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exercises:2016_uzh_cmest:login [2016/09/21 10:49]
tmueller [Module loading]
exercises:2016_uzh_cmest:login [2016/09/22 09:08]
tmueller [Make module loading persistent]
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-====== ​Your first simulation ​======+====== ​First Login ======
  
-In this exercise you will learn how to run your first calculation.+In this exercise you will learn how to login and run commands on our infrastructure.
  
 ===== Part I: Login ===== ===== Part I: Login =====
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   * a file transfer tool to copy files from/to the server:   * a file transfer tool to copy files from/to the server:
-    * on Linux: put ''​sftp:​////​tcopt3.chem.uzh.ch''​ as the address in your file browser and you should be able to login and browser ​your home directory+    * on Linux: put ''​%%sftp://​tcopt3.chem.uzh.ch%%''​ as the address in your file browser and you should be able to browse ​your home directory ​after logging in
     * on Mac OS X/OSX/macOS Sierra: use [[https://​cyberduck.io/​|Cyberduck]]     * on Mac OS X/OSX/macOS Sierra: use [[https://​cyberduck.io/​|Cyberduck]]
     * one Windows: use [[https://​winscp.net/​|WinSCP]] or [[https://​cyberduck.io/​|Cyberduck]]     * one Windows: use [[https://​winscp.net/​|WinSCP]] or [[https://​cyberduck.io/​|Cyberduck]]
   * a plain text editor to edit input files if you are uncomfortable with using ''​vim'',​ ''​nano''​ or ''​emacs''​ via SSH. Please note: It is important that your editor supports Unix line endings. If in doubt, use one of the mentioned editors on the server, or an advanced plain text editor like [[https://​atom.io/​|Atom]] (plus the [[https://​atom.io/​packages/​line-ending-selector-unix|line-ending-selector-unix]] plugin) or [[https://​notepad-plus-plus.org/​|Notepad++]] on your local machine.   * a plain text editor to edit input files if you are uncomfortable with using ''​vim'',​ ''​nano''​ or ''​emacs''​ via SSH. Please note: It is important that your editor supports Unix line endings. If in doubt, use one of the mentioned editors on the server, or an advanced plain text editor like [[https://​atom.io/​|Atom]] (plus the [[https://​atom.io/​packages/​line-ending-selector-unix|line-ending-selector-unix]] plugin) or [[https://​notepad-plus-plus.org/​|Notepad++]] on your local machine.
  
-Use the instructions giving in the lecture/​available via OLAT to login on the server ''​tcopt3.chem.uzh.ch''​.+Use the instructions giving in the lecture/​available via OLAT to login on the server ''​tcopt3.chem.uzh.ch'' ​using your assigned student account.
  
 <note important>​Change the password of your account after your first login, using: <note important>​Change the password of your account after your first login, using:
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 <​code>​ <​code>​
-$ cp2k.popt --help+$ cp2k.sopt --help
 </​code>​ </​code>​
  
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 <​code>​ <​code>​
- cp2k.popt [-c|--check] [-e|--echo] [-h|--help] [--html-manual]+ cp2k.sopt [-c|--check] [-e|--echo] [-h|--help] [--html-manual]
            [-i] <​input_file>​            [-i] <​input_file>​
            ​[-mpi-mapping|--mpi-mapping] <​method>​            ​[-mpi-mapping|--mpi-mapping] <​method>​
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  ​starts the CP2K program, see <​https://​www.cp2k.org/>​  ​starts the CP2K program, see <​https://​www.cp2k.org/>​
  
- The easiest way is cp2k.popt <​input_file>​+ The easiest way is cp2k.sopt <​input_file>​
  
  The following options can be used:  The following options can be used:
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 </​code>​ </​code>​
  
-Another program we need is [[http://​www.ks.uiuc.edu/​Research/​vmd/​|VMD]].+Another program we need for visualization ​is [[http://​www.ks.uiuc.edu/​Research/​vmd/​|VMD]].
  
 Load the respective module (since there is only one version available, the shorthand ''​vmd''​ can be used when specifying the module to load) and start it using: Load the respective module (since there is only one version available, the shorthand ''​vmd''​ can be used when specifying the module to load) and start it using:
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 +===== Part III: Advanced account configuration =====
 +
 +==== Make module loading persistent ====
 +
 +Upon login, the shell (''​bash''​ in our case) executes a number of files if they exist. One of them is the ''​.bashrc''​. To prepare it for management using the the ''​module''​ command, simply execute the following **once**:
 +
 +<​code>​
 +$ echo '​module load ' >> ~/.bashrc
 +</​code>​
 +
 +after that you can add and remove modules to be loaded at startup using ''​module initadd''​ or ''​module initrm''​.
 +
 +To add ''​vmd''​ and ''​cp2k'',​ run for example:
 +
 +<​code>​
 +$ module initadd vmd
 +$ module initadd cp2k/​r17408_2016_09_19
 +</​code>​
 +
 +to remove ''​vmd''​ again from the list of modules to load:
 +
 +<​code>​
 +$ module initrm vmd
 +</​code>​
 +
 +Alternatively you can of course simply edit ''​.bashrc''​ using your favorite editor and add a line like ''​module load vmd cp2k/​r17408_2016_09_19''​ by yourself.
exercises/2016_uzh_cmest/login.txt ยท Last modified: 2016/09/22 09:48 by tmueller