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Task #2371

mtop searching needs reconsideration

Added by Mark Abraham 4 months ago. Updated 4 months ago.

Status:
New
Priority:
Normal
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-
Category:
core library
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Description

At https://gerrit.gromacs.org/#/c/6216/ we discussed some of the issues associated with how gmx_mtop objects are used, often in a not-very-const way that can invalidate the derived data that is stored alongside the raw topology information.

In writing and reviewing that patch, we did not remember that membed edits a topology, and so did not add the required call to the finalization routine, leading to #2364. Perhaps insert-molecules or genion is similarly broken? (check that for 2018, then re-target this task)

When we have API-driven simulations, we will need to have the ability to let the user do arbitrary operations on the topology, and for that to lead to correctly rebuilding whatever is required thereafter.

In the discussion at the above issue, I proposed that we construct an object from an mtop, and use that instead of a raw mtop in those parts of the code that use the derived information for efficient searching. As Teemu noted, that's potentially hundreds of callers, so we should decide carefully how to stage the work to make it manageable. (There are definitely alternative approaches, too)


Related issues

Related to GROMACS - Bug #2364: g_membed not working on gromacs 2018Closed

Associated revisions

Revision e9705c9e (diff)
Added by Mark Abraham 4 months ago

Fix membed by calling the proper mtop finalization routine

Fixes #2364
Refs #2371

Change-Id: I27166acec903e4c0cf3b9a54aaf4b9db7d6974b0

History

#1 Updated by Gerrit Code Review Bot 4 months ago

Gerrit received a related patchset '1' for Issue #2371.
Uploader: Mark Abraham ()
Change-Id: gromacs~release-2018~I27166acec903e4c0cf3b9a54aaf4b9db7d6974b0
Gerrit URL: https://gerrit.gromacs.org/7411

#2 Updated by Mark Abraham 4 months ago

  • Related to Bug #2364: g_membed not working on gromacs 2018 added

#3 Updated by Mark Abraham 4 months ago

  • Description updated (diff)

#4 Updated by Erik Lindahl 4 months ago

  • Target version changed from 2018 to future

Changing target since we should not do the complete redesign of mtop handling in the release branch, and the bug has a separate id.

#5 Updated by Mark Abraham 4 months ago

  • Target version changed from future to 2018

Returning target since I don't think anybody has yet done:

Perhaps insert-molecules or genion is similarly broken? (check that for 2018, then re-target this task)

#6 Updated by Mark Abraham 4 months ago

  • Target version changed from 2018 to future

All the other code that writes .top files (x2top, insert-molecules, genion, pdb2gmx) is OK, mostly because they do simple text-based hacking.

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