Open
Conversation
HaoZeke
force-pushed
the
realDomDec
branch
5 times, most recently
from
5c0cd25 to
d3505c6
Compare
Member
Author
|
This is now consistent, with |
since GMX_LOG is rank 0 only, and cerr is not allowed as per GROMACS style guides
1. The bonded interaction building (make_bondeds_zone) runs for all zones but won't find any cross-zone bondeds when !hasInterAtomicInteractions() — it's a no-op for the extra zones 2. The exclusion building (make_exclusions_zone) correctly builds exclusion entries for all i-zone atoms, satisfying the pairlist assertion Added nzone_bondeds = std::max(nzone_bondeds, numIZonesForExclusions) to ensure the exclusion building loop covers all i-zones when intermolecularExclusionGroup is present. Without this, 3D DD (e.g., 2x2x2 with 8 ranks) has numIZones=4 but nzone_bondeds=1, so exclusion lists are only built for zone 0 atoms while the nbnxm assertion expects them for zones 0-3.
1. localToModelIndex_ sized to numLocalPlusHalo instead of signal.x_.size() (was OOB write) 2. augmentGhostPairs rewritten to correctly identify halo MTA atoms by iterating localToModelIndex_ from numLocalAtoms_ onward, instead of incorrectly slicing the full coordinate array 3. Shift vector computed as pair.dx() - (positions_[B] - positions_[A]) in model-space, then rounded to integer cell shifts and recomputed from box vectors for consistency 4. Deduplication of pairs using std::set<tuple> to handle overlap between signal pairs and augmented halo-halo pairs 5. Timer instrumentation via MetatomicTimer RAII class around key phases
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Look away until
vesin#3nnpotstyle implementation #1Or "real domain decomposition"..
Basically the LAMMPS style where the model loads everywhere, computes on every rank.
WIP. Needs testing to ensure consistency.All set. Closes #7.