From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Feb 14 2014 - 05:12:56 CST
What is the content of "nodelist" after script ran?
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Subbarao Kanchi
Gesendet: Freitag, 14. Februar 2014 11:20
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: Job script for multi node job
Dear All,
I am using compiled version of NAMD_2.9_Linux-x86_64-ibverbs.
The following job script is working for a single node but if I submit with
two/more nodes,job is running but using only one node and not using other
nodes. I am giving the script below and I do not able to figure the mistake
in the script. I will appreciate any suggestions.
Regards,
Subbu.
#!/bin/csh -f
#PBS -l nodes=2:ppn=32
#PBS -o /present_working_dir/out.out
#PBS -e /present_working_dir/err.out
#PBS -N test
cd $PBS_O_WORKDIR
cat $PBS_NODEFILE > temp.1
set nprocs = `wc -l < $PBS_NODEFILE`
echo $nprocs
setenv DO_PARALLEL "/home/NAMD_2.9_Linux-x86_64-ibverbs/charmrun
++remote-shell ssh ++nodelist nodelist +p$nprocs "
setenv exc "/home/NAMD_2.9_Linux-x86_64-ibverbs/namd2 "
set j="e"
set tot=0
echo group main >> nodelist
foreach i ( `cat temp.1` )
echo host $i >> nodelist
if ( $j != $i ) then
ssh -n $i mkdir -p /temp1_dir
ssh -n $i cp -r /present_working_dir/* /temp1_dir
echo "$i " >> t2
ssh -n $i limit >> t2
ssh -n $i limit memorylocked unlimited
endif
set j="$i"
end
cd /temp1_dir
$DO_PARALLEL $exc namd.conf > namd.log
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