avogadrolibs: segfault in SpaceGroupTest.reduceToPrimitive via libsymspg

Avogadro version: 1.95

Avogadrolibs: 1.95.1
Qt: 5.15.2

**Desktop version: **

OS: Debian GNU/Linux
Version debian unstable (Linux 5.10.46)
Compiler g++ 10.2.1

Describe the bug

Running tests for the Debian build of Avogadrolibs: 1.95.1, I get a segfault at SpaceGroupTest.reduceToPrimitive

To Reproduce Steps to reproduce the behavior:

From the avogadrolibs source dir, build tests in a run_test subdir:

mkdir tests/run_test
cd tests/run_test

cmake -DAvogadroLibs_BINARY_DIR=/usr/include/ -Wno-dev ..
make AvogadroTests VERBOSE=1

Then run the tests (from the tests/run_test dir)

./core/AvogadroTests

See error

Expected behavior

All tests are expected to pass without error.

Screenshots A gdb backtrace reports:

...
[----------] 5 tests from SpaceGroupTest
[ RUN      ] SpaceGroupTest.getSpaceGroup
[       OK ] SpaceGroupTest.getSpaceGroup (19 ms)
[ RUN      ] SpaceGroupTest.reduceToPrimitive

Program received signal SIGSEGV, Segmentation fault.
0x00007ffff798e83d in _int_malloc (av=av@entry=0x7ffff7ac4b80 <main_arena>, bytes=bytes@entry=40) at malloc.c:3609
3609	malloc.c: No such file or directory.
(gdb) bt
#0  0x00007ffff798e83d in _int_malloc (av=av@entry=0x7ffff7ac4b80 <main_arena>, bytes=bytes@entry=40) at malloc.c:3609
#1  0x00007ffff7990164 in __GI___libc_malloc (bytes=40) at malloc.c:3058
#2  0x00007ffff78cac78 in ?? () from /lib/x86_64-linux-gnu/libsymspg.so.1
#3  0x00007ffff78cb2b3 in ?? () from /lib/x86_64-linux-gnu/libsymspg.so.1
#4  0x00007ffff78c6b80 in spa_search_spacegroup () from /lib/x86_64-linux-gnu/libsymspg.so.1
#5  0x00007ffff78ba082 in det_determine_all () from /lib/x86_64-linux-gnu/libsymspg.so.1
#6  0x00007ffff78c77ae in ?? () from /lib/x86_64-linux-gnu/libsymspg.so.1
#7  0x00007ffff7f20749 in Avogadro::Core::AvoSpglib::getHallNumber (mol=..., cartTol=1.0000000000000001e-05) at ./avogadro/core/avospglib.cpp:66
#8  0x00007ffff7f20f95 in Avogadro::Core::AvoSpglib::standardizeCell (mol=..., cartTol=1.0000000000000001e-05, toPrimitive=<optimized out>, idealize=<optimized out>) at ./avogadro/core/avospglib.cpp:181
#9  0x000055555566aaac in SpaceGroupTest_reduceToPrimitive_Test::TestBody() ()
#10 0x00005555556bd297 in void testing::internal::HandleExceptionsInMethodIfSupported<testing::Test, void>(testing::Test*, void (testing::Test::*)(), char const*) ()
#11 0x00005555556b267e in testing::Test::Run() ()
#12 0x00005555556b27d5 in testing::TestInfo::Run() ()
#13 0x00005555556b2c69 in testing::TestSuite::Run() ()
#14 0x00005555556b32b2 in testing::internal::UnitTestImpl::RunAllTests() ()
#15 0x00005555556bd807 in bool testing::internal::HandleExceptionsInMethodIfSupported<testing::internal::UnitTestImpl, bool>(testing::internal::UnitTestImpl*, bool (testing::internal::UnitTestImpl::*)(), char const*) ()
#16 0x00005555556b2898 in testing::UnitTest::Run() ()
#17 0x0000555555621b60 in main ()

Additional context

This is with external spglib (libsymspg1) 1.16.2

About this issue

Original URL
State: closed
Created 3 years ago
Comments: 15 (15 by maintainers)

Commits related to this issue

Be careful about assign or copy from molecules with no layers Not sure if this is the perfect solution, but it fixes #800 Might also fix #752 Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.co... — committed to ghutchis/avogadrolibs by ghutchis 3 years ago

Most upvoted comments

If you have other crashes, please create an issue with as much info as you have. I have ideas on a few of them and we can track them down.

#806 isn’t perfect - figuring out the correct solution will take longer - but if it fixes crashes, it’s a useful start.

ghutchis on Oct 6, 2021

Patch #806 seems to be working well enough. Not crashing anymore on SpaceGroupTest.reduceToPrimitive , https://ci.debian.net/data/autopkgtest/testing/amd64/a/avogadrolibs/15790439/log.gz

There’s a separate runtime crash related to changing the crystal cell, but I’m not certain how to reproduce it reliably. I guess it’s not related to this spglib crash anyway, certainly not in the unit tests.

I think we can consider this bug resolved by #806 .

drew-parsons on Oct 6, 2021

As for the spglib segfault, it’s reproduced on the debian CI machines on amd64, arm64, i386 at https://ci.debian.net/packages/a/avogadrolibs/ https://ci.debian.net/data/autopkgtest/testing/amd64/a/avogadrolibs/15777229/log.gz https://ci.debian.net/data/autopkgtest/testing/arm64/a/avogadrolibs/15777518/log.gz

[ RUN      ] SpaceGroupTest.reduceToPrimitive
malloc(): unaligned fastbin chunk detected 3
/tmp/autopkgtest-lxc.nu2ju37t/downtmp/build.KOt/src/debian/tests/test-avogadrolibs-cpp: line 9: 18678 Aborted                 ./core/AvogadroTests

drew-parsons on Oct 4, 2021

OK, let me know if there’s anything you need to to check or patch. I’ll upload avogadrolibs 1.95.1 now to check if clean builds on the Debian servers reproduce it. I guess the rest of the code is safe, so long as getHallNumber is not used.

drew-parsons on Oct 4, 2021