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<p>Hi Dave, All</p>
<p><br>
</p>
<p>I will work through the Python shell of the GUI in the next few days, but I need to do a satisfactory viz now. </p>
<p>I may have <span style="font-size:12pt">a working solution which is not perfect.</span></p>
<p><br>
</p>
<p>Looking into the mailing list's archives and doing a general google search, I found that Delete 'ing</p>
<p>the view and the object makes it easier on the memory, and I get a fast viz simulation.</p>
<p>However, the viz does progressively slow down. Files 1 to 100 come out at 50 per second.</p>
<p>Files 2000 to 2100 come out 10 per second.</p>
<p><br>
</p>
<p>cheers</p>
<p>Sanjay</p>
<p></p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> David E DeMarle <dave.demarle@kitware.com><br>
<b>Sent:</b> 25 July 2015 08:34<br>
<b>To:</b> Kharche, Sanjay<br>
<b>Cc:</b> paraview@paraview.org<br>
<b>Subject:</b> Re: [Paraview] non-interactive viz on cluster</font>
<div> </div>
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<div dir="ltr">Try to do this with some similar data in the python GUI's Tools->Python Shell on your local machine.
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<div>That way you get tab completion and can see things happen in the GUI to help you learn the syntax.
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<div class="gmail_extra"><br clear="all">
<div>
<div class="gmail_signature">David E DeMarle<br>
Kitware, Inc.<br>
R&D Engineer<br>
21 Corporate Drive<br>
Clifton Park, NY 12065-8662<br>
Phone: 518-881-4909</div>
</div>
<br>
<div class="gmail_quote">On Sat, Jul 25, 2015 at 4:29 PM, Kharche, Sanjay <span dir="ltr">
<<a href="mailto:S.R.Kharche@exeter.ac.uk" target="_blank">S.R.Kharche@exeter.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="ltr">
<div style="font-size:12pt; color:#000000; background-color:#ffffff; font-family:Calibri,Arial,Helvetica,sans-serif">
<p>that was one of the combinations I tried, and it didnt work.</p>
<p><br>
</p>
<p>I am looking at the ParaView wiki right now. Appareltly there is a Delete(XX)</p>
<p>which should be used to delete objects. I am trying to work out what to</p>
<p>Delete and what not to delete.<br>
</p>
<br>
<br>
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<div dir="ltr"><font color="#000000" face="Calibri, sans-serif" style="font-size:11pt"><span class=""><b>From:</b> David E DeMarle <<a href="mailto:dave.demarle@kitware.com" target="_blank">dave.demarle@kitware.com</a>><br>
</span><b>Sent:</b> 25 July 2015 08:24
<div>
<div class="h5"><br>
<b>To:</b> Kharche, Sanjay<br>
<b>Cc:</b> <a href="mailto:paraview@paraview.org" target="_blank">paraview@paraview.org</a><br>
<b>Subject:</b> Re: [Paraview] non-interactive viz on cluster</div>
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<div class="h5">
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<div dir="ltr">You are making a new reader, but never connecting it to the View.
