AW: Job script for multi node job

From: Norman Geist (
Date: Fri Feb 14 2014 - 05:12:56 CST

What is the content of "nodelist" after script ran?


Von: [] Im Auftrag
von Subbarao Kanchi
Gesendet: Freitag, 14. Februar 2014 11:20
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.









#!/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



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



                set j="$i"


cd /temp1_dir


$DO_PARALLEL $exc namd.conf > namd.log


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