Re: running NAMD on beowulf cluster

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Thu Apr 06 2006 - 00:09:18 CDT

It looks like you don't have the script. You need to write one then to
create a nodelist file from $PBS_NODEFILE.
A sample script is like:

#!/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

This will create a nodelist file under your home direcotry named
namd.$PBS_JOBID

Gengbin

Nitin Bhardwaj wrote:

>thanks Gengbin,
> you were right. the output files were being generated in the other
>directory. But in the output file there, it said:
>
>make-namd-nodelist: Command not found.
>
>Where is this command coming from in the batch file. I found the
>sample batch file here:
>
>http://biowulf.nih.gov/apps/namd/
>
>How can i avoid this?
>
>thanks a lot.
>Nitin
>On 05/04/06, Gengbin Zheng <gzheng_at_ks.uiuc.edu> wrote:
>
>
>>You have to consult the sysadmin of your cluster (or who writes the
>>make-namd-nodelist script)
>>I suspect the script created the nodelist file under your work directory
>>instead of the home directory, which was why charmrun can not find it.
>>
>>Gengbin
>>
>>Nitin Bhardwaj wrote:
>>
>>
>>
>>>Dear NAMD users,
>>> I am having trouble running NAMD on a beowulf cluster. I am using
>>>this batch file to run NAMD (this is a modified version of the batch
>>>file i found on the web).
>>>
>>>______________________________________
>>>#!/bin/csh
>>>#PBS -N NAMD
>>>#PBS -k oe
>>>#PBS -m be
>>>#
>>>set path=(/home/homes53/nbhard2/C2/wrong/namd2 $path .)
>>>cd $PBS_O_WORKDIR
>>>
>>>make-namd-nodelist
>>>charmrun /home/homes53/nbhard2/C2/wrong/namd2 +p$np ++nodelist
>>>~/namd.$PBS_JOBID wrong_y_90.conf >& test.out
>>>----------------------------------------------------------------------
>>>
>>>
>>>I run it by saying:
>>>
>>>qsub -v np=8 -l nodes=4:smp wrong_y_90.in2
>>>
>>>
>>>or run this batch file (worng_y_90.in2) file with any 4 nodes having
>>>dual processor.
>>>
>>>The error it gives is:
>>>
>>>ERROR> No such nodelist file
>>>/home/homes53/nbhard2/namd.12746.argo-new.cc.uic.edu
>>>
>>>Please let me know where I am going wrong. I also do not understand
>>>the function of the command 'make-namd-nodelist' in my batch file.
>>>
>>>Any help would be greatly appreciated.
>>>
>>>thanks a lot in advance.
>>>Nitin
>>>
>>>
>>>
>>>
>>
>>
>
>
>--
>$B&-(BI+I$B'*(B
>
>

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