Hi, Justin,<br><br>Thank you so much. Now it works well.<br><br>Yi<br><br><div class="gmail_quote">On Mon, May 24, 2010 at 7:59 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5"><br>
<br>
Yi Peng wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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>
#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>
</blockquote>
<br></div></div>
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:<br>
<br>
<a href="http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps" target="_blank">http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps</a><br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thanks!<br>
<br>
Yi<br>
<br>
</blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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</div></div></blockquote></div><br>