Gromacs on Caviness

Templates for Slurm job submission scripts are available for batch GROMACS jobs in /opt/shared/templates/slurm/applications/gromacs. Copy and edit the template based on your job by following the usage described in gromacs.qs.

On Caviness, the template (/opt/shared/templates/slurm/applications/gromacs.qs) provides a number of options to provide the best performance, but you must read the comments and set the options accordingly for your job. By default the template uses double-precision (md_rund), however commenting out GROMACS_DOUBLE_PRECISION=YES will specify the single-precision version (md_run) instead.

When running long GROMACS jobs on Caviness, users may need to restart simulations after jobs are preempted or reach the time limit. With GROMACS v2023.2, users may encounter the following error when attempting to append to a previous run:

System I/O error: 
File locking is not supported on this system.

The cause of this issue is the file locking, which is not supported by the Lustre system on Caviness. This issue does not typically occur with older versions such as GROMACS v2018. In GROMACS v2018, when checkpoint files are read, the program attempts to establish a lock on the log file. If the lock fails, the program will continue executing if the -append flag was used. In GROMACS 2023, the log file code (and locking) was moved to a different source file and the option to ignore a failed lock was completely removed. This change persists in the most-recent source code on github (https://github.com/gromacs/gromacs/blob/main/src/gromacs/mdrunutility/handlerestart.cpp). Users can disable file locking by

export GMX_NO_FILE_LOCKING=1

then users can run command as usual, e.g.:

gmx mdrun -cpi npt_6 -deffnm npt_6 -append