[petsc-dev] issue with v3.21.5 build
Jeffrey Hyman
hymanjd at gmail.com
Tue Apr 29 09:09:01 CDT 2025
did 1 - 4, now I'm getting an error configuring hdf5. configure.log
attached,
On Tue, Apr 29, 2025 at 9:41 AM Matthew Knepley <knepley at gmail.com> wrote:
> On Tue, Apr 29, 2025 at 9:28 AM Jeffrey Hyman <hymanjd at gmail.com> wrote:
>
>> I know he and Richard have it on the to do list. But I'll encourage them
>> at a meeting tomorrow. : )
>>
>> That file for the make to work, but the check failed. Looks like MPI
>> might have gotten crossed up in all the installs?
>>
>
> Yes, I would
>
> 1) Preserve the reconfigure-***.py and gmakegen.py
>
> 2) Remove the whole $PETSC_DIR
>
> 3) Get rid of the preinstalled OpenMPI you have. It is usually somewhat
> broken and not helping.
>
> 4) Reclone and rebuild
>
> THanks,
>
> Matt
>
>
>> Thanks, Matt! Feels close.
>> J
>>
>>
>> On Tue, Apr 29, 2025 at 9:20 AM Matthew Knepley <knepley at gmail.com>
>> wrote:
>>
>>> On Tue, Apr 29, 2025 at 9:17 AM Jeffrey Hyman <hymanjd at gmail.com> wrote:
>>>
>>>> Unfortunately, Pflotran hasn't been updated to use 3.22 yet. So I'm
>>>> stuck with 3.21.5. Can I hack the python path?
>>>>
>>>
>>> Tell Glenn to get in gear :)
>>>
>>> I think you can just get this file:
>>>
>>> https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-__;!!G_uCfscf7eWS!dAFA2mugYMCgUctVmaXgBDyXbPxSz-0PIn0dvTg2qr7tKeAq2tBKU2F_YNura6cI6zU9v3eNwyny4fwL0vMa$
>>> /blob/release-3.22/config/gmakegen.py?ref_type=heads
>>>
>>> and put it in $PETSC_DIR/config/gmakegen.py
>>>
>>> Finger crossed,
>>>
>>> Matt
>>>
>>>
>>>> J
>>>>
>>>>
>>>> On Tue, Apr 29, 2025 at 9:14 AM Matthew Knepley <knepley at gmail.com>
>>>> wrote:
>>>>
>>>>> On Tue, Apr 29, 2025 at 9:08 AM Jeffrey Hyman <hymanjd at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> This configure worked
>>>>>>
>>>>>> ./configure --COPTFLAGS='-O3' --CXXOPTFLAGS='-O3' --FOPTFLAGS='-O3
>>>>>> -Wno-unused-function -fallow-argument-mismatch' --with-debugging=no
>>>>>> --download-mpich=yes --download-hdf5=yes
>>>>>> --download-hdf5-fortran-bindings=yes --download-fblaslapack=yes
>>>>>> --download-metis=yes --download-parmetis=yes --download-cmake=
>>>>>> https://urldefense.us/v3/__https://gitlab.kitware.com/cmake/cmake/-/archive/v3.31.7/cmake-v3.31.7.tar.gz__;!!G_uCfscf7eWS!dAFA2mugYMCgUctVmaXgBDyXbPxSz-0PIn0dvTg2qr7tKeAq2tBKU2F_YNura6cI6zU9v3eNwyny4SvoSOm1$
>>>>>> \
>>>>>> --download-cmake-cc=clang --download-cmake-cxx=clang++
>>>>>>
>>>>>> but then it failed on the make. configure and make attached.
>>>>>>
>>>>>
>>>>> We could backport a check for this. The Python is newer than the
>>>>> release 3.21.5, so we are using something that went away. If you use 3.22
>>>>> or higher this is fixed.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Matt
>>>>>
>>>>>
>>>>>> Thanks again for the help. Much appreciated.
