From: Lina M Nilsson (linan_at_u.washington.edu)
Date: Thu Mar 03 2005 - 16:06:13 CST
Hi.
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).
Thanks,
Lina Nilsson
Output message:
# LSBATCH: User input
./script2_gi
------------------------------------------------------------
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
COMPLILING PROTOCOL
I) Build fftw:
--------------
./configure --enable-type-prefix --enable-float
--prefix=/asgard/home/phys/gianluca/NAMD/fftw-2.1.5/gcc
make
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:
FFTDIR=/asgard/home/phys/gianluca/NAMD/fftw/gcc
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++
make
-----------------------------------
didnt work, then:
in NAMD_2.5_Source/arch/Linux-amd64-g++.arch
instead:
CXXOPTS = -O3 -march=k8 -m64 -fexpensive-optimizations -ffast-math
CXXOPTS = -O0 -march=k8 -m64 -fexpensive-optimizations -ffast-math
instead:
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"
------------------------------------
tried:
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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