[alcf-discuss] [Fwd: Re: Parallel hdf5 I/O of strided data]

[Tim Tautges]

[forwarding 'cuz it might be useful to have archived...]


-------- Original Message --------
Subject: Re: [alcf-discuss] Parallel hdf5 I/O of strided data
Date: Wed, 6 May 2009 16:46:40 -0500
From: Rob Latham <robl at mcs.anl.gov>
To: Tim Tautges <tautges at mcs.anl.gov>
References: <4A01FE12.20909 at mcs.anl.gov> 
<20090506213103.GA21963 at mcs.anl.gov> <4A02034F.4060402 at mcs.anl.gov>

On Wed, May 06, 2009 at 04:38:23PM -0500, Tim Tautges wrote:
> Is that right?  The website you pointed to earlier  
> (http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetDxplMpio)  
> implies the opposite, at least in the documentation for  
> H5Pset_dxpl_mpio_collective_opt...

>>
>> HDF5 disables collective I/O to a dataset by default, which is not
>> ideal on bluegene. 

OK, I see where the confusion lies.  We're talking about two different
functions here.

H5Pset_dxpl_mpio() sets up a property list that will guide how HDF5
does dataset access: it can either be independent (the default) or
collective.  Every HDF5 application on BlueGene should call this, set
the H5FD_MPIO_COLLECTIVE flag, and pass the resulting property list to
the HDF5 read/write routines.

H5Pset_dxpl_mpio_collective_opt() is something else altogether.  Note
"This function should be used only when H5FD_MPIO_COLLECTIVE  has been
set through H5Pset_dxpl_mpio".    I don't have any idea why anybody
would ever call H5Pset_dxpl_mpio_collective_opt() but I presume the
HDF5 guys had a good reason.

My advice: don't ever call H5Pset_dxpl_mpio_collective_opt() -- it
doesn't do what you think it will do, and what it *does* do isn't good
for BlueGene anyway.

==rob

-- 
Rob Latham
Mathematics and Computer Science Division
Argonne National Lab, IL USA


-- 
================================================================
"You will keep in perfect peace him whose mind is
   steadfast, because he trusts in you."               Isaiah 26:3

              Tim Tautges            Argonne National Laboratory
          (tautges at mcs.anl.gov)      (telecommuting from UW-Madison)
          phone: (608) 263-8485      1500 Engineering Dr.
            fax: (608) 263-4499      Madison, WI 53706