dolfin team mailing list archive

["Garth N. Wells" <gnw20@xxxxxxxxx>]

On 26/08/11 02:39, Anders Logg wrote:
> On Thu, Aug 25, 2011 at 05:57:51PM -0400, Garth N. Wells wrote:
>>
>>
>> On 25/08/11 16:53, Anders Logg wrote:
>>> On Thu, Aug 25, 2011 at 09:59:44AM -0400, Garth N. Wells wrote:
>>>
>>>>>>> How about using DOM everywherme and reserve the use of SAX for an
>>>>>>> XML->HDF5 converter?
>>>>>>>
>>>>>>
>>>>>> That could be OK, but if we have the to implement a SAX parser it's
>>>>>> probably easiest to have it in DOLFIN anyway. I don't see the advantage
>>>>>> over having the SAX parser with the io code.
>>>>>
>>>>> I agree we should keep it in DOLFIN, but if the only thing it needs to
>>>>> do is extract data and spit out HDF5, I imagine it can be simpler than
>>>>> the current parser since it doesn't need to be parallel. (?)
>>>>>
>>>>
>>>> To make things clearer, I've just renamed the LocalMeshData parsers to
>>>>
>>>>   XMLLocalMeshDOM (was XMLLocalMeshData)
>>>>
>>>> and
>>>>
>>>>   XMLLocalMeshSAX (was XMLLocalMeshDataDistributed)
>>>
>>> That's good.
>>>
>>>> When XMLLocalMeshSAX is complete, it may be desirable to remove
>>>> XMLLocalMeshDOM.
>>>
>>> Either way is fine for me, as long as we decide which one to use. I
>>> initially wanted to use SAX (as before) but the DOM looks easier and
>>> may be enough if we plan to use HDF5 for large-scale problems anyway.
>>> Or is it the case that DOM is a limitation even for medium sized
>>> problems?
>>>
>>
>> It works for 'medium' (very arbitrary) size problems.
>>
>>>> I don't know what you mean by parallel - the XMLLocalMeshSAX works in
>>>> the same way as the old parser (each process reading a chunk). I don't
>>>> see how it can be made simpler by reading a XML file and then converting
>>>> to HDF5. The steps that are there now will all still be required to read
>>>> the XML mesh before writing a HDF file.
>>>
>>> I don't know HDF, but I imagine one could write one single file and
>>> HDF will handle parallel parsing of that file later. Then the
>>> conversion script we write does not need to do anything parallel, just
>>> read line by line and convert from one format to another.
>>>
>>
>> It may not be possible to do it line-by-line (I don't know, but I
>> wouldn't want to bank on it). Even if line-by-line is technically
>> possible, it could turn out to be terribly slow. We should support that
>> a mesh can be read into memory (distributed), and written to HDF5.
>>
>> Since we'll have support for writing HDF5 meshes, if we can read a large
>> XML mesh then we can re-use the HDF5 output code to make the conversion.
>>
>> I've removed the DOM-based LocalMeshData parser - there is no point to
>> it since we can just read the mesh on one process using XMLMesh and use
>> it to construct a dolfin::XMLLocalMeshData object.
> 
> ok, looks good.
> 
> How should we store boundary indicators? I'm not sure whether it needs
> to be stored as part of ParallelData. Is it really "parallel data"?
> ParallelData will for sure need to be used to compute it (convert
> somehow from the input) but it seems it can then be stored
> locally. 

OK. It's not really parallel data (but perhaps ParallelData should be
renamed).

> Each facet just needs to know its indicator value.
> 
> The input is a list of triples:
> 
>   (indicator, facet_cell, facet_number)
> 
> This indicates that local facet number `facet_number` of the cell
> `facet_cell` should have the indicator value (sub domain number)
> `indicator`.
> 

Let's make it generic:

  (parent_cell_index, entity_dim, local_entity_index, indicator/value)

It could go into MeshData (possibly with what's in ParallelData), and
the current MeshData could be renamed to something like 'UserMeshData'.

Garth

> This is currently store as three MeshFunctions and is converted to
> a MeshFunction over facets ("exterior_facet_domains") upon reading in
> the mesh (in serial).
> 
> --
> Anders