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?
Best,
David
> > On Aug 8, 2018, at 12:41 PM, David Knezevic <david.kneze...@akselos.com>
> wrote:
> >
> > Hi all,
> >
> > I received an ExodusII mesh that uses netcdf4 format, and currently when
> I
> > try to read it in using my libMesh installation I get this error:
> >
> > EXODUS: Error: Attempting to open the netcdf-4 file:
> > 'mesh.exo'
> > with a netcdf library that does not support netcdf-4
> >
> > When I configured libMesh I used --enable-everything and I did not
> > explicitly disable netcdf-4, but from the config.log it seems that it was
> > disabled automatically since my config.log contains
> "--disable-netcdf-4". I
> > haven't installed any extra netcdf package, so I assume I'm using the one
> > in contrib.
> >
> > I was wondering if anyone can provide a suggestion on what I need to do
> to
> > configure with netcdf4 enabled?
> >
> > Thanks!
> > David
> > ------------------------------------------------------------
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>
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