Anders Logg wrote: > 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.) >
It could very well happen, for example reading data in on one process to manipilate it, restart a computation with a different number of processes, etc. >>>> 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". > That's not my point. If I have a directory full of foo_*.xml how can I know which ones make up the vector? It precisely analogous to VTK. My directory can be full of .vtu files, but by opening .pvd I can always correctly visualise a result. Garth > -- > 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> >>>>>>> _______________________________________________ Mailing list: https://launchpad.net/~dolfin Post to : [email protected] Unsubscribe : https://launchpad.net/~dolfin More help : https://help.launchpad.net/ListHelp
