From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Feb 14 2014 - 06:03:47 CST
So do you have 64 procs only on node 3?
Norman Geist.
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 12:23
An: Norman Geist
Cc: Namd Mailing List
Betreff: Re: namd-l: Job script for multi node job
Hi Norman Geist,
Thank you for quick reply. hear is the nodelist
file. we have 32 procs in each node and job went to node 3 and node 6 but it
is not using both with the above script.
Regards,
subbu.
group main
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On Fri, Feb 14, 2014 at 4:42 PM, Norman Geist
<norman.geist_at_uni-greifswald.de> wrote:
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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