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
========================================
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