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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
@@ Line 1: / Line 1: @@
 ====== NAMD on Caviness ======
-[[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 =====
-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
+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)
+.14               compiled with Intel 2020, Open MPI 4.1.4
+.0b3              compiled with Intel 2020, Open MPI 4.1.4
+.0b3:cuda-11.3.1  compiled with Intel 2020, CUDA 11
+.0b3:cuda-12.1.1  compiled with Intel 2020, CUDA 12
 </code>
-===== 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
-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 ${CUDA_VISIBLE_DEVICES} ...
+</code>
-<note tip>It is a good idea to periodically check if the template ''/opt/templates/gridengine/namd'' has changed as we learn more about what works well on a particular cluster.</note>
+Documentation for ''namd'' indicates ''+idlepoll'' must always be used for runs using CUDA devices. Slurm sets ''CUDA_VISIBLE_DEVICES'' to the device indices your job was granted, and ''SLURM_CPUS_ON_NODE'' to the number of CPUs granted to you. Also ''${UD_MPIRUN}'' is setup as part of the job script template provided in ''/opt/shared/templates/slurm/generic/mpi/openmpi/openmpi.qs'' file.
+<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|}}