<html>
<head>
<!-- Template generated by Exclaimer Mail Disclaimers on 02:37:04 Wednesday, 4 January 2017 -->
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<style type="text/css" style="display:none"><!--P{margin-top:0;margin-bottom:0;} --></style>
</head>
<body dir="ltr" style="font-size:12pt;color:#000000;background-color:#FFFFFF;font-family:Calibri,Arial,Helvetica,sans-serif;">
<p></p>
<p>I've tried with:</p>
<p><br>
</p>
<p> --LIBS=/cm/shared/apps/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64_lin/libifcore.a -lstdc++</p>
<p><br>
</p>
<p>but that doesn't seem to make a difference. </p>
<p><br>
</p>
<p>With the option --with-cxx=0 the configure part does work(!), but then I get </p>
<p><br>
</p>
<p>**************************ERROR*************************************<br>
Error during compile, check Linux-x86_64-Intel/lib/petsc/conf/make.log<br>
Send it and Linux-x86_64-Intel/lib/petsc/conf/configure.log to petsc-maint@mcs.anl.gov<br>
*******************************************************************</p>
<p><br>
</p>
<p>See the attached log files.<br>
</p>
<p><br>
</p>
<p>Chris<br>
</p>
<p><br>
</p>
<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>
<font style="font-family:Verdana;font-size:9pt;color:#7D7D7D;font-weight:bold;">MARIN</font><font style="font-family:Verdana;font-size:8pt;color:#7D7D7D;"> | T
</font><font style="font-family:Verdana;font-size:8pt;color:#7D7D7D;">+31 317 49 33 44</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="" target="" style="font-family:Verdana;font-size:8pt;"><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="" target="" style="font-family:Verdana;font-size:8pt;"><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=""><img width="16" height="16" style="border: 0px Solid ; " src="cid:image215e33.PNG@c0ac80f9.4bad8e56" alt="LinkedIn"></a> <a href="http://www.youtube.com/marinmultimedia" target=""><img width="16" height="16" style="border: 0px Solid ; " src="cid:image3607b7.PNG@b9f0a48e.4bb78f1c" alt="YouTube"></a> <a href="https://twitter.com/MARIN_nieuws" target=""><img width="16" height="16" style="border: 0px Solid ; " src="cid:image1b081f.PNG@b2f6ca20.4094b04d" alt="Twitter"></a> <a href="https://www.facebook.com/marin.wageningen" target=""><img width="16" height="16" style="border: 0px Solid ; " src="cid:image17dbf5.PNG@de58fdd8.4dbff7dd" 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/MARIN-Report-119-highlighting-naval-research-projects.htm" title="" target="" style="font-family:Verdana;font-size:8pt;"><span style="font-family:Verdana; font-size:8pt;">MARIN
Report 119: highlighting naval research projects</span></a></span></font></font>
<p></p>
<p></p>
<div style="color: rgb(33, 33, 33);">
<hr tabindex="-1" style="display:inline-block; width:98%">
<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 1:43 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>
<div> </div>
</div>
<div>
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Wed, Jan 4, 2017 at 4:32 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">
Satish,<br>
<br>
I tried your suggestion:<br>
<br>
--with-clib-autodetect=0 --with-fortranlib-autodetect=0 --with-cxxlib-autodetect=0 LIBS=LIBS=/path_to/libifcore.a<br>
<br>
I guess I don't really need "LIBS= " twice (?) so I've used this line:<br>
<br>
LIBS=/cm/shared/apps/intel/<wbr>compilers_and_libraries_2016.<wbr>3.210/linux/compiler/lib/<wbr>intel64_lin/libifcore.a<br>
<br>
Unfortunately, this approach also fails (attached log):<br>
</blockquote>
<div><br>
</div>
<div>Ah, this error is much easier:</div>
<div><br>
</div>
<div>
<div>Executing: mpif90 -o /tmp/petsc-3GfeyZ/config.compilers/conftest -fPIC -g -O3 /tmp/petsc-3GfeyZ/config.compilers/conftest.o /tmp/petsc-3GfeyZ/config.compilers/cxxobj.o /tmp/petsc-3GfeyZ/config.compilers/confc.o -ldl /cm/shared/apps/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64_lin/libifcore.a</div>
