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Task #2829

mdrun appends when checkpoint specified by -cpi is not found

Added by Joe Jordan 6 days ago. Updated 5 days ago.

Status:
New
Priority:
Normal
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Category:
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Target version:
-
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Description

If I invoke mdrun with all paths correctly specified:

gmx mdrun -s md.part0001.tpr -cpi md.part0001.cpt -noappend

I get the expected behavior of creating a bunch of files named md.part0002*. However, if I have a typo I will get unexpected behavior:

gmx mdrun -s md.part0001.tpr -cpi md.part001.cpt -noappend

In this case, md.part0001* files will be backed up and the simulation will just start from the tpr as if the simulation has not started yet.

There is a note which seems to be about this in the mdrun help text

There are three scenarios with
-cpi:

  • no files with matching names are present: new output files are written

but this seems like unexpected behavior if I have explicitly specified -noappend. If I have no cpt file and I give the -append flag to mdrun it will throw an error, so it seems like the reverse case of saying -noappend while not giving an actual file to -cpi should also throw an error.

History

#1 Updated by Berk Hess 5 days ago

This is a special case of our intended, but not ideal behavior. We allow mdrun -cpi to run when no checkpoint file is found for simplifying resubmit scripts.
We can consider not allowing this when -noappend is set explicitly.

#2 Updated by Mark Abraham 5 days ago

Note that this is a subcase of case 4 I listed at https://redmine.gromacs.org/issues/1889

Berk Hess wrote:

This is a special case of our intended, but not ideal behavior. We allow mdrun -cpi to run when no checkpoint file is found for simplifying resubmit scripts.

Another user problem created by that behaviour: https://redmine.gromacs.org/issues/2344#note-13

We can consider not allowing this when -noappend is set explicitly.

That would be inconsistent. If

gmx mdrun -s md.part0001.tpr -cpi md.part001.cpt

when the cpt file is missing starts from the tpr (thus we cannot append) and writes to default filenames (I forget what they are), then

gmx mdrun -s md.part0001.tpr -cpi md.part001.cpt -noappend

should have identical behaviour because all the user did was restrict GROMACS to the behaviour it would have done anyway.

That the user has adopted the .part000n naming for their .tpr is and should be irrelevant.

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