Arkansas High Performace Computing Center [hpcwiki]

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markdowntest [2022/02/08 23:10] – created rootmarkdowntest [2025/10/15 19:51] (current) – external edit 127.0.0.1
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 faster with the `+setcpuaffinity +isomalloc_sync` options. charmrun faster with the `+setcpuaffinity +isomalloc_sync` options. charmrun
 `++ppn` should match PBS `ppn=`. `++ppn` should match PBS `ppn=`.
 +
 +***
  
     module load namd/2.12  [or 2.11]     module load namd/2.12  [or 2.11]
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     charmrun ++remote-shell ssh ++ppn 16 `which namd2` \     charmrun ++remote-shell ssh ++ppn 16 `which namd2` \
     +p $NP +setcpuaffinity +isomalloc_sync apoa1.namd >apoa1.logfile     +p $NP +setcpuaffinity +isomalloc_sync apoa1.namd >apoa1.logfile
 +
 +***
  
 This is for single-node run using only the shared-memory program This is for single-node run using only the shared-memory program
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     NP=$(wc -l <$PBS_O_WORKDIR)     NP=$(wc -l <$PBS_O_WORKDIR)
     namd2 +p $NP apoa1.namd +setcpuaffinity +isomalloc_sync >apoa1.logfile     namd2 +p $NP apoa1.namd +setcpuaffinity +isomalloc_sync >apoa1.logfile
 +
 +***
  
 ##### Benchmarks ##### Benchmarks
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 version didn't show any useful scaling for more than 2 nodes, and AMD version didn't show any useful scaling for more than 2 nodes, and AMD
 not very useful scaling for more than 3 nodes. not very useful scaling for more than 3 nodes.
 +
 +***
  
     Node Type      ppn  version  p  Nodes Bench WallClock  UCSD Bench     Node Type      ppn  version  p  Nodes Bench WallClock  UCSD Bench
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     32-core AMD    32   2.12    32    3   2.29    127        n/a     32-core AMD    32   2.12    32    3   2.29    127        n/a
     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
 +
 +***
  
 ##### 2020 Update ##### 2020 Update
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