[torqueusers] HELP setup on>>charmrun/mpirun & NAMD via torque

Daniel.G.Roberts at sanofi-aventis.com Daniel.G.Roberts at sanofi-aventis.com
Wed Jul 25 08:17:51 MDT 2007


Hello All
I am trying to perform namd runs using Torque/maui and Ihave several
questions regaring the charmrun/mpirun portion especially.
 
When I submit the script below>
 
qsub script.txt
 
I see this in this running inthe queue
[nm67371 at bwdl01-m001 Test06Proc]$ qstat -n
 
bwdl01-m001.brw.pharma.aventis.com:
                                                                   Req'd
Req'd   Elap
Job ID               Username Queue    Jobname    SessID NDS   TSK
Memory Time  S Time
-------------------- -------- -------- ---------- ------ ----- ---
------ ----- - -----
69.bwdl01-m001.brw.p nm67371  ghts     TEST-Webex   9559     2  --    --
336:0 R 00:05
   bwdl01-n014/1+bwdl01-n014/0+bwdl01-n013/1+bwdl01-n013/0
[nm67371 at bwdl01-m001 Test06Proc]$

But, when I do a ps on both nodes 14 and 13 I only can find my PID on
node 14 and not node 13.
So any ideas on how I can properly parrellize my jobs?
What is the relationship between mpirun and charmrun?
Thanks for any advice!
Dan
PS..
The two different scripts below have the same type of behaviour


EXAMPLE Script #0ne
Script.txt

#!/bin/bash
#PBS -l nodes=2:ppn=2,walltime=336:00:00
#PBS -N TEST-Webexample
cd /global/bwsn001/home/users1/Dan/Muzet/Test06Proc
#
TMPDIR=/scratch/$PBS_JOBID
#
PROG=/global/bwsn002/software/ia32/namd/NAMD_2.6b1_Linux-i686/namd2
ARGS="+strategy USE_GRID"
IFILE="/global/bwsn001/home/users1/Dan/Muzet/Test06Proc/test.conf"
OFILE="/global/bwsn001/home/users1/Dan/Muzet/Test06Proc/test.log"
#
# # NP should always be: nodes*ppn from #PBS -l above
let NP=1*2
#
# # Full path to charmrun
CHARMRUN=/global/bw_2/software/ia32/namd/NAMD_2.6b1_Linux-i686/charmrun
#
# # Preparing nodelist file for charmrun
  export NODES=`cat $PBS_NODEFILE`
  export NODELIST=nodelist
  echo group main > $NODELIST
       for node in $NODES ; do
           echo host $node ++shell ssh >> $NODELIST
       done
#
# # Execute the job using charmrun
$CHARMRUN $PROG $ARGS $IFILE +p$NP ++nodelist $NODELIST > $OFILE

OR
EXAMPLE Script #TWO
#PBS -N DAN2
#PBS -l nodes=2:ppn=2,walltime=48:00:00

#change to input directory
cd /global/bwsn001/home/users1/Dan/Muzet/Test06Proc

#run namd2  (this assumes namd2 is in my $PATH)
#mpirun -np 4 namd2 <configfile>

/global/bw_2/software/ia32/namd/NAMD_2.6b1_Linux-i686/charmrun ++p 6
++verbose ++nodelist $PBS_NODEFILE \
/global/bwsn002/software/ia32/namd/NAMD_2.6b1_Linux-i686/namd2\
/global/bwsn001/home/users1/nm67371/Muzet/Test06Proc/test.conf



#end 




More information about the torqueusers mailing list