On 8/5/13 6:36 AM, suhani nagpal wrote:
Sir
Yeah, I meant to use twice the hardware and i have already invoked
mpiexec_mpt.
the pbs script works fine if i start afresh mdrun of the tprs but if i
extend the simulation run by -cpi filename -noappend the run doesnt take
place.
AFAIK, you can't change the number of processors mid-job and then try to use
mdrun -cpi since information related to DD, etc is stored in the checkpoint
files, which now do not match the previous run.
-Justin
On Mon, Aug 5, 2013 at 3:22 PM, Mark Abraham <mark.j.abra...@gmail.com>wrote:
Not sure what you're asking, but if you're providing twice as much
hardware, then invoke mpiexec_mpt suitably to tell it to use all of
that. Then, if you invoke mdrun_mpi the same way as you do now, it
will work out it can use twice as much hardware per replica.
Mark
On Mon, Aug 5, 2013 at 7:55 AM, suhani nagpal <suhani.nag...@gmail.com>
wrote:
Greetings
I'm running REMD of 96 replicas where the run.pbs is the following:
#!/bin/tcsh
#PBS -S /bin/tcsh
#PBS -l walltime=00:15:00
#PBS -q workq
#PBS -l select=8:ncpus=12:mpiprocs=12
#PBS -l place=scatter:excl
#PBS -V
# Go to the directory from which you submitted the job
cd $PBS_O_WORKDIR
setenv MPI_GROUP_MAX 1024
setenv MPI_UNBUFFERED_STDIO 1
#mpiexec_mpt -np 24 ./exefile
mpiexec_mpt -np 96
/lustre/applications/GROMACS/gromacs-4.5.5/bin/mdrun_mpi
-s md_.tpr -multi 96 -replex 2000 -cpi state_.cpt -noappend
So each replica runs at one processor.
Now, I want to run the remd at 16 nodes ( double ) so that each replica
is
subjected to 2 processors.
Kindly assist !
Thanks
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
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