[Bug 1903817] Re: Clustalo 1.2.4-6 segfaults on s390x

[Christian Ehrhardt ]

** 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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Title:
  Clustalo 1.2.4-6 segfaults on s390x

Status in Ubuntu on IBM z Systems:
  New
Status in clustalo package in Ubuntu:
  New
Status in gcc-10 package in Ubuntu:
  New

Bug description:
  Hi,
  with gcc-10.2 clustalo segfaults on s390x.

  First of all I beg your pardon, but I didn't find an upstream  bug tracker for custalo but
  think you should be aware. But furthermore I think this might eventually be a gcc bug (or at least needs the s390x gcc experts to look at).
  I decided to open this bug to track things and have a joint conversation, but then ping the custalo mail about it and let it be mirrored to IBM.

  Issue:
  I see this with the test used in Debian:
    # Run additional test from python-biopython package to verify that
    # this will work as well
    src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal --force

  We run into this segfault:
  Thread 9 "clustalo" received signal SIGSEGV, Segmentation fault.
  [Switching to Thread 0x3fff9ef8870 (LWP 55818)]
  0x000002aa000176e2 in PairDistances._omp_fn.0 () at pair_dist.c:353
  353	                KTuplePairDist((*distmat), mseq, iChunkStarts[iChunk], 
  (gdb) bt
  #0  0x000002aa000176e2 in PairDistances._omp_fn.0 () at pair_dist.c:353
  #1  0x000003fffdaa2066 in gomp_thread_start (xdata=<optimized out>) at ../../../src/libgomp/team.c:123
  #2  0x000003fffd709556 in start_thread (arg=0x3fff9ef8870) at pthread_create.c:463
  #3  0x000003fffd921d46 in thread_start () at ../sysdeps/unix/sysv/linux/s390/s390-64/clone.S:65

  Debugging showed that this is depending on the optimization, when I build
  with -O0 (for debugging) the problem goes away.

  A usual build uses -O3 (from the build system) followed by -g -O2 (from the
  default Debian build flags). For the time being we can avoid the issue by
  setting -O0 there. But I wanted to ask if this is something you could look into?

  In valgrind I see this reported as "Invalid read of size 4"

  In the backtrace it is:
  gdb) p $_siginfo
  $3 = {si_signo = 11, si_errno = 0, si_code = 1, _sifields = {_pad = {0, -16384, 0 <repeats 26 times>}, _kill = {si_pid = 0, si_uid = 4294950912}, _timer = {si_tid = 0, si_overrun = -16384,
        si_sigval = {sival_int = 0, sival_ptr = 0x0}}, _rt = {si_pid = 0, si_uid = 4294950912, si_sigval = {sival_int = 0, sival_ptr = 0x0}}, _sigchld = {si_pid = 0, si_uid = 4294950912,
        si_status = 0, si_utime = 0, si_stime = 0}, _sigfault = {si_addr = 0xffffc000}, _sigpoll = {si_band = 4294950912, si_fd = 0}}}

  The instructions are
  │   0x2aa000176d6 <PairDistances._omp_fn.0+246>     lg      %r2,40(%r9)                                                                                                                       │
  │   0x2aa000176dc <PairDistances._omp_fn.0+252>     sllg    %r1,%r10,2                                                                                                                        │
  │  >0x2aa000176e2 <PairDistances._omp_fn.0+258>     lgf     %r5,0(%r1,%r3)                                                                                                                    │
  │   0x2aa000176e8 <PairDistances._omp_fn.0+264>     lgf     %r4,0(%r1,%r8)

  So it tries to load from
  r3             0xffffcf80          4294954880
  + r1             0x24                36
  into r5

  And that matches the segfault address of si_addr = 0xffffc000

  @IBM
  to reproduce:
  1. get an Ubuntu 20.10 system on s390x (or anything with gcc-10.2 while OTOH it seems gcc-10 was fine).
  2. edit /etc/apt/sources.list
    2a) add deb-src lines to be able to get the source
    2b) enable proposed to be able to get custalo 1.2.4-6
  3. run the build
    $ ./debian/rules build
  This will end in the crash that is to debug.

  @Custalo people:
  If you need s390x system access please check out the IBM Community cloud [1][2]
  which should give you a free VM.

  [1]: https://developer.ibm.com/components/ibm-linuxone/gettingstarted/?_ga=2.85909726.636290536.1605082467-259352313.1597225455
  [2]: https://zcloud.marist.edu/#/login

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