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[netCDF #IBL-547564]: NetCDF build error

Hi Yunlan,

> I  have build NetCDF as follows:
> 1.  Build Zlib-1.2.5
> CC=icc CXX=icpc  CFLAGS='-O -fPIC '   ./configure 
> --prefix=/home/yun70/app/netcdf-4.0.1
> make check install
> 2. Build Hdf5-1.8.6
> CC=icc CXX=icpc FC=ifort  ./configure 
> --with-zlib=/home/yun70/app/netcdf-4.0.1 
> --prefix=/home/yun70/app/netcdf-4.0.1  --disable-shared
> make check install
> 3. Build NetCDF-4.0.1
> CC=icc CXX=icpc  FC=ifort  CPPFLAGS=-I/home/yun70/app/netcdf-4.0.1/include  
> LDFLAGS=-L/home/yun70/app/netcdf-4.0.1/lib    ./configure  --enable-netcdf-4  
>  --with-hdf5=/home/yun70/app/netcdf-4.0.1   
> --with-zlib=/home/yun70/app/netcdf-4.0.1   
> --prefix=/home/yun70/app/netcdf-4.0.1
> make check install
> The result shows that?
> =========================================
> 1 of 45 tests failed
> Please report to address@hidden<mailto:address@hidden>
> =========================================
> make[2]: *** [check-TESTS] Error 1
> make[2]: Leaving directory `/home/yun70/software/try/netcdf-4.0.1/libsrc4'
> make[1]: *** [check-am] Error 2
> make[1]: Leaving directory `/home/yun70/software/try/netcdf-4.0.1/libsrc4'
> make: *** [check-recursive] Error 1
> Please find the detailed output of configure and "make check install" in the 
> attachment. Can you give me some advise how to solve it ?

The output of "make check" for netCDF-4.0.1 shows

  *** Checking HDF5 deflate filter setting and getting...10 failures
  *** Checking HDF5 deflate, fletcher32, shuffle filter setting and 
getting...11 failures
  *** Checking HDF5 endianness control...35 failures
  56 errors detected! Sorry!
  FAIL: tst_h_vars

which indicate problems with the HDF5 library.  In particular, it appears that
the HDF5 library is not finding the zlib library.  Please look in the directory
containing libhdf5.a or libhdf5.so and see if there is a file named 
If so, check if it includes the line

         I/O filters (external): deflate(zlib)

If not, then you'll have to rebuild the hdf5 library and make sure it's built 
the zlib filter.

Maybe the problem is caused by specifying --disable-shared for the HDF5 library,
which is OK but means that you will have to make sure "-lz" is explicitly 
when linking netCDF.  This can be accomplished by including the environment 


with the other environment settings for the netCDF ./configure script.  If other
libraries needed at runtime are missing, you may need to add additional 
to the LDLIBS environment variable.


Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu

Ticket Details
Ticket ID: IBL-547564
Department: Support netCDF
Priority: Normal
Status: Closed

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