=== Namd ====

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=''.

<code>
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
</code>

This is for single-node run using only the shared-memory program ''namd2''.
<code>
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
</code>

== 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.

<code>
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
</code>

== 2020 Update ==

Replicated a couple of old benchmarks and added some new versions and machines
<code>
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
</code>