H5Part development and discussion

[Kurt Stockinger <kstockinger AT lbl.gov>]

Hi Johns,

H5Block allows you to store 3D scalar and vector fields. Internally,
H5Block stores a 3D scalar field as a 3D dataset. A 3D vector field is
stored as three 3-D datasets. Andreas has recently sent me some H5Block
dataset. See an example of the HDF5 file structure below for the 3D
scalar field "potential" and the 3D vector field "Electrical Field".


   GROUP "Block" {
         GROUP "Potential" {
            DATASET "0" {
               DATATYPE  H5T_IEEE_F64LE
               DATASPACE  SIMPLE { ( 128, 16, 16 ) / ( 128, 16, 16 ) }
            }
         }
         GROUP "Electrical Field" {
            DATASET "0" {
               DATATYPE  H5T_IEEE_F64LE
               DATASPACE  SIMPLE { ( 128, 16, 16 ) / ( 128, 16, 16 ) }
            }
            DATASET "1" {
               DATATYPE  H5T_IEEE_F64LE
               DATASPACE  SIMPLE { ( 128, 16, 16 ) / ( 128, 16, 16 ) }
            }
            DATASET "2" {
               DATATYPE  H5T_IEEE_F64LE
               DATASPACE  SIMPLE { ( 128, 16, 16 ) / ( 128, 16, 16 ) }
            }


Unlike in H5Part, where the processor layout is automatically specified
based on the numberOfParticles, in H5Block you need to define the "field
layout", i.e. the partitioning strategy of your 3D dataset. In the
dataset below, the scalar field "Potential" has the dimensionality 16,
16, 128. A possibly partitioning strategy for two processors is:

if (processor == 0)
    H5BlockDefine3DFieldLayout(fh, 0, 15, 0, 15, 0, 63);
else
    H5BlockDefine3DFieldLayout(fh, 0, 15, 0, 15, 64, 127);

The data can then be read with:

H5Block3dReadScalarField ( f, "Potential", data );

H5Block3dRead3dVectorField (f, "ElectricalField", xval, yval, zval);
 
Kurt

John Shalf wrote:
>
> But of course, you would be the first H5block "user".
> It'll be interesting to see if it meets your needs. :-)
>
> -john
>
> On Jun 15, 2007, at 1:53 PM, John Shalf wrote:
>> I think H5Block provides the capability that you are looking for.  It
>> provides the ability to store the block-structured grids that are
>> associated with the PIC calculation together with the particle data.
>>
>> The H5Block interface should automatically re-integrate the chunks
>> (the 64 volumes) into the single/un-domain-decomposed logical volume
>> used in the calculation.
>>
>> -john
>>
>> On Jun 15, 2007, at 9:03 AM, John Biddiscombe wrote:
>>> I've been happily using H5Part particles for some time, but I need
>>> to write a bunch of volume chunks into HDF as well.
>>> I have (say) 64 volumes which abut each other - the points along the
>>> edges are not duplicated (0->7, 8->15, 16->23, 24->31 etc etc). I
>>> was about to start a little utility to dump these volume chunks into
>>> hdf files and I thought. I wonder if this is what H5Block does?
>>>
>>> What is H5Block ? I have not looked at it at all (yet).
>>>
>>> thanks
>>>
>>> JB
>>>
>>> --John Biddiscombe,                            email:biddisco @ cscs.ch
>>> http://www.cscs.ch/about/BJohn.php
>>> CSCS, Swiss National Supercomputing Centre  | Tel:  +41 (91) 610.82.07
>>> Via Cantonale, 6928 Manno, Switzerland      | Fax:  +41 (91) 610.82.82
>>>
>>> _______________________________________________
>>> H5Part mailing list
>>> H5Part AT lists.psi.ch
>>> https://lists.web.psi.ch/mailman/listinfo/h5part
>> _______________________________________________
>> H5Part mailing list
>> H5Part AT lists.psi.ch
>> https://lists.web.psi.ch/mailman/listinfo/h5part
> _______________________________________________
> H5Part mailing list
> H5Part AT lists.psi.ch
> https://lists.web.psi.ch/mailman/listinfo/h5part


-- 
Kurt Stockinger
Computational Research Division
Lawrence Berkeley National Laboratory
Mail Stop 50F-1650, 1 Cyclotron Road
Berkeley, California 94720, USA

Tel: +1 (510) 486 5519, Fax: +1 (510) 486 5812
email: KStockinger AT lbl.gov
http://vis.lbl.gov/~kurts