dolfin team mailing list archive

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

On Fri, 2010-08-06 at 21:06 +0200, Anders Logg wrote:
> On Fri, Aug 06, 2010 at 07:55:54PM +0100, Garth N. Wells wrote:
> > On Fri, 2010-08-06 at 20:53 +0200, Anders Logg wrote:
> > > On Fri, Aug 06, 2010 at 07:51:18PM +0100, Garth N. Wells wrote:
> > > > On Fri, 2010-08-06 at 20:36 +0200, Anders Logg wrote:
> > > > > On Fri, Aug 06, 2010 at 04:55:44PM +0100, Garth N. Wells wrote:
> > > > > > On Fri, 2010-08-06 at 08:42 -0700, Johan Hake wrote:
> > > > > > > On Friday August 6 2010 08:16:26 you wrote:
> > > > > > > > ------------------------------------------------------------
> > > > > > > > revno: 4896
> > > > > > > > committer: Garth N. Wells <gnw20@xxxxxxxxx>
> > > > > > > > branch nick: dolfin-all
> > > > > > > > timestamp: Fri 2010-08-06 16:13:29 +0100
> > > > > > > > message:
> > > > > > > >   Add simple Stokes solver for parallel testing.
> > > > > > > >
> > > > > > > >   Other Stokes demos don't run in parallel because MeshFunction io is not
> > > > > > > >   supported in parallel.
> > > > > > >
> > > > > > > Does anyone have an overview of what is needed for this to be fixed. I
> > > > > > > couldn't find a blueprint on it.
> > > > > > >
> > > > > >
> > > > > > Here it is:
> > > > > >
> > > > > >     https://blueprints.launchpad.net/dolfin/+spec/parallel-io
> > > > > >
> > > > > > > I am interested in getting this fixed :)
> > > > > > >
> > > > > >
> > > > > > Me too! We need to look at all the io since much of it is broken in
> > > > > > parallel.
> > > > > >
> > > > > > We need to settle on how to handle XML data. I favour (and I know Niclas
> > > > > > Janson does too) the VTK approach in which we have a 'master file' that
> > > > > > points to other XML files which contain portions of the vector/mesh,
> > > > > > etc. Process zero can read the 'master file' and then instruct the other
> > > > > > processes on which file(s) they should read in.
> > > > >
> > > > > This only works if the data is already partitioned. Most of our demos
> > > > > assume that we have the mesh in one single file which is then
> > > > > partitioned on the fly.
> > > > >
> > > >
> > > > The approach does work for data which is not partitioned. Just like with
> > > > VTK, one can read the 'master file' or the individual files.
> > > >
> > > > > The initial plan was to support two different ways of reading data in parallel:
> > > > >
> > > > > 1. One file and automatic partitioning
> > > > >
> > > > > DOLFIN gets one file "mesh.xml", each process reads one part of it (just
> > > > > skipping other parts of the file), then the mesh is partitioned and
> > > > > redistributed.
> > > > >
> > > > > 2. Several files and no partitioning
> > > > >
> > > > > DOLFIN get multiple files and each process reads one part. In this
> > > > > case, the mesh and all associated data is already partitioned. This
> > > > > should be very easy to fix since everything that is needed is already
> > > > > in place; we just need to fix the logic. In particular, the data
> > > > > section of each local mesh contains all auxilliary parallel data.
> > > > >
> > > > > This can be handled in two different ways. Either a user specifies the
> > > > > name of the file as "mesh*.xml", in which case DOLFIN appends say
> > > > >
> > > > >   "_%d" % MPI::process_number()
> > > > >
> > > > > on each local process.
> > > > >
> > > > > The other way is to have a master file which lists all the other
> > > > > files. In this case, I don't see a need for process 0 to take any kind
> > > > > of responsibility for communicating file names. It would work fine for
> > > > > each process to read the master file and then check which file it
> > > > > should use. Each process could also check that the total number of
> > > > > processes matches the number of partitions in the file. We could let
> > > > > process 0 handle the parsing of the master file and then communicate
> > > > > the file names but maybe that is an extra complication.
> > > > >
> > > >
> > > > This fails when the number of files differs from the number of
> > > > processes. It's very important to support m files on n processes. We've
> > > > discussed this at length before.
> > >
> > > I don't remember. Can you remind me of what the reasons are?
> > >
> >
> > I perform a simulation using m processes, and write the result to m
> > files. Later I want to use the result later in another computation using
> > n processors.
> 
> I assume you did your first simulation (with m processors) starting
> from one big file?
> 

What do you mean? The first simulation might not read in any file.

> Can't you just restart from that file when you later want to run with
> n processors? It would not be much extra work, and maybe it would even
> be faster considering all the extra communication.
> 

The communication cost is negligible when reading a vector just once and
distributing.

It will be very easy to read m files on n processes, so I don't get why
would we wish to prevent it? 

Also, we can't rely in the data that we read in being suitably
partitioned.

Garth

> I imagine the process would otherwise be something like this (assuming
> m < n).
> 
> 1. Each of the first m processes reads its corresponding file.
> 
> 2. The data is redistributed to n processes.
> 
> 3. Call ParMETIS and continued as when reading from one single file.
> 
> Step (2) would be involve exra work.
> 
> --
> Anders