HDF5 is turned off by default, even with --enable-everything. You need to additionally feed --enabled-hdf5 to configure now.
https://github.com/libMesh/libmesh/pull/1766 On Wed, Aug 8, 2018 at 3:31 PM David Knezevic <david.kneze...@akselos.com> wrote: > On Wed, Aug 8, 2018 at 3:18 PM, David Knezevic <david.kneze...@akselos.com > > > wrote: > > > On Wed, Aug 8, 2018 at 1:58 PM, Kirk, Benjamin (JSC-EG311) < > > benjamin.k...@nasa.gov> wrote: > > > >> netcdf-4 requires an underlying hdf5 library be found on your system; > was > >> that properly detected by ./configure? > >> > > > > Thanks, that's helpful! I just installed libhdf-5-dev in Ubuntu "apt-get > > install libhdf-5-dev") and now ./configure seems to detects netcdf-4, > > e.g. I get this output during configure: > > > > <<< Configuring library with NetCDF version 4 support >>> > > defining -DNOT_NETCDF4 for our Exodus build > > > > ... > > > > === configuring in contrib/netcdf/v4 (/home/dknez/software/libmesh_ > > build/opt_real/contrib/netcdf/v4) > > configure: running /bin/bash /home/dknez/software/libmesh- > > src/contrib/netcdf/v4/configure --disable-option-checking > > '--prefix=/home/dknez/software/libmesh_install/opt_real/libmesh' > > '--enable-everything' '--enable-slepc' '--with-metis=PETSc' > > '--with-subdomain-id-bytes=4' '--with-boundary-id-bytes=4' > '--disable-glpk' > > '--enable-unique-id' '--with-unique-id-bytes=4' > '--with-nlopt-include=/home/ > > dknez/software/libmesh_install/nlopt/include' > > '--with-nlopt-lib=/home/dknez/software/libmesh_install/nlopt/lib' > > '--with-capnproto=/home/dknez/software/libmesh_install/capnp' > > '--disable-parmetis' '--disable-ifem' '--with-methods=opt' > > '--enable-shared' '--disable-netcdf-4' '--disable-testsets' 'CXX=mpicxx' > > 'CC=mpicc' 'F77=mpif77' 'FC=mpif90' 'CPPFLAGS= ' 'LIBS= -ldl ' > > --cache-file=/dev/null --srcdir=/home/dknez/software/ > > libmesh-src/contrib/netcdf/v4 > > configure: netCDF 4.4.1.1 > > > > ... > > > > Optional Packages: > > boost............................ : yes > > capnproto........................ : yes > > cppunit.......................... : yes > > curl............................. : no > > eigen............................ : yes > > exodus........................... : yes > > version....................... : v5.22 > > fparser.......................... : yes > > build from version............ : release > > glpk............................. : no > > gmv.............................. : yes > > gzstream......................... : yes > > hdf5............................. : no > > laspack.......................... : no > > libhilbert....................... : yes > > metis............................ : yes > > mpi.............................. : yes > > nanoflann........................ : yes > > nemesis.......................... : yes > > version....................... : v5.22 > > netcdf........................... : yes > > version....................... : 4 > > nlopt............................ : yes > > parmetis......................... : no > > petsc............................ : no > > qhull............................ : yes > > sfcurves......................... : no > > slepc............................ : no > > thread model..................... : pthread > > c++ rtti ........................ : yes > > tecio............................ : no > > tecplot...(vendor binaries)...... : no > > tetgen........................... : no > > triangle......................... : no > > trilinos......................... : no > > vtk.............................. : no > > > > > > However, I then tried to read the same netcdf-4 ExodusII file, and I > still > > get the same error as before. So I guess ExodusII hasn't been configured > > with netcdf-4 after all? The line "defining -DNOT_NETCDF4 for our Exodus > > build" in the configure output seems to suggest that exodus is not using > > netcdf-4, which would explain my issue, do you know what I should do to > > resolve this? > > > > > I gather that the issue is that my hdf5 build is not being detected by > ./configure properly after all, since I have > "hdf5............................. > : no:. I'll try installing hdf5 from source and see if that fixes it. > > David > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Libmesh-users mailing list > Libmesh-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/libmesh-users > ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
