tune_pme in gromacs 5 does not use "gmx mdrun" by default.
When running gmx tune_pme without setting $MDRUN it tries to run mdrun instead of gmx mdrun.
gmx tune_pme -ntmpi 28 -s ion_channel.tpr ...
Cannot execute mdrun. Please check benchtest.log for problems!
sh: 1: mdrun: not found
Require tune_pme to take -mdrun parameter
The transition away from many binaries in 5.0, and the removal of
symlinks in 5.1 mean there is even less chance that a sensible default
command line for calling mdrun can be provided. In general, mdrun
might be in either precision, with or without MPI, with or without
some custom suffix, inside the wrapper binary or from an mdrun-only
build, or from a custom directory.
Thus, the user is now required to say what command to call to run the
simulation they want to optimize. The MDRUN environment variable
remains as an undocumented and deprecated convenience feature for 5.1.
#4 Updated by Mark Abraham almost 5 years ago
- Category set to core library
- Status changed from New to Feedback wanted
- Assignee set to Mark Abraham
- Target version set to 5.1
- Affected version - extra info set to problem gets worse in 5.1-rc1
- Affected version changed from 5.x to 5.0.7
My fix is targeted at 5.1, because there are no longer symlinks available there.
In 5.0.x, I think Ake's use case should be solved by setting MDRUN if somehow there is not a symlink to mdrun available.