<div dir="ltr">Guilherme,<div><br></div><div>here is my debug configuration (with shared libraries) in PETSc on a XC40</div><div><br></div><div>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--CFLAGS=-mkl=sequential -g -O0 </span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--CXXFLAGS=-mkl=sequential -g -O0 </span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--FFLAGS=-mkl=sequential -g -O0 -lstdc++</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--LDFLAGS=-dynamic</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--download-metis-cmake-arguments=-DCMAKE_C_COMPILER_FORCED=1</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--download-metis=1</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--download-parmetis-cmake-arguments=-DCMAKE_C_COMPILER_FORCED=1</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--download-parmetis=1</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-bits-per-byte=8</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-has-attribute-aligned=1</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-level1-dcache-assoc=8</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-level1-dcache-linesize=64</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-level1-dcache-size=32768</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-memcmp-ok=1</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-mpi-c-double-complex=1</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-mpi-int64_t=1</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-mpi-long-double=1</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-mpi-shared-libraries=0</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-sdot-returns-double=0</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-sizeof-MPI_Comm=4</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-sizeof-MPI_Fint=4</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-sizeof-char=1</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-sizeof-double=8</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-sizeof-float=4</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-sizeof-int=4</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-sizeof-long-long=8</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-sizeof-long=8</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-sizeof-short=2</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-sizeof-size_t=8</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-sizeof-void-p=8</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--known-snrm2-returns-double=0</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--with-ar=ar</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--with-batch=1</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--with-cc=/opt/cray/craype/2.4.2/bin/cc</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--with-clib-autodetect=0</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--with-cmake=/home/zampins/local/bin/cmake</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--with-cxx=/opt/cray/craype/2.4.2/bin/CC</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--with-cxxlib-autodetect=0</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--with-debugging=1</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--with-dependencies=0</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--with-etags=0</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--with-fc=/opt/cray/craype/2.4.2/bin/ftn</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--with-fortran-datatypes=0</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--with-fortran-interfaces=0</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--with-fortranlib-autodetect=0</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--with-pthread=0</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--with-ranlib=ranlib</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--with-scalar-type=real</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--with-shared-ld=ar</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">--with-shared-libraries=1</span><span class="gmail-s1">',</span></p>
