32n1001, which means that user has direct access to
"**r38u31n1000-mic0**" and "**>r38u32n1001-mic0**"
accelerators.
->Please note: At this point user can connect to any of the
+Please note: At this point user can connect to any of the
allocated nodes or any of the allocated MIC accelerators using ssh:
- to connect to the second node : ** $
ssh >r38u32n1001**
->- to connect to the accelerator on the first node from the first
+- to connect to the accelerator on the first node from the first
node: **$ ssh
->r38u31n1000-mic0**</span> or **
+r38u31n1000-mic0** or **
$ ssh mic0**
-** to connect to the accelerator on the second node from the first
node: **$ ssh
->r38u32n1001-mic0**
+r38u32n1001-mic0**
->At this point we expect that correct modules are loaded and binary
+At this point we expect that correct modules are loaded and binary
is compiled. For parallel execution the mpiexec.hydra is used.
Again the first step is to tell mpiexec that the MPI can be executed on
MIC accelerators by setting up the environmental variable "I_MPI_MIC",
@@ -929,7 +929,7 @@ don't forget to have correct FABRIC and PROVIDER defined.
$ export I_MPI_FABRICS=shm:dapl
$ export I_MPI_DAPL_PROVIDER_LIST=ofa-v2-mlx4_0-1u,ofa-v2-scif0,ofa-v2-mcm-1
->The launch the MPI program use:
+The launch the MPI program use:
$ mpirun -genv LD_LIBRARY_PATH $MIC_LD_LIBRARY_PATH
-host r38u31n1000-mic0 -n 4 ~/mpi-test-mic
@@ -962,15 +962,15 @@ The same way MPI program can be executed on multiple hosts:Â
-host r38u31n1000 -n 4 ~/mpi-test
: -host r38u32n1001 -n 6 ~/mpi-test
-### >Symmetric model
+###Symmetric model
->In a symmetric mode MPI programs are executed on both host
+In a symmetric mode MPI programs are executed on both host
computer(s) and MIC accelerator(s). Since MIC has a different
architecture and requires different binary file produced by the Intel
compiler two different files has to be compiled before MPI program is
executed.
->In the previous section we have compiled two binary files, one for
+In the previous section we have compiled two binary files, one for
hosts "**mpi-test**" and one for MIC accelerators "**mpi-test-mic**".
These two binaries can be executed at once using mpiexec.hydra:
@@ -984,20 +984,20 @@ environment variables for execution. The third line specifies binary
that is executed on host (here r38u32n1001) and the last line specifies
the binary that is execute on the accelerator (here r38u32n1001-mic0).
->The output of the program is:
+The output of the program is:
Hello world from process 0 of 4 on host r38u32n1001
Hello world from process 1 of 4 on host r38u32n1001
Hello world from process 2 of 4 on host r38u32n1001-mic0
Hello world from process 3 of 4 on host r38u32n1001-mic0
->The execution procedure can be simplified by using the mpirun
+The execution procedure can be simplified by using the mpirun
command with the machine file a a parameter. Machine file contains list
of all nodes and accelerators that should used to execute MPI processes.
->An example of a machine file that uses 2 >hosts (r38u32n1001
+An example of a machine file that uses 2 >hosts (r38u32n1001
and r38u33n1002) and 2 accelerators **(r38u32n1001-mic0** and
->>r38u33n1002-mic0**) to run 2 MPI processes
+r38u33n1002-mic0**) to run 2 MPI processes
on each of them:
$ cat hosts_file_mix
@@ -1006,7 +1006,7 @@ on each of them:
r38u33n1002:2
r38u33n1002-mic0:2
->In addition if a naming convention is set in a way that the name
+In addition if a naming convention is set in a way that the name
of the binary for host is **"bin_name"**Â and the name of the binary
for the accelerator is **"bin_name-mic"** then by setting up the
environment variable **I_MPI_MIC_POSTFIX** to **"-mic"** user do not
@@ -1025,7 +1025,7 @@ suffix to get a name of the binary for accelerator (i..e.
-machinefile hosts_file_mix
~/mpi-test
->A possible output of the MPI "hello-world" example executed on two
+A possible output of the MPI "hello-world" example executed on two
hosts and two accelerators is:
Hello world from process 0 of 8 on host r38u31n1000
@@ -1042,11 +1042,11 @@ Using the PBS automatically generated node-files
PBS also generates a set of node-files that can be used instead of
manually creating a new one every time. Three node-files are genereated:
-Host only node-file:**
+**Host only node-file:**
 - /lscratch/${PBS_JOBID}/nodefile-cn
-MIC only node-file**:
+MIC only node-file:
 - /lscratch/${PBS_JOBID}/nodefile-mic
-Host and MIC node-file**:
+Host and MIC node-file:
 - /lscratch/${PBS_JOBID}/nodefile-mix
Please note each host or accelerator is listed only per files. User has
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diff --git a/converted/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md b/converted/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md
index 9a76d02d5e7868b66462d6549d9e286eada26ba8..856a3e95e6d41dbbe6eb756762fa53fa50ed2164 100644
--- a/converted/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md
+++ b/converted/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md
@@ -136,7 +136,7 @@ later) the following variables may be used for Intel or GCC:
$ export OMP_PROC_BIND=true
$ export OMP_PLACES=coresÂ
->OpenMPI Process Mapping and Binding
+OpenMPI Process Mapping and Binding
------------------------------------------------
The mpiexec allows for precise selection of how the MPI processes will
diff --git a/converted/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.pdf b/converted/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.pdf
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diff --git a/converted/docs.it4i.cz/salomon/software/mpi-1/mpi.md b/converted/docs.it4i.cz/salomon/software/mpi-1/mpi.md
index 2617fd0b4b705daca582e5db5f779052eea6c551..13c3f15090e589d6a7d3983f0a98a9c220ff0f92 100644
--- a/converted/docs.it4i.cz/salomon/software/mpi-1/mpi.md
+++ b/converted/docs.it4i.cz/salomon/software/mpi-1/mpi.md
@@ -10,7 +10,7 @@ The Salomon cluster provides several implementations of the MPI library:
-------------------------------------------------------------------------
MPI Library Thread support
- ------------------------------------ ------------------------------------
+ ------ |---|---|---
**Intel MPI 4.1** Full thread support up to
MPI_THREAD_MULTIPLE
@@ -44,7 +44,7 @@ The defaults are selected via the modules in following way
--------------------------------------------------------------------------
Module MPI Compiler suite
- ------------------------ ------------------------ ------------------------
+ ------------------ |---|---|-------------- ------------------------
impi-5.0.3.048-iccifort- Intel MPI 5.0.3
2015.3.187
@@ -166,7 +166,7 @@ operating system might still migrate OpenMP threads between cores. You
want to avoid this by setting the KMP_AFFINITY or GOMP_CPU_AFFINITY
environment variables.
