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<p>Our sysadmin says that SL7 does not provide the debug version of glibc.<br>
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<p>Chris<br>
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<font style="font-family:Verdana;font-size:8pt;color:#7D7D7D;font-weight:bold;">dr. ir.</font><font style="font-family:Verdana;font-size:8pt;color:#7D7D7D;font-weight:bold;">
</font><font style="font-family: Verdana;font-size:8pt;color:#7D7D7D;font-weight:bold;">Christiaan</font><font style="font-family: Verdana;font-size:8pt;color:#7D7D7D;font-weight:bold;">
</font><font style="font-family:Verdana;font-size:8pt;color:#7D7D7D;font-weight:bold;">Klaij</font><font size="3" face="Segoe UI"></font><font style="font-family:Verdana;font-size:8pt;color:#7D7D7D;font-weight:bold;"> |
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri, sans-serif"><b>From:</b> Matthew Knepley <knepley@gmail.com><br>
<b>Sent:</b> Wednesday, January 04, 2017 1:40 PM<br>
<b>To:</b> Klaij, Christiaan<br>
<b>Cc:</b> petsc-users; Satish Balay<br>
<b>Subject:</b> Re: [petsc-users] problems after glibc upgrade to 2.17-157</font>
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<div class="gmail_quote">On Wed, Jan 4, 2017 at 3:16 AM, Klaij, Christiaan <span dir="ltr">
<<a href="mailto:C.Klaij@marin.nl" target="_blank">C.Klaij@marin.nl</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
Well, a bit clearer perhaps. It seems the relevant ERROR is on<br>
line 31039. So I did this case by hand using the compile and link<br>
lines from the log, then run it in gdb:<br>
<br>
$ pwd<br>
/tmp/petsc-Q0URwQ/config.<wbr>setCompilers<br>
$ ls<br>
confdefs.h conffix.h conftest conftest.F conftest.o<br>
$ gdb<br>
GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-80.el7<br>
Copyright (C) 2013 Free Software Foundation, Inc.<br>
License GPLv3+: GNU GPL version 3 or later <<a href="http://gnu.org/licenses/gpl.html" rel="noreferrer" target="_blank">http://gnu.org/licenses/gpl.<wbr>html</a>><br>
This is free software: you are free to change and redistribute it.<br>
There is NO WARRANTY, to the extent permitted by law. Type "show copying"<br>
and "show warranty" for details.<br>
This GDB was configured as "x86_64-redhat-linux-gnu".<br>
For bug reporting instructions, please see:<br>
<<a href="http://www.gnu.org/software/gdb/bugs/" rel="noreferrer" target="_blank">http://www.gnu.org/software/<wbr>gdb/bugs/</a>>.<br>
(gdb) file conftest<br>
Reading symbols from /tmp/petsc-Q0URwQ/config.<wbr>setCompilers/conftest...done.<br>
(gdb) run<br>
Starting program: /tmp/petsc-Q0URwQ/config.<wbr>setCompilers/conftest<br>
<br>
Program received signal SIGSEGV, Segmentation fault.<br>
0x00002aaaae32f65e in ?? ()<br>
Missing separate debuginfos, use: debuginfo-install glibc-2.17-157.el7.x86_64<br>
(gdb) bt<br>
#0 0x00002aaaae32f65e in ?? ()<br>
#1 0x00002aaaaaab7675 in _dl_relocate_object ()<br>
from /lib64/ld-linux-x86-64.so.2<br>
#2 0x00002aaaaaaae792 in dl_main () from /lib64/ld-linux-x86-64.so.2<br>
#3 0x00002aaaaaac1e36 in _dl_sysdep_start () from /lib64/ld-linux-x86-64.so.2<br>
#4 0x00002aaaaaaafa31 in _dl_start () from /lib64/ld-linux-x86-64.so.2<br>
#5 0x00002aaaaaaac1e8 in _start () from /lib64/ld-linux-x86-64.so.2<br>
#6 0x0000000000000001 in ?? ()<br>
#7 0x00007fffffffd4e2 in ?? ()<br>
#8 0x0000000000000000 in ?? ()<br>
(gdb)<br>
<br>
Does this make any sense to you?</blockquote>
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<div>No. It looks like there is something deeply wrong with the dynamic loader. You might try</div>
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<div> debuginfo-install glibc-2.17-157.el7.x86_64</div>
