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

[Abhishek Acharya]

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