Re: [gmx-users] REMD run on higher nodes.
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 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 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD run on higher nodes.
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. On Mon, Aug 5, 2013 at 3:22 PM, Mark Abraham 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 > 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 > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD run on higher nodes.
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 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 > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] REMD run on higher nodes.
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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
