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<p class="MsoNormal">Yes, I followed the exact instructions. I’m using bash. I put the environmental variable in the .bashrc file. This only happens to my intel i129700 workstation. Is it because of the hardware?</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Sijie </p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">
Mail</a> for Windows</p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="border:none;padding:0in"><b>From: </b><a href="mailto:knepley@gmail.com">Matthew Knepley</a><br>
<b>Sent: </b>Wednesday, January 11, 2023 7:40 PM<br>
<b>To: </b><a href="mailto:bsmith@petsc.dev">Barry Smith</a><br>
<b>Cc: </b><a href="mailto:zhan2355@purdue.edu">Sijie Zhang</a>; <a href="mailto:petsc-users@mcs.anl.gov">
petsc-users@mcs.anl.gov</a><br>
<b>Subject: </b>Re: [petsc-users] PETSC install</p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black">----
<b>External Email</b>: Use caution with attachments, links, or sharing data ----<o:p></o:p></span></p>
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<p class="MsoNormal">On Wed, Jan 11, 2023 at 2:33 PM Barry Smith <<a href="mailto:bsmith@petsc.dev">bsmith@petsc.dev</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"> Did you do exactly: <o:p></o:p></p>
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<pre style="line-height:12.3pt;box-sizing:border-box;border-radius:0.25rem;padding:1rem;overflow:auto" id="m_1508981105543049089codecell36"><span style="color:black">export</span><span style="color:#F8F8F8"> </span><span style="color:black">HWLOC_HIDE_ERRORS</span><b><span style="color:#CE5C00">=</span><span style="color:#0000CF">2</span></b><span style="color:#323232"><o:p></o:p></span></pre>
<pre style="line-height:12.3pt;box-sizing:border-box;border-radius:0.25rem;padding:1rem;overflow:auto" id="m_1508981105543049089codecell36"><b><span style="color:#0000CF">make check</span></b><span style="color:#323232"><o:p></o:p></span></pre>
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<p class="MsoNormal">Also, what shell are you using? The command above is for bash, but if you use csh it is different.<o:p></o:p></p>
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<p class="MsoNormal"> Thanks,<o:p></o:p></p>
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<p class="MsoNormal"> Matt<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<pre style="line-height:12.3pt;box-sizing:border-box;border-radius:0.25rem;padding:1rem;overflow:auto" id="m_1508981105543049089codecell36"><b><span style="color:#0000CF">?</span></b><span style="color:#323232"><o:p></o:p></span></pre>
<pre style="line-height:12.3pt;box-sizing:border-box;border-radius:0.25rem;padding:1rem;overflow:auto" id="m_1508981105543049089codecell36"><b><span style="color:#0000CF"><br><br></span></b><span style="color:#323232"><o:p></o:p></span></pre>
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<p class="MsoNormal">On Jan 11, 2023, at 6:51 PM, Sijie Zhang <<a href="mailto:zhan2355@purdue.edu" target="_blank">zhan2355@purdue.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">Hi,<br>
<br>
I tried that but it's showing the same error. Can you help me to take a look at that?<br>
<br>
Thanks.<br>
<br>
Sijie<br>
<br>
+++++++++++++++++++++++++++++++++++++++++++++++++++++<br>
<br>
Running check examples to verify correct installation<br>
Using PETSC_DIR=/home/zhangsijie1995/Documents/Package/petsc-3.18.3 and PETSC_ARCH=arch-linux-c-debug<br>
Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process<br>
See <a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a><br>
hwloc/linux: Ignoring PCI device with non-16bit domain.<br>
Pass --enable-32bits-pci-domain to configure to support such devices<br>
(warning: it would break the library ABI, don't enable unless really needed).<br>
lid velocity = 0.0016, prandtl # = 1., grashof # = 1.<br>
Number of SNES iterations = 2<br>
Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes<br>
