Bug#970344: ncbi-blast+: tblastn segfaults intermittently with multiple threads
Hi Aaron, Aaron M. Ucko, on 2020-09-15 16:01:33 -0400: > 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. Sounds good to me, we may work the issue around by single threading execution of tblastn in the meantime, and use this bug as reference when we hit this problem again. Thanks for your investigations, -- Étienne Mollier Old rsa/3072: 5ab1 4edf 63bb ccff 8b54 2fa9 59da 56fe fff3 882d New rsa/4096: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/2, please excuse my verbosity. signature.asc Description: PGP signature
Bug#970344: ncbi-blast+: tblastn segfaults intermittently with multiple threads
u...@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=89479 [2] https://www.ncbi.nlm.nih.gov/viewvc/v1?view=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/?a...@monk.mit.edu
Bug#970344: ncbi-blast+: tblastn segfaults intermittently with multiple threads
Étienne Mollier writes: > * temp_gene_seqs.fasta, which I try to attach to the present > report if the engine accepts attachments of 264 kiB; it is 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. -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu
