Paraview Visualization

An embarrassingly parallel part surface extraction script using a MPI enabled build of pvpython follows. Copy this code into a file named extractSurface.py and run it with the command:

mpirun -np numProcesses pvpython ./extractSurface.py /path/to/input/dir/someMesh.pvtu /path/to/output/dir

Assuming all goes well pvtp file and directories containing vtp files will be created in the /path/to/output/dir directory. It is critical that pvpython have MPI support. See the CCI wiki for info on the ParaView install.

Follow the CCI wiki instructions to visualize the *vtp files in Parallel on the CCI.

#### import the simple module from the paraview
from paraview.simple import *
import sys
import os
from mpi4py import MPI

#### disable automatic camera reset on 'Show'
paraview.simple._DisableFirstRenderCameraReset()

inputDir = sys.argv[2]
outputDir = sys.argv[3]
f = open(inputDir+'/'+sys.argv[1],'r')

def setUpPVTP(piece):
  # create a new 'XML Unstructured Grid Reader'
  part = XMLUnstructuredGridReader(FileName=[inputDir+'/'+piece])

  # create a new 'Extract Surface'
  surface = ExtractSurface(Input=part)

  # this is going to be REALLY hacky
  # create a temporary pvtp file, that contains the field info, but only one source
  # go in later, and put all the piece info correctly in it
  v = XMLPPolyDataWriter(FileName='temp.pvtp', Input=surface,DataMode=0)
  v.UpdatePipeline()


  Delete(surface)
  del surface

  Delete(part)
  del part

def extract(piece,id):

  # create a new 'XML Unstructured Grid Reader'
  part = XMLUnstructuredGridReader(FileName=[inputDir+'/'+piece])

  # create a new 'Extract Surface'
  surface = ExtractSurface(Input=part)
  # save data
  fn=outputDir+'/'+str(int(id/1000))+'/'+piece[:-4]+'.vtp'
  w = XMLPolyDataWriter(FileName=fn, Input=surface)
  w.UpdatePipeline()

  Delete(surface)
  del surface

  Delete(part)
  del part

def extractSet(pieces,start,end):
  for i in range(start,end):
    extract(pieces[i],i)

rank = MPI.COMM_WORLD.Get_rank()

n = MPI.COMM_WORLD.size

# read in the pvtu file
lines = f.readlines()
first = True
pieces = []
for line in lines:
  if '<Piece Source=' in line:
    pieces.append(line[15:-4])
f.close()

if(rank == 0):
  setUpPVTP(pieces[0])

if(rank == 0):
  numDir = int(len(pieces)/1000)
  if not os.path.exists(outputDir):
    os.makedirs(outputDir)
  for i in range(numDir+1):
    if not os.path.exists(outputDir+'/'+str(i)):
      os.makedirs(outputDir+'/'+str(i))

MPI.COMM_WORLD.Barrier()

# all processes can compute the split, and figure it out for themselves.  
piecesPerProc = len(pieces)/n
procSplit = []

for i in range(n):
  procSplit.append((i*(piecesPerProc),(i+1)*piecesPerProc))
# include the remainder on the last core
procSplit[n-1] = (procSplit[n-2][1],len(pieces))

extractSet(pieces,procSplit[rank][0],procSplit[rank][1])

if(rank == 0):
  temp = open('temp.pvtp','r')
  templines = temp.readlines()
  pvtp = open(outputDir+'/'+sys.argv[1][:-5]+'.pvtp','w')

  for line in templines:
    if '<Piece Source=' in line:
      break
    else:
      pvtp.write(line)

  temp.close()

  for i in range(len(pieces)):
    pvtp.write('<Piece Source="'+str(int(i/1000))+'/'+pieces[i][:-4]+'.vtp"/>\n')

  pvtp.write('</PPolyData>\n</VTKFile>\n')
  pvtp.close()
  os.system('rm temp.pvtp')