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namd [2017/07/06 15:41]
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namd [2017/08/07 20:57]
root
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 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 [[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.
  
-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.+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]
namd.txt · Last modified: 2017/08/07 20:57 by root