H5Part development and discussion

[Achim Gsell <achim AT cybercity.ch>]

On Thursday 19 April 2007 20:18, John Shalf wrote:
> On Apr 19, 2007, at 10:45 AM, Achim Gsell wrote:
> > On Thursday 19 April 2007 17:53, John Biddiscombe wrote:
> >> 2) Added option to use INDEPENDENT_IO instead of
> >> COLLECTIVE_IO, I need this when using it on a system with a
> >> non-parallel file-system, using collective IO causes too
> >> large performance drop on our cluster.
> >
> > INDEPENDENT_IO vs COLLECTIVE_IO in H5Part, good point. A
> > couple of weeks ago a college found a bug in H5Part
> > concerning COLLECTIVE_IO (or we understand something
> > completely wrong): The H5FD_MPIO_COLLECTIVE property is
> > added to the property list f->xfer_prop, but this property
> > list is not used in I/O calls. Thus we are using independent
> > I/O. It's the same in version 1.0! John (Shalf), any
> > idea/comments about this?
>
> Either it is a mistake or a misunderstanding about the
> operation of parallelIO with HDF5.  I was under the impression
> that if you open a file with the COLLECTIVE_IO property, that
> the implicit mode of operation for the files is collective
> unless you tell it otherwise. If this is not the case, then we
> should make sure the collective property is added to all of
> the xfer lists (but I assume it is implicit if the file was
> opened in collective mode).

The xfer_prop list is neither used in the open/create calls nor 
in the read/write calls!

> Lets do some regression testing with the benchmark (bench.c)
> to see if there is in fact a difference or not.

We already run some regression test on our XT3 system at CSCS 
with another test program and compared the results with results 
we got from Bench.c. Our conclusion is that H5Part uses 
independent I/O. If you use collective I/O. you must set the 
right MPI hints. Otherwise the performance is very, very poor. 
With Bench.c you can set MPI hints to whatever you want without 
impact to the I/O performance.

Achim