-24 MPI** processes per node, using 1 thread each bound to processor
+**24 MPI** processes per node, using 1 thread each bound to processor
core is most suitable for highly scalable applications with low
communication demand.
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diff --git a/converted/docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python.md b/converted/docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python.md
index 0373645fa9bb7fb120b4867a3d85fc332ca103d8..00577440a001d32dfa7ed93554daa66b1c3136d4 100644
--- a/converted/docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python.md
+++ b/converted/docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python.md
@@ -45,7 +45,7 @@ to run
$ mpiexec python <script>.py
->For example
+For example
$ mpiexec python hello_world.py
@@ -62,7 +62,7 @@ Examples
comm.Barrier() Â # wait for everybody to synchronize
-### >Collective Communication with NumPy arrays
+###Collective Communication with NumPy arrays
from __future__ import division
from mpi4py import MPI
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index 8139cfdf2c65f7b9e1f01f81376682ea47acd931..c713cd7c96b544ea722d8e74537cb78e3b1b1edd 100644
--- a/converted/docs.it4i.cz/salomon/software/numerical-languages/matlab.md
+++ b/converted/docs.it4i.cz/salomon/software/numerical-languages/matlab.md
@@ -70,7 +70,7 @@ To use Distributed Computing, you first need to setup a parallel
profile. We have provided the profile for you, you can either import it
in MATLAB command line:
- >> parallel.importProfile('/apps/all/MATLAB/2015b-EDU/SalomonPBSPro.settings')
+ > parallel.importProfile('/apps/all/MATLAB/2015b-EDU/SalomonPBSPro.settings')
ans =
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diff --git a/converted/docs.it4i.cz/salomon/software/numerical-languages/octave.epub b/converted/docs.it4i.cz/salomon/software/numerical-languages/octave.epub
index 5f25f2c43b43fa34b656b014b22ccef37adbd5ef..9ee0c1aa682f4177914849abf461c70250bf7564 100644
Binary files a/converted/docs.it4i.cz/salomon/software/numerical-languages/octave.epub and b/converted/docs.it4i.cz/salomon/software/numerical-languages/octave.epub differ
diff --git a/converted/docs.it4i.cz/salomon/software/numerical-languages/octave.md b/converted/docs.it4i.cz/salomon/software/numerical-languages/octave.md
index a122b43876fd96a6dcb863c7d0bbb61616172496..6bb5f2d8480cd01e620cf6d387803b0e7eca1c46 100644
--- a/converted/docs.it4i.cz/salomon/software/numerical-languages/octave.md
+++ b/converted/docs.it4i.cz/salomon/software/numerical-languages/octave.md
@@ -11,12 +11,12 @@ for data visualization and manipulation. Octave is normally used through
its interactive command line interface, but it can also be used to write
non-interactive programs. The Octave language is quite similar to Matlab
so that most programs are easily portable. Read more on
-<http://www.gnu.org/software/octave/>****
+<http://www.gnu.org/software/octave/>***
Two versions of octave are available on the cluster, via module
Status Version module
- ------------ -------------- --------
+ ------ |---|---|---- --------
**Stable** Octave 3.8.2 Octave
Â
diff --git a/converted/docs.it4i.cz/salomon/software/numerical-languages/octave.pdf b/converted/docs.it4i.cz/salomon/software/numerical-languages/octave.pdf
index f95562ba77e7eb40547d199ffb7668428b237a1e..8dfcef848b11f49191e55c166f197c92c0a86026 100644
Binary files a/converted/docs.it4i.cz/salomon/software/numerical-languages/octave.pdf and b/converted/docs.it4i.cz/salomon/software/numerical-languages/octave.pdf differ
diff --git a/converted/docs.it4i.cz/salomon/software/numerical-languages/r.epub b/converted/docs.it4i.cz/salomon/software/numerical-languages/r.epub
index 22ceb1e6bfb85b019a3320525a97ad69341f37d7..70735a82429f28ab99320250939b7f14a399b124 100644
Binary files a/converted/docs.it4i.cz/salomon/software/numerical-languages/r.epub and b/converted/docs.it4i.cz/salomon/software/numerical-languages/r.epub differ
diff --git a/converted/docs.it4i.cz/salomon/software/numerical-languages/r.md b/converted/docs.it4i.cz/salomon/software/numerical-languages/r.md
index 111a3736c29a3e3f085a6733291fd76633178a55..85e34b69199ad4b1bdb78d498e7c98aa89845b9b 100644
--- a/converted/docs.it4i.cz/salomon/software/numerical-languages/r.md
+++ b/converted/docs.it4i.cz/salomon/software/numerical-languages/r.md
@@ -30,12 +30,12 @@ Modules
-------
**The R version 3.1.1 is available on the cluster, along with GUI
-interface Rstudio
+interface Rstudio**
- Application Version module
- ------------- -------------- ---------------------
- **R** R 3.1.1 R/3.1.1-intel-2015b
- **Rstudio** Rstudio 0.97 Rstudio
+ |Application|Version|module|
+ ------- |---|---|---- ---------------------
+ |**R**|R 3.1.1|R/3.1.1-intel-2015b|
+ |**Rstudio**|Rstudio 0.97|Rstudio|
$ module load R
