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=.
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
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
Replicated a couple of old benchmarks and added some new versions and machines
Cores Node Type ppn GPU version nodes WallClock 16 Intel Razor 16 2.12 1 242 32 AMD Trestles 32 2.12 1 315 32 Intel G6130 32 2.12 1 127 32 Intel G6130 32 2.13 1 127 48 AMD Epyc 7402 48 2.13 1 89 32 Intel G6130 32 2.15a1-AVX512 1 76 32 Intel G6130 32 V100 3.0a7-cuda 1 39 48 AMD Epyc 7402 48 2.15a1-AVX2 needs recompilation