dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

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?

> 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.

--
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>
> >>>

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