<div>Possible ERROR while running linker: exit code 256</div>
<div>stderr:</div>
<div>/tmp/petsc-3GfeyZ/config.compilers/cxxobj.o:(.gnu.linkonce.d.DW.ref.__gxx_personality_v0+0x0): undefined reference to `__gxx_personality_v0'</div>
</div>
<div><br>
</div>
<div>Intel as lazy writing its C++ compiler, so it uses some of g++. If you want to use C++, you will need to add -lstdc++ to your LIBS variable (I think).</div>
<div>Otherwise, please turn it off using --with-cxx=0.</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">
******************************<wbr>******************************<wbr>*******************<br>
UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):<br>
------------------------------<wbr>------------------------------<wbr>-------------------<br>
Fortran could not successfully link C++ objects<br>
******************************<wbr>******************************<wbr>*******************<br>
<br>
There are multiple libifcore.a in the intel compiler lib: one in intel64_lin and one in intel64_lin_mic. Tried both, got same error.<br>
<br>
Chris<br>
<span class="gmail-"><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>
<br>
</span>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/<wbr>News-items/Comparison-of-<wbr>uRANS-and-BEMBEM-for-<wbr>propeller-pressure-pulse-<wbr>prediction.htm</a><br>
<span class="gmail-"><br>
______________________________<wbr>__________<br>
From: Satish Balay <<a href="mailto:balay@mcs.anl.gov">balay@mcs.anl.gov</a>><br>
</span>Sent: Tuesday, January 03, 2017 4:37 PM<br>
To: Klaij, Christiaan<br>
Cc: <a href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a><br>
<span class="gmail-">Subject: Re: [petsc-users] problems after glibc upgrade to 2.17-157<br>
<br>
</span>Do you have similar issues with gnu compilers?<br>
<br>
It must be some incompatibility with intel compilers with this glibc change.<br>
<br>
>>>>>>>>><br>
compilers: Check that C libraries can be used from Fortran<br>
Pushing language FC<br>
Popping language FC<br>
Pushing language FC<br>
Popping language FC<br>
Pushing language FC<br>
Popping language FC<br>
**** Configure header /tmp/petsc-rOjdnN/confdefs.h ****<br>
<<<<<<<<<<<br>
<br>
Thre is a bug in configure [Matt?] that eats away some of the log - so<br>
I don't see the exact error you are getting.<br>
<br>
If standalone micc/mpif90 etc work - then you can try the following additional options:<br>
<br>
--with-clib-autodetect=0 --with-fortranlib-autodetect=0 --with-cxxlib-autodetect=0 LIBS=LIBS=/path_to/libifcore.a<br>
<br>
[replace "path_to" with the correct path to the ifort lubifcore.a library]<br>
<br>
Note: I have a RHEL7 box with this glibc - and I don't see this issue.<br>
<br>
>>>><br>
-bash-4.2$ cat /etc/redhat-release<br>
Red Hat Enterprise Linux Server release 7.3 (Maipo)<br>
-bash-4.2$ rpm -q glibc<br>
glibc-2.17-157.el7_3.1.x86_64<br>
glibc-2.17-157.el7_3.1.i686<br>
-bash-4.2$ mpiicc --version<br>
icc (ICC) 17.0.0 20160721<br>
Copyright (C) 1985-2016 Intel Corporation. All rights reserved.<br>
<br>
-bash-4.2$<br>
<<<<<br>
<br>
Satish<br>
<br>
On Tue, 3 Jan 2017, Klaij, Christiaan wrote:<br>
<br>
><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>
><br>
> 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>
<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>
</span>> 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/<wbr>News-items/Comparison-of-<wbr>uRANS-and-BEMBEM-for-<wbr>propeller-pressure-pulse-<wbr>prediction.htm</a><br>
><br>
><br>
<br>
</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>
</div>
</div>
</EXCLAIMER:ORIGINAL_BODY_AFTER>
<p></p>
</EXCLAIMER:TEXT_ONLY></EXCLAIMER:AD></EXCLAIMER:AD>
</body>
</html>