On Tue, Apr 29, 2025 at 10:27 AM Jeffrey Hyman <hyma...@gmail.com> wrote:
> Oh, I remember that now. conda used to be so helpful. It always gets me > when I try to rebuild. > > I removed it and got stuck in hdf5 again. Anaconda is gone, but it looks > lille mpif90 was not found. > > 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 conftest.f90 >&5 > ./configure: line 2482: mpif90: command not found > > > should I try --download-mpich= > https://urldefense.us/v3/__https://www.mpich.org/static/downloads/4.3.0/mpich-4.3.0.tar.gz__;!!G_uCfscf7eWS!cDvE4p90Pi6N-WhVuvrgR4IQn2Kxr371XDH4TjfFr4LlPOf0MNBj35pqc-x3pR8JQeEdeMaUot6sPQDDAIj0$ > . that > Satish suggested? > Yes, since now it seems you do not have an MPI. THanks, Matt > J > > > > On Tue, Apr 29, 2025 at 10:12 AM Matthew Knepley <knep...@gmail.com> > wrote: > >> 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 $PETSC_DIR >>>> >>>> 3) Get rid of the preinstalled OpenMPI you have. It is usually somewhat >>>> broken and not helping. >>>> >>>> 4) Reclone and rebuild >>>> >>>> THanks, >>>> >>>> Matt >>>> >>>> >>>>> Thanks, Matt! Feels close. >>>>> J >>>>> >>>>> >>>>> On Tue, Apr 29, 2025 at 9:20 AM Matthew Knepley <knep...@gmail.com> >>>>> wrote: >>>>> >>>>>> On Tue, Apr 29, 2025 at 9:17 AM Jeffrey Hyman <hyma...@gmail.com> >>>>>> wrote: >>>>>> >>>>>>> Unfortunately, Pflotran hasn't been updated to use 3.22 yet. So I'm >>>>>>> stuck with 3.21.5. Can I hack the python path? >>>>>>> >>>>>> >>>>>> Tell Glenn to get in gear :) >>>>>> >>>>>> I think you can just get this file: >>>>>> >>>>>> https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-__;!!G_uCfscf7eWS!cDvE4p90Pi6N-WhVuvrgR4IQn2Kxr371XDH4TjfFr4LlPOf0MNBj35pqc-x3pR8JQeEdeMaUot6sPfUqSjEg$ >>>>>> >>>>>> /blob/release-3.22/config/gmakegen.py?ref_type=heads >>>>>> >>>>>> and put it in $PETSC_DIR/config/gmakegen.py >>>>>> >>>>>> Finger crossed, >>>>>> >>>>>> Matt >>>>>> >>>>>> >>>>>>> J >>>>>>> >>>>>>> >>>>>>> On Tue, Apr 29, 2025 at 9:14 AM Matthew Knepley <knep...@gmail.com> >>>>>>> wrote: >>>>>>> >>>>>>>> On Tue, Apr 29, 2025 at 9:08 AM Jeffrey Hyman <hyma...@gmail.com> >>>>>>>> wrote: >>>>>>>> >>>>>>>>> This configure worked >>>>>>>>> >>>>>>>>> ./configure --COPTFLAGS='-O3' --CXXOPTFLAGS='-O3' --FOPTFLAGS='-O3 >>>>>>>>> -Wno-unused-function -fallow-argument-mismatch' --with-debugging=no >>>>>>>>> --download-mpich=yes --download-hdf5=yes >>>>>>>>> --download-hdf5-fortran-bindings=yes --download-fblaslapack=yes >>>>>>>>> --download-metis=yes --download-parmetis=yes --download-cmake= >>>>>>>>> https://urldefense.us/v3/__https://gitlab.kitware.com/cmake/cmake/-/archive/v3.31.7/cmake-v3.31.7.tar.gz__;!!G_uCfscf7eWS!cDvE4p90Pi6N-WhVuvrgR4IQn2Kxr371XDH4TjfFr4LlPOf0MNBj35pqc-x3pR8JQeEdeMaUot6sPaCh2cof$ >>>>>>>>> >>>>>>>>> \ >>>>>>>>> --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!cDvE4p90Pi6N-WhVuvrgR4IQn2Kxr371XDH4TjfFr4LlPOf0MNBj35pqc-x3pR8JQeEdeMaUot6sPa-bQHi0$ >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> ********************************************************************************************* >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> 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!cDvE4p90Pi6N-WhVuvrgR4IQn2Kxr371XDH4TjfFr4LlPOf0MNBj35pqc-x3pR8JQeEdeMaUot6sPQDDAIj0$ >>>>>>>>>>>>> >>>>>>>>>>>>> \ >>>>>>>>>>>>> --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!cDvE4p90Pi6N-WhVuvrgR4IQn2Kxr371XDH4TjfFr4LlPOf0MNBj35pqc-x3pR8JQeEdeMaUot6sPaCh2cof$ >>>>>>>>>>>>> >>>>>>>>>>>>> \ >>>>>>>>>>>>> --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!cDvE4p90Pi6N-WhVuvrgR4IQn2Kxr371XDH4TjfFr4LlPOf0MNBj35pqc-x3pR8JQeEdeMaUot6sPdGgiC5s$ >>>>>>>>>>>> >>>>>>>>>>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cDvE4p90Pi6N-WhVuvrgR4IQn2Kxr371XDH4TjfFr4LlPOf0MNBj35pqc-x3pR8JQeEdeMaUot6sPeyDBuoL$ >>>>>>>>>>>> > >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> 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!cDvE4p90Pi6N-WhVuvrgR4IQn2Kxr371XDH4TjfFr4LlPOf0MNBj35pqc-x3pR8JQeEdeMaUot6sPdGgiC5s$ >>>>>>>> >>>>>>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cDvE4p90Pi6N-WhVuvrgR4IQn2Kxr371XDH4TjfFr4LlPOf0MNBj35pqc-x3pR8JQeEdeMaUot6sPeyDBuoL$ >>>>>>>> > >>>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> 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!cDvE4p90Pi6N-WhVuvrgR4IQn2Kxr371XDH4TjfFr4LlPOf0MNBj35pqc-x3pR8JQeEdeMaUot6sPdGgiC5s$ >>>>>> >>>>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cDvE4p90Pi6N-WhVuvrgR4IQn2Kxr371XDH4TjfFr4LlPOf0MNBj35pqc-x3pR8JQeEdeMaUot6sPeyDBuoL$ >>>>>> > >>>>>> >>>>> >>>> >>>> -- >>>> 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!cDvE4p90Pi6N-WhVuvrgR4IQn2Kxr371XDH4TjfFr4LlPOf0MNBj35pqc-x3pR8JQeEdeMaUot6sPdGgiC5s$ >>>> >>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cDvE4p90Pi6N-WhVuvrgR4IQn2Kxr371XDH4TjfFr4LlPOf0MNBj35pqc-x3pR8JQeEdeMaUot6sPeyDBuoL$ >>>> > >>>> >>> >> >> -- >> 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!cDvE4p90Pi6N-WhVuvrgR4IQn2Kxr371XDH4TjfFr4LlPOf0MNBj35pqc-x3pR8JQeEdeMaUot6sPdGgiC5s$ >> >> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cDvE4p90Pi6N-WhVuvrgR4IQn2Kxr371XDH4TjfFr4LlPOf0MNBj35pqc-x3pR8JQeEdeMaUot6sPeyDBuoL$ >> > >> > -- 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!cDvE4p90Pi6N-WhVuvrgR4IQn2Kxr371XDH4TjfFr4LlPOf0MNBj35pqc-x3pR8JQeEdeMaUot6sPdGgiC5s$ <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cDvE4p90Pi6N-WhVuvrgR4IQn2Kxr371XDH4TjfFr4LlPOf0MNBj35pqc-x3pR8JQeEdeMaUot6sPeyDBuoL$ >
