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exercises:2016_uzh_cmest:first_simulation_run [2016/09/21 10:49] – [Module loading] tmuellerexercises:2016_uzh_cmest:login [2016/09/22 09:06] – [Make module loading persistent] tmueller
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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 through 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''. For example:
 +
 +<code>
 +$ module initadd vmd
 +$ module initadd cp2k/r17408_2016_09_19
 +</code>
 +
 +to remove ''vmd'' from the list of modules to load at login:
 +
 +<code>
 +$ module initrm vmd
 +</code>
exercises/2016_uzh_cmest/login.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1