rucni merge s upravami od RUS016

docs.it4i/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access.md

@@ -51,8 +51,12 @@ After logging in, you will see the command prompt:
 Last login: Tue Jul  9 15:57:38 2013 from your-host.example.com
 [username@login2.anselm ~]$
 ```
-!!! Note "Note"
-	The environment is **not** shared between login nodes, except for [shared filesystems](../storage/storage/#section-1).
+
+Example to the cluster login:
+
+<tty-player controls src=/src/anselm/login_anselm.ttyrec></tty-player>
+
+>The environment is **not** shared between login nodes, except for [shared filesystems](../storage/storage/#section-1).
 
 Data Transfer
 -------------
@@ -82,6 +86,8 @@ On linux or Mac, use scp or sftp client to transfer the data to Anselm:
 ```bash
 local $ scp -i /path/to/id_rsa my-local-file username@anselm.it4i.cz:directory/file
 ```
+For example how to using scp command:
+<tty-player controls src=/src/anselm/transfer_scp_anselm.ttyrec></tty-player>
 
 ```bash
 local $ scp -i /path/to/id_rsa -r my-local-dir username@anselm.it4i.cz:directory
@@ -92,6 +98,8 @@ or
 ```bash
 local $ sftp -o IdentityFile=/path/to/id_rsa username@anselm.it4i.cz
 ```
+For example how to using sftp command:
+<tty-player controls src=/src/anselm/transfer_sftp_anselm.ttyrec></tty-player>
 
 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)
 

docs.it4i/anselm-cluster-documentation/environment-and-modules.md

@@ -76,6 +76,9 @@ PrgEnv-gnu sets up the GNU development environment in conjunction with the bullx
 
 PrgEnv-intel sets up the INTEL development environment in conjunction with the Intel MPI library
 
+How to using modules in examples:
+<tty-player controls src=/src/anselm/modules_anselm.ttyrec></tty-player>
+
 ### Application Modules Path Expansion
 
 All application modules on Salomon cluster (and further) will be build using tool called [EasyBuild](http://hpcugent.github.io/easybuild/ "EasyBuild"). In case that you want to use some applications that are build by EasyBuild already, you have to modify your MODULEPATH environment variable.

docs.it4i/salomon/accessing-the-cluster/accessing-the-cluster.md

@@ -42,24 +42,7 @@ On **Windows**, use [PuTTY ssh client](../get-started-with-it4innovations/access
 
 After logging in, you will see the command prompt:
 
-```bash
-                    _____       _
-                   / ____|     | |
-                  | (___   __ _| | ___  _ __ ___   ___  _ __
-                   \___ \ / _` | |/ _ \| '_ ` _ \ / _ \| '_ \
-                   ____) | (_| | | (_) | | | | | | (_) | | | |
-                  |_____/ \__,_|_|\___/|_| |_| |_|\___/|_| |_|
-
-
-                        http://www.it4i.cz/?lang=en
-
-
-Last login: Tue Jul  9 15:57:38 2013 from your-host.example.com
-[username@login2.salomon ~]$
-```
-<div id="page-wrap">
-<tty-player controls src=/src/login.ttyrec></tty-player>
-</div>
+<tty-player controls src=/src/salomon/login_salomon.ttyrec></tty-player>
 
 !!! Note "Note"
 	The environment is **not** shared between login nodes, except for [shared filesystems](storage/storage/).
@@ -90,6 +73,9 @@ 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
 ```
 
+For example how to using scp command:
+<tty-player controls src=/src/salomon/transfer_scp_salomon.ttyrec></tty-player>
+
 ```bash
 local $ scp -i /path/to/id_rsa -r my-local-dir username@salomon.it4i.cz:directory
 ```
@@ -100,6 +86,9 @@ or
 local $ sftp -o IdentityFile=/path/to/id_rsa username@salomon.it4i.cz
 ```
 
+For example how to using sftp command:
+<tty-player controls src=/src/salomon/transfer_sftp_salomon.ttyrec></tty-player>
+
 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)
 
 ```bash
@@ -108,9 +97,6 @@ local $ sshfs -o IdentityFile=/path/to/id_rsa username@salomon.it4i.cz:. mountpo
 
 Using sshfs, the users Salomon home directory will be mounted on your local computer, just like an external disk.
 
-Example to transfer data
-<tty-player controls src=/src/transfer.ttyrec></tty-player>
-
 Learn more on ssh, scp and sshfs by reading the manpages
 