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<div><span style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">not:</span></div>
<div><span style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px"> HumanSAN000001_vtk = LegacyVTKReader( FileNames=['HumanSAN%06i.vtk' % (j)] )</span></div>
<div><font color="#000000" face="Calibri, Arial, Helvetica, sans-serif" size="3">rather</font></div>
<div><span style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px"> HumanSAN000001_vtk.FileNames=['HumanSAN%06i.vtk' % (j)]</span></div>
<div><font color="#000000" face="Calibri, Arial, Helvetica, sans-serif"><font size="3"><br>
</font></font></div>
<div><font color="#000000" face="Calibri, Arial, Helvetica, sans-serif"><font size="3">try that<br>
</font></font>
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<div class="gmail_extra"><br clear="all">
<div>
<div>David E DeMarle<br>
Kitware, Inc.<br>
R&D Engineer<br>
21 Corporate Drive<br>
Clifton Park, NY 12065-8662<br>
Phone: <a href="tel:518-881-4909" value="+15188814909" target="_blank">518-881-4909</a></div>
</div>
<br>
<div class="gmail_quote">On Sat, Jul 25, 2015 at 4:18 PM, Kharche, Sanjay <span dir="ltr">
<<a href="mailto:S.R.Kharche@exeter.ac.uk" target="_blank" title="mailto:S.R.Kharche@exeter.ac.uk
Cmd+Click or tap to follow the link">S.R.Kharche@exeter.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
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<p>I think I started celebrations too soon. The images are identical to the</p>
<p>first image. I have tried a few combinations, but could not find any solution.</p>
<p><br>
</p>
<p>The script:</p>
<p><br>
</p>
<p><span>try: paraview.simple<br>
except: from paraview.simple import *<br>
paraview.simple._DisableFirstRenderCameraReset()<br>
<br>
</span>i = 1<span><br>
RenderView1 = GetRenderView()<br>
HumanSAN000001_vtk = LegacyVTKReader( FileNames=['HumanSAN%06i.vtk' % (i)] )<br>
RenderView1.CenterAxesVisibility = 0<br>
RenderView1.OrientationAxesVisibility = 0<br>
RenderView1.Background2 = [0.0, 0.0, 0.16470588235294117]<br>
RenderView1.Background = [1.0, 1.0, 1.0]<br>
DataRepresentation1 = Show()<br>
DataRepresentation1.ScalarOpacityUnitDistance = 2.184824466829962<br>
DataRepresentation1.Representation = 'Outline'<br>
DataRepresentation1.EdgeColor = [0.0, 0.0, 0.5000076295109483]<br>
RenderView1.CenterOfRotation = [63.5, 63.5, 59.0]<br>
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
)<br>
a1_voltage_PiecewiseFunction = CreatePiecewiseFunction()<br>
RenderView1.CameraPosition = [63.5, -351.65487519135064, 59.0]<br>
RenderView1.CameraViewUp = [0.0, 0.0, 1.0]<br>
RenderView1.CameraFocalPoint = [63.5, 63.5, 59.0]<br>
RenderView1.CameraClippingRange = [284.63832643943715, 580.4496983192209]<br>
RenderView1.CameraParallelScale = 107.44998836668155<br>
DataRepresentation1.Representation = 'Volume'<br>
DataRepresentation1.ScalarOpacityFunction = a1_voltage_PiecewiseFunction<br>
DataRepresentation1.ColorArrayName = 'voltage'<br>
DataRepresentation1.LookupTable = a1_voltage_PVLookupTable<br>
Render()<br>
WriteImage("Endo_dir_%06i.png" % (i))<br>
</span>for j in range (2,3998):<br>
HumanSAN000001_vtk = LegacyVTKReader( FileNames=['HumanSAN%06i.vtk' % (j)] )<span><br>
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
)<br>
Render()<br>
</span> WriteImage("Endo_dir_%06i.png" % (j))<br>
<br>
</p>
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<br>
<div style="color:rgb(26,26,26)">
<hr style="display:inline-block; width:98%">
<div dir="ltr"><font color="#000000" face="Calibri, sans-serif" style="font-size:11pt"><span><b>From:</b> David E DeMarle <<a href="mailto:dave.demarle@kitware.com" target="_blank">dave.demarle@kitware.com</a>><br>
