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" <ba...@mcs.anl.gov <mailto:ba...@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@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 <pie...@joliv.et <mailto:pie...@joliv.et>> > Date: Friday, January 6, 2023 at 7:59 AM > To: Danyang Su <danyang...@gmail.com <mailto:danyang...@gmail.com>> > Cc: <petsc-users@mcs.anl.gov <mailto:petsc-users@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...@gmail.com > <mailto:danyang...@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 > > > > >
