mdrun -nsteps option does not work correctly
I have a run with data up till and checkpoint at 200000 steps. Running mdrun -cpi -nsteps 300000 gives:
Program: gmx mdrun, version 2019.1-dev-20190124-085e8c261
Source file: src/gromacs/fileio/checkpoint.cpp (line 2775)
The input requested 100000 steps, however the checkpoint file has already
reached step 200000. The simulation will not proceed, because either your
simulation is already complete, or your combination of input files don't
So it first seems to check for: nsteps_requested - step_checkpoint < nsteps_requested
which doesn't make sense
Make mdrun -nsteps work again.
The mdrun -nsteps option was only functional in some cases,
because it modified ir->nsteps after the checkpoint loading
Note that this option is deprecated, but is should either work
or be removed.
#2 Updated by Mark Abraham about 2 months ago
- Assignee deleted (
gmx convert-tpr -nsteps is the supported way to do this, which the error message could be improved to recommend.
As nobody has yet written down what nsteps is supposed to do in concert with the dozen things that it has to work well with, and written tests for it, we can't implement or maintain this feature. And we already deprecated it at #2569.
#5 Updated by Berk Hess about 2 months ago
- Status changed from New to Fix uploaded
- Assignee set to Berk Hess
I pushed up a fix.
I think that the description on the -nsteps option is clear from a user point of the view. The fundamental issue is that the checkpointing code modifies init_step and nsteps. That makes it difficult to reason about any meaning of these parameters in the code.
#7 Updated by Mark Abraham 17 days ago
mdrun documents -nsteps as "Run this number of steps, overrides .mdp file option". This is slightly ambiguous, as it could refer to
1) the number of steps this invocation of mdrun should perform from the checkpoint configuration, or
2) it could mean to replace the number of steps described .tpr with the new value and simulate from the step in the checkpoint configuration up to the new required number of steps.
This ambiguity only arises when
-cpi is used. Berk's bug report implies he intends the latter interpretation.
The failing test uses
mdrun -nsteps 2 -cpi with a checkpoint file that will normally done more than 2 steps. When I wrote the test, I intended it to do two more steps ie. the former interpretation.
Note that if Berk had implemented his intent to do 100000 more steps according to the former interpretation (ie. with
mdrun -nsteps 100000 -cpi), then he still would have met the error, so the code does not conform to my interpretation regardless of the value passed to
mdrun -nsteps. Berk's fix works for the latter interpretation regardless of the size of
I think we should clarify the documentation regardless. If we want Berk's interpretation, then I suggest "Run this total number of steps, overrides .mdp nsteps" and to remove the call to
-nsteps on line 83 of src/programs/mdrun/tests/terminationhelper.cpp