[petsc-users] PETSC install

Satish Balay balay at mcs.anl.gov
Wed Jan 11 23:41:26 CST 2023 

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: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/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 <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/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/>
> 
>

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