<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div><br></div> If you put the variable in the .bashrc file then you mush <div><br></div><div> source ~/.bashrc </div><div><br></div><div> before running the </div><div><br></div><div> make check</div><div><br></div><div><br></div><div> Barry</div><div><br><div><br><blockquote type="cite"><div>On Jan 11, 2023, at 11:52 PM, Sijie Zhang <zhan2355@purdue.edu> wrote:</div><br class="Apple-interchange-newline"><div><meta charset="UTF-8"><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">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?</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">Thanks.</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">Sijie<span class="Apple-converted-space"> </span></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">Sent from<span class="Apple-converted-space"> </span><a href="https://go.microsoft.com/fwlink/?LinkId=550986" style="color: blue; text-decoration: underline;">Mail</a><span class="Apple-converted-space"> </span>for Windows</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(225, 225, 225); padding: 3pt 0in 0in;"><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif; border: none; padding: 0in;"><b>From:<span class="Apple-converted-space"> </span></b><a href="mailto:knepley@gmail.com" style="color: blue; text-decoration: underline;">Matthew Knepley</a><br><b>Sent:<span class="Apple-converted-space"> </span></b>Wednesday, January 11, 2023 7:40 PM<br><b>To:<span class="Apple-converted-space"> </span></b><a href="mailto:bsmith@petsc.dev" style="color: blue; text-decoration: underline;">Barry Smith</a><br><b>Cc:<span class="Apple-converted-space"> </span></b><a href="mailto:zhan2355@purdue.edu" style="color: blue; text-decoration: underline;">Sijie Zhang</a>;<span class="Apple-converted-space"> </span><a href="mailto:petsc-users@mcs.anl.gov" style="color: blue; text-decoration: underline;">petsc-users@mcs.anl.gov</a><br><b>Subject:<span class="Apple-converted-space"> </span></b>Re: [petsc-users] PETSC install</div></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><table class="MsoNormalTable" border="0" cellspacing="3" cellpadding="0" width="100%" style="width: 1047px; background-color: rgb(255, 240, 160);"><tbody><tr><td style="padding: 3.75pt;"><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><span style="font-size: 10pt; font-family: Verdana, sans-serif;">----<span class="Apple-converted-space"> </span><b>External Email</b>: Use caution with attachments, links, or sharing data ----<o:p></o:p></span></div></td></tr></tbody></table><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div><div><div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">On Wed, Jan 11, 2023 at 2:33 PM Barry Smith <<a href="mailto:bsmith@petsc.dev" style="color: blue; text-decoration: underline;">bsmith@petsc.dev</a>> wrote:<o:p></o:p></div></div><div><blockquote style="border-style: none none none solid; border-left-width: 1pt; border-left-color: rgb(204, 204, 204); padding: 0in 0in 0in 6pt; margin-left: 4.8pt; margin-right: 0in;"><div><div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"> Did you do exactly:<span class="Apple-converted-space"> </span><o:p></o:p></div><div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div></div><div><pre id="m_1508981105543049089codecell36" style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New"; line-height: 12.3pt; box-sizing: border-box; border-radius: 0.25rem; padding: 1rem; overflow: auto;"><span style="">export</span><span style="color: rgb(248, 248, 248);"> </span><span style="">HWLOC_HIDE_ERRORS</span><b><span style="color: rgb(206, 92, 0);">=</span><span style="color: rgb(0, 0, 207);">2</span></b><span style="color: rgb(50, 50, 50);"><o:p></o:p></span></pre><pre id="m_1508981105543049089codecell36" style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New"; line-height: 12.3pt; box-sizing: border-box; border-radius: 0.25rem; padding: 1rem; overflow: auto;"><b><span style="color: rgb(0, 0, 207);">make check</span></b><span style="color: rgb(50, 50, 50);"><o:p></o:p></span></pre></div></div></blockquote><div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div></div><div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">Also, what shell are you using? The command above is for bash, but if you use csh it is different.<o:p></o:p></div></div><div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div></div><div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"> Thanks,<o:p></o:p></div></div><div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div></div><div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"> Matt<o:p></o:p></div></div><div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"> <o:p></o:p></div></div><blockquote style="border-style: none none none solid; border-left-width: 1pt; border-left-color: rgb(204, 204, 204); padding: 0in 0in 0in 6pt; margin-left: 4.8pt; margin-right: 0in;"><div><div><pre id="m_1508981105543049089codecell36" style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New"; line-height: 12.3pt; box-sizing: border-box; border-radius: 0.25rem; padding: 1rem; overflow: auto;"><b><span style="color: rgb(0, 0, 207);">?</span></b><span style="color: rgb(50, 50, 50);"><o:p></o:p></span></pre><pre id="m_1508981105543049089codecell36" style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New"; line-height: 12.3pt; box-sizing: border-box; border-radius: 0.25rem; padding: 1rem; overflow: auto;"><b><span style="color: rgb(0, 0, 207);"><br><br></span></b><span style="color: rgb(50, 50, 50);"><o:p></o:p></span></pre><div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><br><br><o:p></o:p></div><blockquote style="margin-top: 5pt; margin-bottom: 5pt;"><div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">On Jan 11, 2023, at 6:51 PM, Sijie Zhang <<a href="mailto:zhan2355@purdue.edu" target="_blank" style="color: blue; text-decoration: underline;">zhan2355@purdue.edu</a>> wrote:<o:p></o:p></div></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div><div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">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<span class="Apple-converted-space"> </span><a href="https://petsc.org/release/faq/" target="_blank" style="color: blue; text-decoration: underline;">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<span class="Apple-converted-space"> </span><a href="https://petsc.org/release/faq/" target="_blank" style="color: blue; text-decoration: underline;">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<span class="Apple-converted-space"> </span><a href="https://petsc.org/release/faq/" target="_blank" style="color: blue; text-decoration: underline;">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<span class="Apple-converted-space"> </span><a href="https://petsc.org/release/faq/" target="_blank" style="color: blue; text-decoration: underline;">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" style="color: blue; text-decoration: underline;">bsmith@petsc.dev</a>><br>Sent: Wednesday, January 11, 2023 8:22 AM<br>To: Sijie Zhang<br>Cc:<span class="Apple-converted-space"> </span><a href="mailto:petsc-users@mcs.anl.gov" target="_blank" style="color: blue; text-decoration: underline;">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" style="color: blue; text-decoration: underline;">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" style="color: blue; text-decoration: underline;">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<span class="Apple-converted-space"> </span><a href="https://petsc.org/release/faq/" target="_blank" style="color: blue; text-decoration: underline;">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<span class="Apple-converted-space"> </span><a href="https://petsc.org/release/faq/" target="_blank" style="color: blue; text-decoration: underline;">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<span class="Apple-converted-space"> </span><a href="https://petsc.org/release/faq/" target="_blank" style="color: blue; text-decoration: underline;">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<span class="Apple-converted-space"> </span><a href="https://petsc.org/release/faq/" target="_blank" style="color: blue; text-decoration: underline;">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></div></div></div></blockquote></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div></div></div></blockquote></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><br clear="all"><o:p></o:p></div><div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">--<span class="Apple-converted-space"> </span><o:p></o:p></div><div><div><div><div><div><div><div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">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></div></div><div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div></div></div></div></div></div></div></div></div></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank" style="color: blue; text-decoration: underline;">https://www.cse.buffalo.edu/~knepley/</a></div></div></div></blockquote></div><br></div></body></html>