Re: Does the bowtie2 2.3.5.1-1 package work for anyone else?

2019-10-15 Thread Michael Crusoe 
On Mon, Oct 14, 2019 at 9:21 PM Alex Mestiashvili 
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
> > 7f14b12a393d sp 7fff11b4c000 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 0x77a3b414 in dlsym () from /lib/x86_64-linux-gnu/libdl.so.2
#196486 0x77f3a2eb in free () from
/usr/lib/x86_64-linux-gnu/libtbbmalloc_proxy.so.2
#196487 0x77a3b9bd in ?? () from /lib/x86_64-linux-gnu/libdl.so.2
These three lines repeat until the stack overflows

#196488 0x77a3b414 in dlsym () from /lib/x86_64-linux-gnu/libdl.so.2
#196489 0x77f3a2eb in free () from
/usr/lib/x86_64-linux-gnu/libtbbmalloc_proxy.so.2
#196490 0x77a737b9 in ?? () from /lib/x86_64-linux-gnu/libc.so.6
#196491 0x77a3b88c in dlerror () from
/lib/x86_64-linux-gnu/libdl.so.2
#196492 0x77fc092d in ?? () from /usr/lib/cowdancer/libcowdancer.so
#196493 0x77fc13a3 in fopen () from
/usr/lib/cowdancer/libcowdancer.so
#196494 0x7799d78d in void parseFile<100, 2>(char const*,
parseFileItem const (&) [2]) () from
/usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2
#196495 0x7799c35a in ?? () from
/usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2
#196496 0x7799c65d in ?? () from
/usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2
#196497 0x7799c870 in ?? () from
/usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2
#196498 0x7799c93c in scalable_calloc () from
/usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2
#196499 0x77f3a299 in calloc () from
/usr/lib/x86_64-linux-gnu/libtbbmalloc_proxy.so.2
#196500 0x77a3ba45 in ?? () from /lib/x86_64-linux-gnu/libdl.so.2
#196501 0x77a3b2e6 in dlopen () from
/lib/x86_64-linux-gnu/libdl.so.2
#196502 0x77990375 in ?? () from
/usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2
#196503 0x77fe45ba in ?? () from /lib64/ld-linux-x86-64.so.2
#196504 0x77fe46b9 in ?? () from /lib64/ld-linux-x86-64.so.2
#196505 0x77fd60ca in ?? () from /lib64/ld-linux-x86-64.so.2
#196506 0x0001 in ?? ()
#196507 0x7fffe477 in ?? ()
#196508 0x 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

https://orcid.org/-0002-2961-9670

m...@commonwl.org
+1 480 627 9108

Re: Does the bowtie2 2.3.5.1-1 package work for anyone else?

2019-10-15 Thread Michael Crusoe 
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 
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
>> > 7f14b12a393d sp 7fff11b4c000 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 0x77a3b414 in dlsym () from
> /lib/x86_64-linux-gnu/libdl.so.2
> #196486 0x77f3a2eb in free () from
> /usr/lib/x86_64-linux-gnu/libtbbmalloc_proxy.so.2
> #196487 0x77a3b9bd in ?? () from /lib/x86_64-linux-gnu/libdl.so.2
> These three lines repeat until the stack overflows
>
> #196488 0x77a3b414 in dlsym () from
> /lib/x86_64-linux-gnu/libdl.so.2
> #196489 0x77f3a2eb in free () from
> /usr/lib/x86_64-linux-gnu/libtbbmalloc_proxy.so.2
> #196490 0x77a737b9 in ?? () from /lib/x86_64-linux-gnu/libc.so.6
> #196491 0x77a3b88c in dlerror () from
> /lib/x86_64-linux-gnu/libdl.so.2
> #196492 0x77fc092d in ?? () from /usr/lib/cowdancer/libcowdancer.so
> #196493 0x77fc13a3 in fopen () from
> /usr/lib/cowdancer/libcowdancer.so
> #196494 0x7799d78d in void parseFile<100, 2>(char const*,
> parseFileItem const (&) [2]) () from
> /usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2
> #196495 0x7799c35a in ?? () from
> /usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2
> #196496 0x7799c65d in ?? () from
> /usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2
> #196497 0x7799c870 in ?? () from
> /usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2
> #196498 0x7799c93c in scalable_calloc () from
> /usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2
> #196499 0x77f3a299 in calloc () from
> /usr/lib/x86_64-linux-gnu/libtbbmalloc_proxy.so.2
> #196500 0x77a3ba45 in ?? () from /lib/x86_64-linux-gnu/libdl.so.2
> #196501 0x77a3b2e6 in dlopen () from
> /lib/x86_64-linux-gnu/libdl.so.2
> #196502 0x77990375 in ?? () from
> /usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2
> #196503 0x77fe45ba in ?? () from /lib64/ld-linux-x86-64.so.2
> #196504 0x77fe46b9 in ?? () from /lib64/ld-linux-x86-64.so.2
> #196505 0x77fd60ca in ?? () from /lib64/ld-linux-x86-64.so.2
> #196506 0x0001 in ?? ()
> #196507 0x7fffe477 in ?? ()
> #196508 0x 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
> 
> https://orcid.org/-0002-2961-9670
> 
> m...@commonwl.org
> +1 480 627 9108
>


-- 
Michael R. Crusoe
Co-founder & Lead, Common Workflow Language project

https://orcid.org/-0002-2961-9670

m...@commonwl.org
+1 480 627 9108