** Changed in: ubuntu-z-systems
Status: Triaged => Fix Released
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https://bugs.launchpad.net/bugs/1903817
Title:
Clustalo 1.2.4-6 segfaults on s390x
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Thanks - build and migrated in Ubuntu as well
https://launchpad.net/ubuntu/+source/clustalo/1.2.4-7
** Changed in: clustalo (Ubuntu)
Status: Triaged => Fix Released
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Fixed in Debain unstable clustalo 1.2.4-7
** Changed in: clustalo (Debian)
Importance: Unknown => Undecided
** Changed in: clustalo (Debian)
Status: Unknown => New
** Changed in: clustalo (Debian)
Remote watch: Debian Bug tracker #975511 => None
** Changed in: clustalo (Debian)
FYI fixed in 1.2.4-7 which is coming our way via auto-sync
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Title:
Clustalo 1.2.4-6 segfaults on s390x
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FYI: Also filed as Debian bug (linked here) and got a response on the
Debian MR.
** Bug watch added: Debian Bug tracker #975511
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=975511
** Also affects: clustalo (Debian) via
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=975511
** Changed in: ubuntu-z-systems
Importance: High => Medium
** Changed in: ubuntu-z-systems
Status: New => Triaged
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Title:
Clustalo
Thank you Andreas and Stefan,
I've pinged the Debian MR [1] and upstream (via Mail which you are on CC) about
it.
Let us see how things evolve from here.
[1]: https://salsa.debian.org/med-team/clustalo/-/merge_requests/1
** Changed in: gcc-10 (Ubuntu)
Status: New => Invalid
** Changed
Segfault avoidable (thanks AndiKr) if we set OMP_NUM_THREADS, but that
is just hiding the underlying issue which probably is code that isn't
s390x compatible.
OMP_NUM_THREADS=1 src/clustalo -i debian/tests/biopython_testdata/f002
--guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal
The crash happens in 5.4.0-51-generic and a Hirsute LXD container therein.
But also in a Hirsute VM under 5.8.0-25-generic
On the latter the crash looks like (similar):
[520179.980824] report_user_fault: 5 callbacks suppressed
[520179.980827] User process fault: interruption code 003b ilc:3 in
In a discussion with Andreas we failed to break it in his environment
but it reliably failed in mine. Then I found the crash in dmesg, there
it looks like this:
[2431454.082712] User process fault: interruption code 003b ilc:2 in
clustalo[2aa2d00+d4000]
[2431454.082725] Failing address:
** Attachment added: "Core dump gatheres in a Hirsute s390x VM with
5.8.0-25-generic - matches the source/build tarball formerly attached"
https://bugs.launchpad.net/ubuntu/+source/clustalo/+bug/1903817/+attachment/5435116/+files/core.0.84593.1605606619.tar.gz
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As discussed via IRC here a tarball of my build result (the whole tree)
Executing this in it segfaults:
src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out
temp_test.dnd -o temp_test.aln --outfmt clustal --force
** Attachment added: "tar of the built tree that contains the
TL;DR: "-O2 -fno-strict-aliasing is as broken as -O2, while -O0 still works"
I'll attach logs of the three cases ...
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Title:
Clustalo 1.2.4-6
** Attachment added: "buildlog O2 - failing"
https://bugs.launchpad.net/ubuntu/+source/clustalo/+bug/1903817/+attachment/5435051/+files/O2.buildlog
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As I said it is 100% reproducible and should be for you as well if you
follow my steps I mentioned in the report.
Let me know if you see anything in the logs that you need me to work on,
otherwise all that is left for me is wishing you best luck with
debugging.
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** Attachment added: "buildlog O0 - working"
https://bugs.launchpad.net/ubuntu/+source/clustalo/+bug/1903817/+attachment/5435050/+files/O0.buildlog
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** Attachment added: "buildlog O2 fno-strict-aliasing - failing as well"
https://bugs.launchpad.net/ubuntu/+source/clustalo/+bug/1903817/+attachment/5435052/+files/O2-fno-strict-aliasing.buildlog
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I haven't seen any suspicious warnings myself, but I can retry
with/without -fno-strict-aliasing and attach the log for your own
consideration.
And BTW o/ Andreas :-)
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** Tags added: architecture-s39064 bugnameltc-189191 severity-high
targetmilestone-inin2004
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Title:
Clustalo 1.2.4-6 segfaults on s390x
To
** Changed in: ubuntu-z-systems
Importance: Undecided => High
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Title:
Clustalo 1.2.4-6 segfaults on s390x
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** Also affects: ubuntu-z-systems
Importance: Undecided
Status: New
** Changed in: ubuntu-z-systems
Assignee: (unassigned) => Frank Heimes (fheimes)
** Changed in: ubuntu-z-systems
Assignee: Frank Heimes (fheimes) => bugproxy (bugproxy)
** Tags added: reverse-proxy-bugzilla
@Frank - could you get this properly tagged and mirrored so that the IBM
gcc people could have a look?
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Title:
Clustalo 1.2.4-6 segfaults on
FYI: Temporary mitigation forwarded to Debian clustalo packaging at
https://salsa.debian.org/med-team/clustalo/-/merge_requests/1
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