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" <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 > > > > > > > > > > > > > >
