[petsc-users] PETSC install

Barry Smith bsmith at petsc.dev
Thu Jan 12 09:29:27 CST 2023 

  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 <zhan2355 at purdue.edu> 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:knepley at gmail.com>
> Sent: Wednesday, January 11, 2023 7:40 PM
> To: Barry Smith <mailto:bsmith at petsc.dev>
> Cc: Sijie Zhang <mailto:zhan2355 at purdue.edu>; petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>
> 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 <bsmith at petsc.dev <mailto: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 <mailto: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 <mailto:bsmith at petsc.dev>>
> Sent: Wednesday, January 11, 2023 8:22 AM
> To: Sijie Zhang
> Cc: petsc-users at mcs.anl.gov <mailto: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 <mailto: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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