See <a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a><br>
hwloc/linux: Ignoring PCI device with non-16bit domain.<br>
Pass --enable-32bits-pci-domain to configure to support such devices<br>
(warning: it would break the library ABI, don't enable unless really needed).<br>
hwloc/linux: Ignoring PCI device with non-16bit domain.<br>
Pass --enable-32bits-pci-domain to configure to support such devices<br>
(warning: it would break the library ABI, don't enable unless really needed).<br>
lid velocity = 0.0016, prandtl # = 1., grashof # = 1.<br>
Number of SNES iterations = 2<br>
*******************Error detected during compile or link!*******************<br>
See <a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a><br>
/home/zhangsijie1995/Documents/Package/petsc-3.18.3/src/snes/tutorials ex5f<br>
*********************************************************<br>
/opt/intel/oneapi/mpi/2021.8.0/bin/mpif90 -fPIC -Wall -ffree-line-length-none -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -g -O0 -I/home/zhangsijie1995/Documents/Package/petsc-3.18.3/include -I/home/zhangsijie1995/Documents/Package/petsc-3.18.3/arch-linux-c-debug/include
-I/opt/intel/oneapi/mkl/2023.0.0/include -I/opt/intel/oneapi/mpi/2021.8.0/include ex5f.F90 -Wl,-rpath,/home/zhangsijie1995/Documents/Package/petsc-3.18.3/arch-linux-c-debug/lib -L/home/zhangsijie1995/Documents/Package/petsc-3.18.3/arch-linux-c-debug/lib
-Wl,-rpath,/opt/intel/oneapi/mkl/2023.0.0/lib/intel64 -L/opt/intel/oneapi/mkl/2023.0.0/lib/intel64 -Wl,-rpath,/home/zhangsijie1995/Documents/Package/petsc-3.18.3/I_MPI_SUBSTITUTE_INSTALLDIR/lib/release -L/home/zhangsijie1995/Documents/Package/petsc-3.18.3/I_MPI_SUBSTITUTE_INSTALLDIR/lib/release
-Wl,-rpath,/home/zhangsijie1995/Documents/Package/petsc-3.18.3/I_MPI_SUBSTITUTE_INSTALLDIR/lib -L/home/zhangsijie1995/Documents/Package/petsc-3.18.3/I_MPI_SUBSTITUTE_INSTALLDIR/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11
-lpetsc -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lm -lstdc++ -ldl -lmpifort -lmpi -lrt -lpthread -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -o ex5f<br>
f951: Warning: Nonexistent include directory ‘I_MPI_SUBSTITUTE_INSTALLDIR/include/gfortran/11.1.0’ [-Wmissing-include-dirs]<br>
f951: Warning: Nonexistent include directory ‘I_MPI_SUBSTITUTE_INSTALLDIR/include’ [-Wmissing-include-dirs]<br>
Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI process<br>
See <a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a><br>
hwloc/linux: Ignoring PCI device with non-16bit domain.<br>
Pass --enable-32bits-pci-domain to configure to support such devices<br>
(warning: it would break the library ABI, don't enable unless really needed).<br>
Number of SNES iterations = 3<br>
Completed test examples<br>
Error while running make check<br>
gmake[1]: *** [makefile:149: check] Error 1<br>
make: *** [GNUmakefile:17: check] Error 2<br>
<br>
________________________________________<br>
From: Barry Smith <<a href="mailto:bsmith@petsc.dev" target="_blank">bsmith@petsc.dev</a>><br>
Sent: Wednesday, January 11, 2023 8:22 AM<br>
To: Sijie Zhang<br>
Cc: <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br>
Subject: Re: [petsc-users] PETSC install<br>
<br>
---- External Email: Use caution with attachments, links, or sharing data ----<br>
<br>
<br>
<a href="https://petsc.org/release/faq/#what-does-the-message-hwloc-linux-ignoring-pci-device-with-non-16bit-domain-mean" target="_blank">https://petsc.org/release/faq/#what-does-the-message-hwloc-linux-ignoring-pci-device-with-non-16bit-domain-mean</a><br>
<br>
On Jan 11, 2023, at 5:03 AM, Sijie Zhang <<a href="mailto:zhan2355@purdue.edu" target="_blank">zhan2355@purdue.edu</a>> wrote:<br>
<br>
Hi,<br>
<br>
When I try to install petsc on my workstation, I got the following error. Can you help me with that?<br>
<br>
Thank you and best regards.<br>
<br>
Sijie<br>
<br>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>
<br>
Running check examples to verify correct installation<br>
