Steve,
Thanks for your quick reply.
However, I don't have the intel compilers. I have the default compilers
that come with the Centos distribution, I have mpi compilers that come with
the ROCKS distribution and I have Portland Group compilers.
On Tue, Mar 4, 2014 at 3:37 PM, Steven Hart <steven.hart@xxxxxxxxxxxx>wrote:
>
> This website proved extremely helpful in setting up NetCDF 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
>
>
>
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