Python coprocessing example

This example is used to demonstrate how the co-processing library can be used with a python based simulation code. Note that this example requires MPI to be available on your system as well as pyMPI to initialize and finalize MPI from the python script. The executable takes in a python co-processing script and a number of time steps to be run for. Note to remember to set your system environment properly. See [[1]] for details.

Serial python driver code

<source lang="python"> import sys if len(sys.argv) != 3:

   print "command is 'python <python driver code> <script name> <number of time steps>'"
   sys.exit(1)

import paraview import paraview.vtk as vtk

def coProcess(grid, time, step, scriptname):

   import vtkCoProcessorPython # import libvtkCoProcessorPython for older PV versions
   if scriptname.endswith(".py"):
       scriptname = scriptname[0:len(scriptname)-3]#scriptname.rstrip(".py")
   try:
       cpscript = __import__(scriptname)
   except:
       print 'Cannot find ', scriptname, ' -- no coprocessing will be performed.'
       return

   datadescription = vtkCoProcessorPython.vtkCPDataDescription()
   datadescription.SetTimeData(time, step)
   datadescription.AddInput("input")
   cpscript.RequestDataDescription(datadescription)
   inputdescription = datadescription.GetInputDescriptionByName("input")
   if inputdescription.GetIfGridIsNecessary() == False:
       return

   inputdescription.SetGrid(grid)
   inputdescription.SetWholeExtent(grid.GetWholeExtent())
   cpscript.DoCoProcessing(datadescription)

try:

   numsteps = int(sys.argv[2])

except ValueError:

   print 'the last argument should be a number, setting the number of time steps to 10'
   numsteps = 10

for step in range(numsteps):

   # assume simulation time starts at 0
   time = step/float(numsteps)

   # create the input to the coprocessing library.  normally
   # this will come from the adaptor
   imageData = vtk.vtkImageData()
   imageData.SetOrigin(0, 0, 0)
   imageData.SetSpacing(.1, .1, .1)
   imageData.SetExtent(0, 10, 0, 12, 0, 12)
   imageData.SetWholeExtent(imageData.GetExtent())
   pointArray = vtk.vtkDoubleArray()
   pointArray.SetNumberOfTuples(imageData.GetNumberOfPoints())
   for i in range(imageData.GetNumberOfPoints()):
       pointArray.SetValue(i, i)
   pointArray.SetName("pointData")
   imageData.GetPointData().AddArray(pointArray)

   # "perform" coprocessing.  results are outputted only if
   # the passed in script says we should at time/step
   coProcess(imageData, time, step, sys.argv[1])

</source>

Parallel python driver code

<source lang="python"> import sys if len(sys.argv) != 3:

 print "command is 'mpirun -np <#> pyMPI parallelexample.py <script name> <number of time steps>'"
 sys.exit(1)

import paraview import paraview.vtk as vtk

import mpi mpi.initialized()

import paraview import libvtkParallelPython import paraview.simple import vtk

1. set up ParaView to properly use MPI

pm = paraview.servermanager.vtkProcessModule.GetProcessModule() globalController = pm.GetGlobalController() if globalController == None or globalController.IsA("vtkDummyController") == True:

 globalController = vtk.vtkMPIController()
 globalController.Initialize()
 globalController.SetGlobalController(globalController)

def coProcess(grid, simtime, simstep, scriptname):

 # the name of the library was changed so for previous version of ParaView
 # you have to import libvtkCoProcessorPython instead of vtkCoProcessorPython
 #import libvtkCoProcessorPython as vtkCoProcessorPython
 import vtkCoProcessorPython
 if scriptname.endswith(".py"):
   scriptname = scriptname[0:len(scriptname)-3]#scriptname.rstrip(".py")
 try:
   cpscript = __import__(scriptname)
 except:
   print 'Cannot find ', scriptname, ' -- no coprocessing will be performed.'
   return

 datadescription = vtkCoProcessorPython.vtkCPDataDescription()
 datadescription.SetTimeData(simtime, simstep)
 datadescription.AddInput("input")
 cpscript.RequestDataDescription(datadescription)
 inputdescription = datadescription.GetInputDescriptionByName("input")
 if inputdescription.GetIfGridIsNecessary() == False:
   return
 import paraview.simple
 extents = grid.GetWholeExtent()
 inputdescription.SetWholeExtent(extents)
 inputdescription.SetGrid(grid)
 cpscript.DoCoProcessing(datadescription)

def createGrid(time):

