AW: Job script for multi node job

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

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

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host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-3

host compute-0-6

host compute-0-6

host compute-0-6

host compute-0-6

host compute-0-6

host compute-0-6

host compute-0-6

host compute-0-6

host compute-0-6

host compute-0-6

host compute-0-6

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host compute-0-6

host compute-0-6

host compute-0-6

host compute-0-6

host compute-0-6

host compute-0-6

host compute-0-6

host compute-0-6

host compute-0-6

host compute-0-6

host compute-0-6

host compute-0-6

host compute-0-6

host compute-0-6

host compute-0-6

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host compute-0-6

host compute-0-6

 

 

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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