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 [email protected] > >> 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 [EMAIL PROTECTED] > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _______________________________________________ gmx-users mailing list [email protected] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