diff --git a/converted/docs.it4i.cz/salomon/software/numerical-languages/r.pdf b/converted/docs.it4i.cz/salomon/software/numerical-languages/r.pdf
index 512a0bfdb298fe9a9d8914cdfe81e27c704904be..3e34bc24fd27180f96c0ca7f113481f0eb07bd87 100644
Binary files a/converted/docs.it4i.cz/salomon/software/numerical-languages/r.pdf and b/converted/docs.it4i.cz/salomon/software/numerical-languages/r.pdf differ
diff --git a/converted/docs.it4i.cz/salomon/software/operating-system.epub b/converted/docs.it4i.cz/salomon/software/operating-system.epub
index 3bf9308fc187b2969cd4714a009d211148f227c2..b5ef2c5657c5f196f8e6fd030c07364d10fdcad1 100644
Binary files a/converted/docs.it4i.cz/salomon/software/operating-system.epub and b/converted/docs.it4i.cz/salomon/software/operating-system.epub differ
diff --git a/converted/docs.it4i.cz/salomon/software/operating-system.md b/converted/docs.it4i.cz/salomon/software/operating-system.md
index 5af5a79b0bbf35600bc189590c89ae106ac8b481..9cadb41ffdceb80ea618038b186e10be74f1752b 100644
--- a/converted/docs.it4i.cz/salomon/software/operating-system.md
+++ b/converted/docs.it4i.cz/salomon/software/operating-system.md
@@ -7,7 +7,7 @@ The operating system, deployed on Salomon cluster
The operating system on Salomon is Linux - CentOS 6.6.
->The CentOS Linux distribution is a stable, predictable, manageable
+The CentOS Linux distribution is a stable, predictable, manageable
and reproducible platform derived from the sources of Red Hat Enterprise
Linux (RHEL).
diff --git a/converted/docs.it4i.cz/salomon/software/operating-system.pdf b/converted/docs.it4i.cz/salomon/software/operating-system.pdf
index 952a69f9d92687baec4e4148128d576f65449475..e438e42fb61ad55dfd243d7fb19c24cd251e1acc 100644
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diff --git a/converted/docs.it4i.cz/salomon/storage/cesnet-data-storage.epub b/converted/docs.it4i.cz/salomon/storage/cesnet-data-storage.epub
index 0774fcd6772d50d8f3db96119a7e167bb9ef3976..616d1cea6fca5b7691cbe1d893f746643a6f2fe1 100644
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diff --git a/converted/docs.it4i.cz/salomon/storage/cesnet-data-storage.pdf b/converted/docs.it4i.cz/salomon/storage/cesnet-data-storage.pdf
index c120d1be71c5340e86db767c524c312d6465c19d..fefc9074cc92a2377eb660127d7ba888cd9c201c 100644
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diff --git a/converted/docs.it4i.cz/salomon/storage/storage.epub b/converted/docs.it4i.cz/salomon/storage/storage.epub
index e845ce80e8cc58e6364e5d99acdd6dc7d4ddbd0d..171eacb58974e2a8502ff26a5d91fc70b88f3ca6 100644
Binary files a/converted/docs.it4i.cz/salomon/storage/storage.epub and b/converted/docs.it4i.cz/salomon/storage/storage.epub differ
diff --git a/converted/docs.it4i.cz/salomon/storage/storage.md b/converted/docs.it4i.cz/salomon/storage/storage.md
index f8aafac9d8103ef9acb5b1c9ccf61ff7d258b635..b170dd2ff3635cd9064fccc64fb5331b2e83bfdc 100644
--- a/converted/docs.it4i.cz/salomon/storage/storage.md
+++ b/converted/docs.it4i.cz/salomon/storage/storage.md
@@ -6,11 +6,8 @@ Storage
Introduction
------------
-There are two main shared file systems on Salomon cluster, the [
+There are two main shared file systems on Salomon cluster, the [HOME](storage.html#home)and [SCRATCH](storage.html#shared-filesystems).
-HOME](storage.html#home)
-and [
-SCRATCH](storage.html#shared-filesystems).
All login and compute nodes may access same data on shared filesystems.
Compute nodes are also equipped with local (non-shared) scratch, ramdisk
and tmp filesystems.
@@ -18,7 +15,7 @@ and tmp filesystems.
Policy (in a nutshell)
----------------------
-Use [HOME](storage.html#home) for your most valuable data
+Use [ for your most valuable data
and programs.
Use [WORK](storage.html#work) for your large project
files
@@ -140,14 +137,14 @@ setstripe command for setting the stripe parameters to get optimal I/O
performance The correct stripe setting depends on your needs and file
access patterns.Â
-```
+`
$ lfs getstripe dir|filename
$ lfs setstripe -s stripe_size -c stripe_count -o stripe_offset dir|filename
-```
+`
Example:
-```
+`
$ lfs getstripe /scratch/work/user/username
/scratch/work/user/username
stripe_count: 1 stripe_size: 1048576 stripe_offset: -1
@@ -156,7 +153,7 @@ $ lfs setstripe -c -1 /scratch/work/user/username/
$ lfs getstripe /scratch/work/user/username/
/scratch/work/user/username/
stripe_count: -1 stripe_size: 1048576 stripe_offset: -1
-```
+`
In this example, we view current stripe setting of the
/scratch/username/ directory. The stripe count is changed to all OSTs,
@@ -166,10 +163,10 @@ all (54) OSTs
Use lfs check OSTs to see the number and status of active OSTs for each
filesystem on Salomon. Learn more by reading the man page
-```
+`
$ lfs check osts
$ man lfs
-```
+`
### Hints on Lustre Stripping
@@ -202,19 +199,19 @@ on a single-stripe file.
