From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Wed Apr 05 2006 - 16:42:46 CDT
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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