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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Berk,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks very much for looking into this. Look forward to trying things out whenever they’re ready.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">DT<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Consolas;color:black">--</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><br>
David Trudgian Ph.D.<br>
Computational Scientist, BioHPC<br>
UT Southwestern Medical Center<br>
Dallas, TX 75390-9039<br>
Tel: (214) 648-4833</span><span style="font-size:11.0pt;font-family:Consolas;color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Berk Geveci [mailto:berk.geveci@kitware.com]
<br>
<b>Sent:</b> Monday, September 28, 2015 9:58 AM<br>
<b>To:</b> David Trudgian <David.Trudgian@UTSouthwestern.edu><br>
<b>Cc:</b> ParaView Mailing List <paraview@paraview.org><br>
<b>Subject:</b> Re: [Paraview] Volume Rendering 17GB 8.5 billion cell volume<o:p></o:p></span></p>
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<p class="MsoNormal">Hi David,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I have been trying to find some cycles to check this out myself with ParaView 4.4. Thanks to hardware issues (i.e. my big workstation's disk dying), I haven't been able to. Good news is that I found issues with OSMesa + OpenGL2 that we
are working through. Give me another 1-1.5 weeks.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Best,<o:p></o:p></p>
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<p class="MsoNormal">-berk<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Mon, Sep 28, 2015 at 10:46 AM, David Trudgian <<a href="mailto:David.Trudgian@utsouthwestern.edu" target="_blank">David.Trudgian@utsouthwestern.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Berk,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Finally managed to grab an allocation of some Tesla K40 nodes on our cluster, to check GPU rendering
of the full 17GB file with 2 x 12GB GPUs. I see the same thing as I did with OSMesa rendering.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">The 9GB downsampled version works great, across 2 nodes both with a single K40. Go up to the 17GB original
file and nothing is rendered, no errors. Same behavior with OPENGL or OPENGL2 backends.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">This is all on paraview 4.3.1 still – I need to find time to build OSMesa / MPI versions of 4.4 here.
But, does 4.4. have any fixes that would be expected to affect this?</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:Consolas;color:black">--</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><br>
David Trudgian Ph.D.<br>
Computational Scientist, BioHPC<br>
UT Southwestern Medical Center<br>
Dallas, TX 75390-9039<br>
Tel: <a href="tel:%28214%29%20648-4833" target="_blank">(214) 648-4833</a></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Berk Geveci [mailto:<a href="mailto:berk.geveci@kitware.com" target="_blank">berk.geveci@kitware.com</a>]
<br>
<b>Sent:</b> Tuesday, September 15, 2015 2:43 PM<br>
<b>To:</b> David Trudgian <<a href="mailto:David.Trudgian@UTSouthwestern.edu">David.Trudgian@UTSouthwestern.edu</a>><br>
<b>Cc:</b> ParaView Mailing List <<a href="mailto:paraview@paraview.org" target="_blank">paraview@paraview.org</a>><br>
<b>Subject:</b> Re: [Paraview] Volume Rendering 17GB 8.5 billion cell volume</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hey David,<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I am hoping to have some time to play around with volume rendering and hopefully tracking this issue, one thing that I wanted to clarify: it sounds from you description that you
have a short (2 byte) value. Is that correct?<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thanks,<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">-berk<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">On Wed, Sep 9, 2015 at 5:00 PM, David Trudgian <<a href="mailto:david.trudgian@utsouthwestern.edu" target="_blank">david.trudgian@utsouthwestern.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hi,<br>
<br>
We have been experimenting with using Paraview to display very volumes from very<br>
large TIFF stacks generated by whole-brain microscopy equipment. The test stack<br>
has dimensions of 5,368x10,695x150. Stack is assembled in ImageJ from individual<br>
TIFFs, exported as a RAW and loaded into paraview. Saved as a .vti for<br>
convenience. Can view slices fine in standalone paraview client on a 256GB machine.<br>
<br>
When we attempt volume rendering on this data across multiple nodes with MPI<br>
nothing appears in the client. Surface view works as expected. On switching to<br>
volume rendering the client's display will show nothing. There are no messages<br>
from the client or servers - no output.<br>
<br>
This is happening when running pvserver across GPU nodes with NVIDIA Tesla<br>
cards, or using CPU only with OSMESA. pvserver memory usage is well below what<br>
we have on the nodes - no memory warnings/errors.<br>
<br>
Data is about 17GB, 8 billion cells. If we downsize to ~4GB or ~9GB then we can<br>
get working volume rendering. The 17GB never works regardless of scaling<br>
nodes/mpi processes. The 4/9GB will work on 1 or 2 nodes.<br>
<br>
Am confused by the lack of rendering, as we don't have memory issues, or an<br>
other messages at all. Am wondering if there are any inherent limitation, or I'm<br>
missing something stupid.<br>
<br>
Thanks,<br>
<br>
Dave Trudgian<br>
<br>
<br>
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<p align="right" style="text-align:right"><b><span style="font-size:17.0pt;font-family:"Helvetica",sans-serif;color:#0054A0;letter-spacing:-2.25pt">UT</span></b><b><span style="font-size:17.0pt;font-family:"Helvetica",sans-serif;color:#0054A0"> Southwestern</span></b>
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<p align="right" style="text-align:right"><span style="font-size:13.0pt;font-family:"Helvetica",sans-serif;color:#666D70">Medical Center</span><o:p></o:p></p>
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<p align="right" style="text-align:right"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#666D70">The future of medicine, today.</span><o:p></o:p></p>
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