<div dir="ltr"><div dir="ltr">On Wed, Jan 11, 2023 at 2:33 PM Barry Smith <<a href="mailto:bsmith@petsc.dev">bsmith@petsc.dev</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div><br></div>  Did you do exactly:<div><br></div><div><pre id="m_1508981105543049089codecell36" style="box-sizing:border-box;overflow:auto;clear:both;font-size:13.125px;margin-top:0px;margin-bottom:0px;color:rgb(50,50,50);border-radius:0.25rem;line-height:16.4062px;padding:1rem"><span style="box-sizing:border-box;color:rgb(0,0,0)">export</span><span style="box-sizing:border-box;color:rgb(248,248,248)"> </span><span style="box-sizing:border-box;color:rgb(0,0,0)">HWLOC_HIDE_ERRORS</span><span style="box-sizing:border-box;color:rgb(206,92,0);font-weight:bold">=</span><span style="box-sizing:border-box;color:rgb(0,0,207);font-weight:bold">2</span></pre><pre id="m_1508981105543049089codecell36" style="box-sizing:border-box;overflow:auto;clear:both;font-size:13.125px;margin-top:0px;margin-bottom:0px;color:rgb(50,50,50);border-radius:0.25rem;line-height:16.4062px;padding:1rem"><span style="box-sizing:border-box;color:rgb(0,0,207);font-weight:bold">make check</span></pre></div></div></blockquote><div><br></div><div>Also, what shell are you using? The command above is for bash, but if you use csh it is different.</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"><div><div><pre id="m_1508981105543049089codecell36" style="box-sizing:border-box;overflow:auto;clear:both;font-size:13.125px;margin-top:0px;margin-bottom:0px;color:rgb(50,50,50);border-radius:0.25rem;line-height:16.4062px;padding:1rem"><span style="box-sizing:border-box;color:rgb(0,0,207);font-weight:bold">?</span></pre><pre id="m_1508981105543049089codecell36" style="box-sizing:border-box;overflow:auto;clear:both;font-size:13.125px;margin-top:0px;margin-bottom:0px;color:rgb(50,50,50);border-radius:0.25rem;line-height:16.4062px;padding:1rem"><span style="box-sizing:border-box;color:rgb(0,0,207);font-weight:bold"><br></span></pre><div><br><blockquote type="cite"><div>On Jan 11, 2023, at 6:51 PM, Sijie Zhang <<a href="mailto:zhan2355@purdue.edu" target="_blank">zhan2355@purdue.edu</a>> wrote:</div><br><div><div>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><span id="m_1508981105543049089cid:0FC0F0C1-E145-4FDF-85A4-A2BD55922E70"><configure.log></span><span id="m_1508981105543049089cid:03EE1ABB-BAE4-4915-9099-FC91D8B80F79"><make.log></span></div></div></blockquote></div><br></div></div></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><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><div><br></div><div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>