Re: [Libmesh-users] Enabling netcdf4?

[David K. <dav...@ak...>]

On Wed, Aug 8, 2018 at 3:18 PM, David Knezevic <dav...@ak...>
wrote:

> On Wed, Aug 8, 2018 at 1:58 PM, Kirk, Benjamin (JSC-EG311) <
> ben...@na...> 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