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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 > > > _______________________________________________ > netcdfgroup mailing listnetcdfgroup@xxxxxxxxxxxxxxxx > For list information or to unsubscribe, visit: > http://www.unidata.ucar.edu/mailing_lists/ > > > -- > Steve Hart > Systems Administrator > Colorado Center for Astrodynamics Research > University of Colorado Boulder > Steven.Hart@xxxxxxxxxxxx > (303)492-8109 > > > > _______________________________________________ > netcdfgroup mailing list > netcdfgroup@xxxxxxxxxxxxxxxx > For list information or to unsubscribe, visit: > http://www.unidata.ucar.edu/mailing_lists/ >
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