User Tools

Site Tools


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.

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=.

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

The NAMD website has benchmarks run on Trestles while at UCSD http://www.ks.uiuc.edu/Research/namd/performance.html, 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. On this problem, the Intel version didn't show any useful scaling for more than 2 nodes, and AMD not very useful scaling for more than 3 nodes.

Node Type      ppn  version  p  Nodes Bench WallClock  UCSD Bench
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   0.90    146        n/a
16-core Intel  16   2.12    16    3   1.32    146        n/a
32-core AMD    32   2.12    32    1   1.95    317        1.9
32-core AMD    32   2.12    32    2   2.22    185        2.0
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
namd.txt · Last modified: 2017/08/07 20:57 by root