[netCDF #BWM-262177]: Installation error with parallel netCDF

Hello Graham,

A couple of things leap out at me.  First, when building libhdf5, you need to 
pass the '--enable-hl' flag as well, to enable the high-level interface.  It is 
puzzling that the serial netcdf build did not complain about this.  
Additionally, you might try setting your LD_LIBRARY_PATH to include the 
appropriate location for the build, e.g.:

$ CPPFLAGS=-I/scratch/dione/packages_parallel/include 
LDFLAGS=-L/scratch/dione/packages_parallel/lib 
LD_LIBRARY_PATH=/scratch/dione/packages_parallel/lib ./configure

Note that unless you add LD_LIBRARY_PATH to your environmental variables via 
'export', or in a system config file, you will also need to specify it when you 
run 'make check'.

If this does not resolve the issue, can you please provide the 'configure.log' 
generated when you run the configure script? This will provide some insight as 
to the specific problem.

Thanks, I hope this helps,

-Ward


> Hello,
> 
> I am trying to compile and install netCDF with a parallel build of HDF5.
> 
> First I installed an up to date zlib then I installed a serial HDF5 and
> a parallel HDF5 so that
> 
> /scratch/dione/packages/  ... contains the HDF5 and zlib lib, include,
> bin folders.
> 
> /scratch/dione/packages_parallel ...  contains the parallel HDF5 and
> zlib lib, include and bin folders.
> 
> ZLIB INSTALL:
> ./configure --prefix=/scratch/dione/packages
> make
> make test
> make install prefix=/scratch/dione/packages
> &
> ./configure --prefix=/scratch/dione/packages_parallel
> make
> make test
> make install prefix=/scratch/dione/packages_parallel
> 
> HDF5 INSTALL:
> ./configure --prefix=/scratch/dione/packages --enable-fortran
> --with-zlib=/scratch/dione/packages/include,/scratch/dione/packages/lib
> make
> make check
> make install prefix=/scratch/dione/packages
> &
> ./configure --prefix=/scratch/dione/packages_parallel --enable-parallel
> --enable-fortran
> --with-zlib=/scratch/dione/packages_parallel/include,/scratch/dione/packages_parallel/lib
> make
> make check
> make install prefix=/scratch/dione/packages_parallel
> 
> ________
> 
> 
> Then, to install the serial netCDF I used
> 
> ./configure --prefix=/scratch/dione/packages
> CPPFLAGS=-I/scratch/dione/packages/include
> LDFLAGS=-L/scratch/dione/packages/lib
> make
> make check
> make install prefix=/scratch/dione/packages
> 
> This worked successfully.
> 
> However, when I tried to do the same for parallel netCDF I ran into errors.
> I used
> ./configure --prefix=/scratch/dione/packages_parallel
> CPPFLAGS=-I/scratch/dione/packages_parallel/include
> LDFLAGS=-L/scratch/dione/packages_parallel/lib
> 
> and I get the error:
> checking hdf5.h usability ... no
> checking hdf5.h presence ... no
> checking for hdf5.h ... no
> configure: error: Compiling a test with HDF5 failed. Either hdf5.h
> cannot be found, or config.log should be checked for other reason
> 
> I also tried
> ./configure --prefix=/scratch/dione/packages_parallel
> --with-hdf5=/scratch/dione/packages_parallel/
> --with-zlib=/scratch/dione/packages_parallel/lib
> 
> but I get the error message quoted above.
> 
> Do you know why the parallel version might be having trouble finding the
> HDF5 library?
> 
> best,
> Graham
> 
> --
> Graham Kerr
> Solar Physics PhD Student
> 
> Rm 604 Kelvin Building,
> SUPA School of Physics and Astronomy
> University of Glasgow,
> Glasgow,
> G12 8QQ
> 
> T: +44 141 330 2960
> E: address@hidden
> W: http://www.astro.gla.ac.uk/?p=1417
> 
> 
> 

Ticket Details
===================
Ticket ID: BWM-262177
Department: Support netCDF
Priority: Normal
Status: Closed