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

[Satish Balay]

Glad it worked! Thanks for the update!

Satish

On Fri, 6 Jan 2023, Danyang Su wrote:

> 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.
> > 
> > 
> > 
> > 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
> > 
> > 
> > 
> > 
> > 
> 
> 
> 
>