[cctbxbb] CentOS7 - fixed

Wed Sep 30 05:39:38 PDT 2015

Thanks for your suggestions. They did not do the trick though.

Some more detective work got me down to
  ../base/bin/python ../modules/cctbx_project/libtbx/configure.py dials
failing and both
  libtbx.python ../modules/cctbx_project/libtbx/configure.py dials
and
  LD_LIBRARY_PATH=lib ../base/bin/python ../modules/cctbx_project/libtbx/configure.py dials
succeeding.

A run with LD_DEBUG=files identified the problem:
     /lib64/libboost_python.so: error: symbol lookup error: undefined symbol: PyUnicodeUCS4_FromEncodedObject (fatal)

CentOS7 comes with its own set of incompatible boost libraries.

I've put a fix in: http://sourceforge.net/p/cctbx/code/22986/
Installation on CentOS7 now works for me. As far as I could tell this does not break other things.

-Markus

________________________________
From: cctbxbb-bounces at phenix-online.org [cctbxbb-bounces at phenix-online.org] on behalf of Nigel Moriarty [nwmoriarty at lbl.gov]
Sent: Tuesday, September 29, 2015 18:36
To: cctbx mailing list
Subject: Re: [cctbxbb] CentOS7 bugs (cont.)

libtbx.configure --scan-boost phenix

Cheers

Nigel

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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<http://CCI.LBL.gov>

On Tue, Sep 29, 2015 at 10:20 AM, Nicholas Sauter <nksauter at lbl.gov<mailto: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<mailto: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<tel:510-486-5709>     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909<tel:510-486-5909>       Web  : CCI.LBL.gov<http://CCI.LBL.gov>

On Tue, Sep 29, 2015 at 8:29 AM, <markus.gerstel at diamond.ac.uk<mailto: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> [mailto: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<mailto: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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