David,
Thanks for your response. It's much clearer how it all works, but I'm
still unsure how it fits together.
I don't actually need to know the interprocess links -- I have a list of
blocks to read and that list needs to be split over the processors. So each
processor needs to identify itself and the total number of procs, but that's
all. So I can definitely do that with the mpi4py, I was unaware that would
work inside the filter and I didn't know the paraview.vtk.parallel existed.
I'm not actually splitting the structured data; I'm splitting the
vtkMultiBlockDataSet. So each processor is responsible for populating a
portion of the dataset. For instance, in serial when the file (say, with 8
blocks) is read, we end up with one vtkMultiBlockDataset with 8
vtkStructuredData's inside it. If I have a parallel reader (with 8
processes), I have a hunch I'll end up with 8 vtkMultiBlockDataSet's with
one vtkStructuredData under each. Is this correct? Will this cause problems
for other filters downstream? If for fun, I wanted to merge it such that
each processor still only retains it's block, but they share a common parent
vtkMultiBlockDataset, is that possible?
I appreciate your help with this. Maybe these are stupid questions
answered somewhere else, but I can't seem to find them!
Tim
----- Original Message -----
From: "David E DeMarle"<dave.dema...@kitware.com>
To: gtg0...@mail.gatech.edu
Cc: "ParaView list"<paraview@paraview.org>
Sent: Thursday, August 11, 2011 9:54:24 AM
Subject: Re: [Paraview] Programmable filter in parallel
ParaView tries to do no aggregation other than rendering onto the same
screen. Each processor is told what portion it is responsible for via
the UPDATE_EXTENT or UPDATE_PIECE/UPDATE_NUMBER_OF_PIECES keys and are
supposed to only produce what it is asked for. (See
http://paraview.org/Wiki/Writing_ParaView_Readers for more of the
story.)
Filters that need cross communication to work properly (beyond what
they can get from ghost cells) do so by accessing the
vtkMultiProcessController that connects all of the nodes in the server
(or sometimes via MPI directly but that isn't recommended).
Try the following for two means of getting a hold of the interprocess
links.
import paraview.vtk.parallel
#print(dir(paraview.vtk.parallel))
#print(dir(paraview.vtk.parallel.vtkMultiProcessController))
controller =
paraview.vtk.parallel.vtkMultiProcessController.GetGlobalController()
print controller.GetLocalProcessId()
print controller.GetNumberOfProcesses()
from mpi4py import MPI
#print(dir(MPI))
#print(help(MPI))
print MPI.COMM_WORLD.Get_rank()
print MPI.COMM_WORLD.Get_size()
Note also that there is a "feature" in the python programmable filter
that comes into play with structured data. That feature says that
structured data is not split at all by default. If you want structured
data to actually be parallel you need to put this code in your python
programmable filter.
from paraview import util
self.GetExecutive().SetExtentTranslator(self.GetExecutive().GetOutputInformation(0),
vtk.vtkExtentTranslator())
David E DeMarle
Kitware, Inc.
R&D Engineer
28 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-371-3971 x109
On Wed, Aug 3, 2011 at 11:09 AM, Tim Gallagher<tim.gallag...@gatech.edu>
wrote:
I guess I sort of answered my own question -- the entire script runs on
each processor, so I ended up with 8 copies of my data in memory (or I would
have, had I not filled the 12 GB of RAM and 20 GB of swap space and my
system crashed).
So is there some way to query the processor information? Probably
something in the RequestInformation script -- find out how many processors
there are and then the prog. filter determines based on processor ID and
number of processors what section of the data to load.
In that case, how does the aggregation of the data work? The exact
pipeline is:
DataObjectGenerator("MB{}")
ProgrammableFilter
in serial, the PF appends blocks into the input and passes that through
to the output. In parallel, that same pipeline would create a MB{} on each
CPU that gets filled with that CPU's data, but at the end of this step I
would want a single MB{} object, not NCPU MB{}'s.
Hopefully that makes sense... I've never used PV in parallel, so I'm not
sure how it all works.
Tim
----- Original Message -----
From: "Tim Gallagher"<tim.gallag...@gatech.edu>
To: "ParaView list"<paraview@paraview.org>
Sent: Wednesday, August 3, 2011 9:24:25 AM
Subject: [Paraview] Programmable filter in parallel
Hi,
I know many of the built-in readers/filters already work in parallel,
but how does one write a parallel programmable filter?
Our data files are XDMF and split into blocks of data. We have a single
XDMF file that we can read that reads all the blocks and generates a
vtkMultiBlockDataset (this works with the built in XDMF reader).
However, each block has some ghost cells around it that are needed to do
the CellDataToPointData interpolation. For large numbers of blocks, this
creates far too many grid points for our machines to load. So, I've written
a programmable filter that does:
start with empty vtkMultiBlockDataset
for each block in restart file
read block file with XDMFReader
CellDataToPointData
strip off the extra layers of cells
append to output vtkMultiBlockDataset
If I run this in parallel, what exactly is parallel? Is the reading and
CD2PD done in parallel on each block? Is none of it parallel? Ideally, I
would have the loop over blocks done in parallel, but I don't know how to
indicate that in the programmable filter (if it's possible).
Any advice would be great,
Tim
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Please keep messages on-topic and check the ParaView Wiki at:
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Follow this link to subscribe/unsubscribe:
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_______________________________________________
Powered by www.kitware.com
Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html
Please keep messages on-topic and check the ParaView Wiki at:
http://paraview.org/Wiki/ParaView
Follow this link to subscribe/unsubscribe:
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