On Wed, Aug 8, 2018 at 4:25 PM, David Knezevic <david.kneze...@akselos.com> wrote:
> On Wed, Aug 8, 2018 at 3:49 PM, Paul T. Bauman <ptbau...@gmail.com> wrote: > >> 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 >> >> > OK, but I'm having trouble getting configure to detect hdf5, even with > --enable-hdf5. I tried installing ubuntu packages for hdf5 but that > apparently didn't work, so I built it from source instead, but I'm not sure > if there's an option for specifying the location? Is > --with-hdf5=/path/to/hdf5 option? I don't really want to install into a > system directory in this case. > > Do you use hdf5 with libMesh? If so, what is your approach? > Sorry for the spam. I see that there is a --with-hdf5 option, and that does work, so all good. Best, David > > >> 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
