installing NAMD on opteron cluster with MPI

From: Lina M Nilsson (
Date: Thu Mar 03 2005 - 16:06:13 CST

We are trying to install NAMD on a Beowulf opteron 64-bit cluster with MPI but have not gotten NAMD install correctly / generate any of the normal output files. Instead, we get the “broken pipe” error message below. Does anyone have any idea what we could try? (Our install procedure, which worked fine on another cluster that uses opteron 64 processors, is listed below).
Lina Nilsson

Output message:

# LSBATCH: User input

Successfully completed.

Resource usage summary:

CPU time : 3.41 sec.
Max Memory : 2 MB
Max Swap : 11 MB

Max Processes : 1
Max Threads : 1

The output (if any) follows:

nodes: 4 proc: 8
cp: omitting directory `/hreidar/home/werk/pechmann/talin/job'
cp: omitting directory `/hreidar/home/werk/pechmann/talin/NAMD'
starting from n417
companion nodes: n356 n351 n349
/usr/local/apli/mpich/bin/mpirun: line 1: 14291 Broken pipe /hreidar/home/werk/pechmann/NAMD/NAMD_2.5_Source/Linux-amd64-g++//namd2 "min.template.inp" -p4pg /scratch/werk/pechmann/PI14081 -p4wd /scratch/werk/pechmann


I) Build fftw:

./configure --enable-type-prefix --enable-float


make install

II) Build charm++

Go to NAMD_2.5_Source and untar there the newest version of charm++ (e.g.
charm-5.8, delete the charm.tar delivered with the NAMD-tarball!)

tar xvfz charm-5.8.tar.gz

ln -s charm-5.8 charm

cd charm

setenv PATH /usr/local/apli/mpich/bin:{$PATH}

./build charm++ mpi-linux --incdir=/usr/local/apli/mpich/include
--libdir=/usr/local/apli/mpich/lib --no-shared -O -DCMK_OPTIMIZE=1

cd ../../../../

vi Make.charm:
CHARMBASE = /asgard/home/phys/gianluca/NAMD/NAMD_2.5_Source/charm

vi arch/Linux-amd64.fftw:

vi arch/Linux-amd64-g++.arch:
CHARMARCH = mpi-linux
CXXOPTS = -O3 -march=k8 -m64 -fexpensive-optimizations -ffast-math
COPTS = -O3 -march=k8 -m64 -fexpensive-optimizations -ffast-math

./config fftw Linux-amd64-g++

cd Linux-amd64-g++

didnt work, then:

in NAMD_2.5_Source/arch/Linux-amd64-g++.arch

CXXOPTS = -O3 -march=k8 -m64 -fexpensive-optimizations -ffast-math

CXXOPTS = -O0 -march=k8 -m64 -fexpensive-optimizations -ffast-math

COPTS = -O3 -march=k8 -m64 -fexpensive-optimizations -ffast-math

COPTS = -O0 -march=k8 -m64 -fexpensive-optimizations -ffast-math

  "-march=athlon" instead of "-march=k8".
dropp "-fexpensive-optimizations -ffast-math"


COPTS = -O0 -march=k8 -m64

Lina Nilsson

Research Assistant
Department of Bioengineering
University of Washington, Seattle
p:(206) 685-4432
f:(206) 685-4434

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