[gmx-users] Problems with parallel run
Hi all My apologies for the lack of detail in my previous e-mail. I am trying to run gromacs-4.0.7 for a system that I am studying. I have ran several simulations on serial on my own computer that have to date worked fine. I am now however trying to run the simulations on our local cluster in parallel using mpich-1.2.7 and experiencing some difficulty. Please note that the version of gromacs mentioned above is installed in parallel. Right when I run a short simulation of 500 steps in one two or three nodes the simulations runs fine (takes about 10 seconds) and all the data is written to the log file. However when I increase the nodes to 4 there is no stepwise info written and the simulation does not progress. I realise that this maybe a cluster problem, but if anyone has experienced similar issues I would be grateful of some feedback. Here is the script I use: #!/bin/bash #PBS -N hex #PBS -r n #PBS -q longterm #PBS -l walltime=00:30:00 #PBS -l nodes=4 cd $PBS_O_WORKDIR export P4_GLOBMEMSIZE=1 /usr/local/bin/mpiexec mdrun -s Also here is my path: # Gromacs export GMXLIB=/k/gavin/gromacs-4.0.7-parallel/share/gromacs/top export PATH=$PATH:/k/gavin/gromacs-4.0.7-parallel/bin Cheers Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems with parallel run
This email (as well as the two others) have found their way to the list. No need to post several times! On Wed, Mar 3, 2010 at 12:47, Gavin Melaugh gmelaug...@qub.ac.uk wrote: Hi all My apologies for the lack of detail in my previous e-mail. I am trying to run gromacs-4.0.7 for a system that I am studying. I have ran several simulations on serial on my own computer that have to date worked fine. I am now however trying to run the simulations on our local cluster in parallel using mpich-1.2.7 and experiencing some difficulty. Please note [...] If you would have searched the mailing list for posts with terms like parallel problem, you probably would have found several posts that report people having serious problems with mpich-1.2.x and the advise to use mpich2, openMPI or LAM/MPI instead. Check with the admins of your Cluster which alternative MPI lib is available or have them install one of the suggested. Oliver -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems with parallel run
Hi Oliver Thanks very much. Sorry about the other two e-mails that was a mistake, I had checked the list after I sent the first one and it wasn't on so I thought it wasn't received. I was reading many of those posts today and did realise that there were problems with mpich-1.2.x but they seemed to be for earlier versions of gromacs and it was on this point that I was unsure. Thanks anyway for providing some insight on the matter. Cheers Gavin Oliver Stueker wrote: This email (as well as the two others) have found their way to the list. No need to post several times! On Wed, Mar 3, 2010 at 12:47, Gavin Melaugh gmelaug...@qub.ac.uk wrote: Hi all My apologies for the lack of detail in my previous e-mail. I am trying to run gromacs-4.0.7 for a system that I am studying. I have ran several simulations on serial on my own computer that have to date worked fine. I am now however trying to run the simulations on our local cluster in parallel using mpich-1.2.7 and experiencing some difficulty. Please note [...] If you would have searched the mailing list for posts with terms like parallel problem, you probably would have found several posts that report people having serious problems with mpich-1.2.x and the advise to use mpich2, openMPI or LAM/MPI instead. Check with the admins of your Cluster which alternative MPI lib is available or have them install one of the suggested. Oliver -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