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Tue, Apr 29, 2025 at 8:53 AM Jeffrey Hyman <hymanjd at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> I updated brew llvm to the latest clang
>>>>>>>
>>>>>>> Homebrew clang version 20.1.3
>>>>>>> Target: arm64-apple-darwin24.3.0
>>>>>>> Thread model: posix
>>>>>>> InstalledDir: /opt/homebrew/Cellar/llvm/20.1.3/bin
>>>>>>> Configuration file: /opt/homebrew/etc/clang/arm64-apple-darwin24.cfg
>>>>>>>
>>>>>>> and that seems happier with gfortran. I'm guessing that updating my
>>>>>>> mac OS to sequoia mixed stuff up.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Tue, Apr 29, 2025 at 8:24 AM Jeffrey Hyman <hymanjd at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> I had tried with clang as well, but was getting this error. Looks
>>>>>>>> like something with the arm64. Maybe remove and reinstall gfortran?
>>>>>>>>
>>>>>>>>
>>>>>>>> =============================================================================================
>>>>>>>> TESTING: checkFortranNameMangling from
>>>>>>>> config.compilers(config/BuildSystem/config/compilers.py:78
>>>>>>>>
>>>>>>>> *********************************************************************************************
>>>>>>>> UNABLE to CONFIGURE with GIVEN OPTIONS (see
>>>>>>>> configure.log for details):
>>>>>>>>
>>>>>>>> ---------------------------------------------------------------------------------------------
>>>>>>>> Unknown Fortran name mangling: Are you sure the C and Fortran
>>>>>>>> compilers are compatible?
>>>>>>>> Perhaps one is 64-bit and one is 32-bit?
>>>>>>>> See https://urldefense.us/v3/__https://petsc.org/release/faq/*macos-gfortran__;Iw!!G_uCfscf7eWS!dAFA2mugYMCgUctVmaXgBDyXbPxSz-0PIn0dvTg2qr7tKeAq2tBKU2F_YNura6cI6zU9v3eNwyny4a_nh9C7$
>>>>>>>>
>>>>>>>> *********************************************************************************************
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Tue, Apr 29, 2025 at 7:56 AM Matthew Knepley <knepley at gmail.com>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> On Mon, Apr 28, 2025 at 10:02 PM Satish Balay <
>>>>>>>>> balay.anl at fastmail.org> wrote:
>>>>>>>>>
>>>>>>>>>> What do you have for:
>>>>>>>>>>
>>>>>>>>>> clang --version
>>>>>>>>>>
>>>>>>>>>> Try:
>>>>>>>>>>
>>>>>>>>>> ./configure COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS="-O3
>>>>>>>>>> -Wno-unused-function -fallow-argument-mismatch" \
>>>>>>>>>> --with-debugging=no --download-mpich=
>>>>>>>>>> https://urldefense.us/v3/__https://www.mpich.org/static/downloads/4.3.0/mpich-4.3.0.tar.gz__;!!G_uCfscf7eWS!dAFA2mugYMCgUctVmaXgBDyXbPxSz-0PIn0dvTg2qr7tKeAq2tBKU2F_YNura6cI6zU9v3eNwyny4VBSvX_G$ \
>>>>>>>>>> --download-hdf5=yes --with-hdf5-fortran-bindings=yes
>>>>>>>>>> --download-fblaslapack=yes \
>>>>>>>>>> --download-metis=yes --download-parmetis=yes \
>>>>>>>>>> CC=gcc-14 CXX=g++-14 FC=gfortran-14 --download-make=yes \
>>>>>>>>>> --download-cmake=