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<div>as it says so that we can see the stack trace. Considering that the error happens inside of</div>
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<div> _dl_sysdep_start () from /lib64/ld-linux-x86-64.so.2</div>
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<div>I am guessing that it is indeed connected to your upgrade of glibc. Since it only happens when</div>
<div>you are not using compiler libraries, I think your compiler has pointers back to old things in the</div>
<div>OS. I would recommend either a) using GNU as Satish says, or b) reinstalling the whole compiler</div>
<div>suite.</div>
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<div>I will look at the new problem when not using compiler libraries.</div>
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<div> Thanks,</div>
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<div> Matt</div>
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<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
<span class="gmail-"><br>
<br>
dr. ir. Christiaan Klaij | CFD Researcher | Research & Development<br>
MARIN | T <a href="tel:%2B31%20317%2049%2033%2044" value="+31317493344">+31 317 49 33 44</a> | mailto:<a href="mailto:C.Klaij@marin.nl">C.Klaij@marin.nl</a> |
<a href="http://www.marin.nl" rel="noreferrer" target="_blank">http://www.marin.nl</a><br>
<br>
MARIN news: <a href="http://www.marin.nl/web/News/News-items/Software-seminar-in-Shanghai-for-the-first-time-March-28.htm" rel="noreferrer" target="_blank">
http://www.marin.nl/web/News/<wbr>News-items/Software-seminar-<wbr>in-Shanghai-for-the-first-<wbr>time-March-28.htm</a><br>
<br>
______________________________<wbr>__________<br>
</span>From: Klaij, Christiaan<br>
Sent: Wednesday, January 04, 2017 9:26 AM<br>
To: Matthew Knepley; petsc-users; Satish Balay<br>
<span class="gmail-im gmail-HOEnZb">Subject: Re: [petsc-users] problems after glibc upgrade to 2.17-157<br>
<br>
</span><span class="gmail-im gmail-HOEnZb">So I've applied the patch to my current 3.7.4 source, the new<br>
configure.log is attached. It's slightly larger but not much<br>
clearer too me...<br>
<br>
Chris<br>
</span>
<div class="gmail-HOEnZb">
<div class="gmail-h5">______________________________<wbr>__________<br>
From: Satish Balay <<a href="mailto:balay@mcs.anl.gov">balay@mcs.anl.gov</a>><br>
Sent: Tuesday, January 03, 2017 5:00 PM<br>
To: Matthew Knepley<br>
Cc: Klaij, Christiaan; <a href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a><br>
Subject: Re: [petsc-users] problems after glibc upgrade to 2.17-157<br>
<br>
On Tue, 3 Jan 2017, Matthew Knepley wrote:<br>
<br>
> Or get the new tarball when it spins tonight, since Satish has just<br>
> added the fix to maint.<br>
<br>
We don't spin 'maint/patch-release' tarballs everynight. Its every 1-3<br>
months - [partly depending upon the number of outstanding patches - or<br>
their severity]<br>
<br>
-rw-r--r-- 1 petsc pdetools 23194357 Jan 1 10:41 petsc-3.7.5.tar.gz<br>
-rw-r--r-- 1 petsc pdetools 23189526 Oct 2 22:06 petsc-3.7.4.tar.gz<br>
-rw-r--r-- 1 petsc pdetools 23172670 Jul 24 12:22 petsc-3.7.3.tar.gz<br>
-rw-r--r-- 1 petsc pdetools 23111802 Jun 5 2016 petsc-3.7.2.tar.gz<br>
-rw-r--r-- 1 petsc pdetools 23113397 May 15 2016 petsc-3.7.1.tar.gz<br>
-rw-r--r-- 1 petsc pdetools 22083999 Apr 25 2016 petsc-3.7.0.tar.gz<br>
<br>
Satish<br>
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-- <br>
<div class="gmail_signature">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener</div>
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