Charm++ parallel programming system

["Bohm, Eric J" <ebohm AT illinois.edu>]

The poor performance may be arising from thread oversubscription.  Regardless, PPN 38 is a high ratio of worker threads to communication threads for NAMD.

Jim suggested :"May want to change pemap from 1-19,21-39,41-59,61-79 to 1-19+40,21-39+40 depending on how OS is mapping hyperthreads, or use logical to be safe: +pemap L2-39,42-79 +commap L0,40"

3:24

May want to change pemap from 1-19,21-39,41-59,61-79 to 1-19+40,21-39+40 depending on how OS is mapping hyperthreads, or use logical to be safe: +pemap L2-39,42-79 +commap L0,40

On Aug 26, 2020, at 10:22 AM, Dan Kokron <dkokron AT gmail.com> wrote:

I am working with some researchers who are running some COVID19 simulations using NAMD.  I have performed an extensive search of the parameter space trying to find the best performance for their case.  I am asking this question here because the performance of this case depends greatly on communication.

Eric Bohm suggested that UCX+SMP would provide the best scaling yet that configuration (or my use of it) falls significantly behind native UCX.  See attached.

Hardware:

multi-node Xeon (skylake), each node has 2 Gold 6148 (40 hardware cores with HT enabled)

nodes are connected with EDR Infiniband

Software:

NAMD git/master

CHARM++ 6.10.2

HPCX 2.7.0 (OpenMPI + UCX-1.9.0)

Intel 2019.5.281 compiler

CHARM++  for the UCX+SMP build was built with

setenv base_charm_opts "-O3 -ip -g -xCORE-AVX512"

./build charm++ ucx-linux-x86_64 icc ompipmix smp --suffix avx512 --with-production $base_charm_opts --basedir=$HPCX_UCX_DIR --basedir=$HPCX_MPI_DIR -j12

The native UCX build was the same except without the 'smp' option.

The UCX+SMP build of NAMD was built with

FLOATOPTS = -ip -O3 -xCORE-AVX512 -qopt-zmm-usage=high -fp-model fast=2 -no-prec-div -qoverride-limits -DNAMD_DISABLE_SSE -qopenmp-simd -DNAMD_AVXTILES

./config Linux-x86_64-icc --charm-arch ucx-linux-x86_64-ompipmix-smp-icc-avx512 --with-fftw3 --fftw-prefix /fftw-3.3.8/install/namd --charm-opts -verbose

Simulation Case:

1764532 atoms (See attached output listing)

UCX+SMP launch

mpiexec -np $nsockets --map-by ppr:1:socket --bind-to core -x UCX_TLS="rc,xpmem,self"  /Linux-x86_64-icc-ucx-smp-xpmem-avx512/namd2 +ppn 38 +pemap 1-19,21-39,41-59,61-79 +commap 0,20 +setcpuaffinity +showcpuaffinity restart.namd

Would you expect native UCX to outperform UCX_SMP in this scenario?

Can you suggest some ways to improve the performance of my UCX+SMP build?

Dan

<NAMD_UCX+SMP_vs_Native_UCX.png><skxOnskx.UCX.XPMEM.SMP.48s>