Hi, Justin, Thank you so much. Now it works well.
Yi On Mon, May 24, 2010 at 7:59 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Yi Peng wrote: > >> Hi, everyone, >> >> Recently our school upgraded the clusters for us. And they install the >> Gromacs-4.0.7 for us. Before I always used Gromacs-4.0.3, the scripts used >> for parallel running works well. >> >> My script is as follows: >> >> #PBS -l nodes=4:ppn=2 >> #PBS -N pr-impd1-wt >> #PBS -j oe >> module load gromacs >> module load openmpi-intel >> cd $PBS_O_WORKDIR >> NPROCS=`wc -l < $PBS_NODEFILE` >> /usr/local/bin/pbsdcp -s pr.tpr $TMPDIR >> cd $TMPDIR >> mpiexec mdrun -multi $NPROCS -maxh 100 -s pr.tpr -e pr.edr -o pr.trr -g >> pr.log -c pr.gro >> /usr/local/bin/pbsdcp -g '*' $PBS_O_WORKDIR >> cd $PBS_O_WORKDIR >> >> But today I tried to use Gromacs-4.0.7 for this. It always has the error >> message as follows: >> ------------------------------------------------------- >> Program mdrun, VERSION 4.0.7 >> Source code file: gmxfio.c, line: 737 >> >> Can not open file: >> pr7.tpr >> ------------------------------------------------------- >> >> "Your Bones Got a Little Machine" (Pixies) >> >> Error on node 7, will try to stop all the nodes >> Halting parallel program mdrun on CPU 7 out of 8 >> >> gcq#212: "Your Bones Got a Little Machine" (Pixies) >> >> >> ------------------------------------------------------- >> Program mdrun, VERSION 4.0.7 >> Source code file: gmxfio.c, line: 737 >> >> Can not open file: >> pr5.tpr >> ------------------------------------------------------- >> >> "Your Bones Got a Little Machine" (Pixies) >> >> >> gcq#212: "Your Bones Got a Little Machine" (Pixies) >> >> Error on node 5, will try to stop all the nodes >> Halting parallel program mdrun on CPU 5 out of 8 >> >> ------------------------------------------------------- >> Program mdrun, VERSION 4.0.7 >> Source code file: gmxfio.c, line: 737 >> >> Can not open file: >> pr4.tpr >> ------------------------------------------------------- >> >> "Your Bones Got a Little Machine" (Pixies) >> >> >> gcq#212: "Your Bones Got a Little Machine" (Pixies) >> >> Error on node 4, will try to stop all the nodes >> Halting parallel program mdrun on CPU 4 out of 8 >> -------------------------------------------------------------------------- >> MPI_ABORT was invoked on rank 6 in communicator MPI_COMM_WORLD >> with errorcode -1. >> >> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >> You may or may not see output from other processes, depending on >> exactly when Open MPI kills them. >> -------------------------------------------------------------------------- >> >> How can I solve this problem. Where can I add number to each input file >> for pr.tpr? >> >> > The use of -multi implies that you have a series of .tpr files beginning > with zero, i.e. pr0.tpr, pr1.tpr, etc. So the input files have to be named > as mdrun expects them to be. The name given to the -s flag is a prefix. > See, for instance: > > http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps > > -Justin > > Thanks! >> >> Yi >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 >
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