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The namd-verbs-smp binary 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.

module load namd/2.12  [or 2.11]
NP=$(wc -l <$PBS_NODEFILE)
rm -f nodelist
for node in `cat $PBS_NODEFILE | sort | uniq`
  echo "host ${node}" >> nodelist
charmrun ++remote-shell ssh ++ppn 16 `which namd2` +p $NP apoa1.namd >apoa1.logfile

This is for single-node run using only the shared-memory program namd2.

module load namd/2.12  [or 2.11]
NP=$(wc -l <$PBS_O_WORKDIR)
namd2 +p $NP apoa1.namd >apoa1.logfile

The NAMD website has benchmarks run on Trestles while at UCSD, but they don't have any info on how the scores were obtained (namd2, charmrun, or mpi). These are shown as benchmark time*cores. Best results for charmrun here were obtained with multiple nodes using ppn=cores/node,p=total cores (or ppn*nodes). Single nodes running namd2 were both p=cores and are comparable with the published benchmarks. Version 2.12 is substantially faster than 2.11. The downloaded verbs-smp version is set by the module as it is faster than the ibverbs-smp version.

Node Type      ppn  version  p  Nodes Bench WallClock  Trestles
16-core Intel  16   2.11    16    1   1.21    383        n/a
16-core Intel  16   2.12    16    1   0.76    256        n/a
16-core Intel  16   2.12    16    2   0.92    151        n/a
32-core AMD    32   2.12    32    1   2.05    340        1.9
32-core AMD    32   2.12    32    2   2.34    189        2.0
namd.1499289069.txt.gz · Last modified: 2017/07/05 21:11 by root