On 23/11/2019 20.30, Andreas Beckmann wrote: > Control: affects 941933 + src:polymake > Control: retitle -1 polymake: FTBFS with normaliz 3.8.1: segfaults during > tests > > On 23/11/2019 10.45, Benjamin Lorenz wrote: >> On 22/11/2019 22.06, Andreas Beckmann wrote: >>> polymake FTBFS against perl 5.30: > >> This was already reported and should be fixed with >> https://bugs.debian.org/941933 >> but it seems that the builds need to be triggered again as the logs are >> older than the normaliz 3.8.1+ds-1 upload. > > OK, tried my first self-served give-backs ... > > ... some architectures succeeed (arm64, s390x), some had tests failing > with segmentation faults (amd64, i386, armhf, ppc64el), mips*el is > still building. > > https://buildd.debian.org/status/package.php?p=polymake&suite=unstable > > Andreas >
tldr: please rebuild normaliz and then try polymake again. This is very weird but after some digging through backtraces, headers and bugzilla I am quite sure that this is caused by: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=92267 The effect is that using the same std::deque template instantiation in different libraries built with gcc 8 and gcc 9 can cause segfaults because of an ABI incompatibility. In this case libppl.so.14.0.0 was built with gcc 8 and libnormaliz with gcc 9 (9.2.1-12), both of them are using std::deque<bool>. My build for polymake was with gcc 9 (9.2.1-19). So I rebuilt ppl which to my surprise didn't help, but then I noticed that debian already backported the fix for the gcc bug to gcc 9.2.1-16 (see https://tracker.debian.org/news/1075824/accepted-gcc-9-921-16-source-into-unstable/). This means that instead of ppl only normaliz needed to be rebuilt with gcc >= 9.2.1-16. Some logs from my experiments (rebuilding polymake is not necessary for testing this, just switching out the other libraries): ### current normaliz build from unstable (ppl as well): $ file /usr/lib/x86_64-linux-gnu/libnormaliz.so.3.8.1 /usr/lib/x86_64-linux-gnu/libnormaliz.so.3.8.1: ELF 64-bit LSB shared object, x86-64, version 1 (GNU/Linux), dynamically linked, BuildID[sha1]=49042b16a0c8fd0e5ecec9aa50e4fcf70842b8d5, stripped $ objdump -s -j .comment /usr/lib/debug/.build-id/49/042b16a0c8fd0e5ecec9aa50e4fcf70842b8d5.debug Contents of section .comment: 0000 4743433a 20284465 6269616e 20392e32 GCC: (Debian 9.2 0010 2e312d31 32292039 2e322e31 20323031 .1-12) 9.2.1 201 0020 39313032 3200 91022. lorenz@debian-unstable-amd64:~/polymake-3.2r4$ perl perl/polymake --script run_testcases --applications polytope --examples totally_dual_integral *** Testing in application polytope *** testing Examples: [ /functions/Optimization/totally_dual_integral ] 1Segmentation fault ### Installing my new local normaliz build: # dpkg -i libnormaliz-dev_3.8.1+ds-1_amd64.deb libnormaliz-dev-common_3.8.1+ds-1_all.deb libnormaliz3_3.8.1+ds-1_amd64.deb libnormaliz3-dbgsym_3.8.1+ds-1_amd64.deb $ file /usr/lib/x86_64-linux-gnu/libnormaliz.so.3.8.1 /usr/lib/x86_64-linux-gnu/libnormaliz.so.3.8.1: ELF 64-bit LSB shared object, x86-64, version 1 (GNU/Linux), dynamically linked, BuildID[sha1]=836dd385fe81deb4ca8b25dc9552a677ec24cc48, stripped $ objdump -s -j .comment /usr/lib/debug/.build-id/83/6dd385fe81deb4ca8b25dc9552a677ec24cc48.debug Contents of section .comment: 0000 4743433a 20284465 6269616e 20392e32 GCC: (Debian 9.2 0010 2e312d31 39292039 2e322e31 20323031 .1-19) 9.2.1 201 0020 39313130 3900 91109. $ perl perl/polymake --script run_testcases --applications polytope --examples "totally_dual_integral" *** Testing in application polytope *** testing Examples: [ /functions/Optimization/totally_dual_integral ] 1 OK *** Summary *** *** All tests successful *** For reference the top of the backtrace for the segfault with some weird values for __n and __pos for the std::deque: [ /functions/Optimization/totally_dual_integral ] 1 Program received signal SIGSEGV, Segmentation fault. 0x00007ffff114972c in std::deque<bool, std::allocator<bool> >::_M_fill_insert (this=0x7fffffffab88, __pos=<error reading variable: Cannot access memory at address 0x14>, __n=140737488330560, __x=<error reading variable>) at /usr/include/c++/8/bits/deque.tcc:305 305 /usr/include/c++/8/bits/deque.tcc: No such file or directory. (gdb) bt #0 0x00007ffff114972c in std::deque<bool, std::allocator<bool> >::_M_fill_insert (this=0x7fffffffab88, __pos=<error reading variable: Cannot access memory at address 0x14>, __n=140737488330560, __x=<error reading variable>) at /usr/include/c++/8/bits/deque.tcc:305 #1 0x00007ffff0f110af in std::deque<bool, std::allocator<bool> >::resize (this=0x7fffffffab88, __new_size=<optimized out>, __x=<optimized out>) at /usr/include/c++/9/bits/stl_deque.h:757 #2 0x00007ffff0f14a77 in libnormaliz::Full_Cone<long long>::Full_Cone (this=0x7fffffffa0f0, M=..., do_make_prime=<optimized out>) at /usr/include/c++/9/bits/stl_vector.h:915 #3 0x00007ffff0e579cf in libnormaliz::Cone<__gmp_expr<__mpz_struct [1], __mpz_struct [1]> >::compute_full_cone<long long> (this=this@entry=0x7fffffffc380, ToCompute=...) at ../../source/libnormaliz/cone.cpp:2899 Benjamin
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