<p class="gmail-p1"><span class="gmail-s1"> '</span><span class="gmail-s2">PETSC_ARCH=arch-intel-debug</span><span class="gmail-s1">',</span></p></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">2017-06-13 15:34 GMT+02:00 Vaz, Guilherme <span dir="ltr"><<a href="mailto:G.Vaz@marin.nl" target="_blank">G.Vaz@marin.nl</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr" style="font-size:12pt;color:#000000;background-color:#ffffff;font-family:Calibri,Arial,Helvetica,sans-serif">
<p></p>
<p>Dear Matthew,<br>
</p>
<p><br>
</p>
<p>Thanks. It went further, but now I get:<br>
</p>
<div>TESTING: configureMPIEXEC from config.packages.MPI(/zhome/<wbr>academic/HLRS/pri/iprguvaz/<wbr>ReFRESCO/Dev/trunk/Libs/build/<wbr>petsc-3.7.5/config/<wbr>BuildSystem/config/packages/<wbr>MPI.py:143)</div><span class="">
<div>******************************<wbr>******************************<wbr>*******************</div>
<div> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):</div>
<div>------------------------------<wbr>------------------------------<wbr>-------------------</div>
</span><div>Must give a default value for known-mpi-shared-libraries since executables cannot be run</div>
<div>******************************<wbr>******************************<wbr>*******************<br>
</div>
<div><br>
</div>
<div>Last lines from the log:<br>
</div>
<div>
<div> File "./config/configure.py", line 405, in petsc_configure</div>
<div> framework.configure(out = sys.stdout)</div>
<div> File "/zhome/academic/HLRS/pri/<wbr>iprguvaz/ReFRESCO/Dev/trunk/<wbr>Libs/build/petsc-3.7.5/config/<wbr>BuildSystem/config/framework.<wbr>py", line 1090, in configure</div>
<div> self.processChildren()</div>
<div> File "/zhome/academic/HLRS/pri/<wbr>iprguvaz/ReFRESCO/Dev/trunk/<wbr>Libs/build/petsc-3.7.5/config/<wbr>BuildSystem/config/framework.<wbr>py", line 1079, in processChildren</div>
<div> self.serialEvaluation(self.<wbr>childGraph)</div>
<div> File "/zhome/academic/HLRS/pri/<wbr>iprguvaz/ReFRESCO/Dev/trunk/<wbr>Libs/build/petsc-3.7.5/config/<wbr>BuildSystem/config/framework.<wbr>py", line 1060, in serialEvaluation</div>
<div> child.configure()</div>
<div> File "/zhome/academic/HLRS/pri/<wbr>iprguvaz/ReFRESCO/Dev/trunk/<wbr>Libs/build/petsc-3.7.5/config/<wbr>BuildSystem/config/package.py"<wbr>, line 791, in configure</div>
<div> self.executeTest(self.<wbr>checkSharedLibrary)</div>
<div> File "/zhome/academic/HLRS/pri/<wbr>iprguvaz/ReFRESCO/Dev/trunk/<wbr>Libs/build/petsc-3.7.5/config/<wbr>BuildSystem/config/base.py", line 126, in executeTest</div>
<div> ret = test(*args,**kargs)</div>
<div> File "/zhome/academic/HLRS/pri/<wbr>iprguvaz/ReFRESCO/Dev/trunk/<wbr>Libs/build/petsc-3.7.5/config/<wbr>BuildSystem/config/packages/<wbr>MPI.py", line 135, in checkSharedLibrary</div>
<div> self.shared = self.libraries.checkShared('#<wbr>include <mpi.h>\n','MPI_Init','MPI_<wbr>Initialized','MPI_Finalize',<wbr>checkLink = self.checkPackageLink,<wbr>libraries = self.lib, defaultArg = 'known-mpi-shared-libraries', ex</div>
<div>ecutor = self.mpiexec)</div>
<div> File "/zhome/academic/HLRS/pri/<wbr>iprguvaz/ReFRESCO/Dev/trunk/<wbr>Libs/build/petsc-3.7.5/config/<wbr>BuildSystem/config/libraries.<wbr>py", line 471, in checkShared</div>
<div> if self.checkRun(defaultIncludes, body, defaultArg = defaultArg, executor = executor):</div>
<div> File "/zhome/academic/HLRS/pri/<wbr>iprguvaz/ReFRESCO/Dev/trunk/<wbr>Libs/build/petsc-3.7.5/config/<wbr>BuildSystem/config/base.py", line 628, in checkRun</div>
<div> (output, returnCode) = self.outputRun(includes, body, cleanup, defaultArg, executor)</div>
<div> File "/zhome/academic/HLRS/pri/<wbr>iprguvaz/ReFRESCO/Dev/trunk/<wbr>Libs/build/petsc-3.7.5/config/<wbr>BuildSystem/config/base.py", line 598, in outputRun</div>
<div> raise ConfigureSetupError('Must give a default value for '+defaultOutputArg+' since executables cannot be run')</div>
<div><br>
<span style="font-size:12pt">Any ideas? Something related with </span>
<div>
<div> --with-shared-libraries=0 \ </div>
<div> --with-batch=1 \</div>
<div>The first I set because it was in the cray example, and the second because aprun (the mpiexec of Cray) is not available in the frontend. <br>
</div>
</div>
<div><br>
</div>
</div>
</div><span class="">
<div>Thanks,<br>
</div>
<div><br>
</div>
<div>Guilherme V.<br>
</div>
<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">Guilherme</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 style="display:inline-block;width:98%">
