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
>
