[gmx-users] Error running mdrun (v-5.1.4) on a linux cluster.

[Abhishek Acharya]

Thanks Mark for your response. I looked into the PBS script and it does
have a line pointing to the PBS workdir.

But what you said seems right. Somehow, the execution of the script is not
happening correctly. As it turns out, I realized that I was submitting the
script within a qlogin session, the same I had to use for compilations.
Seems to me that PBS env variables were not set correctly within that
session. When I submit the job outside of qlogin session, it works as
expected.

Thank again for pointing towards the right direction.

Abhishek Acharya
Research Associate,
Department of Molecular Nutrition
CSIR-Central Food Technological Research Institute,
Mysuru-570020

On Tue, Jun 19, 2018 at 1:12 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> You aren't running mdrun_mpi from the working directory in which
> testfile.tpr is found. Probably you need to set some flag in your
> submission script to change to the directory from which you submitted
>
> Mark
>
> On Tue, Jun 19, 2018 at 7:41 AM Abhishek Acharya <abhi117acharya at gmail.com
> >
> wrote:
>
> > Dear GROMACS users,
> >
> > I installed mpi-enabled GROMACS (mdrun only) on a linux cluster. The
> > administrators recommended using Intel MPI so I used that. I also
> installed
> > a local version of gcc-5.5.0 (with required dependencies), as the version
> > available system-wide (4.4.6 I believe) was not compatible with C11
> > standard. Using FFTW-3.3.7 and latest BLAS and LAPACK libraries. The
> > compilation ran without any errors.
> >
> > I could not run any regtests as runs are only allowed via PBS scripts.
> > However, I tried to run a test simulation using a tpr file generated
> using
> > the same gromacs version.
> >
> > On submitting the job using qsub, I find that the queue status is C. The
> > output err file shows the following error, which I have never seen
> before.
> >
> > .....
> > .....
> > GROMACS:      mdrun_mpi, VERSION 5.1.4
> > Executable:   /home/acusers/pbalaji/install/
> gromacs-514-impi/bin/mdrun_mpi
> >
> > -------------------------------------------------------
> > Program:     mdrun_mpi, VERSION 5.1.4
> >
> > -------------------------------------------------------
> > Program:     mdrun_mpi, VERSION 5.1.4
> > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
> > Function:    void gmx::CommandLineParser::parse(int*, char**)
> >
> >
> > -------------------------------------------------------
> > Program:     mdrun_mpi, VERSION 5.1.4
> > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
> > Function:    void gmx::CommandLineParser::parse(int*, char**)
> >
> >
> > -------------------------------------------------------
> > Program:     mdrun_mpi, VERSION 5.1.4
> > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
> > Function:    void gmx::CommandLineParser::parse(int*, char**)
> >
> > Error in user input:
> >
> > -------------------------------------------------------
> > Program:     mdrun_mpi, VERSION 5.1.4
> > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
> > Function:    void gmx::CommandLineParser::parse(int*, char**)
> >
> > Error in user input:
> >
> > -------------------------------------------------------
> > Program:     mdrun_mpi, VERSION 5.1.4
> > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
> > Function:    void gmx::CommandLineParser::parse(int*, char**)
> >
> > Error in user input:
> > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
> > Function:    void gmx::CommandLineParser::parse(int*, char**)
> >
> > Error in user input:
> > Invalid command-line options
> > Error in user input:
> > Invalid command-line options
> > Error in user input:
> > Invalid command-line options
> > Invalid command-line options
> > Invalid command-line options
> > Invalid command-line options
> >   In command-line option -s
> >     File 'testfile.tpr' does not exist or is not accessible.
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> > Halting parallel program mdrun_mpi on rank 3 out of 12
> >   In command-line option -s
> >     File 'testfile.tpr' does not exist or is not accessible.
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> > Halting parallel program mdrun_mpi on rank 5 out of 12
> >   In command-line option -s
> >     File 'testfile.tpr' does not exist or is not accessible.
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> > Halting parallel program mdrun_mpi on rank 6 out of 12
> >
> > -------------------------------------------------------
> > Program:     mdrun_mpi, VERSION 5.1.4
> > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
> > Function:    void gmx::CommandLineParser::parse(int*, char**)
> >
> >   In command-line option -s
> >     File 'testfile.tpr' does not exist or is not accessible.
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> > Halting parallel program mdrun_mpi on rank 11 out of 12
> > .....
> > .....
> > and more of the same.
> >
> > Some clues to how this issue can be solved would certainly help.
> >
> > Thanks in advance.
> >
> > Abhishek
> > --
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