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[netCDF #NCP-653180]: Request to help

> I am using hdf-5 1.8.13, but my folder is named as hdf-5 1.8.14.
> I have attached the configure files of both hdf5 and netcdf4. Also
> h5_test/test-suite.log and hdf5/src/libhdf5.settings are also attached.

I see the problem.  You have invoked the netCDF configure command as

   ./configure --with-hdf5=/usr/local/bin/hdf5-1.8.14/lib 
--prefix=/usr/local/bin/netcdf-4.3.3.1

but the netCDF configure doesn't understand the "--with-hdf5=" option, 
and even emits an error message about it:

    configure:20429: WARNING: unrecognized options: --with-hdf5

that should have appeared at the end of the output from configure.
You can see all the options the netCDF configure accepts by invoking
"./configure --help".

Instead, you need to use the environment variables CPPFLAGS and LDFLAGS,
as in the examples in the installation instructions:

   
http://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html#building

For example, in your case you could use:

   $ H5DIR=/usr/local/bin/hdf5-1.8.14
   $ ZDIR=/usr/local/bin
   $ NCDIR=/usr/local/bin/netcdf-4.3.3.1
   $ CPPFLAGS="-I${H5DIR}/include -I${ZDIR}/include" LDFLAGS="-L${H5DIR}/lib 
-L${ZDIR}/lib" ./configure --prefix=${NCDIR}

That should work OK, but note that "bin" in an unconventional 
location in which to store libraries and include files.  Typically,
one would install libraries in /usr/local/lib/.
The /usr/local/bin/directory is conventionally used for programs 
and utilities and /usr/local/include/ for header files. That's just a 
convention, but the way you are doing it will result in netCDF
utilities such as ncdump being stored in 

  /usr/local/bin/netcdf-4.3.3.1/bin/necdump

with two "bin" subdirectories in the path, for example.

