[Bug 1903817] [NEW] Clustalo 1.2.4-6 segfaults on s390x
Christian Ehrhardt
1903817 at bugs.launchpad.net
Wed Nov 11 08:46:05 UTC 2020
Public bug reported:
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
** Affects: ubuntu-z-systems
Importance: Undecided
Assignee: bugproxy (bugproxy)
Status: New
** Affects: clustalo (Ubuntu)
Importance: Undecided
Status: New
** Affects: gcc-10 (Ubuntu)
Importance: Undecided
Status: New
** Tags: reverse-proxy-bugzilla s390x update-excuse
** Also affects: gcc-10 (Ubuntu)
Importance: Undecided
Status: New
** Tags added: update-excuse
--
You received this bug notification because you are a member of Ubuntu
Foundations Bugs, which is subscribed to gcc-10 in Ubuntu.
https://bugs.launchpad.net/bugs/1903817
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
To manage notifications about this bug go to:
https://bugs.launchpad.net/ubuntu-z-systems/+bug/1903817/+subscriptions
More information about the foundations-bugs
mailing list