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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hello cctbx folks,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">We are having problems running, building and/or installing DIALS on CentOS7. Running the linux installer unceremoniously ends in a segfault.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The installer is even broken when it is build on the same system using bootstrapped cctbx/dials.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The installer can be successfully “fixed” by deleting build/lib/boost_python_meta_ext.so during the installation.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">So I see two issues here:<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><span style="mso-list:Ignore">1.<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">What is broken with build/lib/boost_python_meta_ext.so that it causes segfaults on CentOS7?<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><span style="mso-list:Ignore">2.<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Why is this not covered by any test? Neither of the following caught anything:<o:p></o:p></span></p>
<p class="MsoListParagraph" style="margin-left:72.0pt;text-indent:-18.0pt;mso-list:l0 level2 lfo1">
<![if !supportLists]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><span style="mso-list:Ignore">a.<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">python bootstrap.py builder=dials tests<o:p></o:p></span></p>
<p class="MsoListParagraph" style="margin-left:72.0pt;text-indent:-18.0pt;mso-list:l0 level2 lfo1">
<![if !supportLists]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><span style="mso-list:Ignore">b.<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">libtbx.run_tests_parallel module=cctbx module=dials module=boost_adaptbx<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">[NB: The previously reported 3 broken tests on CentOS7 are red herrings and are all fixed by running ‘yum update’]<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I don’t know how to proceed from here.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">-Markus<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><a name="_MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></a></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> markus.gerstel@diamond.ac.uk [mailto:markus.gerstel@diamond.ac.uk]
<br>
<b>Sent:</b> 29 September 2015 13:29<br>
<b>To:</b> dials-support@lists.sourceforge.net<br>
<b>Subject:</b> Re: [Dials-support] CentOS7 bugs (cont.)<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:black">Hello everyone,</span><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">(..)<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="color:#1F497D">Sorry, I hit ctrl+enter by accident…<br>
<br>
In addition to these failed tests the installer dies a boost-related death according to strace:<br>
</span>(..)<o:p></o:p></p>
<p class="MsoPlainText">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<o:p></o:p></p>
<p class="MsoPlainText">--- 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}])<o:p></o:p></p>
<p class="MsoPlainText">close(13) = 0<o:p></o:p></p>
<p class="MsoPlainText">close(15) = 0<o:p></o:p></p>
<p class="MsoPlainText">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<o:p></o:p></p>
<p class="MsoPlainText">--- SIGSEGV {si_signo=SIGSEGV, si_code=SEGV_MAPERR, si_addr=0x18a86} ---<o:p></o:p></p>
<p class="MsoPlainText">+++ killed by SIGSEGV (core dumped) +++<o:p></o:p></p>
<p class="MsoPlainText">Segmentation fault (core dumped)<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Not sure if relevant, but CentOS7 compiler is<br>
GCC 4.8.3 20140911 (Red Hat 4.8.3-9) <br>
<br>
compared to RHEL6<br>
GCC 4.4.7 20120313 (Red Hat 4.4.7-11)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Anybody have any ideas?<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">-Markus<o:p></o:p></span></p>
<p> <o:p></o:p></p>
<p>-- <o:p></o:p></p>
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