>>>>>>>>>> https://urldefense.us/v3/__https://gitlab.kitware.com/cmake/cmake/-/archive/v3.31.7/cmake-v3.31.7.tar.gz__;!!G_uCfscf7eWS!dAFA2mugYMCgUctVmaXgBDyXbPxSz-0PIn0dvTg2qr7tKeAq2tBKU2F_YNura6cI6zU9v3eNwyny4SvoSOm1$
>>>>>>>>>> \
>>>>>>>>>> --download-cmake-cc=clang --download-cmake-cxx=clang++
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> You could use clang. Your g++ is broken:
>>>>>>>>>
>>>>>>>>> Error when bootstrapping CMake:
>>>>>>>>>
>>>>>>>>> Problem while running make
>>>>>>>>>
>>>>>>>>> ---------------------------------------------
>>>>>>>>>
>>>>>>>>> Log of errors:
>>>>>>>>> /Users/hymanjd/src/petsc/arch-darwin-c-debug/externalpackages/cmake-3.29.0/Bootstrap.cmk/cmake_bootstrap.log
>>>>>>>>>
>>>>>>>>> ---------------------------------------------
>>>>>>>>>
>>>>>>>>> stdout:
>>>>>>>>>
>>>>>>>>> In file included from
>>>>>>>>> /opt/homebrew/Cellar/gcc/14.2.0_1/include/c++/14/ext/string_conversions.h:43,
>>>>>>>>>
>>>>>>>>> from
>>>>>>>>> /opt/homebrew/Cellar/gcc/14.2.0_1/include/c++/14/bits/basic_string.h:4154,
>>>>>>>>>
>>>>>>>>> from
>>>>>>>>> /opt/homebrew/Cellar/gcc/14.2.0_1/include/c++/14/string:54,
>>>>>>>>>
>>>>>>>>> from
>>>>>>>>> /Users/hymanjd/src/petsc/arch-darwin-c-debug/externalpackages/cmake-3.29.0/Source/cmTimestamp.h:9,
>>>>>>>>>
>>>>>>>>> from
>>>>>>>>> /Users/hymanjd/src/petsc/arch-darwin-c-debug/externalpackages/cmake-3.29.0/Source/cmTimestamp.cxx:15:
>>>>>>>>>
>>>>>>>>> /opt/homebrew/Cellar/gcc/14.2.0_1/include/c++/14/cstdlib:141:11:
>>>>>>>>> error: 'at_quick_exit' has not been declared in '::'
>>>>>>>>>
>>>>>>>>> 141 | using ::at_quick_exit;
>>>>>>>>>
>>>>>>>>> | ^~~~~~~~~~~~~
>>>>>>>>>
>>>>>>>>> /opt/homebrew/Cellar/gcc/14.2.0_1/include/c++/14/cstdlib:164:11:
>>>>>>>>> error: 'quick_exit' has not been declared in '::'
>>>>>>>>>
>>>>>>>>> 164 | using ::quick_exit;
>>>>>>>>>
>>>>>>>>> | ^~~~~~~~~~
>>>>>>>>>
>>>>>>>>> make: *** [cmTimestamp.o] Error 1
>>>>>>>>>
>>>>>>>>> make: *** Waiting for unfinished jobs....
>>>>>>>>>
>>>>>>>>> Error running configure on CMAKE: Could not
>>>>>>>>> execute "['./configure
>>>>>>>>> --prefix=/Users/hymanjd/src/petsc/arch-darwin-c-debug --parallel=8
>>>>>>>>> CC="/opt/homebrew/bin/gcc-14" CXX="/opt/homebrew/bin/g++-14" --
>>>>>>>>> -DCMAKE_USE_OPENSSL=OFF']":
>>>>>>>>>
>>>>>>>>> Anything that includes <string> looks like it will break.
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>>
>>>>>>>>> Matt
>>>>>>>>>
>>>>>>>>> Satish
>>>>>>>>>>
>>>>>>>>>> On Mon, 28 Apr 2025, Jeffrey Hyman wrote:
>>>>>>>>>>
>>>>>>>>>> > Thanks, I'll give it a spin and let you know how it goes.
>>>>>>>>>> >
>>>>>>>>>> > JDH
>>>>>>>>>> >
>>>>>>>>>> > On Mon, Apr 28, 2025 at 8:43 PM Matthew Knepley <
>>>>>>>>>> knepley at gmail.com> wrote:
>>>>>>>>>> >
>>>>>>>>>> > > On Mon, Apr 28, 2025 at 8:34 PM Jeffrey Hyman <
>>>>>>>>>> hymanjd at gmail.com> wrote:
>>>>>>>>>> > >
>>>>>>>>>> > >> Hi,
>>>>>>>>>> > >>
>>>>>>>>>> > >> I am trying to build v3.21.5 to use with pflotran. I'm
>>>>>>>>>> running into
>>>>>>>>>> > >> issues with cmake. configure log attached. Any suggestions?