 """
 Create a vtkImageData and a point data field called 'pointData'.
 time is used to make the field time varying. The grid is
 partitioned in slices in the x-direction here but that is
 not required.
 """
 imageData = vtk.vtkImageData()
 imageData.Initialize()
 imageData.SetOrigin(0, 0, 0)
 imageData.SetSpacing(.1, .1, .1)
 imageData.SetWholeExtent(0, 2*mpi.size, 0, 5, 0, 5)
 imageData.SetExtent(mpi.rank*2, (mpi.rank+1)*2, 0, 5, 0, 5)
 pointArray = vtk.vtkDoubleArray()
 pointArray.SetNumberOfTuples(imageData.GetNumberOfPoints())
 for i in range(imageData.GetNumberOfPoints()):
   pointArray.SetValue(i, i+time)
 pointArray.SetName("pointData")
 imageData.GetPointData().AddArray(pointArray)

 return imageData

try:

 numsteps = int(sys.argv[2])

except ValueError:

 print 'the last argument should be a number, setting the number of time steps to 10'
 numsteps = 10

for step in range(numsteps):

 # assume simulation time starts at 0
 time = step/float(numsteps)

 # create the input to the coprocessing library.  normally
 # this will come from the adaptor
 grid = createGrid(time)

 # "perform" coprocessing.  results are outputted only if
 # the passed in script says we should at time/step
 coProcess(grid, time, step, sys.argv[1])

globalController.SetGlobalController(None) globalController = None mpi.finalized() </source>

Sample coprocessing script

<source lang="python"> try: paraview.simple except: from paraview.simple import *

def RequestDataDescription(datadescription):

   "Callback to populate the request for current timestep"
   timestep = datadescription.GetTimeStep()
   input_name = 'input'
   if (timestep % 1 == 0) :
       datadescription.GetInputDescriptionByName(input_name).AllFieldsOn()
       datadescription.GetInputDescriptionByName(input_name).GenerateMeshOn()
   else:
       datadescription.GetInputDescriptionByName(input_name).AllFieldsOff()
       datadescription.GetInputDescriptionByName(input_name).GenerateMeshOff()

def DoCoProcessing(datadescription):

   "Callback to do co-processing for current timestep"
   cp_writers = []
   timestep = datadescription.GetTimeStep()

   grid = CreateProducer( datadescription, "input" )
   ImageWriter1 = CreateWriter( XMLPImageDataWriter, "input_grid_%t.pvti", 1, cp_writers )

   for writer in cp_writers:
       if timestep % writer.cpFrequency == 0:
           writer.FileName = writer.cpFileName.replace("%t", str(timestep))
           writer.UpdatePipeline()

   # explicitly delete the proxies -- we do it this way to avoid problems with prototypes
   tobedeleted = GetNextProxyToDelete()
   while tobedeleted != None:
       Delete(tobedeleted)
       tobedeleted = GetNextProxyToDelete()

def GetNextProxyToDelete():

   proxyiterator = servermanager.ProxyIterator()
   for proxy in proxyiterator:
       group = proxyiterator.GetGroup()
       if group.find("prototypes") != -1:
           continue
       if group != 'timekeeper' and group.find("pq_helper_proxies") == -1 :
           return proxy
   return None

def CreateProducer(datadescription, gridname):

   "Creates a producer proxy for the grid"
   if not datadescription.GetInputDescriptionByName(gridname):
       raise RuntimeError, "Simulation input name '%s' does not exist" % gridname
   grid = datadescription.GetInputDescriptionByName(gridname).GetGrid()
   producer = PVTrivialProducer()
   producer.GetClientSideObject().SetOutput(grid)
   if grid.IsA("vtkImageData") == True or grid.IsA("vtkStructuredGrid") == True or grid.IsA("vtkRectilinearGrid") == True:
       extent = datadescription.GetInputDescriptionByName(gridname).GetWholeExtent()
       producer.WholeExtent= [ extent[0], extent[1], extent[2], extent[3], extent[4], extent[5] ]
   producer.UpdatePipeline()
   return producer

def CreateWriter(proxy_ctor, filename, freq, cp_writers):

   writer = proxy_ctor()
   writer.FileName = filename
   writer.add_attribute("cpFrequency", freq)
   writer.add_attribute("cpFileName", filename)
   cp_writers.append(writer)
   return writer

</source>