Read more on
<http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html>
->Disk usage and quota commands
+Disk usage and quota commands
------------------------------------------
->User quotas on the Lustre file systems (SCRATCH) can be checked
+User quotas on the Lustre file systems (SCRATCH) can be checked
and reviewed using following command:
-```
+`
$ lfs quota dir
-```
+`
Example for Lustre SCRATCH directory:
-```
+`
$ lfs quota /scratch
Disk quotas for user user001 (uid 1234):
Filesystem kbytes quota limit grace files quota limit grace
@@ -222,7 +219,7 @@ Disk quotas for user user001 (uid 1234):
Disk quotas for group user001 (gid 1234):
Filesystem kbytes quota limit grace files quota limit grace
/scratch    8    0    0    -    3    0    0    -
-```
+`
In this example, we view current quota size limit of 100TB and 8KB
currently used by user001.
@@ -243,13 +240,13 @@ Example output:
To have a better understanding of where the space is exactly used, you
can use following command to find out.
-```
+`
$ du -hs dir
-```
+`
Example for your HOME directory:
-```
+`
$ cd /home
$ du -hs * .[a-zA-z0-9]* | grep -E "[0-9]*G|[0-9]*M" | sort -hr
258M cuda-samples
@@ -257,23 +254,23 @@ $ du -hs * .[a-zA-z0-9]* | grep -E "[0-9]*G|[0-9]*M" | sort -hr
13M .mozilla
5,5M .eclipse
2,7M .idb_13.0_linux_intel64_app
-```
+`
This will list all directories which are having MegaBytes or GigaBytes
of consumed space in your actual (in this example HOME) directory. List
is sorted in descending order from largest to smallest
files/directories.
->To have a better understanding of previous commands, you can read
+To have a better understanding of previous commands, you can read
manpages.
-```
+`
$ man lfs
-```
+`
-```
+`
$ man du
-```
+`
Extended Access Control List (ACL)
----------------------------------
@@ -288,7 +285,7 @@ ACLs on a Lustre file system work exactly like ACLs on any Linux file
system. They are manipulated with the standard tools in the standard
manner. Below, we create a directory and allow a specific user access.
-```
+`
[vop999@login1.salomon ~]$ umask 027
[vop999@login1.salomon ~]$ mkdir test
[vop999@login1.salomon ~]$ ls -ld test
@@ -313,7 +310,7 @@ user:johnsm:rwx
group::r-x
mask::rwx
other::---
-```
+`
Default ACL mechanism can be used to replace setuid/setgid permissions
on directories. Setting a default ACL on a directory (-d flag to
@@ -331,7 +328,7 @@ Shared Workspaces
Users home directories /home/username reside on HOME filesystem.
Accessible capacity is 0.5PB, shared among all users. Individual users
are restricted by filesystem usage quotas, set to 250GB per user.
->If 250GB should prove as insufficient for particular user, please
+If 250GB should prove as insufficient for particular user, please
contact [support](https://support.it4i.cz/rt),
the quota may be lifted upon request.
@@ -499,18 +496,18 @@ Summary
----------
- -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
- Mountpoint Usage Protocol Net Capacity Throughput Limitations Access Services
- ---------------------------------------------- -------------------------------- ------------- -------------- ------------ ------------- ------------------------- -----------------------------
- /home home directory NFS, 2-Tier 0.5 PB 6 GB/s Quota 250GB Compute and login nodes backed up
+ --------------------------------------------------
+ |Mountpoint|Usage|Protocol|Net|Capacity|Throughput|Limitations|Access|
+ ---------------------------------------- |---|---|---------------------- ------------- -------------- ------------ ------------- ---------- |**Version**|**Module**|------
+ | /home|home directory|NFS, 2-Tier|0.5 PB|6 GB/s|Quota 250GB|Compute and login nodes|backed up|
- /scratch/work large project files Lustre 1.69 PB 30 GB/s Quota Compute and login nodes none
- 1TB
+ |/scratch/work|large project files|Lustre|1.69 PB|30 GB/s|Quota|Compute and login nodes|none|
+
- /scratch/temp job temporary data Lustre 1.69 PB 30 GB/s Quota 100TB Compute and login nodes files older 90 days removed
+ |/scratch/temp|job temporary data|Lustre|1.69 PB|30 GB/s|Quota 100TB|Compute and login nodes|files older 90 days removed|
- /ramdisk job temporary data, node local local 120GB 90 GB/s none Compute nodes purged after job ends
- -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+ |/ramdisk|job temporary data, node local|local|120GB|90 GB/s|none|Compute nodes|purged after job ends|
+ --------------------------------------------------
Â
diff --git a/converted/docs.it4i.cz/salomon/storage/storage.pdf b/converted/docs.it4i.cz/salomon/storage/storage.pdf
index 0894339d01903ba808dea03a9fd7b1edbb04eab9..1d00b5eea5a8c5e13d5c67b75f3419fddb38b18b 100644
Binary files a/converted/docs.it4i.cz/salomon/storage/storage.pdf and b/converted/docs.it4i.cz/salomon/storage/storage.pdf differ
diff --git a/html_md.sh b/html_md.sh
index c81f705fe8be4ac683e9990b811aad57b2078cee..0dd90261a9acc54f5fa8e229aa61c25326096747 100755
--- a/html_md.sh
+++ b/html_md.sh
@@ -2,8 +2,8 @@
### DOWNLOAD AND CONVERT DOCUMENTATION
# autor: kru0052
-# version: 0.51
-# change: export pdf, epub
+# version: 0.52
+# change: repait bugs
# bugs: bad internal links
###
@@ -23,12 +23,7 @@ if [ "$1" = "-e" ]; then
echo "$(tput setaf 12)($counter/$count)$(tput setaf 11)$a => $(tput setaf 13)${a%.*}.epub$(tput setaf 15)"
counter=$((counter+1))
cd "$b"
- #if [ $a = "job-submission-and-execution.md" ]; then
- #!double subscripts problem !!!!!!
