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--- exercises:2019_conexs_newcastle:ex0 [2019/09/10 16:22] – [Using PuTTY] abussy
+++ exercises:2019_conexs_newcastle:ex0 [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 30: / Line 30: @@
 Keep the default `SFTP` file protocol and type `rocket.hpc.ncl.ac.uk` in the `Host name` field, `nconexs##` in `User name` and your password in the corrsponding file. Hit Login and browse!
+===== Going to the proper directory  =====
+In your PuTTY terminal, type the following:
+<code>
+cd /nobackup/nconexs##/
+</code>
+`cd` is the bash command allowing you to move from a directory to another. If you then type the `ls` command, the files contained in this directory will be listed.
+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  =====
+The `cp2k.sh` file contains a set of (machine) instructions that allows you to run a job in parallel on the HPC cluster. You can open and edit this file directly in the PuTTY terminal or through WinSCP.
+<code - cp2k.sh>
+#!/bin/bash
+#SBATCH --ntasks=6
+#SBATCH --tasks-per-node=6
+#SBATCH --job-name=test
+myaccount=tpcss
+export SLURM_ACCOUNT=$myaccount
+export SBATCH_ACCOUNT=$myaccount
+export SALLOC_ACCOUNT=$myaccount
+myres=1
+export SLURM_RESERVATION=${myaccount}_${myres}
+export SBATCH_RESERVATION=${myaccount}_${myres}
+export SALLOC_RESERVATIION=${myaccount}_${myres}
+module load CP2K/6.1-foss-2017b
+export OMP_NUM_THREADS=1
+mpirun -np $SLURM_NTASKS --bind-to core cp2k.popt /nobackup/nconexs03/test.inp > /nobackup/nconexs03/test.out
+</code>
+The first line of this file simply marks it as an executable. The next three lines (starting with `#SBATCH`) indicates how many CPUs will be used for this calculation and the its name. If you were to run 8 cores, the you would need to change the `ntasks` and `tasks-per-node` accordingly.
+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. Note that in principle, you can use either absolute paths or relative paths.
+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`