Re: [netcdfgroup] Failing to configure netcdf-4.3.1.1

• To: netcdfgroup <netcdfgroup@xxxxxxxxxxxxxxxx>
• Subject: Re: [netcdfgroup] Failing to configure netcdf-4.3.1.1
• From: "Doll, Margaret Ann" <margaret_doll@xxxxxxxxx>
• Date: Tue, 4 Mar 2014 16:49:51 -0500

Another problem I see in the configure.log

configure:16382: gcc -o conftest -I/share/apps/include
-I/share/apps/include -L/share/apps/lib -lz conftest.c -lhdf5dll  -lm
-lcurl  >&5
/usr/bin/ld: cannot find -lhdf5dll
collect2: ld returned 1 exit status
configure:16382: $? = 1
configure: failed program was:
| /* confdefs.h */



On Tue, Mar 4, 2014 at 3:06 PM, Doll, Margaret Ann
<margaret_doll@xxxxxxxxx>wrote:

> 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
>

• References:
  • [netcdfgroup] Failing to configure netcdf-4.3.1.1
    • From: Doll, Margaret Ann