[petsc-users] PETSC install

Wed Jan 11 18:40:32 CST 2023

On Wed, Jan 11, 2023 at 2:33 PM Barry Smith <bsmith at petsc.dev> 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 <zhan2355 at purdue.edu> 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 <bsmith at petsc.dev>
> Sent: Wednesday, January 11, 2023 8:22 AM
> To: Sijie Zhang
> Cc: petsc-users at mcs.anl.gov
> 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 <zhan2355 at purdue.edu> 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/>
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