Re: [netcdf-hdf] HDF compile error


I think HDF4 library on your system has NetCDF APIs defined and this creates the conflict.

Would it be possible for you to recompile HDF4 to disable NetCDF APIs?

Here is the configuration you will need to use

./configure --disable-netcdf --with-zlib=/path --with-jpeg=/path... (-- with-szip=/path....)

Please let me know if you have any questions.


On Jun 19, 2009, at 10:30 AM, Blankenship, Clay B. (MSFC-NCC8259) [USRA] wrote:

I am trying to compile LIS-WRF (a coupled land-atmosphere model) on a Linux cluster using Intel Fortran 90 and MPI with NetCDF and HDF libraries.

This is the link command:

mpif90 -o wrf.exe -g -traceback -fpe1 -convert big_endian wrf.o libwrflib.a -L../external/io_netcdf -lwrfio_nf -L/usr/local/other/netcdf/3.6.2_intel-10.1.013/lib -lnetcdf -L../ external/RSL_LITE -lrsl_lite -L../external/io_int -lwrfio_int -L../external/io_grib1 -lio_grib1 -L../external/io_grib_share -lio_grib_share
  ../frame/module_internal_header_util.o ../frame/pack_utils.o
  -L../external/esmf_time_f90 -lesmf_time
../lis/lib/read_grib/readgrib.a ../lis/lib/grib/griblib.a ../lis/ lib/w3lib/libw3.a -L/discover/nobackup/projects/lis/ esmf_2_2_2rp3_intel_10_1_017_impi_3_2_011/lib/libO/ 64.mpi.default
  -lesmf -lnetcdf_stubs -lstdc++ -lrt
-L/usr/local/other/baselibs/ESMF222rp3_NetCDF362b6_10.1.017/Linux/ lib -lhdfeos -lGctp -lmfhdf -ldf -ljpeg -lz -lm -lsz

I get the following warnings:

/usr/local/other/baselibs/ESMF222rp3_NetCDF362b6_10.1.017/Linux/lib/ libmfhdf.a(var.o): In function `NC_var_shape':
var.c:(.text+0x7cc): multiple definition of `NC_var_shape'
/usr/local/other/netcdf/3.6.2_intel-10.1.013/lib/libnetcdf.a(var.o):/ usr/local/other/netcdf-3.6.2/libsrc/var.c:361: first defined hereld: Warning: size of symbol `NC_var_shape' changed from 548 in /usr/ local/other/netcdf/3.6.2_intel-10.1.013/lib/libnetcdf.a(var.o) to 602 in /usr/local/other/baselibs/ESMF222rp3_NetCDF362b6_10.1.017/ Linux/lib/libmfhdf.a(var.o)

What does this mean, exactly? Is there a conflict between HDF and NetCDF, or do I not have the right versions?

I can compile LIS only (without WRF) using the following command, and everthing works fine.

mpif90 -o /home/cbblanke/nobackup//LIS   A_BUNCH_OF_FILES.o
../lib/w3lib/libw3.a ../lib/read_grib/readgrib.a ../lib/grib/ griblib.a -lmpi
  -L/usr/local/other/netcdf/3.6.2_intel-10.1.013/lib -lnetcdf
-L/discover/nobackup/projects/lis/ esmf_2_2_2rp3_intel_10_1_017_impi_3_2_011/lib/libO/ 64.mpi.default
  -lesmf -lnetcdf_stubs -lstdc++ -lrt
-L/usr/local/other/baselibs/ESMF222rp3_NetCDF362b6_10.1.017/Linux/ lib/ -lhdfeos -lGctp -L/usr/local/other/baselibs/ESMF222rp3_NetCDF362b6_10.1.017/Linux/ lib -lmfhdf -ldf -ljpeg -lz -lm -lsz

Any advice would be appreciated.


Clay Blankenship                 * USRA Research Scientist
clay.b.blankenship@xxxxxxxx      * 256-961-7638
320 Sparkman Drive               * Huntsville, AL 35805
National Space Science and Technology Center

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