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

[Danyang Su]

Hi All,

Problem is resolved by Homebrew Gfortran. I use GNU Fortran (GCC) 8.2.0 before. Conda does not cause the problem. 

Thanks,

Danyang

On 2023-01-06, 2:24 PM, "Satish Balay" <balay at mcs.anl.gov <mailto:balay at mcs.anl.gov>> wrote:


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,
> 
> 
> 
> 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,
> 
> 
> 
> Danyang
> 
> 
> 
> From: Pierre Jolivet <pierre at joliv.et <mailto:pierre at joliv.et>>
> Date: Friday, January 6, 2023 at 7:59 AM
> To: Danyang Su <danyang.su at gmail.com <mailto:danyang.su at gmail.com>>
> Cc: <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>>
> Subject: Re: [petsc-users] Error running configure on HDF5 in PETSc-3.18.3
> 
> 
> 
> 
> 
> 
> 
> On 6 Jan 2023, at 4:49 PM, Danyang Su <danyang.su at gmail.com <mailto:danyang.su at gmail.com>> wrote:
> 
> 
> 
> Hi All,
> 
> 
> 
> 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. 
> 
> 
> 
> ./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
> 
> 
> 
> Any idea on this?
> 
> 
> 
> Could you try to reconfigure in a shell without conda being activated?
> 
> You have PATH=/Users/danyangsu/Soft/Anaconda3/bin:/Users/danyangsu/Soft/Anaconda3/condabin:[…] which typically results in a broken configuration.
> 
> 
> 
> Thanks,
> 
> Pierre
> 
> 
> 
> Thanks,
> 
> 
> 
> Danyang
> 
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>