On Wed, Aug 8, 2018 at 3:49 PM, Paul T. Bauman <[email protected]> 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? Thanks, David > On Wed, Aug 8, 2018 at 3:31 PM David Knezevic <[email protected]> > wrote: > >> On Wed, Aug 8, 2018 at 3:18 PM, David Knezevic < >> [email protected]> >> wrote: >> >> > On Wed, Aug 8, 2018 at 1:58 PM, Kirk, Benjamin (JSC-EG311) < >> > [email protected]> 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 >> [email protected] >> 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 [email protected] https://lists.sourceforge.net/lists/listinfo/libmesh-users