- #wkhtmltopdf job-submission-and-execution.md job-submission-and-execution.pdf
- #else
- pandoc ${a%.*}.md -o ${a%.*}.epub
- #fi
+ pandoc ${a%.*}.md -o ${a%.*}.epub
cd "$c"
done
fi
@@ -44,9 +39,23 @@ if [ "$1" = "-e" ]; then
#echo "$b"
counter=$((counter+1))
cd "$b"
+ #!double subscripts problem !!!!!!
+ #ansys-fluent.md
+ #capacity-computing.md
+ #job-submission-and-execution.md
if [ $a = "job-submission-and-execution.md" ]; then
- #!double subscripts problem !!!!!!
- wkhtmltopdf job-submission-and-execution.md job-submission-and-execution.pdf
+ pandoc ${a%.*}.md -o ${a%.*}.epub
+ pandoc ${a%.*}.epub -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf
+ rm "${a%.*}.epub"
+ elif [ $a = "ansys-fluent.md" ]; then
+ #wkhtmltopdf ansys-fluent.md ansys-fluent.pdf
+ pandoc ${a%.*}.md -o ${a%.*}.epub
+ pandoc ${a%.*}.epub -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf
+ rm "${a%.*}.epub"
+ elif [ $a = "capacity-computing.md" ]; then
+ pandoc ${a%.*}.md -o ${a%.*}.epub
+ pandoc ${a%.*}.epub -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf
+ rm "${a%.*}.epub"
else
pandoc ${a%.*}.md -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf
fi
@@ -147,7 +156,7 @@ if [ "$1" = "-c" ]; then
arg1=`echo "$x" | cut -d"&" -f1 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
arg2=`echo "$x" | cut -d"&" -f2 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
- sed -e 's/'"$arg1"'/'"$arg2"'/' "${i%.*}TMP.md" > "${i%.*}TMP.TEST.md";
+ sed -e 's/'"$arg1"'/'"$arg2"'/' "${i%.*}TMP.md" | sed -e 's/^``//g' > "${i%.*}TMP.TEST.md";
cat -s "${i%.*}TMP.TEST.md" > "${i%.*}TMP.md";
done < ./source/formatting
@@ -178,10 +187,20 @@ if [ "$1" = "-c" ]; then
arg1=`echo "$x" | cut -d"&" -f1 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
arg2=`echo "$x" | cut -d"&" -f2 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
- sed -e 's/'"$arg1"'/'"$arg2"'/' "${i%.*}TMP.md" > "${i%.*}.md";
+ sed -e 's/'"$arg1"'/'"$arg2"'/' "${i%.*}TMP.md" | sed -e 's/^>//' > "${i%.*}.md";
cat -s "${i%.*}.md" > "${i%.*}TMP.md";
done < ./source/tabREPLACE
+ # last repair formatting...
+ printf "\t\tlast repair formatting...\n"
+ while read x ; do
+ arg1=`echo "$x" | cut -d"&" -f1 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
+ arg2=`echo "$x" | cut -d"&" -f2 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
+
+ sed -e 's/'"$arg1"'/'"$arg2"'/' "${i%.*}TMP.md" > "${i%.*}TMP.TEST.md";
+ cat -s "${i%.*}TMP.TEST.md" > "${i%.*}TMP.md";
+ done < ./source/lastFilter
+
cat "${i%.*}TMP.md" > "${i%.*}.md";
# delete temporary files
diff --git a/source/formatting b/source/formatting
index cea3e3b9bad821c94cca84283188c26730635477..5ef039f1873c98e6f1e406b544bad0de5887ce03 100644
--- a/source/formatting
+++ b/source/formatting
@@ -47,3 +47,8 @@ Variant Call Format (VCF)**&**Variant Call Format (VCF)**
</span></span>&
/ansys_inc/shared_ les/licensing/lic_admin/anslic_admin&/ansys_inc/shared_les/licensing/lic_admin/anslic_admin
<td align="left">& |
+However, users need only manage User and CA certificates. Note that your&**However, users need only manage User and CA certificates. Note that your
+X.509 PKI certificates for communication with us.&X.509 PKI certificates for communication with us.**
+PuTTYgen**&**PuTTYgen**
+key](../ssh-keys.html) file if Pageant ****SSH&key](../ssh-keys.html) file if Pageant **SSH
+authentication agent is not used.&authentication agent is not used.**
diff --git a/source/lastFilter b/source/lastFilter
new file mode 100644
index 0000000000000000000000000000000000000000..00641541ae06f6de1a53cafb4d66b091ce6d5c1e
--- /dev/null
+++ b/source/lastFilter
@@ -0,0 +1,70 @@
+>key.&key.
