Re: performance on ~1.5 million atoms system

From: Vermaas, Joshua (
Date: Mon Apr 17 2017 - 10:33:04 CDT

Hi Steven,

Does you cluster also have a non-smp build? In my limited experience with SMP, it tends to be slower and scale less well than regular MPI builds do.


On 04/17/2017 12:10 AM, Steven Neumann wrote:
Dear Users,

I am running ~1,5 million atom system on 768 cpus (32 nodes of 24 cpus) and my performance is ~1.3 day/ns. The same system run on 48 cpus (2 nodes of 24 cpus) provides me with better performance of ~0.8 days/ns. Would you please advise the reason? Is it scaling?

My script on 32 nodes:

#PBS -l select=32:ncpus=24:mem=24gb
#PBS -l walltime=24:00:00
#PBS -j oe
#PBS -o log.dat
#PBS -q queue

module purge
module add namd/2.11/ibverbs-smp


echo "USING charmrun: `which charmrun`"
CHARMRUN_BIN=`which charmrun`
echo "USING namd2: `which namd2`"
NAMD2_BIN=`which namd2`

rm -f nodefile
for i in `cat $PBS_NODEFILE`; do
        echo "USING NODE $i"
        echo "host $i" >> nodefile

N_NODES=`wc -l nodefile | cut -f 1 -d\ `
N_CORES=`echo 32*23 | bc`


$CHARMRUN_BIN $NAMD2_BIN ++verbose ++nodelist nodefile +p$N_CORES ++ppn 23 +idlepoll +setcpuaffinity RUN1 > RUN.log

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