Interestingly using docker I can run the package, so it is some sort of chroot/Ubuntu bug :-(
On Tue, Oct 15, 2019 at 10:19 AM Michael Crusoe <michael.cru...@gmail.com> wrote: > > > On Mon, Oct 14, 2019 at 9:21 PM Alex Mestiashvili < > ames...@rsh2.donotuse.de> wrote: > >> On 10/14/19 7:26 PM, Michael Crusoe wrote: >> > I can't get it to build from source in a cowbuilder "sid" chroot on my >> > laptop, which is currently running Ubuntu Bionic with the >> 5.0.0-20-generic >> > #21~18.04.1-Ubuntu kernel. >> > >> > running bowtie2-build --usage (or anything) results in a segfault >> > >> > [34760.926015] bowtie2-align-s[19983]: segfault at 7fff11b4bff8 ip >> > 00007f14b12a393d sp 00007fff11b4c000 error 6 in libdl-2.29.so >> > [7f14b12a3000+1000] >> > [34760.926022] Code: e8 28 f7 ff ff e9 42 ff ff ff e8 3e f7 ff ff 66 66 >> 2e >> > 0f 1f 84 00 00 00 00 00 0f 1f 00 48 83 3d 90 26 00 00 00 41 54 49 89 fc >> > <55> 48 89 f5 53 74 7c 48 8d 35 05 fc ff ff 48 8d 3d 76 27 00 00 e8 >> >> Just managed to build git cloned bowtie2 on Buster and Bionic, both >> work. The one in LXC with Sid is working too. >> As a wild guess, what is ulimit -s for the shell? >> > > In my sid cowbuilder it is > $ ulimit -s > 8192 > > outside it is > $ ulimit -s > 16384 > > >> May be disabling apparmor helps? >> > > Good idea, but no change. > > Here's the backtrace > > #196485 0x00007ffff7a3b414 in dlsym () from > /lib/x86_64-linux-gnu/libdl.so.2 > #196486 0x00007ffff7f3a2eb in free () from > /usr/lib/x86_64-linux-gnu/libtbbmalloc_proxy.so.2 > #196487 0x00007ffff7a3b9bd in ?? () from /lib/x86_64-linux-gnu/libdl.so.2 > These three lines repeat until the stack overflows > > #196488 0x00007ffff7a3b414 in dlsym () from > /lib/x86_64-linux-gnu/libdl.so.2 > #196489 0x00007ffff7f3a2eb in free () from > /usr/lib/x86_64-linux-gnu/libtbbmalloc_proxy.so.2 > #196490 0x00007ffff7a737b9 in ?? () from /lib/x86_64-linux-gnu/libc.so.6 > #196491 0x00007ffff7a3b88c in dlerror () from > /lib/x86_64-linux-gnu/libdl.so.2 > #196492 0x00007ffff7fc092d in ?? () from /usr/lib/cowdancer/libcowdancer.so > #196493 0x00007ffff7fc13a3 in fopen () from > /usr/lib/cowdancer/libcowdancer.so > #196494 0x00007ffff799d78d in void parseFile<100, 2>(char const*, > parseFileItem const (&) [2]) () from > /usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2 > #196495 0x00007ffff799c35a in ?? () from > /usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2 > #196496 0x00007ffff799c65d in ?? () from > /usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2 > #196497 0x00007ffff799c870 in ?? () from > /usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2 > #196498 0x00007ffff799c93c in scalable_calloc () from > /usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2 > #196499 0x00007ffff7f3a299 in calloc () from > /usr/lib/x86_64-linux-gnu/libtbbmalloc_proxy.so.2 > #196500 0x00007ffff7a3ba45 in ?? () from /lib/x86_64-linux-gnu/libdl.so.2 > #196501 0x00007ffff7a3b2e6 in dlopen () from > /lib/x86_64-linux-gnu/libdl.so.2 > #196502 0x00007ffff7990375 in ?? () from > /usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2 > #196503 0x00007ffff7fe45ba in ?? () from /lib64/ld-linux-x86-64.so.2 > #196504 0x00007ffff7fe46b9 in ?? () from /lib64/ld-linux-x86-64.so.2 > #196505 0x00007ffff7fd60ca in ?? () from /lib64/ld-linux-x86-64.so.2 > #196506 0x0000000000000001 in ?? () > #196507 0x00007fffffffe477 in ?? () > #196508 0x0000000000000000 in ?? () > > >> >> > >> > But maybe it is just my system and someone else could confirm on a real >> > Debian sid/unstable system without >> virtualization/chroot/containerization. >> >> There is no point in excluding any kind of >> virtualization/chroot/containerization IMHO. >> > > Agreed; and I wanted to do a sanity check first > > >> >> Best, >> Alex >> >> > > -- > Michael R. Crusoe > Co-founder & Lead, Common Workflow Language project > <http://www.commonwl.org/> > https://orcid.org/0000-0002-2961-9670 > <https://impactstory.org/u/0000-0002-2961-9670> > m...@commonwl.org > +1 480 627 9108 > -- Michael R. Crusoe Co-founder & Lead, Common Workflow Language project <http://www.commonwl.org/> https://orcid.org/0000-0002-2961-9670 <https://impactstory.org/u/0000-0002-2961-9670> m...@commonwl.org +1 480 627 9108
