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Bug #2257

Vsites not constructed for inital decomposition with threads

Added by Berk Hess about 2 years ago. Updated almost 2 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
mdrun
Target version:
Affected version - extra info:
any version with OpenMP threading
Affected version:
Difficulty:
uncategorized
Close

Associated revisions

Revision ccf60bde (diff)
Added by Berk Hess about 2 years ago

Improve vsite parallel checking

The vsite struct now stores internally whether it has been configured
with domain decomposition. This allows for internal checks on valid
commrec, which have now been added.
The vsite constructor now initializes to atom range to invalid values,
so we can check that the thread splitting has been called before
constructing. This would have caught bug #2257.
Removed the vsite struct from the global construct function argument
list, which simplifies the vsite code in several places and
fixes #2257.

Also some general clean-up: removed some snews, added some camelCasing
and doxygen documentation.

More renaming would be beneficial, but should be a separate commit.

Change-Id: I467ec8b8ebfa0da090d4ac0a1d096ad9fab87eb5

History

#1 Updated by Gerrit Code Review Bot about 2 years ago

Gerrit received a related patchset '1' for Issue #2257.
Uploader: Berk Hess ()
Change-Id: gromacs~master~I467ec8b8ebfa0da090d4ac0a1d096ad9fab87eb5
Gerrit URL: https://gerrit.gromacs.org/6965

#2 Updated by Berk Hess about 2 years ago

  • Subject changed from Vsites not constructed for inital coordinates with periodic molecules and threads to Vsites not constructed for inital decomposition with threads
  • Status changed from In Progress to Fix uploaded

At the start of a, non-continuation, simulation the virtual sites are not constructed before the first domain decomposition partitioning when using OpenMP threading. This is because the thread work data structures have a zero work range. There is a second partitioning which occurs after a second, correct virtual site construction, so likely this bug has not lead to any incorrect results.

#3 Updated by Gerrit Code Review Bot about 2 years ago

Gerrit received a related DRAFT patchset '1' for Issue #2257.
Uploader: Berk Hess ()
Change-Id: gromacs~master~I26d0422ac2d95f21dcb6aef297110938acc991d7
Gerrit URL: https://gerrit.gromacs.org/6967

#4 Updated by Gerrit Code Review Bot about 2 years ago

Gerrit received a related DRAFT patchset '1' for Issue #2257.
Uploader: Berk Hess ()
Change-Id: gromacs~master~I60d28af78b26db2d64c77834ca21772b7ec9b825
Gerrit URL: https://gerrit.gromacs.org/6969

#5 Updated by Berk Hess about 2 years ago

  • Status changed from Fix uploaded to Resolved

#6 Updated by Mark Abraham almost 2 years ago

  • Status changed from Resolved to Closed

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