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That should work too. I found it easier having them automatically set in the bashrc but that's cool.
either way, I'd makesure you have them pointing specifically at your HDF install directory.
I'm only guessing but maybe:CFLAGS=-I/share/apps/include CPPFLAGS='-I/share/apps/include -I/share/apps/include/hdf' LDFLAGS='-L/share/apps/lib -L/share/apps/lib/hdf' ./configure --prefix=/share/app --disable-remote-tests
I'm just spit-balling as I really do not know your setup. I had to call HDF specifically in CPPFLAGS and LDFLAGS.
Steve On 03/04/2014 02:04 PM, Doll, Margaret Ann wrote:
Steve, printenv LD_LIBRARY_PATH /opt/gridengine/lib/lx26-amd64:/opt/openmpi/lib:/share/apps/lib:/share/apps/lib I set my CFLAGS, CPPFLAGS and LDFLAGS in the configure line.CFLAGS=-I/share/apps/include CPPFLAGS=-I/share/apps/include LDFLAGS=-L/share/apps/lib ./configure --prefix=/share/app --disable-remote-testsOn Tue, Mar 4, 2014 at 3:53 PM, Steven Hart <steven.hart@xxxxxxxxxxxx <mailto:steven.hart@xxxxxxxxxxxx>> wrote:No problem. Since your installis having trouble seeing the HDF install, make sure that: CPPFLAGS='-I/usr/include -I/usr/include/hdf' (or have it reflect your path to HDF) and LD_LIBRARY_PATH=$LD_LIBRARY_PATH:'/usr/lib64/hdf' (or have it reflect your path to HDF) I found alot of the same errors you are seeing before I had these set correctly. Steve On 03/04/2014 01:48 PM, Doll, Margaret Ann wrote:Steve, Thanks for your quick reply. However, I don't have the intel compilers. I have the default compilers that come with the Centos distribution, I have mpi compilers that come with the ROCKS distribution and I have Portland Group compilers. On Tue, Mar 4, 2014 at 3:37 PM, Steven Hart <steven.hart@xxxxxxxxxxxx <mailto:steven.hart@xxxxxxxxxxxx>> wrote: This website proved extremely helpful in setting upNetCDF on my RHEL6 system. http://www.unidata.ucar.edu/software/netcdf/docs/build_default.html I saw those HDF errors as well, make sure you have all the correct flags defined. Here's what worked for me in my .bashrc: # ENV VAR for intel and netcdf install source /usr/local/intel/bin/compilervars.sh intel64 export CC=icc export CXX=icpc export CFLAGS='-O3 -xHost -ip -no-prec-div -static-intel' export CXXFLAGS='-O3 -xHost -ip -no-prec-div -static-intel' export F77=ifort export FC=ifort export F90=ifort export FFLAGS='-O3 -xHost -ip -no-prec-div -static-intel' export FCFLAGS=-64 export CPP='icc -E' export CXXCPP='icpc -E' export CPPFLAGS='-I/usr/include -I/usr/include/hdf' export LD_LIBRARY_PATH=$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.hH5Apublic.h H5FDlog.h H5IMpublic.h H5PTpublic.h hdf5_hl.hH5Cpublic.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: noconfigure:16477: error: Compiling a test with HDF5 failed. Either hdf5.h cannot be found, or config.log should bechecked 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 list netcdfgroup@xxxxxxxxxxxxxxxx <mailto:netcdfgroup@xxxxxxxxxxxxxxxx>For list information or to unsubscribe, visit:http://www.unidata.ucar.edu/mailing_lists/-- Steve HartSystems Administrator Colorado Center for Astrodynamics Research University of Colorado Boulder Steven.Hart@xxxxxxxxxxxx <mailto:Steven.Hart@xxxxxxxxxxxx> (303)492-8109 <tel:%28303%29492-8109> _______________________________________________ netcdfgroup mailing list netcdfgroup@xxxxxxxxxxxxxxxx <mailto:netcdfgroup@xxxxxxxxxxxxxxxx> For list information or to unsubscribe, visit: http://www.unidata.ucar.edu/mailing_lists/-- Steve HartSystems Administrator Colorado Center for Astrodynamics Research University of Colorado Boulder Steven.Hart@xxxxxxxxxxxx <mailto:Steven.Hart@xxxxxxxxxxxx> (303)492-8109 <tel:%28303%29492-8109> _______________________________________________ netcdfgroup mailing list netcdfgroup@xxxxxxxxxxxxxxxx <mailto:netcdfgroup@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
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