Project

General

Profile

Bug #1631

Triclinic 1xNx1 domain decomposition with Verlet scheme gives incorrect results

Added by Berk Hess almost 5 years ago. Updated over 4 years ago.

Status:
Closed
Priority:
High
Assignee:
Berk Hess
Category:
mdrun
Target version:
4.6.8
Affected version - extra info:
5.0
Affected version:
4.6
Difficulty:
uncategorized
Close

Description

With the Verlet scheme and triclinic boxes, a 1D decomposition over y, i.e. 1xNx1, produces incorrect bounding boxes for the non-bonded grid, which results in missing non-bonded interactions. Unless box angles are very close to 90 degrees, many interactions will be missing and the system will crash after a few steps.
This was never noticed before, because the default 1D domain decomposition is Nx1x1, unless the box is longer in y than in x. Because the high number of missing interactions makes the system crash quickly, this will not lead to silent errors.

Associated revisions

Revision c8d919a3 (diff)
Added by Berk Hess almost 5 years ago

Fixed triclinic 1xNx1 domain decomposition

With the Verlet scheme, 1D triclinic domain decomposition along
dimension y produces incorrect bounding boxes for the non-bonded grid.
This led to a lot of missing non-bonded interactions, which quickly
crashes any simulation affected by this.
Fixes #1631.

Change-Id: I9bd1fc9d983be839e0c9a8e62d47f6cf17684a03

Revision 29b6eedc (diff)
Added by Berk Hess almost 5 years ago

Fix recent bug with trilinic 1D DD

A recent bug-fix (c8d919a3) for triclinic 1D domain decompostion
introduced a bug for boxes with box[YY][XX]!=0.
Fixes #1656.
Refs #1631.

Change-Id: I06b9376212390b73e90a3ce9704dee2bad9693fb

Revision 61f49916 (diff)
Added by Berk Hess almost 5 years ago

Add test cases to show bugs are fixed

  • octahedron adds a fully trilinic test case
  • dd121 adds a test case that will default to more
    ranks in a direction other than X (here, Y)

The reference data is generated with a "last known good" patch from
release-5-0 from before the fix for #1631 was introduced, not that it
really matters. The reference build is unaffected by any of the bugs,
because it runs single-core.

Refs #1631, #1656

Change-Id: I46c63a91aaae19a37bbe39e0c973cb9888019591

History

#1 Updated by Gerrit Code Review Bot almost 5 years ago

Gerrit received a related patchset '1' for Issue #1631.
Uploader: Berk Hess ()
Change-Id: I9bd1fc9d983be839e0c9a8e62d47f6cf17684a03
Gerrit URL: https://gerrit.gromacs.org/4177

#2 Updated by Gerrit Code Review Bot almost 5 years ago

Gerrit received a related patchset '1' for Issue #1631.
Uploader: Berk Hess ()
Change-Id: I06b9376212390b73e90a3ce9704dee2bad9693fb
Gerrit URL: https://gerrit.gromacs.org/4276

#3 Updated by Berk Hess over 4 years ago

  • Status changed from In Progress to Closed

Also available in: Atom PDF