hpc documentation

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
====== NAMD on Caviness ======

===== Batch job =====

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

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 namd: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>

===== Scaling =====

Using ApoA1 as an example, the scaling results are presented. The performance improved with increasing CPU and GPU numbers.

<code bash>
vpkg_require namd/3.0b3
charmrun namd3  +p$SLURM_NTASKS  apoa1.namd > apoa1.log
</code>
{{:software:namd:scaling_namd_cpu.jpg?400|}}

<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|}}