[Paraview] non-interactive viz on cluster

Sun Jul 26 11:30:50 EDT 2015

Hi Dave, All

I will work through the Python shell of the GUI in the next few days, but I need to do a satisfactory viz now.

I may have a working solution which is not perfect.

Looking into the mailing list's archives and doing a general google search, I found that Delete 'ing

the view and the object makes it easier on the memory, and I get a fast viz simulation.

However, the viz does progressively slow down.  Files 1 to 100 come out at 50 per second.

Files 2000 to 2100 come out 10 per second.

cheers

Sanjay

________________________________
From: David E DeMarle <dave.demarle at kitware.com>
Sent: 25 July 2015 08:34
To: Kharche, Sanjay
Cc: paraview at paraview.org
Subject: Re: [Paraview] non-interactive viz on cluster

Try to do this with some similar data in the python GUI's Tools->Python Shell on your local machine.

That way you get tab completion and can see things happen in the GUI to help you learn the syntax.

David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909

On Sat, Jul 25, 2015 at 4:29 PM, Kharche, Sanjay <S.R.Kharche at exeter.ac.uk<mailto:S.R.Kharche at exeter.ac.uk>> wrote:

that was one of the combinations I tried, and it didnt work.

I am looking at the ParaView wiki right now. Appareltly there is a Delete(XX)

which should be used to delete objects. I am trying to work out what to

Delete and what not to delete.

________________________________
From: David E DeMarle <dave.demarle at kitware.com<mailto:dave.demarle at kitware.com>>
Sent: 25 July 2015 08:24

To: Kharche, Sanjay
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Subject: Re: [Paraview] non-interactive viz on cluster

You are making a new reader, but never connecting it to the View.

not:
  HumanSAN000001_vtk = LegacyVTKReader( FileNames=['HumanSAN%06i.vtk' % (j)] )
rather
  HumanSAN000001_vtk.FileNames=['HumanSAN%06i.vtk' % (j)]

try that

David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909<tel:518-881-4909>

On Sat, Jul 25, 2015 at 4:18 PM, Kharche, Sanjay <S.R.Kharche at exeter.ac.uk<mailto:S.R.Kharche at exeter.ac.uk>> wrote:

I think I started celebrations too soon. The images are identical to the

first image. I have tried a few combinations, but could not find any solution.

The script:

try: paraview.simple
except: from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()

i = 1
RenderView1 = GetRenderView()
HumanSAN000001_vtk = LegacyVTKReader( FileNames=['HumanSAN%06i.vtk' % (i)] )
RenderView1.CenterAxesVisibility = 0
RenderView1.OrientationAxesVisibility = 0
RenderView1.Background2 = [0.0, 0.0, 0.16470588235294117]
RenderView1.Background = [1.0, 1.0, 1.0]
DataRepresentation1 = Show()
DataRepresentation1.ScalarOpacityUnitDistance = 2.184824466829962
DataRepresentation1.Representation = 'Outline'
DataRepresentation1.EdgeColor = [0.0, 0.0, 0.5000076295109483]
RenderView1.CenterOfRotation = [63.5, 63.5, 59.0]
a1_voltage_PVLookupTable = GetLookupTableForArray( "voltage", 1, NanColor=[0.25, 0.0, 0.0], RGBPoints=[0.0, 0.23, 0.299, 0.754, 1.0, 0.7059976962405788, 0.016126465515202103, 0.15000112339188484], VectorMode='Magnitude', ColorSpace='Diverging', LockScalarRange=1 )
a1_voltage_PiecewiseFunction = CreatePiecewiseFunction()
RenderView1.CameraPosition = [63.5, -351.65487519135064, 59.0]
RenderView1.CameraViewUp = [0.0, 0.0, 1.0]
RenderView1.CameraFocalPoint = [63.5, 63.5, 59.0]
RenderView1.CameraClippingRange = [284.63832643943715, 580.4496983192209]
RenderView1.CameraParallelScale = 107.44998836668155
DataRepresentation1.Representation = 'Volume'
DataRepresentation1.ScalarOpacityFunction = a1_voltage_PiecewiseFunction
DataRepresentation1.ColorArrayName = 'voltage'
DataRepresentation1.LookupTable = a1_voltage_PVLookupTable
Render()
WriteImage("Endo_dir_%06i.png" % (i))
for j in range (2,3998):
    HumanSAN000001_vtk = LegacyVTKReader( FileNames=['HumanSAN%06i.vtk' % (j)] )
    a1_voltage_PVLookupTable = GetLookupTableForArray( "voltage", 1, NanColor=[0.25, 0.0, 0.0], RGBPoints=[0.0, 0.23, 0.299, 0.754, 1.0, 0.7059976962405788, 0.016126465515202103, 0.15000112339188484], VectorMode='Magnitude', ColorSpace='Diverging', LockScalarRange=1 )
    Render()
    WriteImage("Endo_dir_%06i.png" % (j))

