Dear Erik,
Thank you very much for your reply. I have fixed the problem with
David's helps. Now I am struggling with parallel running with gromacs.
I use
grompp -np 8 -sort -shuffle -f pr -o pr -c after_em -p AceAla5ac to get
pr.tpr
When I submitted a job to the computing center by using the attached
script file, I got the following error message:
Fatal error:
run input file pr.tpr was made for 8 nodes,
while mdrun_mpi expected it to be for 1 nodes.
my script file is:
#PBS -S /bin/ksh -q sp_short
. /etc/profile
module load gromacs
cd $PBS_O_WORKDIR
### CPU number
#PBS -l nodes=8:ppn=1
###Job name
#PBS -N test
mdrun_mpi -np 8 mdrun -np 8 -s pr -o pr -c after_pr -e pr -g pr -v -N 8
Could you please tell me what's wrong? Thanks!
Dongsheng
On Tue, 2006-03-21 at 23:18 +0100, Erik Lindahl wrote:
> Hi,
>
> Sounds like the binary was compiled (and optimized for) one machine,
> but run another. Give us some info both about the command you ran and
> how Gromacs was compiled/installed.
>
> Cheers,
>
> Erik
>
> On Mar 21, 2006, at 6:11 AM, Dongsheng Zhang wrote:
>
> > Dear All,
> >
> > I want to run gromacs in supercomputer center at my school. When I
> > used
> > pdb2gmx, it gave me an error message as follows:
> > illegal instruction (core dumped out)
> >
> > Could anyone give a clue what's happening? Thank you in advance.
> >
> >
> > Dongsheng
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