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[netCDF #MLF-697840]: Parallel NetCDF 4.1.3 compile error finding HDFflush



Hi John,

We recommend this way to build with parallel I/O support:

  http://www.unidata.ucar.edu/netcdf/docs/build_parallel.html

This works for netCDF version 4.3.0, but I don't know for sure
whether it works for the older 4.1.3 release.  Is there some reason
you have to use version 4.1.3?  I notice you're building a separate 
netCDF-Fortran library anyway, which is what you would do if you
first build and install netCDF-C library version 4.3.0, then build
and install netCDF-Fortran version 4.2 according to these instructions:

  http://www.unidata.ucar.edu/netcdf/docs/netcdf-fortran-install.html

paying attention to the parallel I/O instructions in step 4, under the 
"Using Static Libraries" section, if that's what you want to install.

--Russ

> Full Name: John Eylander
> Email Address: address@hidden
> Organization: Army Cold Regions Research & Eng. Lab
> Package Version: 4.1.3
> Operating System: RHEL 6.2 64-bit OS
> Hardware: 64-Bit
> Description of problem: I'm having extreme troubles compiling NetCDF 4.1.3 
> (with parallel I/O support enabled).  I have HDF5 1.8.6 installed and 
> successfully compiled and installed.  I have searched all the google sources 
> I know to try to find the right flag or option to turn off/on with no luck.  
> Here is my NetCDF compile script:
> 
> HDF_DIR=/u/home/eylandej/hdf5
> export CC=/site/intel/impi/4.1.0.024/intel64/bin/mpicc
> export F77=/site/intel/impi/4.1.0.024/intel64/bin/mpif77
> export CXX=/site/intel/impi/4.1.0.024/intel64/bin/mpicxx
> export FC=/site/intel/impi/4.1.0.024/intel64/bin/mpif90
> echo $LD_LIBRARY_PATH
> export LD_LIBRARY_PATH=/u/home/eylandej/hdf5-1.8.6/lib:$LD_LIBRARY_PATH
> export FCFLAGS="-I/u/home/eylandej/hdf5/include 
> -I/u/home/eylandej/zlib-1.2.7/include -I/u/home/eylandej/szip-2.1/include 
> -m64"
> export CPPFLAGS="-I/u/home/eylandej/hdf5/include 
> -I/u/home/eylandej/zlib-1.2.7/include -I/u/home/eylandej/szip-2.1/include 
> -DpgiFortran"
> export FFLAGS="-I/u/home/eylandej/hdf5/include 
> -I/u/home/eylandej/zlib-1.2.7/include -I/u/home/eylandej/szip-2.1/include 
> -m64"
> export LDFLAGS="-L${HDF_DIR}/lib -L/u/home/eylandej/zlib-1.2.7/lib 
> -L/u/home/eylandej/szip-2.1/lib"
> LIBS="-ldl -lz -lm -lhdf5 -lhdf5_hl -lhdf5_fortran -lhdf5hl_fortran"
> ./configure --prefix=/u/home/eylandej/netcdf-4.1.3 
> --with-zlib=/u/home/eylandej/zlib-1.2.7 --with-szip=/u/home/eylandej/szip-2.1 
> \
> --enable-netcdf-4 --enable-pnetcdf4 --disable-dap --disable-shared 
> --enable-static \
> --enable-separate-fortran  --enable-f90 --with-udunits --with-libcf 
> --enable-large-file-tests --enable-parallel-tests
> 
> This is the error I get during the "configure" stage of compiling NetCDF:
> 
> checking for ptrdiff_t... yes
> checking for uchar... no
> checking for longlong... no
> checking whether char is unsigned... no
> checking whether byte ordering is bigendian... no
> checking size of short... 2
> checking size of int... 4
> checking size of long... 8
> checking size of float... 4
> checking size of double... 8
> checking size of off_t... 8
> checking size of size_t... 8
> checking for library containing deflate... none required
> checking for floor in -lm... yes
> checking for library containing H5Fflush... no
> configure: error: Can't find or link to the hdf5 library. Use 
> --disable-netcdf-4, or see config.log for errors.
> + exit
> 
> I need to compile NetCDF 4 with parallel I/O support for WRF version 3.4.1. 
> Any ideas on what I have done wrong with my flags/options?  I've been 
> struggling with this for a couple of weeks...  Thanks in adance!
> 
> 
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: MLF-697840
Department: Support netCDF
Priority: Normal
Status: Closed


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