+</span>&
+`.ssh`&`.ssh` Â directory: 700 (drwx------)
+Authorized_keys,&Authorized_keys, known_hosts and public key (`.pub` file): `644 (-rw-r--r--)`
+Private key&Private key (`id_rsa/id_rsa.ppk` ): `600 (-rw-------)`
+ (gnome-session:23691): WARNING **: Cannot open display:& (gnome-session:23691): WARNING **: Cannot open display:**
+ &
+ &
+Search for the localhost and port number (in this case&**Search for the localhost and port number (in this case
+Preferences](gdmscreensaver.png/@@images/8e80a92f-f691-4d92-8e62-344128dcc00b.png "Screensaver Preferences")](../../../../salomon/gnome_screen.jpg.1)&
+maximum performance**&maximum performance
+Better performance** is obtained by logging on the allocated compute&**Better performance** is obtained by logging on the allocated compute
+ class="discreet">&
+ id="result_box"&
+ class="hps alt-edited">stated &stated in the previous example.
+Water-cooled Compute Nodes With MIC Accelerator**&**Water-cooled Compute Nodes With MIC Accelerator**
+Access from PRACE network:**&**Access from PRACE network:**
+Access from public Internet:**&**Access from public Internet:**
+Access from PRACE network:**&**Access from PRACE network:**
+Access from public Internet:**&**Access from public Internet:**
+>VPN client installation&VPN client installation
+Install](https://docs.it4i.cz/salomon/vpn_web_install_2.png/@@images/c2baba93-824b-418d-b548-a73af8030320.png "VPN Install")](../vpn_web_install_2.png)&
+Â [](Salomon_IB_topology.png)&
+###IB single-plane topology - ICEX Mcell**&###IB single-plane topology - ICEX Mcell
+As shown in a diagram [IB&As shown in a diagram &
+and [ &
+SCRATCH](storage.html#shared-filesystems).&
+There are two main shared file systems on Salomon cluster, the [&There are two main shared file systems on Salomon cluster, the [HOME](storage.html#home)and [SCRATCH](storage.html#shared-filesystems).
+>Disk usage and quota commands&Disk usage and quota commands
+>OpenCL&### OpenCL
+Execution on host**&**Execution on host**
+Execution on host - MPI processes distributed over multiple&**Execution on host - MPI processes distributed over multiple
+Host only node-file:**&**Host only node-file:**
+MIC only node-file**:&MIC only node-file:
+Host and MIC node-file**:&Host and MIC node-file:
+interface Rstudio&interface Rstudio**
+### >&###
+3. >>&3. >
+- >>&- >
+>Usage with MPI&Usage with MPI
+>>&>
+ id="result_box"> &
+<span&
+>Introduction&Introduction
+>Options&Options
+***[ANSYS&**[ANSYS
+Channel partner](http://www.ansys.com/)***&Channel partner](http://www.ansys.com/)**
+Multiphysics)-**Commercial.**&Multiphysics)-**Commercial.
+>1. Common way to run Fluent over pbs file&1. Common way to run Fluent over pbs file
+>2. Fast way to run Fluent from command line&2. Fast way to run Fluent from command line
+**Academic**&**Academic
+***&**
+id="result_box"&
+</span>&
+[](Fluent_Licence_2.jpg)&
+Failed to initialize connection subsystem Win 8.1 - 02-10-15 MS&**Failed to initialize connection subsystem Win 8.1 - 02-10-15 MS
diff --git a/source/repairIMG b/source/repairIMG
index 7bc3a16235a6e0a0e686fd9c4e0474501b4065d1..5a8d1763fd87d5d3e2e40aa52b0ab08aa6e43f75 100644
--- a/source/repairIMG
+++ b/source/repairIMG
@@ -114,7 +114,7 @@ screensaver](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-
[](gnome-compute-nodes-over-vnc.png)&
&
genomic coordinates.](fig6.png.1 "fig6.png")&genomic coordinates.](fig6.png)
-out.](images/fig1.png "Fig 1")&out.](ig1.png)
+out.](images/fig1.png "Fig 1")&out.](fig1.png)
operation.](fig3.png "fig3.png")&operation.](fig3.png)
starts.](images/fig7.png "fig7.png")&starts.](fig7.png)
H).](images/fig7x.png "fig7x.png")&H).](fig7x.png)
diff --git a/source/tabREPLACE b/source/tabREPLACE
index 337add8c392d382d90d3c070d7d4f2fb3432fe4a..7ed3455feb6bc8c41119e9ab92ce8a67644abb74 100644
--- a/source/tabREPLACE
+++ b/source/tabREPLACE
@@ -32,3 +32,116 @@
goolf BLACS, FFTW, GCC, OpenBLAS, OpenMPI, ScaLAPACK&|goolf|BLACS, FFTW, GCC, OpenBLAS, OpenMPI, ScaLAPACK|
>iompi OpenMPI, icc, ifort&|iompi|OpenMPI, icc, ifort|
iccifort icc, ifort&|iccifort|icc, ifort|
+ Login address Port Protocol Login node& |Login address|Port|Protocol|Login node|
+ ------------------------------ ------ ---------- ----------------------------------& |---|---|
+ salomon-prace.it4i.cz 2222 gsissh login1, login2, login3 or login4& |salomon-prace.it4i.cz|2222|gsissh|login1, login2, login3 or login4|
+ login1-prace.salomon.it4i.cz 2222 gsissh login1& |login1-prace.salomon.it4i.cz|2222|gsissh|login1|
+ login2-prace.salomon.it4i.cz 2222 gsissh login2& |login2-prace.salomon.it4i.cz|2222|gsissh|login2|
+ login3-prace.salomon.it4i.cz 2222 gsissh login3& |login3-prace.salomon.it4i.cz|2222|gsissh|login3|
+ login4-prace.salomon.it4i.cz 2222 gsissh login4& |login4-prace.salomon.it4i.cz|2222|gsissh|login4|
