[Debian-med-packaging] Bug#970344: ncbi-blast+: tblastn segfaults intermittently with multiple threads

[Aaron M. Ucko]

ucko at debian.org (Aaron M. Ucko) writes:

> FTR, the BTS accepted this attachment, thanks!  As proposed on -med, I
> will try to reproduce the bug under rr, though doing so isn't quite as
> straightforward as I'd hoped because rr emulates a single CPU; to
> compensate, I must temporarily patch out BLAST+'s logic to limit the
> thread count accordingly.

I captured this crash, but getting to the root cause turned out to be
difficult.  The good news is that the latest upstream 2.10.1 release
should include a pair of commits with promising messages:

  Fix tblastn mt issue (seqdb changes), JIRA:SB-2784 [1]
  Fix tblastn mt issue (engine changes),JIRA:SB-2784 [2]

It also contains at least one x86ism I'll need to conditionalize
appropriately, but that should be straightforward enough.

As such, I plan to put further investigation on hold in hopes that the
upgrade will suffice, and to take care of the latter when I get a chance.

[1] https://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=89479
[2] https://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=89480

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu