Bug #676

g_pme_error does not work with threads

Added by Justin Lemkul over 9 years ago. Updated over 7 years ago.

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


When building the latest version of the manual and calling executables produced with the most recent version in release-4-5-patches, I noticed "Abort trap" when running mkman. It came from g_pme_error, which, when executed by itself, gave:

./g_pme_error -h
tMPI error: Invalid tMPI_Comm
Abort trap

Re-configuring without threads fixed the problem.


#1 Updated by Justin Lemkul over 9 years ago

  • Assignee deleted (David van der Spoel)

#2 Updated by Mark Abraham over 9 years ago

Yes g_pme_error wasn't contributed by a regular GROMACS developer, so probably doesn't follow all the development guidelines. It certainly uses MPI, and its development probably predates the existence of threading in GROMACS.

I'm also aware of at least one array-indexing bug in it, which I'll deal with at some point.

#3 Updated by Florian Dommert about 8 years ago

Have you still an idea, where the indexing bug was. The problem with threads is solved in a new upcoming version, as it now does either compile with MPI support or runs only in serial, if tMPI or OpenMP is requested.

#4 Updated by Mark Abraham about 8 years ago

IIRC it was in generating the lookup index for some table. I thought I still had a repo where I fixed it for my own use, but I can't find that on the machines I can access right now. Will try another machine when I get a chance.

#5 Updated by Florian Dommert about 8 years ago

OK. If it has been in the lookup tables, then it is most probably gone, because the new error estimate is based on another method and uses completely new tables.

#6 Updated by Roland Schulz over 7 years ago

  • Status changed from New to Feedback wanted

It this problem fixed as Florian says? Or does it still occur?

#7 Updated by Justin Lemkul over 7 years ago

  • Status changed from Feedback wanted to Closed

Version 4.5.5 works as expected. Closing the issue.

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