________________________________
From: David E DeMarle <dave.demarle at kitware.com<mailto:dave.demarle at kitware.com>>
Sent: 25 July 2015 03:47
To: Kharche, Sanjay
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Subject: Re: [Paraview] non-interactive viz on cluster

I think your memory usage is growing with each iteration, Try moving everything out of the loop and then just changing what you have to in the fixed pipeline inside the loop.

i = 415
RenderView1 = GetRenderView()
...
Render()
WriteImage("Endo_dir_%06i.png" % (i))
for i in range(416...):
   HumanSAN000001_vtk.FileName='HumanSAN%06i.vtk' % (i)
   a1_voltage_PVLookupTable = GetLookupTableForArray( "voltage", 1, NanColor=[0.25, 0.0, 0.0], RGBPoints=[0.0, 0.23, 0.299, 0.754, 1.0, 0.7059976962405788, 0.016126465515202103, 0.15000112339188484], VectorMode='Magnitude', ColorSpace='Diverging', LockScalarRange=1 )
   Render()
   WriteImage...

David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909<tel:518-881-4909>

On Sat, Jul 25, 2015 at 11:30 AM, Kharche, Sanjay <S.R.Kharche at exeter.ac.uk<mailto:S.R.Kharche at exeter.ac.uk>> wrote:

Dear David, All

I am now using VNC and got my scripts to do non-interactive viz, i.e.
making of png files using the script below. However, I have a question
regarding efficiency of the run.

As of now, I am doing a serial run. The first several png files are produced
swiftly. However, eventually, the run slows down considerably.
e.g. files 1 to 200 are at a rate of 10 per second
but files 300 to 35 are almost 1 every 2 minutes.#

Any ideas why this is, and how to rectify this? Isthis a memory leak and if so
how not do introduce this when making the .py script using the trace option
in the GUI?

cheers
Sanjay

line in pbs script:

# now any X11 traffic is sent to the VNC server.
pvbatch --use-offscreen-rendering sk3d.py &

my sk3d.py script:

try: paraview.simple
except: from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()

for i in range (415,3998):
    RenderView1 = GetRenderView()
    HumanSAN000001_vtk = LegacyVTKReader( FileNames=['HumanSAN%06i.vtk' % (i)] )
    RenderView1.CenterAxesVisibility = 0
    RenderView1.OrientationAxesVisibility = 0
    RenderView1.Background2 = [0.0, 0.0, 0.16470588235294117]
    RenderView1.Background = [1.0, 1.0, 1.0]
    DataRepresentation1 = Show()
    DataRepresentation1.ScalarOpacityUnitDistance = 2.184824466829962
    DataRepresentation1.Representation = 'Outline'
    DataRepresentation1.EdgeColor = [0.0, 0.0, 0.5000076295109483]
    RenderView1.CenterOfRotation = [63.5, 63.5, 59.0]
    a1_voltage_PVLookupTable = GetLookupTableForArray( "voltage", 1, NanColor=[0.25, 0.0, 0.0], RGBPoints=[0.0, 0.23, 0.299, 0.754, 1.0, 0.7059976962405788, 0.016126465515202103, 0.15000112339188484], VectorMode='Magnitude', ColorSpace='Diverging', LockScalarRange=1 )
    a1_voltage_PiecewiseFunction = CreatePiecewiseFunction()
    RenderView1.CameraPosition = [63.5, -351.65487519135064, 59.0]
    RenderView1.CameraViewUp = [0.0, 0.0, 1.0]
    RenderView1.CameraFocalPoint = [63.5, 63.5, 59.0]
    RenderView1.CameraClippingRange = [284.63832643943715, 580.4496983192209]
    RenderView1.CameraParallelScale = 107.44998836668155
    DataRepresentation1.Representation = 'Volume'
    DataRepresentation1.ScalarOpacityFunction = a1_voltage_PiecewiseFunction
    DataRepresentation1.ColorArrayName = 'voltage'
    DataRepresentation1.LookupTable = a1_voltage_PVLookupTable
    Render()
    WriteImage("Endo_dir_%06i.png" % (i))

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