[cctbxbb] CentOS7 bugs (cont.)

Tue Sep 29 10:36:41 PDT 2015

libtbx.configure --scan-boost phenix

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 10:20 AM, Nicholas Sauter <nksauter at lbl.gov> wrote:

> 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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>>
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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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