[Paraview] Volume Rendering 17GB 8.5 billion cell volume

Tue Oct 20 17:55:54 EDT 2015

Here it is. It would be great if someone else try it as well:

----Steps----
1. In src/mesa/main/config.h, there should MAX_TEXTURE_MBYTES defined. I
believe by default it was 1024 Mbytes. Please change it to 4096 or
something higher.

2.  Then Compile and Install MESA again (do not forget to set the
MESA_GL_VERSION_OVERRIDE to 3.2).

3. Compile paraview again (server)

On Tue, Oct 20, 2015 at 5:48 PM, Aashish Chaudhary <
aashish.chaudhary at kitware.com> wrote:

> 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.
>>>
>>>
>>>
>>
>>
>> _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
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>>
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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>*
>

-- 

*| 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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