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

[Barry Smith]

  Please email your latest configure.log  (with no Conda stuff) to petsc-maint at mcs.anl.gov <mailto:petsc-maint at mcs.anl.gov>

  The configuration of HDF5 (done by HDF5) is objecting to some particular aspect of your current Fortran compiler, we need to figure out the exact objection.

  Barry


> On Jan 6, 2023, at 5:14 PM, Danyang Su <danyang.su at gmail.com> 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.
>  
> Any other suggestions?
>  
> 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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