[gmx-users] REMD

[Dongsheng Zhang]

Dear David,

I forgot one more information. The computer administrator told me I did
not need to use mpirun. As I told you in the previous email, I have done
tests for parallel computing. It worked fine.

Dongsheng

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
> >>
> >> _______________________________________________
> >> gmx-users mailing list    gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> Please don't post (un)subscribe requests to the list. Use the 
> >> www interface or send it to gmx-users-request at gromacs.org.
> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
>