[Paraview] Volume Rendering 17GB 8.5 billion cell volume

Tue Oct 20 17:48:30 EDT 2015

Berk,

On Tue, Oct 20, 2015 at 4:00 PM, Berk Geveci <berk.geveci at kitware.com>
wrote:

> Hi folks,
>
> I wanted to close the loop on this. Here are my findings:
>
> * ParaView master (4.4 should also do) + OpenGL2 + NVIDIA Tesla w 12 GB
> memory: I verified that I can volume render data up to the capacity of the
> card. I could volume render a 1400x1400x1400 volume of floats.
>
> * ParaView master (4.4 should also do) + OpenGL2 + Mesa (OSMesa 11,
> llvmpipe, swrast): Mesa has some fairly small limits on 3D texture size,
> which is what we use for volume rendering. So, ~ 1000x1000x1000 will be the
> upper end of what can be done for now. In time, we will implement multiple
> textures / streaming to enable rendering of larger volumes.
>

Did you see my other email? You can change the default for OSMesa. I sent
it last week.

- Aashish

>
> Best,
> -berk
>
> On Mon, Sep 28, 2015 at 11:00 AM, David Trudgian <
> David.Trudgian at utsouthwestern.edu> wrote:
>
>> Berk,
>>
>>
>>
>> Thanks very much for looking into this. Look forward to trying things out
>> whenever they’re ready.
>>
>>
>>
>> DT
>>
>>
>>
>> --
>> David Trudgian Ph.D.
>> Computational Scientist, BioHPC
>> UT Southwestern Medical Center
>> Dallas, TX 75390-9039
>> Tel: (214) 648-4833
>>
>>
>>
>> *From:* Berk Geveci [mailto:berk.geveci at kitware.com]
>> *Sent:* Monday, September 28, 2015 9:58 AM
>>
>> *To:* David Trudgian <David.Trudgian at UTSouthwestern.edu>
>> *Cc:* ParaView Mailing List <paraview at paraview.org>
>> *Subject:* Re: [Paraview] Volume Rendering 17GB 8.5 billion cell volume
>>
>>
>>
>> Hi David,
>>
>>
>>
>> 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.
>>
>>
>>
>> Best,
>>
>> -berk
>>
>>
>>
>> On Mon, Sep 28, 2015 at 10:46 AM, David Trudgian <
>> David.Trudgian at utsouthwestern.edu> wrote:
>>
>> Hi Berk,
>>
>>
>>
>> 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.
>>
>>
>>
>> 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.
>>
>>
>>
>> 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?
>>
>>
>>
>> Thanks,
>>
>>
>>
>> --
>> David Trudgian Ph.D.
>> Computational Scientist, BioHPC
>> UT Southwestern Medical Center
>> Dallas, TX 75390-9039
>> Tel: (214) 648-4833
>>
>>
>>
>> *From:* Berk Geveci [mailto:berk.geveci at kitware.com]
>> *Sent:* Tuesday, September 15, 2015 2:43 PM
>> *To:* David Trudgian <David.Trudgian at UTSouthwestern.edu>
>> *Cc:* ParaView Mailing List <paraview at paraview.org>
>> *Subject:* Re: [Paraview] Volume Rendering 17GB 8.5 billion cell volume
>>
>>
>>
>> Hey David,
>>
>>
>>
>> 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?
>>
>>
>>
>> Thanks,
>>
>> -berk
>>
>>
>>
>> On Wed, Sep 9, 2015 at 5:00 PM, David Trudgian <
>> david.trudgian at utsouthwestern.edu> wrote:
>>
>> Hi,
>>
>> We have been experimenting with using Paraview to display very volumes
>> from very
>> large TIFF stacks generated by whole-brain microscopy equipment. The test
>> stack
>> has dimensions of 5,368x10,695x150. Stack is assembled in ImageJ from
>> individual
>> TIFFs, exported as a RAW and loaded into paraview. Saved as a .vti for
>> convenience. Can view slices fine in standalone paraview client on a
>> 256GB machine.
>>
>> When we attempt volume rendering on this data across multiple nodes with
>> MPI
>> nothing appears in the client. Surface view works as expected. On
>> switching to
>> volume rendering the client's display will show nothing. There are no
>> messages
>> from the client or servers - no output.
>>
>> This is happening when running pvserver across GPU nodes with NVIDIA Tesla
>> cards, or using CPU only with OSMESA. pvserver memory usage is well below
>> what
>> we have on the nodes - no memory warnings/errors.
>>
>> Data is about 17GB, 8 billion cells. If we downsize to ~4GB or ~9GB then
>> we can
>> get working volume rendering. The 17GB never works regardless of scaling
>> nodes/mpi processes. The 4/9GB will work on 1 or 2 nodes.
>>
>> Am confused by the lack of rendering, as we don't have memory issues, or
>> an
>> other messages at all. Am wondering if there are any inherent limitation,
>> or I'm
>> missing something stupid.
>>
>> Thanks,
>>
>> Dave Trudgian
>>
>>
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>>
>> ------------------------------
>>
>> *UT** Southwestern*
>>
>> Medical Center
>>
>> The future of medicine, today.
>>
>>
>>
>
>
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-- 

*| Aashish Chaudhary | Technical Leader         | Kitware Inc.            *
*| http://www.kitware.com/company/team/chaudhary.html
<http://www.kitware.com/company/team/chaudhary.html>*
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