[netCDF #QFD-237189]: netcdf-c-4.3.3 (TWO CHECKS FAILED)

Peter,

> I have given this a go and have now hopefully installed HDF5.

Good!  The next step requires that you build and install the 
netCDF C library before you can build and install netCDF Fortran.

Were you able to build and install the netCDF C library, which
uses the HDF5 library you just installed?

Documentation for how to do this is here:

  
http://www.unidata.ucar.edu/netcdf/docs/getting_and_building_netcdf.html#build_default

and here's an example of how to do this, assuming you're using a
Unix shell that sets environment variables in the standard way:

  $ cd /path/to/netcdf-C/source/directory
  $ NCDIR=/home/mse_sw/netcdf    # where you want to install the netCDF C 
library
  $ H5DIR=/home/mse_sw/hdf5       # where you have already installed the HDF5 
library
  $ CPPFLAGS="-I${H5DIR}/include" LDFLAGS="-L${H5DIR}/lib" ./configure 
--prefix=${NCDIR}
  $ make check
  $ make install

Then you can build and install netCDF-Fortran as described in detail here:

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

An example for how this might look for you is:

  $ cd /path/to/netcdf-Fortran/source/directory
  $ NFDIR=/home/mse_sw/netcdf-4.4.1   # where you want to install the 
netCDF-Fortran library
  $ LD_LIBRARY_PATH=${NCDIR}/lib CPPFLAGS="-I${NCDIR}/include" 
LDFLAGS="-L${NCDIR}/lib"  \
     FC=ifort F77=ifort  ./configure --prefix=${NFDIR}
  $ make check
  $ make install

This is assuming the defaults, installing the HDF5 and netCDF-C libraries as 
shared libraries.

> However, when trying to install NetCDF-Fortran-4.4.1 I tried to configure 
> using the following
> 
> ./configure --prefix=/home/mse_sw/netcdf-4.4.1 --enable-f90 F77=ifort FC=ifort
> 
> We want to link to ifort on the our system so hence the F77 & FC,
> But im not sure this is right or even enough??
> 
> This gives me a WARNING: unrecognized options: --enable-f90
> But seems to run through OK.

Right, --enable-f90 is not one of the options this configure script
understands, because it's not included in the output from invoking

  $ ./configure --help

> When I then try to run make check
> This results in errors which I don't understand

> make[2]: *** [nf_test] Error 1
> make[2]: Leaving directory `/home/SF_SRC/netcdf-fortran-4.4.1/nf_test'
> make[1]: *** [check-am] Error 2
> make[1]: Leaving directory `/home/SF_SRC/netcdf-fortran-4.4.1/nf_test'
> make: *** [check-recursive] Error 1
> [root@fotcluster2 netcdf-fortran-4.4.1]#

I don't understand those errors either, as there's not enough context.

> I'm afraid I don't full understand how to set the various flags such as 
> CPPFLAGS etc.
> Also when linking HDF5 to zlib we used the --with-zlib command.
> 
> But how does NETCDF know where HDF5 and zlib is installed.

It doesn't use the --with-hdf5 option, but instead uses the values of the
CPPFLAGS and LDFLAGS environment variables.

> I'm really sorry for troubling you, but this is a little beyond my knowledge 
> and any help would be most appreciated.
> Also an explanation to setting flags and how to would be most appreciated.

I hope the examples above are sufficient. If you're using csh as your shell 
instead of a standard Unix shell such as bash or ksh, you'll need to use
different syntax, as explained in the building_netcdf_fortran.html doc
referenced above.

--Russ

> Regards
> Peter Mills
> 
> 
> ________________________________________
> From: Peter Mills
> Sent: 22 January 2015 15:32
> To: address@hidden
> Subject: RE: [netCDF #QFD-237189]: netcdf-c-4.3.3 (TWO CHECKS FAILED)
> 
> Hi Russ,
> 
> I have tried to install zlib and hdf5 but get errors during the make check of 
> HDF5.
> I have summarised my steps and have copy the log files to the bottom of this 
> email
> 
> Would you be able to have a look and let me know what the problem is, please.
> 
> Our system is Centos 6.6, with Fortran Compiler and C Compiler installed.
> 
> To access these I loaded a module environment file.
> 
> Steps taken
> 
> I have download and installed zlib.1.2.8
> Configured using the following commands
> 
> ./configure –prefix=home/mse_sw/zlib.1.2.8
> make check
> make install
> 
> this seems to have installed well.
> 
> I then tried to install hdf5 using the following commands to configure
> 
> ./configure --prefix=/home/mse_sw/hdf5 --enable-fortran --enable-cxx 
> --with-zlib=/home/mse_sw/zlib.1.2.8/  >> compile.txt   (SEE BELOW)
> 
> This seems to go well but I get loads of warnings similar to this:
> 
> plugin.c:303: warning: will never be executed
> plugin.c:303: warning: will never be executed
> plugin.c:303: warning: will never be executed
> plugin.c:303: warning: will never be executed
> plugin.c:305: warning: will never be executed
> plugin.c:305: warning: will never be executed
> plugin.c:305: warning: will never be executed
> plugin.c:305: warning: will never be executed
> plugin.c:305: warning: will never be executed
> plugin.c:307: warning: will never be executed
> plugin.c:307: warning: will never be executed
> plugin.c:307: warning: will never be executed
> plugin.c:307: warning: will never be executed
> plugin.c:307: warning: will never be executed
> 
> 
> Then when I try to do a make check, once again this all seems to go wrong - 
> see make _check.txt
> 
> I would be really grateful if you could advise me what is wrong and if I have 
> missed any vital steps.
> 
> I haven’t set any environment variables for flags such as CC , FC etc
> 
> 
> -----------------------------------------------------------------------------------------------------------------------------------------------
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Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: QFD-237189
Department: Support netCDF
Priority: Normal
Status: Closed