The examples appear to run [with extra warnings]. You could assume you have a working install of petsc and start using it [but you will continue to get these messages]..
Wrt the warnings - You have 2 sets of messages. 1. 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). 2. > 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] The env variable HWLOC_HIDE_ERRORS=2 should fix the first one. Are you still getting it? The second one is due to spurious stuff from your MPI wrappers: >>> Executing: /opt/intel/oneapi/mpi/2021.8.0/bin/mpif90 -c -o /tmp/petsc-v6nugevd/config.setCompilers/conftest.o -I/tmp/petsc-v6nugevd/config.setCompilers /tmp/petsc-v6nugevd/config.setCompilers/conftest.F90 Possible ERROR while running compiler:exit code 0 stderr: 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] <<<< Also: >>>>> Executing: /opt/intel/oneapi/mpi/2021.8.0/bin/mpiifort -c -o /tmp/petsc-v6nugevd/config.setCompilers/conftest.o -I/tmp/petsc-v6nugevd/config.setCompilers /tmp/petsc-v6nugevd/config.setCompilers/conftest.F90 Possible ERROR while running compiler: exit code 127 stderr: /opt/intel/oneapi/mpi/2021.8.0/bin/mpiifort: 1: eval: ifort: not found <<<<<< So it would be good if you can fix your Intel compilers and Intel-MPI [to not give the above warnings/errors] - before installing/using PETSc with it. Or - just use gnu compilers (with mpich) - unless you have a really good reason to use Intel compilers/MPI Satish On Thu, 12 Jan 2023, Sijie Zhang 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/Pack age/pets c-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-pci-device-with-non-16bit-domain-mean > > 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/Pack age/pets c-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/> > >
