[petsc-dev] issue with v3.21.5 build

Jeffrey Hyman hymanjd at gmail.com
Tue Apr 29 08:16:58 CDT 2025 

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?
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!cBNLiZjc6oqZZmFbC4HgLmq2tj7O-yjdayOHP5-mzR0CEXbopKmky2s266O5ghDqPYZRmE9xP8XKkhjSU3uk$ 
>> \
>> --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!cBNLiZjc6oqZZmFbC4HgLmq2tj7O-yjdayOHP5-mzR0CEXbopKmky2s266O5ghDqPYZRmE9xP8XKkiz1vVTk$ 
>>>>
>>>> *********************************************************************************************
>>>>
>>>>
>>>>
>>>> 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!cBNLiZjc6oqZZmFbC4HgLmq2tj7O-yjdayOHP5-mzR0CEXbopKmky2s266O5ghDqPYZRmE9xP8XKkmy-3Ce0$  \
>>>>>> --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!cBNLiZjc6oqZZmFbC4HgLmq2tj7O-yjdayOHP5-mzR0CEXbopKmky2s266O5ghDqPYZRmE9xP8XKkhjSU3uk$ 
>>>>>> \
>>>>>> --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!cBNLiZjc6oqZZmFbC4HgLmq2tj7O-yjdayOHP5-mzR0CEXbopKmky2s266O5ghDqPYZRmE9xP8XKkkaw9W8x$ 
>>>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cBNLiZjc6oqZZmFbC4HgLmq2tj7O-yjdayOHP5-mzR0CEXbopKmky2s266O5ghDqPYZRmE9xP8XKkkk3T9lx$ >
>>>>>
>>>>
>
> --
> 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!cBNLiZjc6oqZZmFbC4HgLmq2tj7O-yjdayOHP5-mzR0CEXbopKmky2s266O5ghDqPYZRmE9xP8XKkkaw9W8x$ 
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cBNLiZjc6oqZZmFbC4HgLmq2tj7O-yjdayOHP5-mzR0CEXbopKmky2s266O5ghDqPYZRmE9xP8XKkkk3T9lx$ >
>
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