If you put the variable in the .bashrc file then you mush source ~/.bashrc before running the make check Barry
On Jan 11, 2023, at 11:52 PM, Sijie Zhang <[email protected]> wrote:
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?
Thanks.
Sijie
Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows
From: Matthew Knepley <mailto:[email protected]> Sent: Wednesday, January 11, 2023 7:40 PM To: Barry Smith <mailto:[email protected]> Cc: Sijie Zhang <mailto:[email protected]>; [email protected] <mailto:[email protected]> Subject: Re: [petsc-users] PETSC install
---- External Email: Use caution with attachments, links, or sharing data ----
On Wed, Jan 11, 2023 at 2:33 PM Barry Smith <[email protected] <mailto:[email protected]>> wrote:
Did you do exactly:
export HWLOC_HIDE_ERRORS=2 make check
Also, what shell are you using? The command above is for bash, but if you use csh it is different.
Thanks,
Matt
?
On Jan 11, 2023, at 6:51 PM, Sijie Zhang <[email protected] <mailto:[email protected]>> wrote:
Hi,
I tried that but it's showing the same error. Can you help me to take a look at that?
Thanks.
Sijie
+++++++++++++++++++++++++++++++++++++++++++++++++++++
Running check examples to verify correct installation Using PETSC_DIR=/home/zhangsijie1995/Documents/Package/petsc-3.18.3 and PETSC_ARCH=arch-linux-c-debug Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process See https://petsc.org/release/faq/ hwloc/linux: Ignoring PCI device with non-16bit domain. Pass --enable-32bits-pci-domain to configure to support such devices (warning: it would break the library ABI, don't enable unless really needed). lid velocity = 0.0016, prandtl # = 1., grashof # = 1. Number of SNES iterations = 2 Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes See https://petsc.org/release/faq/ hwloc/linux: Ignoring PCI device with non-16bit domain. Pass --enable-32bits-pci-domain to configure to support such devices (warning: it would break the library ABI, don't enable unless really needed). hwloc/linux: Ignoring PCI device with non-16bit domain. Pass --enable-32bits-pci-domain to configure to support such devices (warning: it would break the library ABI, don't enable unless really needed). lid velocity = 0.0016, prandtl # = 1., grashof # = 1. Number of SNES iterations = 2 *******************Error detected during compile or link!******************* See https://petsc.org/release/faq/ /home/zhangsijie1995/Documents/Package/petsc-3.18.3/src/snes/tutorials ex5f ********************************************************* /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 f951: Warning: Nonexistent include directory ‘I_MPI_SUBSTITUTE_INSTALLDIR/include/gfortran/11.1.0’ [-Wmissing-include-dirs] f951: Warning: Nonexistent include directory ‘I_MPI_SUBSTITUTE_INSTALLDIR/include’ [-Wmissing-include-dirs] Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI process See https://petsc.org/release/faq/ hwloc/linux: Ignoring PCI device with non-16bit domain. Pass --enable-32bits-pci-domain to configure to support such devices (warning: it would break the library ABI, don't enable unless really needed). Number of SNES iterations = 3 Completed test examples Error while running make check gmake[1]: *** [makefile:149: check] Error 1 make: *** [GNUmakefile:17: check] Error 2
________________________________________ From: Barry Smith <[email protected] <mailto:[email protected]>> Sent: Wednesday, January 11, 2023 8:22 AM To: Sijie Zhang Cc: [email protected] <mailto:[email protected]> Subject: Re: [petsc-users] PETSC install
---- External Email: Use caution with attachments, links, or sharing data ----
https://petsc.org/release/faq/#what-does-the-message-hwloc-linux-ignoring-pc...
On Jan 11, 2023, at 5:03 AM, Sijie Zhang <[email protected] <mailto:[email protected]>> wrote:
Hi,
When I try to install petsc on my workstation, I got the following error. Can you help me with that?
Thank you and best regards.
Sijie
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Running check examples to verify correct installation Using PETSC_DIR=/home/zhangsijie1995/Documents/Package/petsc-3.18.3 and PETSC_ARCH=arch-linux-c-debug Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process See https://petsc.org/release/faq/ hwloc/linux: Ignoring PCI device with non-16bit domain. Pass --enable-32bits-pci-domain to configure to support such devices (warning: it would break the library ABI, don't enable unless really needed). lid velocity = 0.0016, prandtl # = 1., grashof # = 1. Number of SNES iterations = 2 Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes See https://petsc.org/release/faq/ hwloc/linux: Ignoring PCI device with non-16bit domain. Pass --enable-32bits-pci-domain to configure to support such devices (warning: it would break the library ABI, don't enable unless really needed). hwloc/linux: Ignoring PCI device with non-16bit domain. Pass --enable-32bits-pci-domain to configure to support such devices (warning: it would break the library ABI, don't enable unless really needed). lid velocity = 0.0016, prandtl # = 1., grashof # = 1. Number of SNES iterations = 2 *******************Error detected during compile or link!******************* See https://petsc.org/release/faq/ /home/zhangsijie1995/Documents/Package/petsc-3.18.3/src/snes/tutorials ex5f ********************************************************* /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 f951: Warning: Nonexistent include directory ‘I_MPI_SUBSTITUTE_INSTALLDIR/include/gfortran/11.1.0’ [-Wmissing-include-dirs] f951: Warning: Nonexistent include directory ‘I_MPI_SUBSTITUTE_INSTALLDIR/include’ [-Wmissing-include-dirs] Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI process See https://petsc.org/release/faq/ hwloc/linux: Ignoring PCI device with non-16bit domain. Pass --enable-32bits-pci-domain to configure to support such devices (warning: it would break the library ABI, don't enable unless really needed). Number of SNES iterations = 3 Completed test examples Error while running make check gmake[1]: *** [makefile:149: check] Error 1 make: *** [GNUmakefile:17: check] Error 2<configure.log><make.log>
<configure.log><make.log>
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener
https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>