[netCDF #JHA-515459]: netCDF-4.3.2 test failure on Scientific Linux 6.5

Dylan,

> Thanks for this - setting the LD_LIBRARY_PATH environment variable to
> include /usr/local/hdf5/lib did the trick (... libhdf5_hl.so.8 did exist
> and was
> readable).
> 
> I have another very similar error message however, when I try to import the
> netCDF4 library in python3 :
> 
> "libhdf5_hl.so.7: cannot open shared object file: No such file or directory"
> 
> This is perhaps completely unrelated - (maybe it is a python3 issue - the
> python2.7 version works fine) ... but given the significant similarities
> with the
> error message below, I thought it might be worth following up with you
> (..is
> there another environment variable that needs to be set?). libhdf5_hl.so.7
> certainly exists in the /usr/local/hdf5/lib directory.

Sorry, I don't know why there would be a difference for Python 3 when it works
with Python 2.7.

However, according to the netcdf4-python Install section here:

  http://unidata.github.io/netcdf4-python/

the environment variables HDF5_DIR, HDF5_INCDIR, and HDF5_LIBDIR 
can be used to define the locations of the headers and libraries.

--Russ

> address@hidden> wrote:
> 
> > Hi Dylan,
> >
> > > I build netCDF-4.3.2 (with zlib-1.2.8 and hdf5-1.2.12) - as per
> > > requirements here:
> > > http://www.unidata.ucar.edu/netcdf/docs/getting_and_building_netcdf.html
> > >
> > > $ CPPFLAGS=-I/usr/local/hdf5/include LDFLAGS=-L/usr/local/hdf5/lib
> > > ./configure --enable-netcdf4 --prefix=/usr/local/netCDF4
> > >
> > > (..and I built zlib and hdf5 using the following configurations
> > > respectively):
> > >
> > > $ ./configure --prefix=/usr/local/zlib
> > >
> > > $./configure --enable-fortran --enable-cxx --with-zlib=/usr/local/zlib
> > > --prefix=/usr/local/hdf5
> >
> > We don't build or test HDF5 with --enable-fortran or --enable-cxx, as
> > those libraries
> > aren't needed by netCDF-C, but I doubt if that is causing the problem
> > you're seeing.
> >
> > > However I received  an error in the 'make check' stage:
> > >
> > > ===========================================
> > > netCDF 4.3.2: nc_test4/test-suite.log
> > > ===========================================
> > >
> > > # TOTAL: 54
> > > # PASS:  53
> > > # SKIP:  0
> > > # XFAIL: 0
> > > # FAIL:  1
> > > # XPASS: 0
> > > # ERROR: 0
> > >
> > > .. contents:: :depth: 2
> > >
> > > FAIL: run_grp_rename.sh
> > > =======================
> > >
> > >
> > > *** Running group_rename test
> > > /#####/#####/Source/netcdf-4.3.2/nc_test4/.libs/lt-renamegroup: error
> > while
> > > loading shared libraries: libhdf5_hl.so.8: cannot open shared object
> > file:
> > > No such file or directory
> >
> > Does libhdf5_hl exist and is it readable in your /usr/local/hdf5/lib/
> > directory?
> > If so, you may need to set your LD_LIBRARY_PATH environment variable to
> > include /usr/local/hdf5/lib before running "make check".
> >
> > --Russ
> >
> > > ***FAIL: attempt to rename /inner/inner_inner failed
> > > /#####/#####//Source/netcdf-4.3.2/nc_test4/.libs/lt-renamegroup: error
> > > while loading shared libraries: libhdf5_hl.so.8: cannot open shared
> > object
> > > file: No such file or directory
> > > ***FAIL: attempt to rename /inner failed
> > > 12c12
> > > < group: renamed {
> > > ---
> > > > group: inner {
> > > 26c26
> > > <   group: inner_renamed {
> > > ---
> > > >   group: inner_inner {
> > > 29,30c29,30
> > > <     } // group inner_renamed
> > > <   } // group renamed
> > > ---
> > > >     } // group inner_inner
> > > >   } // group inner
> > > ***FAIL: output and reference output differ
> > > /#####/#####/Source/netcdf-4.3.2/nc_test4/.libs/lt-renamegroup: error
> > while
> > > loading shared libraries: libhdf5_hl.so.8: cannot open shared object
> > file:
> > > No such file or directory
> > > ***XFAIL : attempt to rename root group failed as expected
> > >
> > >
> > > O.S Details: Scientific Linux release 6.5 (Carbon), Linux
> > > 2.6.32-431.20.3.el6.x86_64 x86_64
> > >
> > > Kind Regards,
> > >
> > > Dylan
> > >
> > > Date:    Fri, 05 Sep 2014 15:58:16 +1000
> > > To:      address@hidden
> > > From:    Dylan McConnell <address@hidden>
> > > Subject: Re: netCDF-4.3.2 test failure on Scientific Linux 6.5
> > > From address@hidden  Thu Sep  4 23: 58:18
> > > 2014
> > >
> > > Apologies, it was build with hdf5-1.8.12 (not hdf5-1.2.12, as in the
> > > original email)
> > >
> > > Dylan
> > >
> > >
> > >
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                      http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: JHA-515459
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> >
> >
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: JHA-515459
Department: Support netCDF
Priority: Normal
Status: Closed