[gmx-users] Running GROMACS on cluster

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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