<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Tue, Jan 3, 2017 at 9:46 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">
<div dir="ltr" style="font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255);font-family:calibri,arial,helvetica,sans-serif">
<p></p>
<p>I've downloaded the tarball on October 24th:</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</p>
<p>(no direct internet access on cluster)</p></div></blockquote><div>That is missing the fix. You can insert those few lines:</div><div><br></div><div> <span style="color:rgb(33,33,33);font-family:calibri,arial,helvetica,sans-serif;font-size:16px"> </span><a href="https://bitbucket.org/petsc/petsc/commits/32cc76960ddbb48660f8e7c667e293c0ccd0e7d7" target="_blank" style="font-family:calibri,arial,helvetica,sans-serif;font-size:16px">https://bitbucket.org/petsc/<wbr>petsc/commits/<wbr>32cc76960ddbb48660f8e7c667e293<wbr>c0ccd0e7d7</a></div><div><br></div><div>Or get the new tarball when it spins tonight, since Satish has just added the fix to maint.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> <br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr" style="font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255);font-family:calibri,arial,helvetica,sans-serif">
<font style="font-family:verdana;font-size:8pt;color:rgb(125,125,125);font-weight:bold">dr. ir.</font><font style="font-family:verdana;font-size:8pt;color:rgb(125,125,125);font-weight:bold">
</font><font style="font-family:verdana;font-size:8pt;color:rgb(125,125,125);font-weight:bold">Christiaan</font><font style="font-family:verdana;font-size:8pt;color:rgb(125,125,125);font-weight:bold">
</font><font style="font-family:verdana;font-size:8pt;color:rgb(125,125,125);font-weight:bold">Klaij</font><font size="3" face="Segoe UI"></font><font style="font-family:verdana;font-size:8pt;color:rgb(125,125,125);font-weight:bold"> |
</font><font style="font-family:verdana;font-size:8pt;color:rgb(125,125,125);font-weight:bold">CFD Researcher</font><font style="font-family:verdana;font-size:8pt;color:rgb(125,125,125);font-weight:bold"> |
</font><font style="font-family:verdana;font-size:8pt;color:rgb(125,125,125);font-weight:bold">Research & Development</font><br>
<font style="font-family:verdana;font-size:9pt;color:rgb(125,125,125);font-weight:bold">MARIN</font><font style="font-family:verdana;font-size:8pt;color:rgb(125,125,125)"> | T
</font><font style="font-family:verdana;font-size:8pt;color:rgb(125,125,125)"><a href="tel:+31%20317%20493%20344" value="+31317493344" target="_blank">+31 317 49 33 44</a></font><font color="#7d7d7d" size="2" face="Segoe UI"></font><font style="font-family:verdana;font-size:8pt"> |
</font><span style="font-family:verdana;font-size:8pt"><a href="mailto:C.Klaij@marin.nl" title="" style="font-family:verdana;font-size:8pt" target="_blank"><span style="font-family:verdana;font-size:8pt">C.Klaij@marin.nl</span></a></span><font color="#7d7d7d" size="2" face="Segoe UI"></font><font style="font-family:verdana;font-size:8pt"> |
</font><span style="font-family:verdana;font-size:8pt"><a href="http://www.marin.nl" title="" style="font-family:verdana;font-size:8pt" target="_blank"><span style="font-family:verdana;font-size:8pt">www.marin.nl</span></a></span><br>
<br>
<a href="https://www.linkedin.com/company/marin" target="_blank"><img width="16" height="16" style="border: 0px solid;" src="cid:image901d0c.PNG@47b19979.46b62169" alt="LinkedIn"></a> <a href="http://www.youtube.com/marinmultimedia" target="_blank"><img width="16" height="16" style="border: 0px solid;" src="cid:image1337f2.PNG@ba1aeacc.449d33e8" alt="YouTube"></a> <a href="https://twitter.com/MARIN_nieuws" target="_blank"><img width="16" height="16" style="border: 0px solid;" src="cid:image75d749.PNG@22a5c14b.4590eb63" alt="Twitter"></a> <a href="https://www.facebook.com/marin.wageningen" target="_blank"><img width="16" height="16" style="border: 0px solid;" src="cid:imagebc4ffe.PNG@99abc7e7.4fab85ff" alt="Facebook"></a><br>
<font style="font-family:verdana;font-size:8pt" color="#7d7d7d" size="2" face="Verdana">MARIN news:
<font style="font-family:verdana;font-size:8pt"><span style="font-family:verdana;font-size:8pt"><a href="http://www.marin.nl/web/News/News-items/Modelling-natural-transition-on-hydrofoils-for-application-in-underwater-gliders-1.htm" title="" style="font-family:verdana;font-size:8pt" target="_blank"><span style="font-family:verdana;font-size:8pt">Modelling
natural transition on hydrofoils for application in underwater gliders</span></a></span></font></font>
<p></p>
<p></p>
<div style="color:rgb(33,33,33)">
<hr style="display:inline-block;width:98%">
<div id="gmail-m_-2722872531146610546divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri, sans-serif"><b>From:</b> Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>><br>
<b>Sent:</b> Tuesday, January 03, 2017 4:36 PM<br>
<b>To:</b> Klaij, Christiaan<br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br>
<b>Subject:</b> Re: [petsc-users] problems after glibc upgrade to 2.17-157</font>
<div> </div>
</div>
<div>
<div dir="ltr">
<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>
<div><br>
</div>
<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" target="_blank">https://bitbucket.org/petsc/<wbr>petsc/commits/<wbr>32cc76960ddbb48660f8e7c667e293<wbr>c0ccd0e7d7</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/d<wbr>ocumentation/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" target="_blank">+31 317 49 33 44</a> | mailto:<a href="mailto:C.Klaij@marin.nl" target="_blank">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/Comparison-of-uRANS-and-BEMBEM-for-propeller-pressure-pulse-prediction.htm" rel="noreferrer" target="_blank">
http://www.marin.nl/web/News/N<wbr>ews-items/Comparison-of-uRANS-<wbr>and-BEMBEM-for-propeller-<wbr>pressure-pulse-prediction.htm</a><br>
<br><span class="gmail-HOEnZb"><font color="#888888">
</font></span></blockquote><span class="gmail-HOEnZb"><font color="#888888">
</font></span></div><span class="gmail-HOEnZb"><font color="#888888">
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div class="gmail-m_-2722872531146610546gmail_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>
</font></span></div>
</div>
</div>
</div>
<u></u>
<p></p>
<u></u><u></u><u></u>
</div>
</blockquote></div><br><br clear="all"><div><br></div>-- <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>
</div></div>