[cctbxbb] CentOS7 bugs (cont.)

Nicholas Sauter nksauter at lbl.gov
Tue Sep 29 10:20:45 PDT 2015


Nigel,

Do remember how to force libtbx.scons to scan the boost directory?

Nick

On Tue, Sep 29, 2015 at 9:25 AM, Nigel Moriarty <nwmoriarty at lbl.gov> wrote:

> Markus
>
> The default usage of libtbx.scons in the build directory does not scan the
> boost directory so maybe that has something to do with the .so not behaving
> on Centos7 - because it was built on Centos5/6?
>
> Cheers
>
> Nigel
>
> ---
> Nigel W. Moriarty
> Building 33R0349, Physical Biosciences Division
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov
>
> On Tue, Sep 29, 2015 at 8:29 AM, <markus.gerstel at diamond.ac.uk> wrote:
>
>> Hello cctbx folks,
>>
>>
>>
>> We are having problems running, building and/or installing DIALS on
>> CentOS7. Running the linux installer unceremoniously ends in a segfault.
>>
>> The installer is even broken when it is build on the same system using
>> bootstrapped cctbx/dials.
>>
>>
>>
>> The broken installer can be traced to the DIALS extension loader, which
>> uses python’s pkgutil loader, which triggers some library scanning routine
>> within python, which in turn falls over boost_python_meta_ext.so and dies
>> with the strace shown in the email below.
>>
>>
>>
>> The installer can be successfully “fixed” by deleting
>> build/lib/boost_python_meta_ext.so during the installation.
>>
>>
>>
>> So I see two issues here:
>>
>> 1.       What is broken with build/lib/boost_python_meta_ext.so that it
>> causes segfaults on CentOS7?
>>
>> 2.       Why is this not covered by any test? Neither of the following
>> caught anything:
>>
>> a.       python bootstrap.py builder=dials tests
>>
>> b.       libtbx.run_tests_parallel module=cctbx module=dials
>> module=boost_adaptbx
>>
>>
>>
>>
>> [NB: The previously reported 3 broken tests on CentOS7 are red herrings
>> and are all fixed by running ‘yum update’]
>>
>>
>>
>> I don’t know how to proceed from here.
>>
>>
>>
>> -Markus
>>
>>
>>
>>
>>
>> *From:* markus.gerstel at diamond.ac.uk [mailto:markus.gerstel at diamond.ac.uk]
>>
>> *Sent:* 29 September 2015 13:29
>> *To:* dials-support at lists.sourceforge.net
>> *Subject:* Re: [Dials-support] CentOS7 bugs (cont.)
>>
>>
>>
>> Hello everyone,
>>
>> (..)
>>
>> Sorry, I hit ctrl+enter by accident…
>>
>> In addition to these failed tests the installer dies a boost-related
>> death according to strace:
>> (..)
>>
>> poll([{fd=13, events=POLLIN|POLLPRI}, {fd=15, events=POLLIN|POLLPRI}], 2,
>> 4294967295) = 1 ([{fd=13, revents=POLLIN}]) read(13, "\tlinux-vdso.so.1 =>
>> (0x00007fff"..., 4096) = 486
>>
>> --- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=7648,
>> si_status=0, si_utime=0, si_stime=0} --- poll([{fd=13,
>> events=POLLIN|POLLPRI}, {fd=15, events=POLLIN|POLLPRI}], 2, 4294967295) = 2
>> ([{fd=13, revents=POLLHUP}, {fd=15, revents=POLLHUP}])
>>
>> close(13)                               = 0
>>
>> close(15)                               = 0
>>
>> wait4(7648, [{WIFEXITED(s) && WEXITSTATUS(s) == 0}], 0, NULL) = 7648
>> stat("$prefix/dials-dev20150928/build/lib/boost_python_meta_ext",
>> 0x7fff6421d3f0) = -1 ENOENT (No such file or directory)
>> open("$prefix/dials-dev20150928/build/lib/boost_python_meta_ext.so",
>> O_RDONLY) = 11 fstat(11, {st_mode=S_IFREG|0775, st_size=200624, ...}) = 0
>>
>> --- SIGSEGV {si_signo=SIGSEGV, si_code=SEGV_MAPERR, si_addr=0x18a86} ---
>>
>> +++ killed by SIGSEGV (core dumped) +++
>>
>> Segmentation fault (core dumped)
>>
>>
>>
>> Not sure if relevant, but CentOS7 compiler is
>>   GCC 4.8.3 20140911 (Red Hat 4.8.3-9)
>>
>> compared to RHEL6
>>   GCC 4.4.7 20120313 (Red Hat 4.4.7-11)
>>
>> Anybody have any ideas?
>>
>> -Markus
>>
>>
>>
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-- 
Nicholas K. Sauter, Ph. D.
Computer Staff Scientist, Physical Biosciences Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd., Bldg. 64R0121
Berkeley, CA 94720-8118
(510) 486-5713
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