 ```bash

docs.it4i/salomon/environment-and-modules.md

@@ -23,12 +23,13 @@ then
  module list # Display loaded modules
 fi
 ```
-Example display informations to standard output
-<tty-player controls src=/src/modules.ttyrec></tty-player>
 
 !!! Note "Note"
 	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 stated in the previous example.
 
+How to using modules in examples:
+<tty-player controls src=/src/salomon/modules_salomon.ttyrec></tty-player>
+
 ### Application Modules
 
 In order to configure your shell for  running particular application on Salomon we use Module package interface.

docs.it4i/src/anselm/login_anselm.screen

+$ termrec login_anselm.ttyrec
+
+# login to Anselm cluster from local linux machine
+
+ssh -i /home/local/.ssh/id_rsa rus016@login1.anselm.it4i.cz
+
+# Welcome to Anselm supercomputer cluster
+
+# run htop command
+
+htop
+
+# logout from the cluster
+
+logout

docs.it4i/src/modules.screen → docs.it4i/src/anselm/modules_anselm.screen

-ssh -i /home/local/.ssh/id_rsa dd-16-12-13@salomon.it4i.cz
+termrec -e 'ssh -i /home/local/.ssh/id_rsa rus016@anselm.it4i.cz' modules_anselm.ttyrec
 
-# working with modules
+# Working with modules
 
 # get the current version of Python
 $ python --version
@@ -27,7 +27,7 @@ python
 # now turn back to old version you have to unload module
 $ module unload Python/3.5.1-intel-2016.01
 
-$ python -- version
+$ python --version
 
 # Python version 2.6.6 is ready to use now
 

docs.it4i/src/anselm/transfer_scp_anselm.screen

+$ termrec transfer_scp_anselm.ttyrec
+
+# File transfer from local machine to Anselm cluster
+
+# create local directory with files
+$ mkdir folder
+$ cd folder
+$ touch test_file.scp
+
+$ mkdir local_dir
+$ touch local_dir/file.txt
+
+# using scp command to transfer a file to the cluster
+$ scp test_file.scp rus016@anselm.it4i.cz:/home/rus016/test_file.scp
+
+# successfully uploaded to the cluster
+
+# using scp command to transfer a directory to the cluster
+$ scp -r local_dir rus016@anselm.it4i.cz:/home/rus016/local_dir
+
+# successfully uploaded to the cluster
+
+# login to Anselm cluster and check all transfered files
+ssh -i /home/local/.ssh/id_rsa rus016@anselm.it4i.cz
+
+$ls -l
+
+# yes, all files and directory are stored in home directory on the cluster
+
+

docs.it4i/src/anselm/transfer_sftp_anselm.screen

+$ termrec transfer_sftp_anselm.ttyrec
+
+# File transfer from local machine to Anselm cluster
+
+# using sftp command
+$ touch test_file.sftp
+$ sftp -o IdentityFile=/home/local/.ssh/id_rsa rus016@anselm.it4i.cz
+
+# list of all commands - help or ?
+sftp> help
+
+# display remote working directory on Anselm cluster
+sftp> pwd
+# display remote directory listing on Anselm cluster
+sftp> ls -la
+# display statistics for remote directory
+sftp> df -h
+
+# display local working directory on local linux machine
+sftp> lpwd
+# display local directory listing on local linux machine
+sftp> lls -la
+
+# now we can upload a file from linux machine to Anselm cluster
+sftp> put test_file.sftp
+
+# and then check if successfully uploaded
+sftp> ls -l
+
+# of course we can download a file from the cluster
+sftp> get demo.tar.gz
+
+# and check in local directory
+sftp> lls -l
+
+# delete local file from sftp
+sftp>!rm demo.tar.gz
+
+# quit sftp
+sftp> exit
+
+# login to Anselm cluster and check all transfered files
+ssh -i /home/local/.ssh/id_rsa rus016@anselm.it4i.cz
+
+$ls -l
+
+# yes, all files are stored in home directory on the cluster
+

docs.it4i/src/login.screen → docs.it4i/src/salomon/login_salomon.screen

+$ termrec login_salomon.ttyrec
+
 # login to Salomon cluster from local linux machine
 
 ssh -i /home/local/.ssh/id_rsa dd-16-12-13@salomon.it4i.cz
 
-# successfull login to cluster
+# Welcome to Salomon supercomputer cluster
 
 # run htop command
 
 htop
 
-# logout from cluster
+# logout from the cluster
 
 logout
 

docs.it4i/src/salomon/modules_salomon.screen

+$ termrec -e 'ssh -i /home/local/.ssh/id_rsa dd-16-12-13@salomon.it4i.cz' modules_salomonn.ttyrec
+
+# Working with modules
+
+# get the current version of Python
+$ python --version
+
+# run Python
+python
+
+# right now is version 2.6.6
+
+# search all available Python's modules
+module avail |& grep Python/
+
+# for example let's choose a new module Python 3.5.1
+$ module load Python/3.5.1-intel-2016.01
+
+# and now get the current version of Python
+$ python --version
+
+# run Python
+python
+
+# that's correct, version 3.5.1
+
+# now turn back to old version you have to unload module
+$ module unload Python/3.5.1-intel-2016.01
+
+$ python --version
+
+# Python version 2.6.6 is ready to use now
+

docs.it4i/src/salomon/transfer_scp_salomon.screen

+$ termrec transfer_scp_salomon.ttyrec
+
+# File transfer from local machine to Salomon cluster
+
+# create local directory with files
+$ mkdir folder
+$ cd folder
+$ touch test_file.scp
+
+$ mkdir local_dir
+$ touch local_dir/file.txt
+
+# using scp command to transfer a file to the cluster
+$ scp test_file.scp dd-16-12-13@salomon.it4i.cz:/home/trainig/dd-16-12-13/test_file.scp
+
+# successfully uploaded to the cluster
+
+# using scp command to transfer a directory to the cluster
+$ scp -r local_dir dd-16-12-13@salomon.it4i.cz:/home/training/dd-16-12-13/local_dir
+
+# successfully uploaded to the cluster
+
+# login to Salomon cluster and check all transfered files
+$ ssh -i /home/local/.ssh/id_rsa dd-16-12-13@salomon.it4i.cz
+
+$ls -l
+
+# yes, all files and directory are stored in home directory on the cluster
+
+