CP2K Open Source Molecular Dynamics

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exercises:2019_conexs_newcastle:ex0 [2019/09/10 16:40] – [Launching a CP2K calculation] abussyexercises:2019_conexs_newcastle:ex0 [2019/09/10 16:59] – [Going to the proper directory] abussy
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 To browse to the same file in WinSCP, use the top right field (currently displaying `nconexs##`) and first go to `/ <root>`, then `nobackup` and finally your `nconexs##` directory. You should see the same files as in the WinSCP terminal. To browse to the same file in WinSCP, use the top right field (currently displaying `nconexs##`) and first go to `/ <root>`, then `nobackup` and finally your `nconexs##` directory. You should see the same files as in the WinSCP terminal.
  
 +
 +**You can edit files, create new files and directories, etc. either directly in the PuTTY terminal or using WinSCP**
 ===== Launching a CP2K calculation  ===== ===== Launching a CP2K calculation  =====
  
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 The next paragraph specifies a bunch of indications for the queue system which we do not need to understand and should not modify. The next paragraph specifies a bunch of indications for the queue system which we do not need to understand and should not modify.
 +
 +The `module load` line indicates which (available) version of CP2K to use and the final line is the actual launch command.
 +
 +Look at the structure of that last line. `/nobackup/nconexs03/test.inp` is the path to your CP2K input file and `/nobackup/nconexs03/test.out` that of your input file. You will have to edit those paths for your own calculation.
 +
 +To launch the calculation, you have to run the `cp2k.sh` file. This is done via the `sbatch` command (to be typed in the PuTTY terminal):
 +
 +
 +<code>
 +sbatch cp2k.sh
 +</code>
 +
 +Note that this specific example will fail, as you do not have access to the `nconexs03` directory.
 +
 +
 +==== Keeping track of your job ====
 +
 +
 +There are a few very useful (terminal) commands that you can use to keep track of your calculations. First of which is the
 +
 +
 +<code>
 +squeue -u nconexs##
 +</code>
 +
 +
 +which informs you about the state of your calculation (whether it is in the queue, or if it is currently running, and also the job id). 
 +
 +If you want to kill your job, you can do so using the `scancel` command:
 +
 +<code>
 +scancel jobid(obtained with squeue)
 +</code>
 +
 +
 +Finally you can also follow the state of your calculation by checking the output file as it is written using the `tail` command:
 +
 +
 +<code>
 +
 +tail -f path_to_your_output_file
 +</code>
 +
 +
 +This command can be exited by pressing `Ctrl+c`
 +
 +
 +
 +
exercises/2019_conexs_newcastle/ex0.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1