+ |Login address|Port|Protocol|Login node|& |Login address|Port|Protocol|Login node|
+ ------------------------ ------ ---------- ----------------------------------& |---|---|
+ salomon.it4i.cz 2222 gsissh login1, login2, login3 or login4& |salomon.it4i.cz|2222|gsissh|login1, login2, login3 or login4|
+ login1.salomon.it4i.cz 2222 gsissh login1& |login1.salomon.it4i.cz|2222|gsissh|login1|
+ login2.salomon.it4i.cz 2222 gsissh login2& |login2-prace.salomon.it4i.cz|2222|gsissh|login2|
+ login3.salomon.it4i.cz 2222 gsissh login3& |login3-prace.salomon.it4i.cz|2222|gsissh|login3|
+ login4.salomon.it4i.cz 2222 gsissh login4& |login4-prace.salomon.it4i.cz|2222|gsissh|login4|
+ Login address Port Node role& |Login address|Port|Node role|
+ ------------------------------- ------ -----------------------------& |---|---|
+ gridftp-prace.salomon.it4i.cz 2812 Front end /control server& |gridftp-prace.salomon.it4i.cz|2812|Front end /control server|
+ lgw1-prace.salomon.it4i.cz 2813 Backend / data mover server& |lgw1-prace.salomon.it4i.cz|2813|Backend / data mover server|
+ lgw2-prace.salomon.it4i.cz 2813 Backend / data mover server& |lgw2-prace.salomon.it4i.cz|2813|Backend / data mover server|
+ lgw3-prace.salomon.it4i.cz 2813 Backend / data mover server& |lgw3-prace.salomon.it4i.cz|2813|Backend / data mover server|
+ Login address Port Node role& |Login address|Port|Node role|
+ ------------------------- ------ -----------------------------& |---|---|
+ gridftp.salomon.it4i.cz 2812 Front end /control server& |gridftp.salomon.it4i.cz|2812|Front end /control server|
+ lgw1.salomon.it4i.cz 2813 Backend / data mover server& |lgw1.salomon.it4i.cz|2813|Backend / data mover server|
+ lgw2.salomon.it4i.cz 2813 Backend / data mover server& |lgw2.salomon.it4i.cz|2813|Backend / data mover server|
+ lgw3.salomon.it4i.cz 2813 Backend / data mover server& |lgw3.salomon.it4i.cz|2813|Backend / data mover server|
+ File system mount point Filesystem Comment& |File system mount point|Filesystem|Comment|
+ ------------------------- ------------ ----------------------------------------------------------------& |---|---|
+ /home Lustre Default HOME directories of users in format /home/prace/login/& |/home|Lustre|Default HOME directories of users in format /home/prace/login/|
+ /scratch Lustre Shared SCRATCH mounted on the whole cluster& |/scratch|Lustre|Shared SCRATCH mounted on the whole cluster|
+ Data type Default path& |Data type|Default path|
+ ------------------------------ ---------------------------------& |---|---|
+ large project files /scratch/work/user/prace/login/& |large project files|/scratch/work/user/prace/login/|
+ large scratch/temporary data /scratch/temp/& |large scratch/temporary data|/scratch/temp/|
+ ---------------------------------------------------------------------------------------------------------------------------------------------&
+ queue Active project Project resources Nodes priority authorization walltime&|queue|Active project|Project resources|Nodes|priority|authorization|walltime default/max|
+ default/max&
+ --------------------- -|---|---|---|--------------------- ---------- --------------- -------------&|---|---|
+ **qexp** no none required 32 nodes, max 8 per user 150 no 1 / 1h& |**qexp** Express queue|no|none required|32 nodes, max 8 per user|150|no|1 / 1h|
+ Express queue&\\
+ **qprace** yes > 0 >1006 nodes, max 86 per job 0 no 24 / 48h&|**qprace** Production queue|yes|> 0|1006 nodes, max 86 per job|0|no|24 / 48h|
+ Production queue&\\
+ **qfree** yes none required 752 nodes, max 86 per job -1024 no 12 / 12h&|**qfree** Free resource queue|yes|none required|752 nodes, max 86 per job|-1024|no|12 / 12h|
+ Free resource queue&\\
+ ---------------------------------------------------------------------------------------------------------------------------------------------&
+ Port Protocol& |Port|Protocol|
+ ------ ----------& |---|---|
+ 22 ssh& |22|ssh|
+ 80 http& |80|http|
+ 443 https& |443|https|
+ 9418 git& |9418|git|
+ Node Count Processor Cores Memory Accelerator& |Node|Count|Processor|Cores|Memory|Accelerator|
+ ----------------- ------- ---------------------------------- ------- -------- --------------------------------------------& |---|---|
+ w/o accelerator 576 2x Intel Xeon E5-2680v3, 2.5GHz 24 128GB -& |w/o accelerator|576|2x Intel Xeon E5-2680v3, 2.5GHz|24|128GB|-|
+ MIC accelerated 432 2x Intel Xeon E5-2680v3, 2.5GHz 24 128GB 2x Intel Xeon Phi 7120P, 61cores, 16GB RAM& |MIC accelerated|432|2x Intel Xeon E5-2680v3, 2.5GHz|24|128GB|2x Intel Xeon Phi 7120P, 61cores, 16GB RAM|
+ Node Count Processor Cores Memory GPU Accelerator& |Node|Count|Processor|Cores|Memory|GPU Accelerator|
+ --------------- ------- --------------------------------- ------- -------- ------------------------------& |---|---|
