netcdf build against parallel HDF5

[Nico Schlömer]

So far, netCDF depends on libhdf5-serial-dev, restricting the I/O to serial. There are a number of parallel HDF5 installation options in Ubuntu already, e.g., libhdf5-mpi-dev or libhdf5-openmpi-dev. NetCDF could as well build against those, allowing for parallel I/O. One change in the configure script is that NetCDF would need to be configured with the respective MPI compiler.
I'm not sure what the cleanest options here would be. Possible a package libnetcdf-openmpi-dev?

[Launchpad Janitor (janitor)]

Status changed to 'Confirmed' because the bug affects multiple users.

[SimonS (schmonzes)]

I support the idea of a package libnetcdf-openmpi-dev. The current state is quite unsatisfying. It took me ages to find out that the library is built with hdf5 support, but not with hdf5-parallel. Surprisingly, the netcdf routines themself did not give any warning, when trying to use parallel I/O and instead just opened the file in serial mode.

[Maui Muc (stefan-mauerberger)]

I'd like to support the idea of having a libnetcdf-openmpi-dev package, too. Having it would be a grate relief.

Well, I tried to build it my own, however, with no success.
Maybe someone could help me out with this?

The following is what I did:
1. Sources and build dependencies
 > apt-get source libnetcdf-dev
 > sudo apt-get build-dep libnetcdf-dev
2. Replace libhdf5-dev (serial) by libhdf5-openmpi-dev
 > sudo apt-get install libhdf5-openmpi-dev
3. Changing build dependencies in debian/control
 line 6: libhdf5-dev -> libhdf5-openmpi-dev
4. Modify /debian/rules
 line 14: --enable-parallel-tests
 line 15: mpif90
 line 16: mpic++
 line 17: mpicc
5. Rebuild package
 > dpkg-buildpackage -us -uc

This however does not work. The build-process terminates with some error messages due to that reason:
> libtool: link: mpif90 -shared .... -L/usr/lib/openmpi/lib -l -L/usr/lib/gcc/x86_64-linux-gnu/4.7 ....
Sure, -l directly followed by -L wont work ...

Does anyone have an idea what is going wrong here?

Cheers,
Stefan

[Nico Schlömer (nschloe)]

I did some work for this in https://launchpad.net/~nschloe/+archive/trilinos-nightly which you may want to check out. It's based off of netCDF's latest dev version which provides a CMake builds, doing away with many of the flaws previously present.

[Gianfranco Costamagna (costamagnagianfranco)]

Hi, can you please forward the patches on a new Debian bug? This should be fixed in Debian before, I think.

I'll be happy to sponsor/sync the package after.