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| software:namd:caviness [2018-11-15 20:04] – [Batch job] anita | software:namd:caviness [2024-03-19 09:45] – [Batch job] anita |
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| ===== Batch job ===== | ===== Batch job ===== |
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| Open MPI Slurm job submission script should be used for NAMD jobs on ''Caviness'' and can be found in ''/opt/templates/slurm/generic/mpi/openmpi''. Copy and edit the template based on your job requirements by following the comments described in the ''openmpi.qs'' file. | Open MPI Slurm job submission script should be used for NAMD jobs on Caviness and can be found in ''/opt/shared/templates/slurm/generic/mpi/openmpi''. Copy and edit the template based on your job requirements by following the comments described in the ''openmpi.qs'' file. |
| | <code bash> |
| | $ vpkg_versions namd |
| |
| <note tip>It is always a good idea to periodically check if the templates in ''/opt/templates/slurm'' have changed especially as we learn more about what works well on a particular cluster.</note> | Available versions in package (* = default version): |
| | |
| | [/opt/shared/valet/2.1/etc/namd.vpkg_yaml] |
| | namd Scalable Molecular Dynamics |
| | 2.12 Version 2.12 |
| | * 2.13 Version 2.13 |
| | 2.13:gpu Version 2.13 (with CUDA support) |
| | 2.14 compiled with Intel 2020, Open MPI 4.1.4 |
| | 3.0b3 compiled with Intel 2020, Open MPI 4.1.4 |
| | 3.0b3:cuda-11.3.1 compiled with Intel 2020, CUDA 11 |
| | 3.0b3:cuda-12.1.1 compiled with Intel 2020, CUDA 12 |
| | </code> |
| | |
| | The ''*'' version is loaded by default when using ''vpkg_require namd''. Make sure you select a GPU variant of the ''namd'' package if you plan to use GPUs, i.e. ''vpkg_require named/2.13:gpu'' and provide the correct options to ''namd'' in the job script |
| | |
| | <code bash> |
| | ${UD_MPIRUN} namd2 +idlepoll +p${SLURM_CPUS_ON_NODE} +devices ${CUDA_VISIBLE_DEVICES} ... |
| | </code> |
| | |
| | Documentation for ''namd'' indicates ''+idlepoll'' must always be used for runs using CUDA devices. Slurm sets ''CUDA_VISIBLE_DEVICES'' to the device indices your job was granted, and ''SLURM_CPUS_ON_NODE'' to the number of CPUs granted to you. Also ''${UD_MPIRUN}'' is setup as part of the job script template provided in ''/opt/shared/templates/slurm/generic/mpi/openmpi/openmpi.qs'' file. |
| | |
| | |
| | <note tip>It is always a good idea to periodically check if the templates in ''/opt/shared/templates/slurm'' have changed especially as we learn more about what works well on a particular cluster.</note> |