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software:namd:caviness [2018-11-15 19:43] – created anita | software:namd:caviness [2024-05-12 15:25] (current) – [Scaling] bkang |
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====== NAMD on Caviness ====== | ====== NAMD on Caviness ====== |
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[[http://www.ks.uiuc.edu/Research/namd/|NAMD]] (NAnoscale Molecular Dynamics) is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | ===== Batch job ===== |
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To determine the available versions of NAMD installed use | 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> |
<code> | |
$ vpkg_versions namd | $ vpkg_versions namd |
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| Available versions in package (* = default version): |
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| [/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> | </code> |
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===== Batch job ===== | 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 namd:gpu'' and provide the correct options to ''namd'' in the job script |
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Templates for Grid Engine queue submission scripts are available for serial or parallel batch NAMD jobs on ''Mills'' & ''Farber'' in ''/opt/templates/gridengine/namd''. Copy and edit the template based on your job by following the usage described in the ''named-serial.qs'' or ''named-parallel.qs'', respectively. | <code bash> |
| ${UD_MPIRUN} namd2 +idlepoll +p${SLURM_CPUS_ON_NODE} +devices ${CUDA_VISIBLE_DEVICES} ... |
| </code> |
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<note tip>It is a good idea to periodically check if the template ''/opt/templates/gridengine/namd'' has changed as we learn more about what works well on a particular cluster.</note> | Documentation for ''namd'' indicates ''+idlepoll'' must always be used for runs using CUDA devices. Slurm sets ''CUDA_VISIBLE_DEVICES'' to the device indices your job was granted, and ''SLURM_CPUS_ON_NODE'' to the number of CPUs granted to you. Also ''${UD_MPIRUN}'' is setup as part of the job script template provided in ''/opt/shared/templates/slurm/generic/mpi/openmpi/openmpi.qs'' file. |
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| <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> |
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| ===== Scaling ===== |
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| Using ApoA1 as an example, the scaling results are presented. The performance improved with increasing CPU and GPU numbers. |
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| <code bash> |
| vpkg_require namd/3.0b3 |
| charmrun namd3 +p$SLURM_NTASKS apoa1.namd > apoa1.log |
| </code> |
| {{:software:namd:scaling_namd_cpu.jpg?400|}} |
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| <code bash> |
| vpkg_require namd/3.0b3:cuda-12.1.1 |
| charmrun namd3 +idlepoll +p$SLURM_CPUS_PER_TASK +devices $CUDA_VISIBLE_DEVICES apoa1.namd > apoa1.log |
| </code> |
| {{:software:namd:scaling_namd_gpu.jpg?400|}} |
| {{:software:namd:scaling_namd_cpu_gpu.jpg?400|}} |