dong at pampas.chem.purdue.edu
Thu Apr 13 15:44:53 CEST 2006
The commands I used are as following:
grompp -f replica0.mdp -c confout.gro -p topol.top -o replica0 to get
grompp -f replica1.mdp -c confout.gro -p topol.top -o replica1 to get
the script I used is:
#PBS -S /bin/ksh -q sp_large
### CPU number
#PBS -l nodes=2:ppn=1
### -lwalltime=0:05:0 would be five minutes.
#PBS -N remd
module load gromacs
mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm
replica -v -N 2
I have done several tests:
1. ran replica0.tpr and replica1.tpr seperately. Both worked fine
2. used grompp -np 2 -sort -shuffle -f replica0.mdp -c confout.gro -p
topol.top -o replica0 to get replica0.tpr. I ran replica0.tpr. It worked
fine. I also tried to use replica1.mdp to get replica1.tpr in the same
way. replica1.tpr worked fine as well.
If you need more information, please let me know. Thank you very much
for your help!
On Thu, 2006-04-13 at 09:52 +0200, David van der Spoel wrote:
> Dongsheng Zhang wrote:
> > dear Mark,
> > Thank you very much for your prompt reply. I try to use parallel
> > computing. It works fine.
> > for example: grompp -f -c -p -o replica0 -np 2 -sort -shuffle
> > to get replica0.tpr
> > then, mdrun_mpi -np 2 -s replica0.tpr
> please give EXACT command line and do use mpirun
> > The error message mentioned in the previous email looks very strange to
> > me. MPI works fine, and individual tpr runs fine. The error message
> > comes out before replica exchange. replica0 stops at step 500, replica1
> > stops at step 400, even the output informatio can't be complted. The
> > last lines in replica1.log is
> > Step Time Lambda
> > 400 0.80000 0.00000
> > Rel. Constraint Deviation: Max between atoms RMS
> > I hope these further information can help you to figure out what's the
> > problem.
> > Best Wishes!
> > Dongsheng
> > On Thu, 2006-04-13 at 15:17 +1000, Mark Abraham wrote:
> >>> Dear gmx users:
> >>> I am trying to run REMD with two replicas (for testing). I used
> >>> grompp -f -c -p -o replica0 to get replica0.tpr
> >>> grompp -f -c -p -o replica1 to get replica1.tpr
> >>> then used
> >>> mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm replica
> >>> -v -N 2
> >>> to run it.
> >> mdrun doesn't take '-N 2' but I'm not sure this is the problem. Otherwise,
> >> looks fine to me.
> >>> I got an error message "Segmentation fault" from my script output, but
> >>> no error message in both log files. When I tried to run individual tpr
> >>> file, it worked fine.
> >>> Could someone can comment why I got "Segmentation fault"? Thank you for
> >>> your help!
> >> Your MPI setup might require you use a command like "mpirun -N 2 mdrun_mpi
> >> ..." to make it work - the segfault might be a gromacs-MPI interaction
> >> problem. If you can run an MPI process from the command line you may get
> >> more helpful feedback.
> >> Mark
> >> _______________________________________________
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