[gmx-users] Running GROMACS on cluster

Yasser Almeida Hernández yasser.almeida.hernandez at chemie.uni-hamburg.de
Fri Mar 17 12:28:17 CET 2017

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.

#$ -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 Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
+49 40 42838 2845
yasser.almeida.hernandez at chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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