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-tests
On 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.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
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--
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 <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
