This website proved extremely helpful in setting upNetCDF on my RHEL6
system.
http://www.unidata.ucar.edu/software/netcdf/docs/build_default.html
I saw those HDF errors as well, make sure you have all the correct flags
defined. Here's what worked for me in my .bashrc:
# 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'
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:'/usr/lib64
/usr/local/intel/composer_xe_2013_sp1.1.106/compiler/lib/intel64
/usr/lib64/hdf /usr/local/netcdf-4.3.1/lib'
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
