From: Sourav Ray (souravray90_at_gmail.com)
Date: Sat Sep 12 2015 - 01:13:32 CDT
#!/bin/bash
#PBS -S /bin/bash
## Set Walltime here in HH:MM:SS Format
#PBS -l walltime=<execution time>
## Set the number of nodes and PROCESSORS PER NODE(ppn)
#PBS -l nodes=<no of nodes>:ppn=<processor per node>
## Mention the Memory required by your job
## Not to exceed 2GB/processor
#PBS -l pmem=<memory>
## The queue in which you want to put the job
#PBS -q <queue>
## Job name that is displayed on qstat
#PBS -N <anme of the job>
## Output file from the PBS SCRIPT
#PBS -o <output file name>
cd $PBS_O_WORKDIR
echo "Current working directory is `pwd`"
echo "Node file:"
echo "---------------------"
cat $PBS_NODEFILE
echo "---------------------"
NPROC=`cat $PBS_NODEFILE|wc -l`
echo "Running on $NPROC processors."
#### Creating Node File for NAMD ####
JobID=`echo $PBS_JOBID | cut -f1 -d'.'`
nodefile=./$JobID.nodelist
echo group main > $nodefile
nodes=`cat $PBS_NODEFILE`
for node in $nodes
do
echo host $node >> $nodefile
done
echo "Created Nodefile : $nodefile"
##The folder/directory where the namd executable are located
NAMDDIR=<path to the namd sourcefile>
export CONV_RSH=ssh
echo "Starting run at: `date`"
#### CHANGE the names for the NAMD input (.conf file) and the output (.log
file) ###
$NAMDDIR/charmrun +p$NPROC ++nodelist $nodefile $NAMDDIR/namd2 *.conf >
*.log
echo "Job finished at: `date`"
Try and let me know, posted the code as Parag's server blocked the text
file.
Regards
Sourav
On Sat, Sep 12, 2015 at 11:41 AM, Sourav Ray <souravray90_at_gmail.com> wrote:
> Hello Parag and Peter
>
> Try this script with NAMD-TCP version on PBS. Worked for me.
>
> On Sat, Sep 12, 2015 at 9:25 AM, Abhishek Tyagi <atyagiaa_at_connect.ust.hk>
> wrote:
>
>> Dear Parag,
>>
>> Have you gone through the mailing list, you may find similar questions
>> asked previously. For multiple node for example cluster, your job examples
>> were given in namd readme file. Just follow the instructions.
>>
>>
>> On 11 Sep, 2015, at 9:02 pm, Parag Khuraswar <parag_k_at_citilindia.com>
>> wrote:
>>
>> Hi,
>>
>>
>> Can anyone help to run 1 job of MAND on multiple node. How to create a
>> node file and command line syntax in PBS job script for NAMD.
>>
>> Regards,
>> Parag
>> +91 8308806004
>>
>> *From:* Parag Khuraswar
>> *Sent:* Wednesday, September , 2015 9:58 AM
>> *To:* namd-l_at_ks.uiuc.edu
>> *Cc:* 'Peter Freddolino'
>> *Subject:* node file for NAMD
>>
>> Hi,
>>
>> Can anyone help me to know how to create PBS node file to run one NAMD
>> job on multiple node. And also command line syntax in PBS job script for
>> NAMD.
>>
>> Regards,
>> Parag
>> +91 8308806004
>>
>>
>>
>
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