From: k.manzoorolajdad (kazem.manzoor_at_gmail.com)
Date: Tue Sep 03 2013 - 02:22:54 CDT
thanks branko
i use your script and submit but say:
ssh: Could not resolve hostname ++nodelist: Name or service not known
i attach all file use and make by pbs
nodelist:
group main
host compute-0-14 ++shell ssh
host compute-0-14 ++shell ssh
host compute-0-14 ++shell ssh
host compute-0-14 ++shell ssh
host compute-0-14 ++shell ssh
host compute-0-14 ++shell ssh
host compute-0-14 ++shell ssh
host compute-0-14 ++shell ssh
is correct or :
group main
compute-0-14
compute-0-14
compute-0-14
compute-0-14
compute-0-14
compute-0-14
compute-0-14
compute-0-14
?
thank
On Sun, Aug 25, 2013 at 7:50 PM, Branko <bdrakuli_at_chem.bg.ac.rs> wrote:
> Manzoor,
>
> In clusters with pbs you usually should put number of nodes and number of
> processors that you need, input and output file names and the line that
> execute script (for example script.sh) all in pbs file. In script you
> should put path to the exe files (charmrun and namd2) as well as to your
> file which give all 'instructions' for namd run. In this way you could
> execute program with 'qsub <file_name>.pbs' , In your scrip it is uncertain
> are charmrun and namd2 are in the same directory. Best solution is to ask
> your system administrator, for example see below
>
> Branko
>
> PBS:
>
> #!/bin/bash
> #PBS -q <your_q>
> #PBS -l nodes=1:ppn=1
> #PBS -l walltime=100:00:00
> #PBS -e ${PBS_JOBID}.err
> #PBS -o ${PBS_JOBID}.out
>
> cd $PBS_O_WORKDIR
> chmod +x job.sh
> ./job.sh
>
> job.sh:
>
> #!/bin/sh -x
>
> PROC_NUM=number_of_procesor_same_as_in_PBS
>
> echo
> "***********************************************************************"
> echo "Running on: $HOSTNAME"
> echo
> "***********************************************************************"
>
> if [ "x$PBS_NODEFILE" != "x" ] ; then
> echo "PBS Nodefile: $PBS_NODEFILE"
> HOST_NODEFILE=$PBS_NODEFILE
> fi
>
>
> if [ "x$HOST_NODEFILE" = "x" ]; then
> echo "No hosts file defined. Exiting..."
> exit
> fi
>
> echo "Creating host file..."
>
> export NODES=`cat $PBS_NODEFILE`
> export NODELIST=nodelist
> echo group main > $NODELIST
> for node in $NODES ; do
> echo host $node ++shell ssh >>
> $NODELIST
> done
>
> echo "Nodelist file:"
> cat $NODELIST
>
> /path_to_charmrun/charmrun ++remote-shell ssh ++nodelist $NODELIST
> +p$PROC_NUM /path_to_namd2/namd2
> /path_to_your_namd_instructive_file/<file_name>.namd
>
>
>
>
>
>
> On 8/25/2013 4:36 PM, k.manzoorolajdad wrote:
>
> Dear NAMD user:
> I use cluster with rock cluster 6 and pbs torque
> and see this address
> http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdOnPBS
> but cant handel
> i write the script below:
> #!/bin/csh
> #PBS -N NAMD
> #PBS -k oe
> #PBS -m be
> #PBS -M kazem.manzoor_at_gmail.com
>
> #set path=(/home/homes53/nbhard2/C2/wrong/namd2 $path .)
> cd $PBS_O_WORKDIR
>
> ./make-namd-nodelist
> ./charmrun ./namd2 +p$np ++nodelist ~/namd.$PBS_JOBID MinEqu.conf >&
> test.log
>
> and create ./make-namd-nodelist :
>
> #!/bin/sh
>
> nodelist=~/namd.$PBS_JOBID
> lists=`cat "$PBS_NODEFILE" | sort`
>
> echo group main > $nodelist
> for i in $lists
> do
> echo host $i >> $nodelist
> done
>
>
> and submit with:
> qsub -v np=40 -l nodes=5 namd.pbs
>
> what's my wrong?
> thanks
> manzoor
>
>
>
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