dolfin team mailing list archive

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

Anders Logg wrote:
> On Sun, Mar 14, 2010 at 08:45:39AM +0000, Garth N. Wells wrote:
>>
>> Anders Logg wrote:
>>> On Sun, Mar 14, 2010 at 08:35:32AM +0000, Garth N. Wells wrote:
>>>> Anders Logg wrote:
>>>>> On Sun, Mar 14, 2010 at 07:39:45AM +0000, Garth N. Wells wrote:
>>>>>> Anders Logg wrote:
>>>>>>> On Fri, Mar 12, 2010 at 06:58:22PM -0000, noreply@xxxxxxxxxxxxx wrote:
>>>>>>>> ------------------------------------------------------------
>>>>>>>> revno: 4635
>>>>>>>> committer: Garth N. Wells <gnw20@xxxxxxxxx>
>>>>>>>> branch nick: dolfin-all
>>>>>>>> timestamp: Fri 2010-03-12 18:53:05 +0000
>>>>>>>> message:
>>>>>>>>   Work on reading Vectors in parallel. Some issues to resolve still.
>>>>>>>>
>>>>>>>>   Some issues:
>>>>>>>>   - How should files be named when in parallel?
>>>>>>>>   - Should we have a 'master' xml file which points to the files
>>>>>>>>   - from different processes?
>>>>>>> I think this should be done in the same way as for Meshes. We
>>>>>>> discussed the following design:
>>>>>>>
>>>>>>> 1. Reading a single file "foo.xml" results in each process reading the
>>>>>>> entire file but skipping data located on another process as determined
>>>>>>> by local_range. This is what is implemented now for meshes (followed
>>>>>>> by communication and mesh partitioning). The difference for vectors
>>>>>>> would be that no extra communication is necessary.
>>>>>>>
>>>>>> OK.
>>>>>>
>>>>>>> 2. Reading a set of files "foo*.xml" results in each process reading
>>>>>>> its portion stored in "foo%d.xml" % p. The File interface then needs
>>>>>>> to check for the occurence of '*' and figure out the correct file name
>>>>>>> based on its process number.
>>>>>>>
>>>>>> I think that are a number of advantages to having a single .xml that
>>>>>> points to the 'sub-files'. An obvious advantage is that we won't need to
>>>>>> distinguish between cases 1 and 2 when reading in a vector.
>>>>>>
>>>>>> Garth
>>>>> I don't feel strongly about either option, but if we go for the
>>>>> master-file/sub-file design I think we should do the same for vectors
>>>>> and meshes.
>>>>>
>>>>> The master file could look something like this for vectors:
>>>>>
>>>>>   <distributed_vector size="1024" num_partitions="16">
>>>>>     <sub_vector partition="0" file="foo_0.xml" offset="0"/>
>>>>>     <sub_vector partition="1" file="foo_1.xml" offset="64"/>
>>>>>     <sub_vector partition="2" file="foo_2.xml" offset="128"/>
>>>>>     ...
>>>>>   </distributed_vector>
>>>>>
>>>> Looks good, except 'offset' should be 'size', or 'local_size'.
>>> Yes, but then maybe it's not needed since the local size will be
>>> available in the local files (which can be standard XML vector data).
>>>
>>> But then won't the master files always be trivial? The only extra
>>> information that is contained in the master file is the total size,
>>> and the number of partitions (which will only be used to check that it
>>> matches the actual number of processes).
>>>
>> The master file is the definitive file. Say a program is run with 4
>> processes, and then with 2.  The files vector_0.xml, vector_1.xml,
>> vector_2.xml and vector_3.xml will be floating around, but which files
>> make up the vector? The master file will point to vector_0.xml and
>> vector_1.xml.
> 
> I don't understand how that would work. Would it repartition the
> entire vector or just use the first two?
>

It would read the first two. What the program does with them from that
point onwards is separate issue.


>> Also, there should be no need to check that the number of 'partitions'
>> matches the number of processes.
> 
> That seems to be the only real use of having a master file, at least
> the only extra information contained in the master file and not
> contained in the local files.
>

The master file *defines* which files are the sub files. For example, a
collection of .xml files could be read by a single process program, just
like ParaView does.

Garth

> --
> Anders
> 
> 
>> Garth
>>
>>
>>>> Garth
>>>>
>>>>> For meshes, we can do this:
>>>>>
>>>>>   <distributed_mesh num_partitions="16">
>>>>>     <sub_mesh partition="0" file="foo_0.xml"/>
>>>>>     <sub_vector partition="1" file="foo_1.xml"/>
>>>>>     <sub_vector partition="2" file="foo_2.xml"/>
>>>>>     ...
>>>>>   </distributed_mesh>
>>>>>