[netcdfgroup] Failing to configure netcdf-4.3.1.1

• To: netcdfgroup@xxxxxxxxxxxxxxxx
• Subject: [netcdfgroup] Failing to configure netcdf-4.3.1.1
• From: "Doll, Margaret Ann" <margaret_doll@xxxxxxxxx>
• Date: Tue, 4 Mar 2014 15:06:55 -0500

I have a ROCKS cluster running Centos 5.

I am building my applications with the prefix of /share/apps.  My ultimate
goal is to build GMT which requires netcdf with hdf5.


I have installed hdf5-1.8.12 and zlig-1.2.8

I am trying to install netcdf-4.3.1.1

I used the following to try to configure netcdf

CFLAGS=-I/share/apps/include CPPFLAGS=-I/share/apps/include
LDFLAGS=-L/share/apps/lib ./configure --prefix=/share/apps

*The compilation fails with*

checking for library containing deflate... none required
checking for floor in -lm... yes
checking for library containing H5Fflush... -lhdf5
checking for library containing H5DSis_scale... -lhdf5_hl
checking /share/apps/include/hdf5.h usability... no
checking /share/apps/include/hdf5.h presence... no
checking for /share/apps/include/hdf5.h... no
configure: error: Compiling a test with HDF5 failed.  Either hdf5.h cannot
be found, or config.log should be checked for other reason.

*hdf5.h is in /share/apps/include*

ls /share/apps/include
curl                   h5ds.mod             H5FDsec2.h
h5lt.mod             H5Spublic.h
deal.II                H5DSpublic.h         H5FDstdio.h
H5LTpublic.h         h5tb.mod
fftw3.f                h5e.mod              h5f.mod
H5MMpublic.h         H5TBpublic.h
fftw3.f03              h5e_provisional.mod  h5fortran_types.mod
h5o.mod              h5t.mod
fftw3.h                H5Epubgen.h          h5f_provisional.mod
h5o_provisional.mod  h5t_provisional.mod
fftw3l.f03             H5Epublic.h          H5Fpublic.h
H5Opublic.h          H5Tpublic.h
fftw3q.f03             H5f90i_gen.h         h5global.mod
H5overflow.h         H5version.h
H5ACpublic.h           H5f90i.h             h5g.mod
H5PLextern.h         h5z.mod
h5a.mod                H5FDcore.h           H5Gpublic.h
h5p.mod              H5Zpublic.h
H5api_adpt.h           H5FDdirect.h         h5im.mod
h5p_provisional.mod  hdf5dll.dll
h5a_provisional.mod    H5FDfamily.h         h5i.mod
H5Ppublic.h          hdf5.h
H5Apublic.h            H5FDlog.h            H5IMpublic.h
H5PTpublic.h         hdf5_hl.h
H5Cpublic.h            H5FDmpi.h            H5Ipublic.h
H5pubconf.h          hdf5.mod
h5_dble_interface.mod  H5FDmpio.h           h5lib.mod
H5public.h           netcdf.h
h5d.mod                h5fdmpio.mod         h5lib_provisional.mod
h5r.mod              zconf.h
H5DOpublic.h           H5FDmpiposix.h       h5l.mod
h5r_provisional.mod  zlib.h
h5d_provisional.mod    H5FDmulti.h          h5l_provisional.mod
H5Rpublic.h
H5Dpublic.h            H5FDpublic.h         H5Lpublic.h            h5s.mod

*From the config.log:*

#define USE_NETCDF4 1
| #define H5_USE_16_API 1
| /* end confdefs.h.  */
#include </share/apps/include/hdf5.h>
configure:16470: result: no
configure:16470: checking for /share/apps/include/hdf5.h
configure:16470: result: no
configure:16477: error: Compiling a test with HDF5 failed.  Either hdf5.h
cannot be found, or config.log should be checked for other reason.

*The lines in configure which are indicated as the problem:*

   for ac_header in hdf5.h
do :
  ac_fn_c_check_header_mongrel "$LINENO" "/share/apps/include/hdf5.h"
"ac_cv_header_hdf5_h" "$ac_includes_default"
if test "x$ac_cv_header_hdf5_h" = xyes; then :
  cat >>confdefs.h <<_ACEOF
#define HAVE_HDF5_H 1
_ACEOF

else
  as_fn_error $? "Compiling a test with HDF5 failed.  Either hdf5.h cannot
be found, or config.log should be checked for other reason." "$LINENO" 5
fi

• Follow-Ups:
  • Re: [netcdfgroup] Failing to configure netcdf-4.3.1.1
    • From: Doll, Margaret Ann
  • Re: [netcdfgroup] Failing to configure netcdf-4.3.1.1
    • From: Ward Fisher
  • Re: [netcdfgroup] Failing to configure netcdf-4.3.1.1
    • From: Doll, Margaret Ann
  • Re: [netcdfgroup] Failing to configure netcdf-4.3.1.1
    • From: Orion Poplawski