On Tue, Apr 29, 2025 at 9:28 AM Jeffrey Hyman <hyma...@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 $PETSC_DIR
3) Get rid of the preinstalled OpenMPI you have. It is usually somewhat
broken and not helping.
4) Reclone and rebuild
THanks,
Matt
> Thanks, Matt! Feels close.
> J
>
>
> On Tue, Apr 29, 2025 at 9:20 AM Matthew Knepley <knep...@gmail.com> wrote:
>
>> On Tue, Apr 29, 2025 at 9:17 AM Jeffrey Hyman <hyma...@gmail.com> wrote:
>>
>>> Unfortunately, Pflotran hasn't been updated to use 3.22 yet. So I'm
>>> stuck with 3.21.5. Can I hack the python path?
>>>
>>
>> Tell Glenn to get in gear :)
>>
>> I think you can just get this file:
>>
>> https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-__;!!G_uCfscf7eWS!aCXYdJa6qIqzbz7bbjecjWzBan_SFbfJfdIaygZj2PaZvFifH1mMrwwpbPzHpv3kDXCyUeQr0942aqmC9XCa$
>>
>> /blob/release-3.22/config/gmakegen.py?ref_type=heads
>>
>> and put it in $PETSC_DIR/config/gmakegen.py
>>
>> Finger crossed,
>>
>> Matt
>>
>>
>>> J
>>>
>>>
>>> On Tue, Apr 29, 2025 at 9:14 AM Matthew Knepley <knep...@gmail.com>
>>> wrote:
>>>
>>>> On Tue, Apr 29, 2025 at 9:08 AM Jeffrey Hyman <hyma...@gmail.com>
>>>> wrote:
>>>>
>>>>> This configure worked
>>>>>
>>>>> ./configure --COPTFLAGS='-O3' --CXXOPTFLAGS='-O3' --FOPTFLAGS='-O3
>>>>> -Wno-unused-function -fallow-argument-mismatch' --with-debugging=no
>>>>> --download-mpich=yes --download-hdf5=yes
>>>>> --download-hdf5-fortran-bindings=yes --download-fblaslapack=yes
>>>>> --download-metis=yes --download-parmetis=yes --download-cmake=
>>>>> https://urldefense.us/v3/__https://gitlab.kitware.com/cmake/cmake/-/archive/v3.31.7/cmake-v3.31.7.tar.gz__;!!G_uCfscf7eWS!aCXYdJa6qIqzbz7bbjecjWzBan_SFbfJfdIaygZj2PaZvFifH1mMrwwpbPzHpv3kDXCyUeQr0942aum8KPZc$
>>>>>
>>>>> \
>>>>> --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 <hyma...@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 <hyma...@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!aCXYdJa6qIqzbz7bbjecjWzBan_SFbfJfdIaygZj2PaZvFifH1mMrwwpbPzHpv3kDXCyUeQr0942ar3KiTnU$
>>>>>>>
>>>>>>>
>>>>>>> *********************************************************************************************
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Tue, Apr 29, 2025 at 7:56 AM Matthew Knepley <knep...@gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> On Mon, Apr 28, 2025 at 10:02 PM Satish Balay <
>>>>>>>> balay....@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!aCXYdJa6qIqzbz7bbjecjWzBan_SFbfJfdIaygZj2PaZvFifH1mMrwwpbPzHpv3kDXCyUeQr0942ajrJha90$
>>>>>>>>> \
>>>>>>>>> --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!aCXYdJa6qIqzbz7bbjecjWzBan_SFbfJfdIaygZj2PaZvFifH1mMrwwpbPzHpv3kDXCyUeQr0942aum8KPZc$
>>>>>>>>>
>>>>>>>>> \
>>>>>>>>> --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 <
>>>>>>>>> knep...@gmail.com> wrote:
>>>>>>>>> >
>>>>>>>>> > > On Mon, Apr 28, 2025 at 8:34 PM Jeffrey Hyman <
>>>>>>>>> hyma...@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!aCXYdJa6qIqzbz7bbjecjWzBan_SFbfJfdIaygZj2PaZvFifH1mMrwwpbPzHpv3kDXCyUeQr0942attehhcz$
>>>>>>>>
>>>>>>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!aCXYdJa6qIqzbz7bbjecjWzBan_SFbfJfdIaygZj2PaZvFifH1mMrwwpbPzHpv3kDXCyUeQr0942alhImLgb$
>>>>>>>> >
>>>>>>>>
>>>>>>>
>>>>
>>>> --
>>>> 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!aCXYdJa6qIqzbz7bbjecjWzBan_SFbfJfdIaygZj2PaZvFifH1mMrwwpbPzHpv3kDXCyUeQr0942attehhcz$
>>>>
>>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!aCXYdJa6qIqzbz7bbjecjWzBan_SFbfJfdIaygZj2PaZvFifH1mMrwwpbPzHpv3kDXCyUeQr0942alhImLgb$
>>>> >
>>>>
>>>
>>
>> --
>> 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!aCXYdJa6qIqzbz7bbjecjWzBan_SFbfJfdIaygZj2PaZvFifH1mMrwwpbPzHpv3kDXCyUeQr0942attehhcz$
>>
>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!aCXYdJa6qIqzbz7bbjecjWzBan_SFbfJfdIaygZj2PaZvFifH1mMrwwpbPzHpv3kDXCyUeQr0942alhImLgb$
>> >
>>
>
--
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!aCXYdJa6qIqzbz7bbjecjWzBan_SFbfJfdIaygZj2PaZvFifH1mMrwwpbPzHpv3kDXCyUeQr0942attehhcz$
<https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!aCXYdJa6qIqzbz7bbjecjWzBan_SFbfJfdIaygZj2PaZvFifH1mMrwwpbPzHpv3kDXCyUeQr0942alhImLgb$
>
