software:namd:caviness

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software:namd:caviness [2024-03-19 09:47] – [Batch job] anitasoftware:namd:caviness [2024-05-12 15:25] (current) – [Scaling] bkang
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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> <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|}}
  • software/namd/caviness.1710856021.txt.gz
  • Last modified: 2024-03-19 09:47
  • by anita