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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-tests On Tue, Mar 4, 2014 at 3:53 PM, Steven Hart <steven.hart@xxxxxxxxxxxx>wrote: > No problem. Since your install is 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=$LD_LIBRARY_PATH:'/usr/lib64/hdf' (or have it reflect your > path to HDF) > > I found alot of the same errors you are seeing before I had these set > correctly. > > Steve > > > > On 03/04/2014 01:48 PM, Doll, Margaret Ann wrote: > > Steve, > > Thanks for your quick reply. > > However, I don't have the intel compilers. I have the default compilers > that come with the Centos distribution, I have mpi compilers that come with > the ROCKS distribution and I have Portland Group compilers. > > > On Tue, Mar 4, 2014 at 3:37 PM, Steven Hart <steven.hart@xxxxxxxxxxxx>wrote: > >> >> This website proved extremely helpful in setting up NetCDF on my RHEL6 >> system. >> >> http://www.unidata.ucar.edu/software/netcdf/docs/build_default.html >> >> I saw those HDF errors as well, make sure you have all the correct flags >> defined. Here's what worked for me in my .bashrc: >> >> # ENV VAR for intel and netcdf install >> source /usr/local/intel/bin/compilervars.sh intel64 >> export CC=icc >> export CXX=icpc >> export CFLAGS='-O3 -xHost -ip -no-prec-div -static-intel' >> export CXXFLAGS='-O3 -xHost -ip -no-prec-div -static-intel' >> export F77=ifort >> export FC=ifort >> export F90=ifort >> export FFLAGS='-O3 -xHost -ip -no-prec-div -static-intel' >> export FCFLAGS=-64 >> export CPP='icc -E' >> export CXXCPP='icpc -E' >> export CPPFLAGS='-I/usr/include -I/usr/include/hdf' >> export LD_LIBRARY_PATH=$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/ >> > > > -- > 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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