+ visualization 2 2x Intel Xeon E5-2695v3, 2.3GHz 28 512GB NVIDIA QUADRO K5000, 4GB RAM& |visualization|2|2x Intel Xeon E5-2695v3, 2.3GHz|28|512GB|NVIDIA QUADRO K5000, 4GB RAM|
+ Hypercube dimension& |Hypercube|dimension|
+ --------------------- -------------------------------------------& |---|---|
+ 1D ehc_1d& |1D|ehc_1d|
+ 2D ehc_2d& |2D|ehc_2d|
+ 3D ehc_3d& |3D|ehc_3d|
+ 4D ehc_4d& |4D|ehc_4d|
+ 5D ehc_5d& |5D|ehc_5d|
+ 6D ehc_6d& |6D|ehc_6d|
+ 7D ehc_7d& |7D|ehc_7d|
+ Node type Count Short name Long name Rack& |Node type|Count|Short name|Long name|Rack|
+ -------------------------------------- ------- ------------------ -------------------------- -------& |---|---|
+ M-Cell compute nodes w/o accelerator 576 cns1 -cns576 r1i0n0 - r4i7n17 1-4& |M-Cell compute nodes w/o accelerator|576|cns1 -cns576|r1i0n0 - r4i7n17|1-4|
+ compute nodes MIC accelerated 432 cns577 - cns1008 r21u01n577 - r37u31n1008 21-38& |compute nodes MIC accelerated|432|cns577 - cns1008|r21u01n577 - r37u31n1008|21-38|
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------&
+ Mountpoint Usage Protocol Net Capacity Throughput Limitations Access Services& |Mountpoint|Usage|Protocol|Net|Capacity|Throughput|Limitations|Access|
+ ---------------------------------------------- -------------------------------- ------------- -------------- ------------ ------------- ------------------------- -----------------------------& |---|---|
+ /home home directory NFS, 2-Tier 0.5 PB 6 GB/s Quota 250GB Compute and login nodes backed up&| /home|home directory|NFS, 2-Tier|0.5 PB|6 GB/s|Quota 250GB|Compute and login nodes|backed up|
+ /scratch/work large project files Lustre 1.69 PB 30 GB/s Quota Compute and login nodes none& |/scratch/work|large project files|Lustre|1.69 PB|30 GB/s|Quota|Compute and login nodes|none|
+ 1TB&
+ /scratch/temp job temporary data Lustre 1.69 PB 30 GB/s Quota 100TB Compute and login nodes files older 90 days removed& |/scratch/temp|job temporary data|Lustre|1.69 PB|30 GB/s|Quota 100TB|Compute and login nodes|files older 90 days removed|
+ /ramdisk job temporary data, node local local 120GB 90 GB/s none Compute nodes purged after job ends& |/ramdisk|job temporary data, node local|local|120GB|90 GB/s|none|Compute nodes|purged after job ends|
+ -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------&
+ Application Version module& |Application|Version|module|
+ ------------- -------------- ---------------------& |---|---|
+ **R** R 3.1.1 R/3.1.1-intel-2015b& |**R**|R 3.1.1|R/3.1.1-intel-2015b|
+ **Rstudio** Rstudio 0.97 Rstudio& |**Rstudio**|Rstudio 0.97|Rstudio|
+ 24 MPI**&**24 MPI**
+ --------------- -----------------------& |**Version**|**Module**|
+**Version** **Module**& |---|---|
+ 2016 Update 2 Advisor/2016_update2& |2016 Update 2|Advisor/2016_update2|
+ 2016 Update 1 Inspector/2016_update1& |2016 Update 1|Inspector/2016_update1|
+ Interface Integer type& |Interface|Integer type|
+ ----------- -----------------------------------------------& |---|---|
+ LP64 32-bit, int, integer(kind=4), MPI_INT& |LP64|32-bit, int, integer(kind=4), MPI_INT|
+ ILP64 64-bit, long int, integer(kind=8), MPI_INT64 & |ILP64|64-bit, long int, integer(kind=8), MPI_INT64|
+ Parameter Value& |Parameter|Value|
+ ------------------------------------------------- -----------------------------& |---|---|
+ >max number of atoms 200& |max number of atoms|200|
+ >max number of valence orbitals 300& |max number of valence orbitals|300|
+ >max number of basis functions 4095& |max number of basis functions|4095|
+ >max number of states per symmmetry 20& |max number of states per symmmetry|20|
+ >max number of state symmetries 16& |max number of state symmetries|16|
+ >max number of records 200& |max number of records|200|
+ >max number of primitives >maxbfn x [2]& |max number of primitives|maxbfn x [2]|
+ Address Port Protocol& |Address|Port|Protocol|
+ -------------------------------------------------- ---------------------------------- -----------------------------------------& |---|---|
+ anselm.it4i.cz 22 scp, sftp& |anselm.it4i.cz|22|scp, sftp|
+ login1.anselm.it4i.cz 22 scp, sftp& |login1.anselm.it4i.cz|22|scp, sftp|
+ login2.anselm.it4i.cz 22 scp, sftp& |login2.anselm.it4i.cz|22|scp, sftp|
+ class="discreet">dm1.anselm.it4i.cz 22 class="discreet">scp, sftp</span>& |dm1.anselm.it4i.cz|22|scp, sftp|
+ Login address Port Protocol Login node& |Login address|Port|Protocol|Login node|
+ ----------------------- ------ ---------- ----------------------------------------------& |---|----|
+ anselm.it4i.cz 22 ssh round-robin DNS record for login1 and login2& |anselm.it4i.cz|22|ssh|round-robin DNS record for login1 and login2|
+ login1.anselm.it4i.cz 22 ssh login1& |login1.anselm.it4i.cz|22|ssh|login1|
+ login2.anselm.it4i.cz 22 ssh login2& |login2.anselm.it4i.cz|22|ssh|login2|