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