[netCDF #RWU-267828]: Netcdf Fortran configure error

Hello,

Looking at the file config.log-netcdf-fortran, I see many messages similar to 
the following:

/usr/local/netcdf-intel-mpi/netcdf-c-4.7.2/lib/libnetcdf.a(libnchdf5_la-hdf5var.o):
 In function `NC4_HDF5_set_var_chunk_cache':
hdf5var.c:(.text+0x5f69): undefined reference to `H5open'
hdf5var.c:(.text+0x5f6f): undefined reference to `H5P_CLS_DATASET_ACCESS_g'
hdf5var.c:(.text+0x5f74): undefined reference to `H5Pcreate'
hdf5var.c:(.text+0x5f9b): undefined reference to `H5Pset_chunk_cache'
hdf5var.c:(.text+0x5fa7): undefined reference to `H5Dclose'
hdf5var.c:(.text+0x5fba): undefined reference to `H5Dopen2'
hdf5var.c:(.text+0x5fc9): undefined reference to `H5Pclose'
/usr/local/netcdf-intel-mpi/netcdf-c-4.7.2/lib/libnetcdf.a(libnchdf5_l

It appears that the linker is trying to link against the static libnetcdf.a 
instead of the dynamic library you compiled.  There are two solutions I can 
think of.

First, you could recompile netcdf-c and in addition to specifying 
--enable-shared, specify --disable-static. This will prevent the static library 
from being built. 

Alternatively, you could modify how you configure netCDF-Fortran as follows:

    $ ./configure --prefix=/usr/local/netcdf-intel-mpi/netcdf-fortran-4.5.2 
--enable-shared --enable-pnetcdf --enable-parallel-tests --host=x86_64 
--disable-dap $(nc-config --libs --static)

Note the addition of "$(nc-config --libs --static)" on the end.  This will 
specify the compiler flags needed to properly link against the downstream 
dependencies when linking against static libnetcdf.  You can invoke 'nc-config 
--libs --static' from the command line if you want to see what the output it. 

Let me know if this doesn't resolve the issue. Have a great day,

-Ward


> Dear all:
> 
> I was tring to compile the NETCDF with parallel support with intel
> compiler. And installation sequence is 1)zlib-1.2.8 2) szip-2.1 3)
> hdf5-1.8.13 4) pnetcdf-1.12.1 5) netcdf-c-4.7.2 6)netcdf-fortran-4.5.2
> . I installed the former 5 parts with no problem. But I encountered with
> configure error when I was trying to configure Netcdf Fortran. And
> the error message is "configure: error: Could not link to netcdf
> C library. Please set LDFLAGS." Which I am quite confused since I
> already set the netcdf-c library path in the LDFLAGS.  The attachment
> is netcdf-fortran config.log and   in case you need it I also upload
> the netcdf-c config.log. Hope you can have some opinion on this
> problem. THANKS.
> 
> Sincerely
> 
> FYI: Here is the sentence I used to configure netcdf-fortran.
> 
> CPPFLAGS="-I/usr/local/netcdf-intel-mpi/hdf5-1.8.13/include 
> -I/usr/local/netcdf-intel-mpi/pnetcdf-1.12.1/include 
> -I/usr/local/netcdf-intel-mpi/netcdf-c-4.7.2/include" 
> LDFLAGS="-L/usr/local/netcdf-intel-mpi/hdf5-1.8.13/lib -lhdf5_hl -lhdf5 -lz 
> -lm -L/usr/local/netcdf-intel-mpi/pnetcdf-1.12.1/lib -lpnetcdf 
> -L/usr/local/netcdf-intel-mpi/netcdf-c-4.7.2/lib 
> -L/opt/impi/5.0.1.035/intel64/lib" ./configure 
> --prefix=/usr/local/netcdf-intel-mpi/netcdf-fortran-4.5.2 --enable-shared 
> --enable-pnetcdf --enable-parallel-tests --host=x86_64 --disable-dap
> 
> 


Ticket Details
===================
Ticket ID: RWU-267828
Department: Support netCDF
Priority: Normal
Status: Closed
===================
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