[petsc-users] Error running configure on HDF5 in PETSc-3.18.3

[Satish Balay]

Likely your installed gfortran is incompatible with hdf5

>>>>
Executing: gfortran --version
stdout:
GNU Fortran (GCC) 8.2.0
<<<<

We generally use brew gfortran - and that works with hdf5 aswell

balay at ypro ~ % gfortran --version
GNU Fortran (Homebrew GCC 11.2.0_1) 11.2.0

Satish

On Fri, 6 Jan 2023, Danyang Su wrote:

> Hi Pierre,
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> I have tried to exclude Conda related environment variables but it does not work. Instead, if I include ‘--download-hdf5=yes’ but exclude ‘--with-hdf5-fortran-bindings’ in the configuration, PETSc can be configured and installed without problem, even with Conda related environment activated. However, since my code requires fortran interface to HDF5, I do need ‘--with-hdf5-fortran-bindings’, otherwise, my code cannot be compiled.
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> Any other suggestions?
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> Thanks,
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> Danyang
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> From: Pierre Jolivet <pierre at joliv.et>
> Date: Friday, January 6, 2023 at 7:59 AM
> To: Danyang Su <danyang.su at gmail.com>
> Cc: <petsc-users at mcs.anl.gov>
> Subject: Re: [petsc-users] Error running configure on HDF5 in PETSc-3.18.3
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> On 6 Jan 2023, at 4:49 PM, Danyang Su <danyang.su at gmail.com> wrote:
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> Hi All,
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> 
> I get ‘Error running configure on HDF5’ in PETSc-3.18.3 on MacOS, but no problem on Ubuntu. Attached is the configuration log file. 
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> ./configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-mumps --download-scalapack --download-parmetis --download-metis --download-ptscotch --download-fblaslapack --download-mpich --download-hypre --download-superlu_dist --download-hdf5=yes --with-debugging=0 --download-cmake --with-hdf5-fortran-bindings
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> Any idea on this?
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> Could you try to reconfigure in a shell without conda being activated?
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> You have PATH=/Users/danyangsu/Soft/Anaconda3/bin:/Users/danyangsu/Soft/Anaconda3/condabin:[…] which typically results in a broken configuration.
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> Thanks,
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> Pierre
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> Thanks,
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> Danyang
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