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

[Christian Ehrhardt ]

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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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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