software:namd:caviness

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software:namd:caviness [2018-11-15 20:04] – [Batch job] anitasoftware:namd:caviness [2024-03-19 09:43] – [Batch job] anita
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 ===== Batch job ===== ===== 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.+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) 
 +</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/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>
  • software/namd/caviness.txt
  • Last modified: 2024-05-12 15:25
  • by bkang