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/
>
