Gromacs 2020.2

Accelerated Computing NGC GPU Cloud Container: HPC
1

HI NVIDIA Team,

I am evaluating Gromacs with docket on DGX1 machine. I am referring to the documentation at GROMACS | NVIDIA NGC.

There are a couple of errors while executing commands as mentioned in the documentation.

user@dgx1:~/amit/containers/gromacs$ docker run -ti --runtime nvidia -v /dev/infiniband:/dev/inifiniband -v $(pwd)/gromacs_benchmarks/adh_cubic:/benchmark --workdir /benchmark nvcr.io/hpc/gromacs:2020.2 sh -c "gmx grompp -f pme_verlet.mdp"
INFO Configured container for NVIDIA GPU architecture sm80
       :-) GROMACS - gmx grompp, 2020.2-dev-20200430-5e78835-unknown (-:

....

GROMACS:      gmx grompp, version 2020.2-dev-20200430-5e78835-unknown
Executable:   /usr/local/gromacs//sm80/bin/gmx
Data prefix:  /usr/local/gromacs//sm80
Working dir:  /benchmark
Command line:
  gmx grompp -f pme_verlet.mdp


-------------------------------------------------------
Program:     gmx grompp, version 2020.2-dev-20200430-5e78835-unknown
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function:    void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
  In command-line option -f
    File 'pme_verlet.mdp' does not exist or is not accessible.
    The file could not be opened.
      Reason: No such file or directory
      (call to fopen() returned error code 2)

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

The second command also results in a similar error.

user@dgx1:~/amit/containers/gromacs$ docker run -ti --runtime nvidia -v /dev/infiniband:/dev/inifiniband -v $(pwd)/gromacs_benchmarks/adh_cubic:/benchmark --workdir /benchmark nvcr.io/hpc/gromacs:2020.2 sh -c "gmx mdrun -v -nsteps 100000 -resetstep 90000 -noconfout -ntmpi 4 -ntomp 10 -nb gpu -bonded gpu -pme gpu -npme 1 -nstlist 400 -s topol.tpr"
INFO Configured container for NVIDIA GPU architecture sm80
        :-) GROMACS - gmx mdrun, 2020.2-dev-20200430-5e78835-unknown (-:

...

GROMACS:      gmx mdrun, version 2020.2-dev-20200430-5e78835-unknown
Executable:   /usr/local/gromacs//sm80/bin/gmx
Data prefix:  /usr/local/gromacs//sm80
Working dir:  /benchmark
Command line:
  gmx mdrun -v -nsteps 100000 -resetstep 90000 -noconfout -ntmpi 4 -ntomp 10 -nb gpu -bonded gpu -pme gpu -npme 1 -nstlist 400 -s topol.tpr


-------------------------------------------------------
Program:     gmx mdrun, version 2020.2-dev-20200430-5e78835-unknown
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function:    void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
  In command-line option -s
    File 'topol.tpr' does not exist or is not accessible.
    The file could not be opened.
      Reason: No such file or directory
      (call to fopen() returned error code 2)

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Please let us know if we are missing any step.

Thanks,
Amit Ruhela