[gmx-users] problem: gromacs run on gpu

leila karami karami.leila1 at gmail.com
Thu Jul 13 07:04:15 CEST 2017

Dear Gromacs users,

I am doing md simulation on Gromacs 5.1.3. on GPU in Rocks cluster system using

gmx_mpi mdrun -nb gpu -v -deffnm gpu -ntomp 16 -gpu_id 0 -pin on

All things are ok.

When I use this command in a script to do md simulation by queuing system:

#$ -S /bin/bash
#$ -q gpu.q
#$ -cwd
#$ -N cell_1
#$ -e error_1.dat
#$ -o output_1.dat
echo "Job started at date"
gmx_mpi mdrun -nb gpu -v -deffnm gpu -ntomp 16 -gpu_id 0 -pin on
echo "Job Ended at date"

I encountered with following error:

Program:     gmx mdrun, VERSION 5.1.3
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
Function:    void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
  In command-line option -pin
    Invalid value: on

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Halting program gmx mdrun
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.


How to resolve this error?
Any help will be highly appreciated

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