Re: [netcdf-hdf] HDF compile error

  • Subject: Re: [netcdf-hdf] HDF compile error
  • From: "Blankenship, Clay B. (MSFC-NCC8259)[USRA]" <clay.b.blankenship@xxxxxxxx>
  • Date: Fri, 19 Jun 2009 14:10:14 -0500
I do need to read HDF files--I'm not sure if they are HDF4. I am trying your suggestion with an HDF library the NCCS help desk provided.

Thanks,
Clay



On Jun 19, 2009, at 2:03 PM, Elena Pourmal wrote:

If your applications doesn't need to read HDF4 files, probably you
don't need to use HDF4 library at all.

Elena
On Jun 19, 2009, at 12:57 PM, Blankenship, Clay B. (MSFC-NCC8259)
[USRA] wrote:

I can try that but I am not sure if the WRF part of LIS-WRF needs the
APIs (whatever those are).  If HDF has NetCDF routines defined in it,
can I take out the HDF library?

Clay
On Jun 19, 2009, at 10:48 AM, Elena Pourmal wrote:

Clay,

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.

Elena

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/Linux.intel.
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/Linux.intel.
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


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







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