James at 20:12, 27 October 2022

2022-10-27T20:12:13Z

James: Created page with "At the CUNY HPC Center CP2K is installed on ANDY. CP2K can be built as a serial, MPI-parallel, or MPI-OpenMP-parallel code. At this time, only the MPI-parallel version of the application has been built for production use at the HPC Center. Further information on CP2K is available at the website here [http://www.cp2k.org/]. Below is an example PBS script that will run the CP2K H2O-32 test case provided with the CP2K distribution. It can be copied from the local insta..."

2022-10-20T19:59:23Z

Created page with "At the CUNY HPC Center CP2K is installed on ANDY. CP2K can be built as a serial, MPI-parallel, or MPI-OpenMP-parallel code. At this time, only the MPI-parallel version of the application has been built for production use at the HPC Center. Further information on CP2K is available at the website here [http://www.cp2k.org/]. Below is an example PBS script that will run the CP2K H2O-32 test case provided with the CP2K distribution. It can be copied from the local insta..."

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At the CUNY HPC Center CP2K is installed on ANDY. CP2K can be built as a serial, MPI-parallel, or
MPI-OpenMP-parallel code. At this time, only the MPI-parallel version of the application has been built for
production use at the HPC Center. Further information on CP2K is available at the website here [http://www.cp2k.org/].

Below is an example PBS script that will run the CP2K H2O-32 test case provided with the CP2K distribution.
It can be copied from the local installation directory to your current location as follows:

<pre>
cp /share/apps/cp2k/2.3/tests/SE/regtest-2/H2O-32.inp .
</pre>

To include all required environmental variables and the path to the CP2K executable run the modules load
command (the modules utility is discussed in detail above).

<pre>
module load cp2k
</pre>

Here is the example SLURM script:

<pre>
#!/bin/bash
#SBATCH -- partition production
#SBATCH -- job-name CP2K_MPI.test
#SBATCH -- nodes=8
#SBATCH -- ntasks
#SBATCH -- mem=2880

# Find out name of master execution host (compute node)
echo ""
echo -n ">>>> SLURM Master compute node is: "
hostname

# Change to working directory
cd $SLURM_SUBMIT_DIR

echo ">>>> Begin CP2K MPI Parallel Run ..."
mpirun -np 8 cp2k.popt ./H2O-32.inp > H2O-32.out 2>&1
echo ">>>> End CP2K MPI Parallel Run ..."
</pre>

This script can be dropped in to a file (say cp2k.job) and started with the command:

<pre>
qsub cp2k.job
</pre>

Running the H2O-32 test case should take less than 5 minutes and will produce PBS output and error files beginning
with the job name 'CP2K_MPI.test'. The CP2K application results will be written into the user-specified file at the end
of the CP2K command line after the greater-than sign. Here it is named 'H2O-32.out'. The expression '2>&1' combines
Unix standard output from the program with Unix standard error. Users should always explicitly specify the name of the
application's output file in this way to ensure that it is written directly into the user's working directory which has much
more disk space than the PBS spool directory on /var.

Details on the meaning of the PBS script are covered above in the PBS section. The most important lines are the '#PBS -l select=8:ncpus=1:mem=2880mb'
and the '#PBS -l pack=free' lines. The first instructs PBS to select 8 resource 'chunks' with 1 processor (core) and 2,880 MBs
of memory in each for the job. The second instructs PBS to place this job wherever the least used resources are found (freely).
The master compute node that PBS finally selects to run your job will be printed in the PBS output file by the 'hostname'
command.

← Older revision		Revision as of 20:12, 27 October 2022
Line 3:		Line 3:
	production use at the HPC Center. Further information on CP2K is available at the website here [http://www.cp2k.org/].		production use at the HPC Center. Further information on CP2K is available at the website here [http://www.cp2k.org/].

	Below is an example ~~PBS~~ script that will run the CP2K H2O-32 test case provided with the CP2K distribution.		Below is an example SLURM script that will run the CP2K H2O-32 test case provided with the CP2K distribution.
	It can be copied from the local installation directory to your current location as follows:		It can be copied from the local installation directory to your current location as follows:

Line 47:		Line 47:
	</pre>		</pre>

	Running the H2O-32 test case should take less than 5 minutes and will produce ~~PBS~~ output and error files beginning		Running the H2O-32 test case should take less than 5 minutes and will produce SLURM output and error files beginning
	with the job name 'CP2K_MPI.test'. The CP2K application results will be written into the user-specified file at the end		with the job name 'CP2K_MPI.test'. The CP2K application results will be written into the user-specified file at the end
	of the CP2K command line after the greater-than sign. Here it is named 'H2O-32.out'. The expression '2>&1' combines		of the CP2K command line after the greater-than sign. Here it is named 'H2O-32.out'. The expression '2>&1' combines
	Unix standard output from the program with Unix standard error. Users should always explicitly specify the name of the		Unix standard output from the program with Unix standard error. Users should always explicitly specify the name of the
	application's output file in this way to ensure that it is written directly into the user's working directory which has much		application's output file in this way to ensure that it is written directly into the user's working directory which has much
	more disk space than the ~~PBS~~ spool directory on /var.		more disk space than the SLURM spool directory on /var.

	Details on the meaning of the ~~PBS~~ script are covered above in the ~~PBS~~ section. The most important lines are the '#~~PBS~~ -l select=8:ncpus=1:mem=2880mb'		Details on the meaning of the SLURM script are covered above in the SLURM section. The most important lines are the '#SLURM -l select=8:ncpus=1:mem=2880mb'
	and the '#~~PBS~~ -l pack=free' lines. The first instructs ~~PBS~~ to select 8 resource 'chunks' with 1 processor (core) and 2,880 MBs		and the '#SLURM -l pack=free' lines. The first instructs SLURM to select 8 resource 'chunks' with 1 processor (core) and 2,880 MBs
	of memory in each for the job. The second instructs ~~PBS~~ to place this job wherever the least used resources are found (freely).		of memory in each for the job. The second instructs SLURM to place this job wherever the least used resources are found (freely).
	The master compute node that ~~PBS~~ finally selects to run your job will be printed in the ~~PBS~~ output file by the 'hostname'		The master compute node that SLURM finally selects to run your job will be printed in the SLURM output file by the 'hostname'
	command.		command.

CP2K - Revision history

James at 20:12, 27 October 2022