>>>>>>>>>> > >>
>>>>>>>>>> > >
>>>>>>>>>> > > The documentation could be clearer here. We cannot use the
>>>>>>>>>> PETSc compilers
>>>>>>>>>> > > to build CMake since it explicitly does not want MPI. Thus
>>>>>>>>>> you need to
>>>>>>>>>> > > specify them yourself. That means you would need
>>>>>>>>>> > >
>>>>>>>>>> > > --download-cmake-cc=/opt/homebrew/bin/gcc-14
>>>>>>>>>> > > --download-cmake-cxx=/opt/homebrew/bin/g++-14
>>>>>>>>>> > >
>>>>>>>>>> > > Thanks,
>>>>>>>>>> > >
>>>>>>>>>> > > Matt
>>>>>>>>>> > >
>>>>>>>>>> > >
>>>>>>>>>> > >> Thanks for the help,
>>>>>>>>>> > >> Jeffrey
>>>>>>>>>> > >>
>>>>>>>>>> > >>
>>>>>>>>>> > >
>>>>>>>>>> > > --
>>>>>>>>>> > > 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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!bZa6EMKsRCbKBAnduL8Vva4vRPvbjUsz_v4OKJW8-c8D8gQcN4fZPfrAaQfZ37j1kQzigfg-TVDeQNOczHyI$
>>>>>>>>>> > > <
>>>>>>>>>> https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!bZa6EMKsRCbKBAnduL8Vva4vRPvbjUsz_v4OKJW8-c8D8gQcN4fZPfrAaQfZ37j1kQzigfg-TVDeQKP18rKz$
>>>>>>>>>> >
>>>>>>>>>> > >
>>>>>>>>>> >
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> 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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dAFA2mugYMCgUctVmaXgBDyXbPxSz-0PIn0dvTg2qr7tKeAq2tBKU2F_YNura6cI6zU9v3eNwyny4fbYSK9n$
>>>>>>>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dAFA2mugYMCgUctVmaXgBDyXbPxSz-0PIn0dvTg2qr7tKeAq2tBKU2F_YNura6cI6zU9v3eNwyny4Q1ci-Np$ >
>>>>>>>>>
>>>>>>>>
>>>>>
>>>>> --
>>>>> 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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dAFA2mugYMCgUctVmaXgBDyXbPxSz-0PIn0dvTg2qr7tKeAq2tBKU2F_YNura6cI6zU9v3eNwyny4fbYSK9n$
>>>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dAFA2mugYMCgUctVmaXgBDyXbPxSz-0PIn0dvTg2qr7tKeAq2tBKU2F_YNura6cI6zU9v3eNwyny4Q1ci-Np$ >
>>>>>
>>>>
>>>
>>> --
>>> 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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dAFA2mugYMCgUctVmaXgBDyXbPxSz-0PIn0dvTg2qr7tKeAq2tBKU2F_YNura6cI6zU9v3eNwyny4fbYSK9n$
>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dAFA2mugYMCgUctVmaXgBDyXbPxSz-0PIn0dvTg2qr7tKeAq2tBKU2F_YNura6cI6zU9v3eNwyny4Q1ci-Np$ >
>>>
>>
>
> --
> 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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dAFA2mugYMCgUctVmaXgBDyXbPxSz-0PIn0dvTg2qr7tKeAq2tBKU2F_YNura6cI6zU9v3eNwyny4fbYSK9n$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dAFA2mugYMCgUctVmaXgBDyXbPxSz-0PIn0dvTg2qr7tKeAq2tBKU2F_YNura6cI6zU9v3eNwyny4Q1ci-Np$ >
>
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