[gmx-users] problem: gromacs run on gpu

[Mark Abraham]

Hi,

Probably you have some strange character after "on" if you edited the file
on Windows or pasted the line from elsewhere

Mark

On Thu, 13 Jul 2017 07:22 Alex <nedomacho at gmail.com> wrote:

> Can you try to open the script in vi, delete the mdrun line and then
> manually retype it?
>
>
> On 7/12/2017 11:03 PM, leila karami wrote:
> > Dear Gromacs users,
> >
> > I am doing md simulation on Gromacs 5.1.3. on GPU in Rocks cluster
> system using
> > command:
> >
> > 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:
> >
> >
> -----------------------------------------------------------------------------------------------------
> > #!/bin/bash
> > #$ -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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