From: Kevin Jander (waverunnergp_at_gmail.com)
Date: Fri Jul 13 2007 - 14:14:05 CDT
I'm having some trouble getting NAMD and SGE to work together. NAMD
will run fine on the command line, but I get the following error when
trying to run it using SGE:
"ERROR> Cannot obtain IP address of compute-0-28.local"
The compute number varies (and sometimes repeats) each run. I thought
the problem might possibly be that it has .local on the end, but I
added that to my nodelist file and then ran it from the command line
and it ran fine. Here is the job script I am using (copied from the
NAMD Wiki):
#$ -cwd
#$ -j y
#$ -S /bin/bash
nodefile=$TMPDIR/namd2.nodelist
echo group main ++shell ssh > $nodefile
awk '{ for (i=0;i<$2;++i) {print "host",$1} }' $PE_HOSTFILE >> $nodefile
dir=/$HOME/Linux-i686-g++
$dir/charmrun ++nodelist $nodefile +p$NSLOTS $dir/namd2
~/gluc_MD/Production.conf.orig
The command im using to submit the job is the same as the one in the wiki:
qsub -pe mpich 32 ./namd.job
I have also tried mpi and lam, and those both have the same error.
I am using a compiled verson of NAMD 2.6 with the net-linux version of
charm and the Linux-i686-g++ architecture for NAMD, and I'm running
Rocks 4.3. Thanks for the help.
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