From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Tue Nov 06 2007 - 21:54:46 CST
Hi Richard,
I use a binary of NAMD compiled from someone else. It works very well. If
you want it, I have copied it to:
/cfs/scratch/users/gianluca/NAMD_2.6_Linux-amd64-MPI/
You might want to copy it to your home directory.
To launch use:
mpirun -machinefile $PBS_NODEFILE -np ${NPROCS} ~/NAMD_2.6_Linux-amd64-MPI/namd2 inputfile > logfile
from your PBS batch script.
Otherwise, consult_at_ncsa.uiuc.edu are very helpful.
Gianluca
On Tue, 6 Nov 2007, Richard Swenson wrote:
> Hi all,
>
>
>
> I am currently attempting to run NAMD on Abe at NCSA by using either Jim
> Phillip's binary directly or by using his submission script
> (http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdAtNCSA). In both
> cases, NAMD loads fine and finishes startup phase 8, but then exits. I have
> briefly looked in the NAMD list archives and wiki, but have not found the
> solution to my problem. Could someone point me to some help?
>
>
>
> Thanks a bunch,
>
> Richard
>
>
>
>
-----------------------------------------------------
Dr. Gianluca Interlandi gianluca_at_u.washington.edu
+1 (206) 685 4435
+1 (206) 714 4303
http://biocroma.unizh.ch/gianluca/
Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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