<div id="m_4042342488001796776divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>><br>
<b>Sent:</b> Tuesday, June 13, 2017 2:34 PM<br>
<b>To:</b> Vaz, Guilherme<br>
<b>Cc:</b> PETSc<br>
<b>Subject:</b> Re: [petsc-users] PETSC on Cray Hazelhen</font>
<div> </div>
</div><div><div class="h5">
<div>
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Tue, Jun 13, 2017 at 3:48 AM, Vaz, Guilherme <span dir="ltr">
<<a href="mailto:G.Vaz@marin.nl" target="_blank">G.Vaz@marin.nl</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr" style="font-size:12pt;color:#000000;background-color:#ffffff;font-family:Calibri,Arial,Helvetica,sans-serif">
<p></p>
<p>Dear all,<br>
</p>
<p><span style="font-size:12pt">I am trying to install PETSC on a Cray XC40 system (Hazelhen) with the usual Cray wrappers for Intel compilers, with some chosen external packages and MKL libraries.</span><br>
</p>
<p>I read some threads in the mailing list about this, and I tried the petsc-3.7.5/config/examples/ar<wbr>ch-cray-xt6-pkgs-opt.py config<wbr>uration options. After trying this (please abstract from my own env vars),<br>
</p>
<div>CONFOPTS="--prefix=$PETSC_INST<wbr>ALL_DIR \</div>
<div> --with-cc=cc \</div>
<div> --with-cxx=CC \</div>
<div> --with-fc=ftn \</div>
<div> --with-clib-autodetect=0 \</div>
<div> --with-cxxlib-autodetect=0 \</div>
<div> --with-fortranlib-autodetect=0 \</div>
<div> --COPTFLAGS=-fast -mp \</div>
<div> --CXXOPTFLAGS=-fast -mp \</div>
<div> --FOPTFLAGS=-fast -mp \<br>
</div>
<div> --with-shared-libraries=0 \ </div>
<div> --with-batch=1 \</div>
<div> --with-x=0 \</div>
<div> --with-mpe=0 \</div>
<div> --with-debugging=0 \</div>
<div> --download-superlu_dist=$SOURC<wbr>E_DIR/$SUPERLU_SOURCE_FILE \</div>
<div> --with-blas-lapack-dir=$BLASDI<wbr>R \</div>
<div> --download-parmetis=$SOURCE_DI<wbr>R/$PARMETIS_SOURCE_FILE \</div>
<div> --download-metis=$SOURCE_DIR/$<wbr>METIS_SOURCE_FILE \</div>
<div> --with-external-packages-dir=$<wbr>INSTALL_DIR \</div>
<div> --with-ssl=0 <span style="font-size:12pt">"</span></div>
<p><br>
</p>
<p>I get the following error:<br>
</p>
<p><br>
</p>
<div>TESTING: checkFortranLinkingCxx from config.compilers(/zhome/academ<wbr>ic/HLRS/pri/iprguvaz/ReFRESCO/<wbr>Dev/trunk/Libs/build/petsc-3.<wbr>7.5/config/BuildSystem/config/<wbr>compilers.py:1097)</div>
<div>******************************<wbr>******************************<wbr>*******************</div>
<div> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):</div>
<div>------------------------------<wbr>------------------------------<wbr>-------------------</div>
<div>Fortran could not successfully link C++ objects</div>
<div>******************************<wbr>******************************<wbr>*******************</div>
<div><br>
Does it ring a bell? Any tips?</div>
</div>
</blockquote>
<div><br>
</div>
<div>You turned off autodetection, so it will not find libstdc++. That either has to be put in LIBS, or I would recommend</div>
<div><br>
</div>
<div> --with-cxx=0</div>
<div><br>
</div>
<div>since nothing you have there requires C++.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr" style="font-size:12pt;color:#000000;background-color:#ffffff;font-family:Calibri,Arial,Helvetica,sans-serif">
<div>Thanks,<br>
</div>
<div>Guilherme V.<br>
</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">Guilherme</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">Vaz</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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<font color="#7d7d7d" size="2" face="Verdana" style="font-family:Verdana;font-size:8pt">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/Maritime-Safety-seminar-September-12-Singapore.htm" title="" style="font-family:Verdana;font-size:8pt" target="_blank"><span style="font-family:Verdana;font-size:8pt">Maritime
Safety seminar, September 12, Singapore</span></a></span></font></font>
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<div>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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<div><a href="http://www.caam.rice.edu/~mk51/" target="_blank">http://www.caam.rice.edu/~<wbr>mk51/</a><br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature">Stefano</div>
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