[cctbxbb] CentOS7 bugs (cont.)

Nigel Moriarty nwmoriarty at lbl.gov
Tue Sep 29 09:25:53 PDT 2015


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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