| Line 9: | Line 9: | ||
Cpmd is provided so jobs can be run in the mpi queue on sharcnet clusters. | Cpmd is provided so jobs can be run in the mpi queue on sharcnet clusters. | ||
| − | =Version Selection= | + | =Usage on Graham= |
| + | ==Version Selection== | ||
<pre>module load cpmd/3.17.1</pre> | <pre>module load cpmd/3.17.1</pre> | ||
| − | =Job Submission= | + | ==Job Submission== |
| + | Graham uses Slurm scheduler, which is different from the sq command used on other Sharcnet clusters. For details about submitting jobs, see [https://docs.computecanada.ca/wiki/Running_jobs Running Jobs]. | ||
| + | |||
| + | Example script for a parallel job | ||
| + | |||
| + | #!/bin/bash | ||
| + | #SBATCH --nodes=1 --ntasks-per-node=32 # 1 node with 32 cpus, MPI job | ||
| + | #SBATCH --mem-per-cpu=2G # memory, should be less than 4G | ||
| + | #SBATCH --time=00-01:00 # time (DD-HH:MM) | ||
| + | #SBATCH --output=%J.log # output .log file | ||
| + | module load cpmd/3.17.1 | ||
| + | srun cpmd-mpi.x inputfile.inp # srun command | ||
| + | |||
| + | You can modify the script to fit your job's requirements for compute resources. | ||
| + | |||
| + | =Usage on Legacy systems= | ||
| + | ==Version Selection== | ||
| + | |||
| + | <pre>module load cpmd/3.17.1</pre> | ||
| + | |||
| + | ==Job Submission== | ||
<pre>sqsub -r 1h -q mpi -n 16 -o ofile%J cpmd-mpi.x methan-fd-nosymm.inp</pre> | <pre>sqsub -r 1h -q mpi -n 16 -o ofile%J cpmd-mpi.x methan-fd-nosymm.inp</pre> | ||
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where <b>2 < -n ncpus < ncpusmax</b> should be established by running scaling tests for ncpu= 2, 4, 8, 16 ... | where <b>2 < -n ncpus < ncpusmax</b> should be established by running scaling tests for ncpu= 2, 4, 8, 16 ... | ||
| − | =Example Job= | + | ==Example Job== |
To run the <b>std/wat32</b> example from <i>cpmd-test.tar.gz</i> do the following: | To run the <b>std/wat32</b> example from <i>cpmd-test.tar.gz</i> do the following: | ||
Revision as of 23:52, 26 September 2017
| CPMD |
|---|
| Description: Parallelized Plane Wave Implementation of DFT |
| SHARCNET Package information: see CPMD software page in web portal |
| Full list of SHARCNET supported software |
Contents
Introduction
Cpmd is provided so jobs can be run in the mpi queue on sharcnet clusters.
Usage on Graham
Version Selection
module load cpmd/3.17.1
Job Submission
Graham uses Slurm scheduler, which is different from the sq command used on other Sharcnet clusters. For details about submitting jobs, see Running Jobs.
Example script for a parallel job
#!/bin/bash #SBATCH --nodes=1 --ntasks-per-node=32 # 1 node with 32 cpus, MPI job #SBATCH --mem-per-cpu=2G # memory, should be less than 4G #SBATCH --time=00-01:00 # time (DD-HH:MM) #SBATCH --output=%J.log # output .log file module load cpmd/3.17.1 srun cpmd-mpi.x inputfile.inp # srun command
You can modify the script to fit your job's requirements for compute resources.
Usage on Legacy systems
Version Selection
module load cpmd/3.17.1
Job Submission
sqsub -r 1h -q mpi -n 16 -o ofile%J cpmd-mpi.x methan-fd-nosymm.inp
where 2 < -n ncpus < ncpusmax should be established by running scaling tests for ncpu= 2, 4, 8, 16 ...
Example Job
To run the std/wat32 example from cpmd-test.tar.gz do the following:
cp -a /opt/sharcnet/cpmd/3.17.1/test/CPMD-test/std /scratch/$USER/std/wat32 cd /scratch/$USER/std/wat32 module load cpmd/3.17.1 sqsub -r 1h -q mpi -n 16 --mpp=500M -o ofile%J cpmd-mpi.x inp-1
Warning: The femd example contains a bug that results in jobs crashing if run under cpmd/3.17.1 described in http://cpmd.org/track-issues/issues-tracker/10.
General Notes
Contributed Files
For convenience contributed files are provided in the contrib directory:
[roberpj@orc-login1:/opt/sharcnet/cpmd/3.17.1/contrib] ls cpmd2cube.tar.gz dev-test-suite.tar.gz non-std-inst.tar.gz pseudo_vdb.tar.gz cpmd2xyz-scripts.tar.gz fourier.tar.gz pseudo_ext.tar.gz README cpmd-test.tar.gz Goedecker.tar.gz pseudo_std.tar.gz Vreco_CPMD.tar.gz
Patches
The patches applied to the respective module can be found in the patches directory:
[roberpj@orc-login1:/opt/sharcnet/cpmd/3.17.1/patches] ls patch_2769_3085 patch_3085_3090 patch_3090_3093 patch_3093_3101 patch_3101_3116 README
References
o CPMD Homepage
http://www.cpmd.org/
o CPMD Documentation (Manual,FAQ,Tutorial)
http://cpmd.org/documentation
o CPDM Downloadable Files
http://cpmd.org/downloadable-files/no-authentication/
o CPMD Mailing List
http://cpmd.org/documentation/mailing-list