dolfin team mailing list archive

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

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').

3. For now, use native PETSc/Epetra HDF5 io for linear algebra objects
in serious parallel computations.  

4. In the future look into using parallel HDF5 to read/write meshes and
other essential data.

Garth 


> Garth
> 
> > --
> > Anders
> 
> 
> 
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