Re: running NAMD on beowulf cluster

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Wed Apr 05 2006 - 16:30:27 CDT

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
>
>

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