Re: [netcdfgroup] Failing to configure netcdf-4.3.1.1

• Subject: Re: [netcdfgroup] Failing to configure netcdf-4.3.1.1
• From: Steven Hart <steven.hart@xxxxxxxxxxxx>
• Date: Tue, 04 Mar 2014 13:53:14 -0700

and

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.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 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 <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

• Follow-Ups:
  • Re: [netcdfgroup] Failing to configure netcdf-4.3.1.1
    • From: Doll, Margaret Ann

• References:
  • Re: [netcdfgroup] Failing to configure netcdf-4.3.1.1
    • From: Steven Hart
  • Re: [netcdfgroup] Failing to configure netcdf-4.3.1.1
    • From: Doll, Margaret Ann