namd2.6b1 has bad scaling

From: Morad Alawneh (
Date: Wed Jan 25 2006 - 11:17:53 CST

Dear everyone,

I have recently compiled namd2.6b1 to have it work in parallel. I have a system of about 92,000 atoms, and when I submit my job for using more than 2 processors I'll get bas scaling and the performance is lower than using 2 processors. Would you help to figure out what is the problem.

Cluster system:
It is a Dell 1855 Linux cluster consisting of 630 nodes. Each node is equipped with two Intel Xeon EM64T processors (3.6GHz) and 4 GB of memory.  Each node runs its own Linux kernel (Red Hat Enterprise Linux 3). The Intel version of MPICH provides message-passing interface (MPI) across all the nodes.

Installation instructions:
charm++ installation:

Edit namd/Make.charm
(set CHARMBASE to the full path to charm-5.9)

Edit the file charm/src/arch/mpi-linux-amd64/ to have the right
path to mpicc and mpiCC (replace mpiCC by mpicxx), use mpich/gnu.

./build charm++ mpi-linux-amd64 gcc --libdir=/opt/mpich/gnu/lib
--incdir=/opt/mpich/gnu/include --no-build-shared -g -O -verbose -tracemode summary
-memory default -DCMK_OPTIMIZE=1

namd Installation:

Edit various configuration files:
namd/arch/Linux-amd64-MPI.arch (fix CHARMARCH to be mpi-linux-amd64-gcc)
namd/arch/Linux-amd64.fftw  (fix path to files, and delete all
                             -I$(HOME)/fftw/include -L$(HOME)/fftw/lib)
namd/arch/Linux-amd64.tcl   (fix path to files, and delete all
                             -I$(HOME)/tcl/include -L$(HOME)/tcl/lib)

Set up build directory and compile:
  ./config tcl fftw Linux-amd64-MPI
  cd Linux-amd64-MPI

Job submission script:

#PBS -l nodes=1:ppn=2,walltime=336:00:00
#PBS -N Huge_gA
#PBS -m abe

# The maximum memory allocation = 2.86 GB
let Memory=128*1024*1024
export P4_GLOBMEMSIZE=$Memory

#cd into the directory where I typed qsub

ARGS="+strategy USE_GRID"

# NP should always be: nodes*ppn from #PBS -l above
let NP=1*2

# Full path to charmrun

# Preparing nodelist file for charmrun
export NODES=`cat $PBS_NODEFILE`
export NODELIST=nodelist
echo group main > $NODELIST
for node in $NODES ; do
  echo host $node ++shell ssh >> $NODELIST

# Execute the job using charmrun

exit 0



Morad Alawneh

Department of Chemistry and Biochemistry


Provo, UT 84602

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