Hi, everyone,<br><br>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. <br><br>My script is as follows:<br>
<br><span class="gI"></span>#PBS -l nodes=4:ppn=2<br>#PBS -N pr-impd1-wt<br>#PBS -j oe<br>module load gromacs<br>module load openmpi-intel<br>cd $PBS_O_WORKDIR<br>NPROCS=`wc -l < $PBS_NODEFILE`<br>/usr/local/bin/pbsdcp -s pr.tpr $TMPDIR<br>
cd $TMPDIR<br>mpiexec mdrun -multi $NPROCS -maxh 100 -s pr.tpr -e pr.edr -o pr.trr -g pr.log -c pr.gro<br>/usr/local/bin/pbsdcp -g '*' $PBS_O_WORKDIR<br>cd $PBS_O_WORKDIR<br><br>But today I tried to use Gromacs-4.0.7 for this. It always has the error message as follows:<br>
-------------------------------------------------------<br>Program mdrun, VERSION 4.0.7<br>Source code file: gmxfio.c, line: 737<br><br>Can not open file:<br>pr7.tpr<br>-------------------------------------------------------<br>
<br>"Your Bones Got a Little Machine" (Pixies)<br><br>Error on node 7, will try to stop all the nodes<br>Halting parallel program mdrun on CPU 7 out of 8<br><br>gcq#212: "Your Bones Got a Little Machine" (Pixies)<br>
<br><br>-------------------------------------------------------<br>Program mdrun, VERSION 4.0.7<br>Source code file: gmxfio.c, line: 737<br><br>Can not open file:<br>pr5.tpr<br>-------------------------------------------------------<br>
<br>"Your Bones Got a Little Machine" (Pixies)<br><br><br>gcq#212: "Your Bones Got a Little Machine" (Pixies)<br><br>Error on node 5, will try to stop all the nodes<br>Halting parallel program mdrun on CPU 5 out of 8<br>
<br>-------------------------------------------------------<br>Program mdrun, VERSION 4.0.7<br>Source code file: gmxfio.c, line: 737<br><br>Can not open file:<br>pr4.tpr<br>-------------------------------------------------------<br>
<br>"Your Bones Got a Little Machine" (Pixies)<br><br><br>gcq#212: "Your Bones Got a Little Machine" (Pixies)<br><br>Error on node 4, will try to stop all the nodes<br>Halting parallel program mdrun on CPU 4 out of 8<br>
--------------------------------------------------------------------------<br>MPI_ABORT was invoked on rank 6 in communicator MPI_COMM_WORLD<br>with errorcode -1.<br><br>NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.<br>
You may or may not see output from other processes, depending on<br>exactly when Open MPI kills them.<br>--------------------------------------------------------------------------<br><br>How can I solve this problem. Where can I add number to each input file for pr.tpr?<br>
<br>Thanks!<br><br>Yi<br>