Re: [netcdf-hdf] netcdf4 and OpenMP

Hi Charlie,

On May 23, 2008, at 8:42 AM, Charlie Zender wrote:

Hi Quincey,

1. Are there benefits to building HDF without --enable-threadsafe?
As Orion mentioned, the C++ and FORTRAN wrappers aren't currently compatible with the threadsafe option. I don't think it would be too hard to address this, but it's probably enough work that we should look for some funding to do it.

I hope HDF finds the resources to keep the C and Fortran API at equivalent levels of functionality.

We do try, yes. For instance the upcoming 1.8.1 release will have many new FORTRAN wrappers for new 1.8 API routines.

The only other downside really is the increased overhead for each HDF5 API call (to perform the semaphore locking that allows threadsafety).

Can you post or point me to numbers that quantify this?

        I don't have any, sorry.

If not, can you make it the HDF/netCDF4 default? at least
on multi-core systems?
That's probably difficult for us to detect at configure time.  :-/

Yes, easier said than done.
One might try imitating how packages like MPICH2 handle this.

Hmm, I'm not familiar with how MPICH2 works for this. Do you have a pointer?

We have learned, I think, to disable our progams' (NCO's)
threading unless it is linked to threadsafe HDF.
Otherwise users will experience unpredictable NCO failure.

2. How should we test, at NCO compile time, whether the
underlying netCDF4/HDF install is threadsafe?
The "H5_HAVE_THREADSAFE" macro will be defined when the "hdf5.h" header is included and threadsafety is enabled.

Good. This token will help us optimize NCO when built from source.

I wanted our NCO programs to have threading available for general
users but the configuration issues seem to dictate otherwise.
For instance, we distribute NCO .debs and RPMs now with threading
enabled by default because it "just works" with libnetcdf3.a.
With netCDF4, however, pre-built binaries like debs and RPMs
will depend on the distribution's libnetcdf4 .deb and RPM
which likely will not be built on top of HDF --threadsafe.

One outcome is that NCO users who rely on .debs and RPMs over custom
installs will lose NCO threading on (at least) netCDF4 files.
That is actually not
a big deal since threading only speeds up math-heavy jobs (ncwa,
ncap2) because I/O bottlenecks and threading overhead combine to
slow down I/O intensive jobs (ncdiff, ncra,..). It's possible
we may force OMP_NUM_THREADS=1 at run-time when input
or output files are netCDF4 format, and only leave threading
enabled for netCDF3 I/O in pre-built executables.

Even when a threadsafe HDF5 is used, and NCO is only reading from netCDF-4 files, you could still have problems for multi-threaded access. For instance, there are probably some global data structures in netCDF-4 that won't be protected by a semaphore and could get corrupted. Maybe Ed can think about this and offer an opinion...

        Quincey


Charlie
--
Charlie Zender, Department of Earth System Science, UC Irvine
Sab. at CNRS/LGGE-Grenoble until 20080815 :) 011+33+476+824236
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