software:namd:caviness

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software:namd:caviness [2024-03-19 09:43] – [Batch job] anitasoftware:namd:caviness [2024-05-12 15:25] (current) – [Scaling] bkang
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 [/opt/shared/valet/2.1/etc/namd.vpkg_yaml] [/opt/shared/valet/2.1/etc/namd.vpkg_yaml]
-namd        Scalable Molecular Dynamics +namd                 Scalable Molecular Dynamics 
-  2.12      Version 2.12 +  2.12               Version 2.12 
-* 2.13      Version 2.13 +* 2.13               Version 2.13 
-  2.13:gpu  Version 2.13 (with CUDA support)+  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> </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+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> <code bash>
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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.1710855825.txt.gz
  • Last modified: 2024-03-19 09:43
  • by anita