On 3/17/17 7:22 AM, Yasser Almeida Hernández wrote:
Hi all, I am strugling to run GROMACS on a cluster with SGE queue system, but I have any acceleration. The verbose output says that it will end is September 2017!!. This is the script I am using to run.
What does your system administrator advise as far as best practices? What benchmarking have you done on this system?
-Justin
**** #!/bin/bash #$ -cwd #$ -pe parallel 24 #$ -q main.q #name of the queue #$ -e stderr.log # redirections for stdout,err #$ -o stdout.log #export LD_LIBRARY_PATH=/home/whoever/mylibdir:$LD_LIBRARY_PATH # any changes you need to the environment #MPIRUN=$I_MPI_ROOT/intel64/bin/mpirun # this is the full path to the correct mpirun installation. #OPENMPI=/opt/openmpi-1.8.1/bin/mpirun -mca btl ^usnic -machinefile hosts -np $NSLOTS # this is the full correct command for open-mpirun #CMD=mdrun_mpi -v -deffnm md_glpg_NG_50ns # command to be executed export I_MPI_FABRICS=shm:ofa mpirun /usr/bin/mdrun_mpi -v -deffnm md_protein_NG_100ns_packmol **** My system is composed by a membrane protein, detergent, water and ions. Thanks in advance Yasser
-- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