</span><span><b>Sent:</b> 25 July 2015 03:47<br>
</span><span><b>To:</b> Kharche, Sanjay<br>
<b>Cc:</b> <a href="mailto:paraview@paraview.org" target="_blank">paraview@paraview.org</a><br>
<b>Subject:</b> Re: [Paraview] non-interactive viz on cluster</span></font>
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<div dir="ltr">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.<br>
<br>
<br>
i = 415<br>
RenderView1 = GetRenderView()<br>
…<br>
Render()<br>
WriteImage("Endo_dir_%06i.png" % (i))<br>
for i in range(416…):<br>
HumanSAN000001_vtk.FileName='HumanSAN%06i.vtk' % (i)<br>
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
)<br>
Render()<br>
WriteImage…
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<div class="gmail_extra"><br clear="all">
<div>
<div>David E DeMarle<br>
Kitware, Inc.<br>
R&D Engineer<br>
21 Corporate Drive<br>
Clifton Park, NY 12065-8662<br>
Phone: <a href="tel:518-881-4909" value="+15188814909" target="_blank">518-881-4909</a></div>
</div>
<br>
<div class="gmail_quote">On Sat, Jul 25, 2015 at 11:30 AM, Kharche, Sanjay <span dir="ltr">
<<a href="mailto:S.R.Kharche@exeter.ac.uk" target="_blank">S.R.Kharche@exeter.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
<div dir="ltr">
<div style="font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255); font-family:Calibri,Arial,Helvetica,sans-serif">
<br>
Dear David, All<br>
<br>
I am now using VNC and got my scripts to do non-interactive viz, i.e.<br>
making of png files using the script below. However, I have a question<br>
regarding efficiency of the run.<br>
<br>
As of now, I am doing a serial run. The first several png files are produced<br>
swiftly. However, eventually, the run slows down considerably.<br>
e.g. files 1 to 200 are at a rate of 10 per second <br>
but files 300 to 35 are almost 1 every 2 minutes.#<br>
<br>
Any ideas why this is, and how to rectify this? Isthis a memory leak and if so<br>
how not do introduce this when making the .py script using the trace option<br>
in the GUI?<br>
<br>
cheers<br>
Sanjay<br>
<br>
<br>
line in pbs script:<br>
<br>
# now any X11 traffic is sent to the VNC server.<br>
pvbatch --use-offscreen-rendering sk3d.py &<br>
<br>
<br>
my sk3d.py script:<span><br>
<br>
try: paraview.simple<br>
except: from paraview.simple import *<br>
paraview.simple._DisableFirstRenderCameraReset()<br>
<br>
</span>for i in range (415,3998):<br>
RenderView1 = GetRenderView()<br>
HumanSAN000001_vtk = LegacyVTKReader( FileNames=['HumanSAN%06i.vtk' % (i)] )<br>
RenderView1.CenterAxesVisibility = 0<br>
RenderView1.OrientationAxesVisibility = 0<br>
RenderView1.Background2 = [0.0, 0.0, 0.16470588235294117]<br>
RenderView1.Background = [1.0, 1.0, 1.0]<br>
DataRepresentation1 = Show()<br>
DataRepresentation1.ScalarOpacityUnitDistance = 2.184824466829962<br>
DataRepresentation1.Representation = 'Outline'<span><br>
DataRepresentation1.EdgeColor = [0.0, 0.0, 0.5000076295109483]<br>
</span> RenderView1.CenterOfRotation = [63.5, 63.5, 59.0]<br>
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
)<br>
a1_voltage_PiecewiseFunction = CreatePiecewiseFunction()<br>
RenderView1.CameraPosition = [63.5, -351.65487519135064, 59.0]<br>
RenderView1.CameraViewUp = [0.0, 0.0, 1.0]<br>
RenderView1.CameraFocalPoint = [63.5, 63.5, 59.0]<br>
RenderView1.CameraClippingRange = [284.63832643943715, 580.4496983192209]<br>
RenderView1.CameraParallelScale = 107.44998836668155<br>
DataRepresentation1.Representation = 'Volume'<br>
DataRepresentation1.ScalarOpacityFunction = a1_voltage_PiecewiseFunction<br>
DataRepresentation1.ColorArrayName = 'voltage'<br>
DataRepresentation1.LookupTable = a1_voltage_PVLookupTable<br>
Render()<br>
WriteImage("Endo_dir_%06i.png" % (i))<br>
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