Bug #2736

bug in domain decomposition of dims without PBC

Added by Berk Hess 15 days ago. Updated 4 days ago.

Target version:
Affected version - extra info:
Affected version:


The aminoacids test, which uses the group scheme, can produce incorrect forces at step 0. Up till now this has only been seen with gcc-8, no GPU. Both release and release-with-debug are affected, both no SIMD and AVX-256. Up till now I have only reproduced this with 6 tMPI ranks, dd 3x1x2, not with 1 or 4.

Related issues

Has duplicate GROMACS - Bug #2745: complex/aminoacids test fails with DD errorClosed

Associated revisions

Revision d536de3b (diff)
Added by Berk Hess 12 days ago

Fix bug with DD for dims without PBC

When using DD along dimensions without PBC, many pair forces could
be missing. This would not cause silent errors, except when only
running a few steps.

Fixes #2736

Change-Id: Ia256b907e25eef811e1c8f348dc0a78aaddb5610


#1 Updated by Berk Hess 15 days ago

Found the point where it goes wrong:
17978 Thread 6:
17978 Conditional jump or move depends on uninitialised value(s)
17978 at 0x4599C5: float const& std::min<float>(float const&, float const&) (stl_algobase.h:200)
17978 by 0x825671: dd_move_cellx(gmx_domdec_t*, gmx_ddbox_t const*, float*, float*) (partition.cpp:371)
17978 by 0x826E50: comm_dd_ns_cell_sizes(gmx_domdec_t*, gmx_ddbox_t*, float*, float*, long) (partition.cpp:822)

#2 Updated by Gerrit Code Review Bot 14 days ago

Gerrit received a related patchset '1' for Issue #2736.
Uploader: Berk Hess ()
Change-Id: gromacs~release-2019~Ia256b907e25eef811e1c8f348dc0a78aaddb5610
Gerrit URL:

#3 Updated by Berk Hess 14 days ago

  • Subject changed from aminoacids test fails with gcc-8 to bug in domain decomposition of dims without PBC
  • Status changed from In Progress to Fix uploaded
  • Assignee set to Berk Hess
  • Priority changed from Normal to High
  • Target version set to 2019-beta3
  • Affected version - extra info set to 2019-beta1
  • Affected version changed from 2019-beta1 to 2019-beta2

#4 Updated by Szilárd Páll 13 days ago

  • Has duplicate Bug #2745: complex/aminoacids test fails with DD error added

#5 Updated by Berk Hess 12 days ago

  • Status changed from Fix uploaded to Resolved

#6 Updated by Berk Hess 4 days ago

  • Status changed from Resolved to Closed

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