dolfin team mailing list archive

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

On Mon, 2010-08-09 at 13:53 +0200, Anders Logg wrote:
> On Mon, Aug 09, 2010 at 12:47:10PM +0100, Garth N. Wells wrote:
> > On Mon, 2010-08-09 at 13:37 +0200, Anders Logg wrote:
> > > On Sat, Aug 07, 2010 at 01:24:44PM +0100, Garth N. Wells wrote:
> > > > On Fri, 2010-08-06 at 19:55 +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've looked a little into parallel io, and looked at what Trilinos and
> > > > PETSc do. Both support HDF5, and HDF5 has been developed to work
> > > > parallel. HDF5 does not advocate the one-file per processes (too awkward
> > > > and complicated they say), but advocates a one file approach. It has
> > > > tools that allow different processes to write to different parts of the
> > > > same file in parallel.
> > > >
> > > > >From reading this, what I propose (for now) is:
> > > >
> > > > 1. We only ever write one XML file for a given object. This file can be
> > > > read by different processes, with each reading in only a chunk.
> > > >
> > > > 2. We should add an XML format for partitioning data (Trilinos calls
> > > > this a 'map'). If a map file is present, it is used to define the
> > > > partitions. It may make sense to have a map file for each process (but
> > > > no need for a 'master file').
> > >
> > > I suggest something slightly different. I'm ok with the one file
> > > approach, but it would be good to store that data in a partitioned
> > > way. Our current model for parallel computing is that each process has
> > > a Mesh and each process has the partitioning data it needs stored in
> > > the data section of the Mesh. So each process has just a regular mesh
> > > with some auxilliary data attached to it. That makes it easy to read
> > > and write using already existing code. (No need for a special parallel
> > > format.)
> > >
> > > But we could easily throw all that data into one big file, something
> > > like this:
> > >
> > > <distributed_mesh num_parts="16">
> > >   <mesh ...>
> > >     ...
> > >   </mesh>
> > >   <mesh ...>
> > >     ...
> > >   </mesh>
> > >   ...
> > > </distributed_mesh>
> > >
> >
> > I would like to separate mesh and partitioning data. A partitioning of a
> > given mesh is not unique to a mesh, so it should be separated. A
> > partition could still go in the same XML file though.
> 
> It is separate from the mesh, but it is stored locally as part of the
> Mesh in MeshData. I think this has proved to be a very good way
> (efficient and simple) to store the data.
> 

This breaks the concept of using a given Mesh on a different number of
processes. For a given mesh, I may want to store and use different
partitions.

The same applied to Vectors. 

> Or do you suggest that we store it differently on file than we do as
> part of the DOLFIN data structures?
> 

I suggest that we decouple the Mesh and the partition data for file
output. It comes back to permitting a variable number of processes.

> I'm not sure that's a good idea. I like the 1-1 correspondence between
> our data structures and the file formats.
> 

Mapping the Mesh or Vector data structure to the file output reflects
the number of processes - we should strive to avoid that.

> But I wouldn't mind an additional file format (like HDF5) if that
> proves to be good for high-performace/very many processes.
> 

It will be needed eventually.

> > > > 3. For now, use native PETSc/Epetra HDF5 io for linear algebra objects
> > > > in serious parallel computations.
> > >
> > > ok.
> > >
> > > > 4. In the future look into using parallel HDF5 to read/write meshes and
> > > > other essential data.
> > >
> > > Perhaps, but I'm not sure how flexible HDF5 is to store and name all
> > > the data we need.
> > >
> >
> > An feature of HDF5 is that anything can be stored - we can just define
> > tags, heirachies, etc. It's XML-like in that respect.
> 
> ok. Is it a candidate for replacing the XML I/O? Or just a complement
> to it?
> 

I would suggest that it complements the XML format for now. It could
probably be used now in place of the BinaryFile format.

Garth

> --
> Anders