On Tue, Apr 29, 2025 at 10:09 AM Jeffrey Hyman <hyma...@gmail.com> wrote:
> did 1 - 4, now I'm getting an error configuring hdf5. configure.log
> attached,
>
I forgot to look at your environment. This is what was causing your MPI
issues. Always turn off all Anaconda stuff in the env when building PETSc.
configure:7444: mpif90 -c -ffree-line-length-none -ffree-line-length-0
-Wno-lto-type-mismatch -O3 -Wno-unused-function -fallow-argument-mismatch
-fallow-argument-mismatch -x f95 conftest.f90 >&5
/Users/hymanjd/opt/anaconda3/bin/mpif90: line 392:
x86_64-apple-darwin13.4.0-gfortran: command not found
configure:7444: $? = 127
configure: failed program was:
| program main
|
| end
configure:7454: result: unknown
configure:7457: error: Fortran could not compile .f90 files
It has ceased to be a force for good.
Thanks,
Matt
On Tue, Apr 29, 2025 at 9:41 AM Matthew Knepley <knep...@gmail.com> wrote:
>
>> 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 $PETSC_DIR
>>
>> 3) Get rid of the preinstalled OpenMPI you have. It is usually somewhat
>> broken and not helping.
>>
>> 4) Reclone and rebuild
>>
>> THanks,
>>
>> Matt
>>
>>
>>> Thanks, Matt! Feels close.
>>> J
>>>
>>>
>>> On Tue, Apr 29, 2025 at 9:20 AM Matthew Knepley <knep...@gmail.com>
>>> wrote:
>>>
>>>> On Tue, Apr 29, 2025 at 9:17 AM Jeffrey Hyman <hyma...@gmail.com>
>>>> wrote:
>>>>
>>>>> Unfortunately, Pflotran hasn't been updated to use 3.22 yet. So I'm
>>>>> stuck with 3.21.5. Can I hack the python path?
>>>>>
>>>>
>>>> Tell Glenn to get in gear :)
>>>>
>>>> I think you can just get this file:
>>>>
>>>> https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-__;!!G_uCfscf7eWS!fqzhNW3Ah4trHzfvrzpKetbDAwv2of8-_XkbNeD14cE73iml5fA0iFSWUe84ajrEBVhue1G_wPXAgxic_Okz$
>>>>
>>>> /blob/release-3.22/config/gmakegen.py?ref_type=heads
>>>>
>>>> and put it in $PETSC_DIR/config/gmakegen.py
>>>>
>>>> Finger crossed,
>>>>
>>>> Matt
>>>>
>>>>
>>>>> J
>>>>>
>>>>>
>>>>> On Tue, Apr 29, 2025 at 9:14 AM Matthew Knepley <knep...@gmail.com>
>>>>> wrote:
>>>>>
>>>>>> On Tue, Apr 29, 2025 at 9:08 AM Jeffrey Hyman <hyma...@gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> This configure worked
>>>>>>>
>>>>>>> ./configure --COPTFLAGS='-O3' --CXXOPTFLAGS='-O3' --FOPTFLAGS='-O3
>>>>>>> -Wno-unused-function -fallow-argument-mismatch' --with-debugging=no
>>>>>>> --download-mpich=yes --download-hdf5=yes
>>>>>>> --download-hdf5-fortran-bindings=yes --download-fblaslapack=yes
>>>>>>> --download-metis=yes --download-parmetis=yes --download-cmake=
>>>>>>> https://urldefense.us/v3/__https://gitlab.kitware.com/cmake/cmake/-/archive/v3.31.7/cmake-v3.31.7.tar.gz__;!!G_uCfscf7eWS!fqzhNW3Ah4trHzfvrzpKetbDAwv2of8-_XkbNeD14cE73iml5fA0iFSWUe84ajrEBVhue1G_wPXAgzCNqLEl$
>>>>>>>
>>>>>>> \
>>>>>>> --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!fqzhNW3Ah4trHzfvrzpKetbDAwv2of8-_XkbNeD14cE73iml5fA0iFSWUe84ajrEBVhue1G_wPXAgwkEHjz1$
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> *********************************************************************************************
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 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!fqzhNW3Ah4trHzfvrzpKetbDAwv2of8-_XkbNeD14cE73iml5fA0iFSWUe84ajrEBVhue1G_wPXAg5v3j-GF$
>>>>>>>>>>>
>>>>>>>>>>> \
>>>>>>>>>>> --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!fqzhNW3Ah4trHzfvrzpKetbDAwv2of8-_XkbNeD14cE73iml5fA0iFSWUe84ajrEBVhue1G_wPXAgzCNqLEl$
>>>>>>>>>>>
>>>>>>>>>>> \
>>>>>>>>>>> --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!fqzhNW3Ah4trHzfvrzpKetbDAwv2of8-_XkbNeD14cE73iml5fA0iFSWUe84ajrEBVhue1G_wPXAg8XLs_cs$
>>>>>>>>>>
>>>>>>>>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fqzhNW3Ah4trHzfvrzpKetbDAwv2of8-_XkbNeD14cE73iml5fA0iFSWUe84ajrEBVhue1G_wPXAg7LeGrsv$
>>>>>>>>>> >
>>>>>>>>>>
>>>>>>>>>
>>>>>>
>>>>>> --
>>>>>> 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!fqzhNW3Ah4trHzfvrzpKetbDAwv2of8-_XkbNeD14cE73iml5fA0iFSWUe84ajrEBVhue1G_wPXAg8XLs_cs$
>>>>>>
>>>>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fqzhNW3Ah4trHzfvrzpKetbDAwv2of8-_XkbNeD14cE73iml5fA0iFSWUe84ajrEBVhue1G_wPXAg7LeGrsv$
>>>>>> >
>>>>>>
>>>>>
>>>>
>>>> --
>>>> 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!fqzhNW3Ah4trHzfvrzpKetbDAwv2of8-_XkbNeD14cE73iml5fA0iFSWUe84ajrEBVhue1G_wPXAg8XLs_cs$
>>>>
>>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fqzhNW3Ah4trHzfvrzpKetbDAwv2of8-_XkbNeD14cE73iml5fA0iFSWUe84ajrEBVhue1G_wPXAg7LeGrsv$
>>>> >
>>>>
>>>
>>
>> --
>> 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!fqzhNW3Ah4trHzfvrzpKetbDAwv2of8-_XkbNeD14cE73iml5fA0iFSWUe84ajrEBVhue1G_wPXAg8XLs_cs$
>>
>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fqzhNW3Ah4trHzfvrzpKetbDAwv2of8-_XkbNeD14cE73iml5fA0iFSWUe84ajrEBVhue1G_wPXAg7LeGrsv$
>> >
>>
>
--
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!fqzhNW3Ah4trHzfvrzpKetbDAwv2of8-_XkbNeD14cE73iml5fA0iFSWUe84ajrEBVhue1G_wPXAg8XLs_cs$
<https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fqzhNW3Ah4trHzfvrzpKetbDAwv2of8-_XkbNeD14cE73iml5fA0iFSWUe84ajrEBVhue1G_wPXAg7LeGrsv$
>