Using PETSC_DIR=/home/zhangsijie1995/Documents/Package/petsc-3.18.3 and PETSC_ARCH=arch-linux-c-debug<br>
Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process<br>
See <a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a><br>
hwloc/linux: Ignoring PCI device with non-16bit domain.<br>
Pass --enable-32bits-pci-domain to configure to support such devices<br>
(warning: it would break the library ABI, don't enable unless really needed).<br>
lid velocity = 0.0016, prandtl # = 1., grashof # = 1.<br>
Number of SNES iterations = 2<br>
Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes<br>
See <a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a><br>
hwloc/linux: Ignoring PCI device with non-16bit domain.<br>
Pass --enable-32bits-pci-domain to configure to support such devices<br>
(warning: it would break the library ABI, don't enable unless really needed).<br>
hwloc/linux: Ignoring PCI device with non-16bit domain.<br>
Pass --enable-32bits-pci-domain to configure to support such devices<br>
(warning: it would break the library ABI, don't enable unless really needed).<br>
lid velocity = 0.0016, prandtl # = 1., grashof # = 1.<br>
Number of SNES iterations = 2<br>
*******************Error detected during compile or link!*******************<br>
See <a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a><br>
/home/zhangsijie1995/Documents/Package/petsc-3.18.3/src/snes/tutorials ex5f<br>
*********************************************************<br>
/opt/intel/oneapi/mpi/2021.8.0/bin/mpif90 -fPIC -Wall -ffree-line-length-none -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -g -O0 -I/home/zhangsijie1995/Documents/Package/petsc-3.18.3/include -I/home/zhangsijie1995/Documents/Package/petsc-3.18.3/arch-linux-c-debug/include
-I/opt/intel/oneapi/mkl/2023.0.0/include -I/opt/intel/oneapi/mpi/2021.8.0/include ex5f.F90 -Wl,-rpath,/home/zhangsijie1995/Documents/Package/petsc-3.18.3/arch-linux-c-debug/lib -L/home/zhangsijie1995/Documents/Package/petsc-3.18.3/arch-linux-c-debug/lib
-Wl,-rpath,/opt/intel/oneapi/mkl/2023.0.0/lib/intel64 -L/opt/intel/oneapi/mkl/2023.0.0/lib/intel64 -Wl,-rpath,/home/zhangsijie1995/Documents/Package/petsc-3.18.3/I_MPI_SUBSTITUTE_INSTALLDIR/lib/release -L/home/zhangsijie1995/Documents/Package/petsc-3.18.3/I_MPI_SUBSTITUTE_INSTALLDIR/lib/release
-Wl,-rpath,/home/zhangsijie1995/Documents/Package/petsc-3.18.3/I_MPI_SUBSTITUTE_INSTALLDIR/lib -L/home/zhangsijie1995/Documents/Package/petsc-3.18.3/I_MPI_SUBSTITUTE_INSTALLDIR/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11
-lpetsc -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lm -lstdc++ -ldl -lmpifort -lmpi -lrt -lpthread -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -o ex5f<br>
f951: Warning: Nonexistent include directory ‘I_MPI_SUBSTITUTE_INSTALLDIR/include/gfortran/11.1.0’ [-Wmissing-include-dirs]<br>
f951: Warning: Nonexistent include directory ‘I_MPI_SUBSTITUTE_INSTALLDIR/include’ [-Wmissing-include-dirs]<br>
Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI process<br>
See <a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a><br>
hwloc/linux: Ignoring PCI device with non-16bit domain.<br>
Pass --enable-32bits-pci-domain to configure to support such devices<br>
(warning: it would break the library ABI, don't enable unless really needed).<br>
Number of SNES iterations = 3<br>
Completed test examples<br>
Error while running make check<br>
gmake[1]: *** [makefile:149: check] Error 1<br>
make: *** [GNUmakefile:17: check] Error 2<configure.log><make.log><br>
<br>
<configure.log><make.log><o:p></o:p></p>
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<p class="MsoNormal">-- <o:p></o:p></p>
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<p class="MsoNormal">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<o:p></o:p></p>
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<p class="MsoNormal"><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><o:p></o:p></p>
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