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<p></p>
<p>So how would I do that? Does LIBS=<string> accept spaces in the string? Something like this perhaps:<br>
</p>
<p><br>
</p>
<p>LIBS="-L/cm/shared/apps/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64_lin -lifcore"
</p>
<p><br>
</p>
<p>But I'm starting to believe that my intel install is somehow broken. I'm getting these intel compilers from rpm's provided by our cluster vendor. On a workstation I can try yum remove and install of the intel packages. Not so easy on a production cluster.
Is this worth a try? Or will it just copy/paste the same broken (?) stuff in the same place?</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;"> |
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<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 3:13 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 7:37 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 tried with:</p>
<p><br>
</p>
<p> --LIBS=/cm/shared/apps/intel/<wbr>compilers_and_libraries_2016.<wbr>3.210/linux/compiler/lib/<wbr>intel64_lin/libifcore.a -lstdc++\\</p>
</div>
</blockquote>
<div>This is likely connected to the problem below, but I would have to see the log. <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">
<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>**************************<wbr>ERROR*************************<wbr>************<br>
Error during compile, check Linux-x86_64-Intel/lib/petsc/<wbr>conf/make.log<br>
Send it and Linux-x86_64-Intel/lib/petsc/<wbr>conf/configure.log to <a href="mailto:petsc-maint@mcs.anl.gov" target="_blank">
petsc-maint@mcs.anl.gov</a><br>
******************************<wbr>******************************<wbr>*******</p>
</div>
</blockquote>
<div>Here is the problem:</div>
<div><br>
</div>
<div>
<div> CLINKER /projects/developers/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.4/Linux-x86_64-Intel/lib/libpetsc.so.3.7.4</div>
<div>ld: /cm/shared/apps/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64_lin/libifcore.a(for_init.o): relocation R_X86_64_32 against `.rodata.str1.4' can not be used when making a shared object; recompile with -fPIC</div>
<div>/cm/shared/apps/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64_lin/libifcore.a: could not read symbols: Bad value</div>
</div>
<div><br>
</div>
<div>Clearly there is something wrong with the compiler install.</div>
<div><br>
</div>
<div>However, can you put a libifcore.so in LIBS instead?</div>
<div><br>
</div>
<div> Matt</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">
<p>See the attached log files.<br>
</p>
<span class="gmail-">
<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: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">
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<p></p>
<p></p>
<div style="color:rgb(33,33,33)">
<hr style="display:inline-block; width:98%">
<div id="gmail-m_-1311841313628239103divRplyFwdMsg" 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> Wednesday, January 04, 2017 1:43 PM<span class="gmail-"><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</span></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/com<wbr>pilers_and_libraries_2016.3.<wbr>210/linux/compiler/lib/intel64<wbr>_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.<wbr>compilers/conftest -fPIC -g -O3 /tmp/petsc-3GfeyZ/config.<wbr>compilers/conftest.o /tmp/petsc-3GfeyZ/config.<wbr>compilers/cxxobj.o /tmp/petsc-3GfeyZ/config.<wbr>compilers/confc.o -ldl /cm/shared/apps/intel/<wbr>compilers_and_libraries_2016.<wbr>3.210/linux/compiler/lib/<wbr>intel64_lin/libifcore.a</div>
<div>Possible ERROR while running linker: exit code 256</div>
<div>stderr:</div>
<div>/tmp/petsc-3GfeyZ/config.<wbr>compilers/cxxobj.o:(.gnu.<wbr>linkonce.d.DW.ref.__gxx_<wbr>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-m_-1311841313628239103gmail-"><span class="gmail-"><br>
<br>
<br>
dr. ir. Christiaan Klaij | CFD Researcher | Research & Development<br>
</span><span class="gmail-">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>
</span></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/N<wbr>ews-items/Comparison-of-uRANS-<wbr>and-BEMBEM-for-propeller-<wbr>pressure-pulse-prediction.htm</a><span class="gmail-"><br>
<span class="gmail-m_-1311841313628239103gmail-"><br>
______________________________<wbr>__________<br>
From: Satish Balay <<a href="mailto:balay@mcs.anl.gov" target="_blank">balay@mcs.anl.gov</a>><br>
</span></span>Sent: Tuesday, January 03, 2017 4:37 PM<br>
To: Klaij, Christiaan<br>
Cc: <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><span class="gmail-"><br>
<span class="gmail-m_-1311841313628239103gmail-">Subject: Re: [petsc-users] problems after glibc upgrade to 2.17-157<br>
<br>
</span></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/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>
<span class="gmail-m_-1311841313628239103gmail-"><span class="gmail-">><br>
><br>
> dr. ir. Christiaan Klaij | CFD Researcher | Research & Development<br>
</span><span class="gmail-">> 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>
</span></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/N<wbr>ews-items/Comparison-of-uRANS-<wbr>and-BEMBEM-for-propeller-<wbr>pressure-pulse-prediction.htm</a><br>
><br>
><br>
<br>
</blockquote>
</div>
<span class="gmail-"><br>
<br clear="all">
<div><br>
</div>
-- <br>
<div class="gmail-m_-1311841313628239103gmail_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>
</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>
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