On Sun, Mar 14, 2010 at 03:42:29PM +0000, Garth N. Wells wrote: > > > 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, [email protected] wrote: > >>>>>>>> ------------------------------------------------------------ > >>>>>>>> revno: 4635 > >>>>>>>> committer: Garth N. Wells <[email protected]> > >>>>>>>> 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.
That seems like a strange situation. Will that ever happen? (Storing data from n processes and then reading back a subset on m < n processes.) > >> 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. Yes, but those files will most likely always have the same numbering scheme (if stored from DOLFIN), something like foo_1.xml, foo_2.xml etc. Then we might as well do "foo_*.xml". -- Anders > Garth > > >> 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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