Commit b5653724 authored by Lukáš Krupčík's avatar Lukáš Krupčík

version 0.52

parent ac99635d
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Převod html dokumentace do md formátu (version 0.51) - BETA
Převod html dokumentace do md formátu (version 0.52) - BETA
===========================================================
Výsledkem projektu by měl být skript pro stažení a převod stávající dokumentace na docs.it4i.cz do md formátu
......@@ -28,8 +28,7 @@ Pro svou práci si naklonujete Gitem repozitář do svého pracovního adresář
|0.45|7m56s|optimalizace|
|0.47|11m7s|přidání filtrů pro opravu a nahrazení tabulek, vylepšení filtrace, ...|
|0.51|16m37s|export do pdf, export do epub, filtry, ...|
|0.52|16m37s|oprava exportu do pdf, nový filtr pro poslední opravu formátování a chyb, ...|
>**Problémy**
> * interní a externí odkazy
......
......@@ -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
......
......@@ -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:b7 (RSA)
 
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
......
......@@ -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
......
......@@ -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.
......
......@@ -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
......
......@@ -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
......
......@@ -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.
......
......@@ -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: