[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
** Changed in: ubuntu-z-systems Status: Triaged => Fix Released -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
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 -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
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) Status: New => Fix Released -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
FYI fixed in 1.2.4-7 which is coming our way via auto-sync -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
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 Importance: Unknown Status: Unknown -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
** Changed in: ubuntu-z-systems Importance: High => Medium ** Changed in: ubuntu-z-systems Status: New => Triaged -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
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 in: clustalo (Ubuntu) Status: New => Triaged ** Changed in: clustalo (Ubuntu) Importance: Undecided => Medium -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
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 --force Never the less, it now feels less an compiler and more like a code issue. I have updated my MP with the new insight but think we can leave it as-is until resolved in the Debian Packaging. [1]: https://salsa.debian.org/med- team/clustalo/-/merge_requests/1#note_203049 -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
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 clustalo[2aa0590+aa000] [520179.980842] Failing address: ddf7c000 TEID: ddf7c800 [520179.980843] Fault in primary space mode while using user ASCE. [520179.980845] AS:28f281c7 R3:0024 [520179.980852] CPU: 1 PID: 83822 Comm: clustalo Not tainted 5.8.0-25-generic #26-Ubuntu [520179.980853] Hardware name: IBM 2964 N63 400 (KVM/Linux) [520179.980855] User PSW : 070520018000 02aa059176e2 [520179.980857]R:0 T:1 IO:1 EX:1 Key:0 M:1 W:0 P:1 AS:0 CC:2 PM:0 RI:0 EA:3 [520179.980858] User GPRS: 0004 03ffddf7c838 ddf7c7d0 [520179.980859]02aa05e2b1d8 0001 02aa05e29f00 [520179.980860]03ffddf7c7e0 03ffddf7c840 0001 [520179.980860]03ffbe7abf98 03ffddf7c998 02aa05917682 03ffddf7c568 [520179.980872] User Code: 02aa059176d0: e330f0c80004 lg %r3,200(%r15) 02aa059176d6: e32090280004 lg %r2,40(%r9) #02aa059176dc: eb1a0002000d sllg %r1,%r10,2 >02aa059176e2: e3513014 lgf %r5,0(%r1,%r3) 02aa059176e8: e3418014 lgf %r4,0(%r1,%r8) 02aa059176ee: 6080f0c0 std %f8,192(%r15) 02aa059176f2: b9040037 lgr %r3,%r7 02aa059176f6: a7ab0001 aghi%r10,1 [520179.980883] Last Breaking-Event-Address: [520179.980893] [<03ffbe28d144>] 0x3ffbe28d144 -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
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: 2d0d5000 TEID: 2d0d5800 [2431454.082727] Fault in primary space mode while using user ASCE. [2431454.082729] AS:000e6fcb41c7 R3:0024 [2431454.082734] CPU: 3 PID: 1359979 Comm: clustalo Tainted: P O 5.4.0-51-generic #56-Ubuntu [2431454.082735] Hardware name: IBM 2964 N63 400 (LPAR) [2431454.082737] User PSW : 070520018000 02aa2d011028 [2431454.082739]R:0 T:1 IO:1 EX:1 Key:0 M:1 W:0 P:1 AS:0 CC:2 PM:0 RI:0 EA:3 [2431454.082741] User GPRS: 03ff0018 0002 2d0d5560 02aa2d0ba8e4 [2431454.082742]02aa2d0ba8e4 0007 0019 2d0d5560 [2431454.082743] 03ff0001 02aa2edaef70 03ff8a6767a0 [2431454.082744]03ff8a62bf98 02aa2d0baa80 02aa2d01a130 03ffcabfc350 [2431454.082753] User Code: 02aa2d01101a: b9040013 lgr %r1,%r3 02aa2d01101e: d207f0c0b028 mvc 192(8,%r15),40(%r11) #02aa2d011024: b9040034 lgr %r3,%r4 >02aa2d011028: 584020c0 l %r4,192(%r2) 02aa2d01102c: 1941 cr %r4,%r1 02aa2d01102e: a7240022 brc 2,02aa2d011072 02aa2d011032: eb110003000d sllg %r1,%r1,3 02aa2d011038: b9080021 agr %r2,%r1 [2431454.082765] Last Breaking-Event-Address: [2431454.082770] [<02aa2d01a12a>] 0x2aa2d01a12a -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
** 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 -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
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 failing binary" https://bugs.launchpad.net/ubuntu/+source/clustalo/+bug/1903817/+attachment/5435112/+files/clustalo-1.2.4-fail.tgz -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
TL;DR: "-O2 -fno-strict-aliasing is as broken as -O2, while -O0 still works" I'll attach logs of the three cases ... -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
** Attachment added: "buildlog O2 - failing" https://bugs.launchpad.net/ubuntu/+source/clustalo/+bug/1903817/+attachment/5435051/+files/O2.buildlog -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
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. -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
** Attachment added: "buildlog O0 - working" https://bugs.launchpad.net/ubuntu/+source/clustalo/+bug/1903817/+attachment/5435050/+files/O0.buildlog -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
** 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 -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
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 :-) -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
** Tags added: architecture-s39064 bugnameltc-189191 severity-high targetmilestone-inin2004 -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
** Changed in: ubuntu-z-systems Importance: Undecided => High -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
** 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 s390x -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
@Frank - could you get this properly tagged and mirrored so that the IBM gcc people could have a look? -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x
FYI: Temporary mitigation forwarded to Debian clustalo packaging at https://salsa.debian.org/med-team/clustalo/-/merge_requests/1 -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1903817 Title: Clustalo 1.2.4-6 segfaults on s390x To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
