Arkansas High Performace Computing Center [hpcwiki]

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namd [2020/09/21 21:58]
root created 		namd [2022/03/14 19:10] (current)
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 === Namd ==== === Namd ====
  
-The namd-verbs-smp binary [[http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD]] version 2.11 or 2.12 is installed in /share/apps/NAMD on [[razor]] and [[trestles]].  It does not use MPI.+The namd-verbs-smp binary [[https://web.archive.org/web/20181127065652/http://www.ks.uiuc.edu/Research/namd/benchmarks/]] version 2.11 or 2.12 is installed in /share/apps/NAMD on [[razor]] and [[trestles]].  It does not use MPI.
  
 This is for multiple-node runs with ''charmrun'' as the distributed component and ''namd2'' on each compute node. We have found most runs are faster with the ''+setcpuaffinity +isomalloc_sync'' options. charmrun ''++ppn'' should match PBS ''ppn=''. This is for multiple-node runs with ''charmrun'' as the distributed component and ''namd2'' on each compute node. We have found most runs are faster with the ''+setcpuaffinity +isomalloc_sync'' options. charmrun ''++ppn'' should match PBS ''ppn=''.
 +
 <code> <code>
 module load namd/2.12  [or 2.11] module load namd/2.12  [or 2.11]
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 32-core AMD    32   2.12    32    4   2.56    104        n/a 32-core AMD    32   2.12    32    4   2.56    104        n/a
 </code> </code>
 +
 +== 2020 Update ==
 +
 +Replicated a couple of old benchmarks and added some new versions and machines
 +<code>
 +Cores Node Type  ppn GPU version     nodes WallClock
 +16 Intel Razor    16      2.12          1   242
 +32 AMD Trestles   32      2.12          1   315
 +32 Intel G6130    32      2.12          1   127
 +32 Intel G6130    32      2.13          1   127
 +48 AMD Epyc 7402  48      2.13          1    89
 +32 Intel G6130    32      2.15a1-AVX512 1    76
 +32 Intel G6130    32 V100 3.0a7-cuda    1    39
 +48 AMD Epyc 7402  48      2.15a1-AVX2 needs recompilation
 +</code>
 +
 +
  
namd.1600725531.txt.gz ยท Last modified: 2020/09/21 21:58 by root

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