version 0.52

README.md

-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

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

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: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

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

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.
 

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

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