--Russ

 
> address@hidden> wrote:
> 
> > Hi Nandithat,
> >
> > Are you using HDF5-1.8.9 or later?  Earlier versions of HDF5 have a problem
> > with recent versions of netCDF-4. You can see what version of HDF5 you have
> > installed by looking at the file libhdf5.settings in the lib/ directory
> > where the
> > HDF5 library is installed.
> >
> > If it's not a problem with an old version of the HDF5 library, could you
> > please send
> > the config.log file generated when the configure script was run, and the
> > h5_test/test-suite.log file that has more details about the failed
> > tst_H_VARS test?
> >
> > Thanks.
> >
> > --Russ
> >
> > > I am facing the following make error. Please help in solving.
> > >
> > > Making check in include
> > > make[1]: Entering directory
> > > `/home/nanditha/Documents/NANDITHA/THESIS/mhm/netcdf-4.3.3.1/include'
> > > make[1]: Nothing to be done for `check'.
> > > make[1]: Leaving directory
> > > `/home/nanditha/Documents/NANDITHA/THESIS/mhm/netcdf-4.3.3.1/include'
> > > Making check in h5_test
> > > make[1]: Entering directory
> > > `/home/nanditha/Documents/NANDITHA/THESIS/mhm/netcdf-4.3.3.1/h5_test'
> > > make  tst_h_files tst_h_files2 tst_h_files4 tst_h_atts tst_h_atts3
> > > tst_h_atts4 tst_h_vars tst_h_vars2 tst_h_vars3 tst_h_grps tst_h_compounds
> > > tst_h_compounds2 tst_h_wrt_cmp tst_h_rd_cmp tst_h_vl tst_h_opaques
> > > tst_h_strings tst_h_strings1 tst_h_strings2 tst_h_ints tst_h_dimscales
> > > tst_h_dimscales1 tst_h_dimscales2 tst_h_dimscales3 tst_h_enums
> > > tst_h_dimscales4
> > > make[2]: Entering directory
> > > `/home/nanditha/Documents/NANDITHA/THESIS/mhm/netcdf-4.3.3.1/h5_test'
> > > make[2]: `tst_h_files' is up to date.
> > > make[2]: `tst_h_files2' is up to date.
> > > make[2]: `tst_h_files4' is up to date.
> > > make[2]: `tst_h_atts' is up to date.
> > > make[2]: `tst_h_atts3' is up to date.
> > > make[2]: `tst_h_atts4' is up to date.
> > > make[2]: `tst_h_vars' is up to date.
> > > make[2]: `tst_h_vars2' is up to date.
> > > make[2]: `tst_h_vars3' is up to date.
> > > make[2]: `tst_h_grps' is up to date.
> > > make[2]: `tst_h_compounds' is up to date.
> > > make[2]: `tst_h_compounds2' is up to date.
> > > make[2]: `tst_h_wrt_cmp' is up to date.
> > > make[2]: `tst_h_rd_cmp' is up to date.
> > > make[2]: `tst_h_vl' is up to date.
> > > make[2]: `tst_h_opaques' is up to date.
> > > make[2]: `tst_h_strings' is up to date.
> > > make[2]: `tst_h_strings1' is up to date.
> > > make[2]: `tst_h_strings2' is up to date.
> > > make[2]: `tst_h_ints' is up to date.
> > > make[2]: `tst_h_dimscales' is up to date.
> > > make[2]: `tst_h_dimscales1' is up to date.
> > > make[2]: `tst_h_dimscales2' is up to date.
> > > make[2]: `tst_h_dimscales3' is up to date.
> > > make[2]: `tst_h_enums' is up to date.
> > > make[2]: `tst_h_dimscales4' is up to date.
> > > make[2]: Leaving directory
> > > `/home/nanditha/Documents/NANDITHA/THESIS/mhm/netcdf-4.3.3.1/h5_test'
> > > make  check-TESTS
> > > make[2]: Entering directory
> > > `/home/nanditha/Documents/NANDITHA/THESIS/mhm/netcdf-4.3.3.1/h5_test'
> > > make[3]: Entering directory
> > > `/home/nanditha/Documents/NANDITHA/THESIS/mhm/netcdf-4.3.3.1/h5_test'
> > > PASS: tst_h_files
> > > PASS: tst_h_files2
> > > PASS: tst_h_files4
> > > PASS: tst_h_atts
> > > PASS: tst_h_atts3
> > > PASS: tst_h_atts4
> > > FAIL: tst_h_vars
> > > PASS: tst_h_vars2
> > > PASS: tst_h_vars3
> > > PASS: tst_h_grps
> > > PASS: tst_h_compounds
> > > PASS: tst_h_compounds2
> > > PASS: tst_h_wrt_cmp
> > > PASS: tst_h_rd_cmp
> > > PASS: tst_h_vl
> > > PASS: tst_h_opaques
> > > PASS: tst_h_strings
> > > PASS: tst_h_strings1
> > > PASS: tst_h_strings2
> > > PASS: tst_h_ints
> > > PASS: tst_h_dimscales
> > > PASS: tst_h_dimscales1
> > > PASS: tst_h_dimscales2
> > > PASS: tst_h_dimscales3
> > > PASS: tst_h_enums
> > > PASS: tst_h_dimscales4
> > > make[4]: Entering directory
> > > `/home/nanditha/Documents/NANDITHA/THESIS/mhm/netcdf-4.3.3.1/h5_test'
> > > make[4]: Nothing to be done for `all'.
> > > make[4]: Leaving directory
> > > `/home/nanditha/Documents/NANDITHA/THESIS/mhm/netcdf-4.3.3.1/h5_test'
> > >
> > ============================================================================
> > > Testsuite summary for netCDF 4.3.3.1
> > >
> > ============================================================================
> > > # TOTAL: 26
> > > # PASS:  25
> > > # SKIP:  0
> > > # XFAIL: 0
> > > # FAIL:  1
> > > # XPASS: 0
> > > # ERROR: 0
> > >
> > ============================================================================
> > > See h5_test/test-suite.log
> > > Please report to address@hidden
> > >
> > ============================================================================
> > > make[3]: *** [test-suite.log] Error 1
> > > make[3]: Leaving directory
> > > `/home/nanditha/Documents/NANDITHA/THESIS/mhm/netcdf-4.3.3.1/h5_test'
> > > make[2]: *** [check-TESTS] Error 2
> > > make[2]: Leaving directory
> > > `/home/nanditha/Documents/NANDITHA/THESIS/mhm/netcdf-4.3.3.1/h5_test'
> > > make[1]: *** [check-am] Error 2
> > > make[1]: Leaving directory
> > > `/home/nanditha/Documents/NANDITHA/THESIS/mhm/netcdf-4.3.3.1/h5_test'
> > > make: *** [check-recursive] Error 1
> > >
> > > Thanks & Regards
> > > --
> > > Nanditha J. S.
> > > 14210029
> > > M. Tech, Civil Engineering
> > > IIT Gandhinagar
> > >
> > >
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                      http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: NCP-653180
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> >
> >
> 
> 
> --
> Nanditha J. S.
> 14210029
> M. Tech, Civil Engineering
> IIT Gandhinagar
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: NCP-653180
Department: Support netCDF
Priority: Normal
Status: Closed