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

[Mark Abraham]

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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