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

[Danyang Su]

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>
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

 

 



On 6 Jan 2023, at 4:49 PM, Danyang Su <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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