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Bug #2386

assertion failure in grompp

Added by Berk Hess over 1 year ago. Updated over 1 year ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
preprocessing (pdb2gmx,grompp)
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

When having an mdp option with both old and current name present in an mdp file, e.g. verlet-buffer-drift and verlet-buffer-tolerance, an assertion fails in grompp.

Program: gmx grompp, version 2018.1-dev-20180116-35654e9af
Source file: src/gromacs/utility/keyvaluetreebuilder.h (line 417)
Function: std::map<std::basic_string<char>, gmx::KeyValueTreeValue>::iterator gmx::KeyValueTreeObjectBuilder::addProperty(const string&, gmx::KeyValueTreeValue&&)

Assertion failed:
Condition: !keyExists(key)
Duplicate key value

Associated revisions

Revision 3a08ebdb (diff)
Added by Berk Hess over 1 year ago

Add check in grompp to avoid assertion failure

With an mdp file with a parameter present with both the current name
and the old name which automatically gets replaced, an assertion
would fail. Now a fatal error is issued.

Fixes #2386

Change-Id: Idc66145afaca6a1e0cb868dd6aba2405e2dd7171

Revision 42878b93 (diff)
Added by Aleksei Iupinov over 1 year ago

Add a death test for the duplicate inputrec keys checking

That was fixed in Idc66145af.

Refs #2386

Change-Id: I4c726989da646ffa5343f4bcdea51dfdf049ef6c

History

#1 Updated by Berk Hess over 1 year ago

  • Status changed from New to Fix uploaded
  • Assignee set to Berk Hess

#2 Updated by Gerrit Code Review Bot over 1 year ago

Gerrit received a related patchset '2' for Issue #2386.
Uploader: Berk Hess ()
Change-Id: gromacs~release-2018~Idc66145afaca6a1e0cb868dd6aba2405e2dd7171
Gerrit URL: https://gerrit.gromacs.org/7488

#3 Updated by Gerrit Code Review Bot over 1 year ago

Gerrit received a related patchset '1' for Issue #2386.
Uploader: Aleksei Iupinov ()
Change-Id: gromacs~master~I4c726989da646ffa5343f4bcdea51dfdf049ef6c
Gerrit URL: https://gerrit.gromacs.org/7489

#4 Updated by Mark Abraham over 1 year ago

I think that the correct behaviour here should be to reject the mdp file, telling the user that their input is inconsistent. We should not be guessing that they got the value right for the current name.

I'd further suggest that even if the value is the same for both names, we should still reject the mdp file because there's likely to be something going on that warrants the user inspecting their file.

#5 Updated by Berk Hess over 1 year ago

  • Status changed from Fix uploaded to Resolved

#6 Updated by Berk Hess over 1 year ago

  • Status changed from Resolved to Closed

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