Arkansas High Performace Computing Center [hpcwiki]

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namd [2020/11/20 20:25]
root 		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]
Line 46: Line 47:
 16 Intel Razor    16      2.12          1   242 16 Intel Razor    16      2.12          1   242
 32 AMD Trestles   32      2.12          1   315 32 AMD Trestles   32      2.12          1   315
-32 Intel Pinnacle 32      2.12          1   127 +32 Intel G6130    32      2.12          1   127 
-32 Intel Pinnacle 32      2.13          1   127 +32 Intel G6130    32      2.13          1   127 
-32 Intel Pinnacle 32      2.15a1-AVX512 1    76 +48 AMD Epyc 7402  48      2.13          1    89 
-32 Intel Pinnacle 32 V100 3.0a7-cuda    1    39 +32 Intel G6130    32      2.15a1-AVX512 1    76 
-48 AMD Epyc 2     48      2.15a1-AVX2 needs recompilation+32 Intel G6130    32 V100 3.0a7-cuda    1    39 
 +48 AMD Epyc 7402  48      2.15a1-AVX2 needs recompilation
 </code> </code>
  
  
  
namd.1605903949.txt.gz · Last modified: 2020/11/20 20:25 by root

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