On Wed, Aug 8, 2018 at 4:48 PM David Knezevic <[email protected]> wrote:
> On Wed, Aug 8, 2018 at 4:25 PM, David Knezevic <[email protected] > > wrote: > >> 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? >> > > Sorry for the spam. I see that there is a --with-hdf5 option, and that > does work, so all good. > Great. Just to close this off, I was going to reply with a couple of thoughts before this. For distro packages, you usually need to install the "dev" version to get the header files (non-dev only have library to link against). Our approach is to build everything locally, including hdf5, and install in non-system locations and use lmod. > > > Best, > 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
