Re: [netcdfgroup] Failing to configure netcdf-4.3.1.1

• To: netcdfgroup@xxxxxxxxxxxxxxxx
• Subject: Re: [netcdfgroup] Failing to configure netcdf-4.3.1.1
• From: Steven Hart <steven.hart@xxxxxxxxxxxx>
• Date: Tue, 04 Mar 2014 13:37:36 -0700

http://www.unidata.ucar.edu/software/netcdf/docs/build_default.html

# ENV VAR for intel and netcdf install
source /usr/local/intel/bin/compilervars.sh intel64
export CC=icc
export CXX=icpc
export CFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export CXXFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export F77=ifort
export FC=ifort
export F90=ifort
export FFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export FCFLAGS=-64
export CPP='icc -E'
export CXXCPP='icpc -E'
export CPPFLAGS='-I/usr/include -I/usr/include/hdf'

Hope that helps

Steve

On 03/04/2014 01:06 PM, Doll, Margaret Ann 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


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--
Steve Hart
Systems Administrator
Colorado Center for Astrodynamics Research
University of Colorado Boulder
Steven.Hart@xxxxxxxxxxxx
(303)492-8109

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