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<p>I've downloaded the tarball on October 24th:</p>
<p><br>
</p>
<p>$ ls -lh petsc-lite-3.7.4.tar.gz <br>
-rw-r--r-- 1 cklaij domain users 8.4M Oct 24 11:07 petsc-lite-3.7.4.tar.gz<br>
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<p>(no direct internet access on cluster)<br>
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<div style="color: rgb(33, 33, 33);"></div>
<br>
<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;"> |
</font><font style="font-family:Verdana;font-size:8pt;color:#7D7D7D;font-weight:bold;">CFD Researcher</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;">Research & Development</font><br>
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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> Tuesday, January 03, 2017 4:36 PM<br>
<b>To:</b> Klaij, Christiaan<br>
<b>Cc:</b> petsc-users@mcs.anl.gov<br>
<b>Subject:</b> Re: [petsc-users] problems after glibc upgrade to 2.17-157</font>
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<div class="gmail_extra">
<div class="gmail_quote">On Tue, Jan 3, 2017 at 9:04 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">
<br>
I've been using petsc-3.7.4 with intel mpi and compilers,<br>
superlu_dist, metis and parmetis on a cluster running<br>
SL7. Everything was working fine until SL7 got an update where<br>
glibc was upgraded from 2.17-106 to 2.17-157.<br>
</blockquote>
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<div>I cannot see the error in your log. We previously fixed a bug with this error reporting:</div>
<div><br>
</div>
<div> <a href="https://bitbucket.org/petsc/petsc/commits/32cc76960ddbb48660f8e7c667e293c0ccd0e7d7">https://bitbucket.org/petsc/petsc/commits/32cc76960ddbb48660f8e7c667e293c0ccd0e7d7</a></div>
<div><br>
</div>
<div>in August. Is it possible that your PETSc is older than this? Could you apply that patch, or</div>
<div>run the configure with 'master'?</div>
<div><br>
</div>
<div>My guess is this is a dynamic library path problem, as it always is after upgrades.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
This update seemed to have broken (at least) parmetis: the<br>
standalone binary gpmetis started to give a segmentation<br>
fault. The core dump shows this:<br>
<br>
Core was generated by `gpmetis'.<br>
Program terminated with signal 11, Segmentation fault.<br>
#0 0x00002aaaac6b865e in memmove () from /lib64/libc.so.6<br>
<br>
That's when I decided to recompile, but to my surprise I cannot<br>
even get past the configure stage (log attached)!<br>
<br>
******************************<wbr>******************************<wbr>*******************<br>
UNABLE to EXECUTE BINARIES for ./configure<br>
------------------------------<wbr>------------------------------<wbr>-------------------<br>
Cannot run executables created with FC. If this machine uses a batch system<br>
to submit jobs you will need to configure using ./configure with the additional option --with-batch.<br>
Otherwise there is problem with the compilers. Can you compile and run code with your compiler 'mpif90'?<br>
See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#libimf" rel="noreferrer" target="_blank">
http://www.mcs.anl.gov/petsc/<wbr>documentation/faq.html#libimf</a><br>
******************************<wbr>******************************<wbr>*******************<br>
<br>
Note the following:<br>
<br>
1) Configure was done with the exact same options that worked<br>
fine before the update of SL7.<br>
<br>
2) The intel mpi and compilers are exactly the same as before the<br>
update of SL7.<br>
<br>
3) The cluster does not require a batch system to run code.<br>
<br>
4) I can compile and run code with mpif90 on this cluster.<br>
<br>
5) The problem also occurs on a workstation running SL7.<br>
<br>
Any clues on how to proceed?<br>
Chris<br>
<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>
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http://www.marin.nl/web/News/<wbr>News-items/Comparison-of-<wbr>uRANS-and-BEMBEM-for-<wbr>propeller-pressure-pulse-<wbr>prediction.htm</a><br>
<br>
</blockquote>
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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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