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 $PBS_O_WORKDIR export P4_GLOBMEMSIZE=100000000 /usr/local/bin/mpiexec mdrun -s Also here is my path: # Gromacs export GMXLIB=/k/gavin/gromacs-4.0.7-parallel/share/gromacs/top export PATH="$PATH:/k/gavin/gromacs-4.0.7-parallel/bin" Cheers Gavin -- gmx-users mailing list gmx-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