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? Thanks! Yi
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