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--- software:namd:caviness [2019-08-29 17:39] – [Batch job] anita
+++ software:namd:caviness [2022-02-04 10:34] – [Batch job] anita
@@ Line 1: / Line 1: @@
-====== 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/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
-.12      Version 2.12
-* 2.13      Version 2.13
-.13:gpu  Version 2.13 (with CUDA support)
-</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 by using ''vpkg_require named:gpu''
-In your job script, you should use the following when you call ''namd''
-<code bash>
-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.
-<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>