[gmx-users] pdb2gmx illegal instruction

[Dongsheng Zhang]

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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