[Paraview] Volume Rendering 17GB 8.5 billion cell volume

Tue Sep 15 12:52:19 EDT 2015

I just realized you are on PV 4.3.1, that version is probably old enough
that we did not have OpenGL2 working with Mesa back then. Updating to a
more recent PV/VTK will be needed to use OpenGL2 with Mesa (I think we got
it working three or four months ago). As far as I know the 10.6 versions of
Mesa should also work fine, anything after 10.5.4 should be good.

Sorry for the confusion

Ken

Ken Martin PhD

Chairman & CFO

Kitware Inc.

28 Corporate Drive

Clifton Park NY 12065

ken.martin at kitware.com

919 869-8871 (w)

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*From:* David Trudgian [mailto:David.Trudgian at UTSouthwestern.edu]
*Sent:* Tuesday, September 15, 2015 12:43 PM
*To:* Ken Martin; paraview at paraview.org
*Subject:* RE: [Paraview] Volume Rendering 17GB 8.5 billion cell volume

Am currently using Mesa 10.5.4 as I’d seen that as a working config
mentioned somewhere on the web, so will try newer. Any reason to avoid the
10.6 series?

I guess I should also try moving to Paraview 4.4 now :-)

--
David Trudgian Ph.D.
Computational Scientist, BioHPC
UT Southwestern Medical Center
Dallas, TX 75390-9039
Tel: (214) 648-4833

*From:* Ken Martin [mailto:ken.martin at kitware.com <ken.martin at kitware.com>]
*Sent:* Monday, September 14, 2015 2:29 PM
*To:* paraview at paraview.org
*Subject:* Re: [Paraview] Volume Rendering 17GB 8.5 billion cell volume

I am not sure about the rest of the email, but the error you included is
typically caused by using too old of a version of mesa. I’m not sure about
specific driver/etc but I usually suggest trying Mesa version 10.5.5 or
later to see if that solves the issue.

Thanks

Ken

Ken Martin PhD

Chairman & CFO

Kitware Inc.

28 Corporate Drive

Clifton Park NY 12065

ken.martin at kitware.com

919 869-8871 (w)

This communication, including all attachments, contains confidential and
legally privileged information, and it is intended only for the use of the
addressee.  Access to this email by anyone else is unauthorized. If you are
not the intended recipient, any disclosure, copying, distribution or any
action taken in reliance on it is prohibited and may be unlawful. If you
received this communication in error please notify us immediately and
destroy the original message.  Thank you.

From: *David Trudgian* <David.Trudgian at utsouthwestern.edu>
Date: Mon, Sep 14, 2015 at 1:35 PM
Subject: RE: [Paraview] Volume Rendering 17GB 8.5 billion cell volume
To: Aashish Chaudhary <aashish.chaudhary at kitware.com>
Cc: Berk Geveci <berk.geveci at kitware.com>, ParaView list <
paraview at paraview.org>

I've now had chance to build paraview 4.3.1 with the OpenGL2 backend.

I've not been able to test on GPU accelerated nodes (cluster is too busy to
get enough right now), but I have also built as an OSMESA with OpenGL2
version. Unfortunately the symptoms are the same. With the largest 16GB VTI
I see wireframe etc, but switching to volume rendering results in nothing
visible in the client. No messages from the server or client. Memory usage
well below RAM in the systems. Runnning across 8 256GB 24-core nodes with
8-mpi tasks per node.

As with the OpenGL backend I go to our 9GB or 4GB downsampled VTIs and
things work as expected. Great rendering performance running across the
8-node allocation with OpenMPI and OSMESA.

I did also come across another issue. Switching back to surface view on the
16GB data I had a crash shortly after I started manipulating the view with
the mouse. I couldn't replicate this crash with the smaller datasets though.

ERROR: In
/home2/dtrudgian/paraview/ParaView-v4.3.1-source/VTK/Rendering/OpenGL2/vtkShaderProgram.cxx,
line 292
vtkShaderProgram (0x6488a60): 0:22(12): warning: extension
`GL_EXT_gpu_shader4' unsupported in fragment shader
0:130(12): error: `gl_PrimitiveID' undeclared
0:130(12): error: operands to arithmetic operators must be numeric
0:130(12): error: operands to arithmetic operators must be numeric
0:131(28): error: operator '%' is reserved in GLSL 1.10 (GLSL 1.30 or GLSL
ES 3.00 required)
0:131(22): error: cannot construct `float' from a non-numeric data type
0:131(22): error: operands to arithmetic operators must be numeric
0:131(17): error: cannot construct `vec4' from a non-numeric data type

Cheers,

--
David Trudgian Ph.D.
Computational Scientist, BioHPC
UT Southwestern Medical Center
Dallas, TX 75390-9039
Tel: (214) 648-4833

-----Original Message-----
From: David Trudgian
Sent: Thursday, September 10, 2015 10:13 AM
To: Aashish Chaudhary <aashish.chaudhary at kitware.com>
Cc: Berk Geveci <berk.geveci at kitware.com>; ParaView list <
paraview at paraview.org>
Subject: RE: [Paraview] Volume Rendering 17GB 8.5 billion cell volume

Aashish,

(sorry - didn't hit reply-all first time)

> Would it be possible for you to try OpenGL2 backend?

Yes - I can try this, but probably next week. I just change
VTK_RENDERING_BACKENDS? Do you know if OSMESA has to be built with any
particularly flags itself?

Thanks,

DT

________________________________________
From: Aashish Chaudhary [aashish.chaudhary at kitware.com]
Sent: Thursday, September 10, 2015 9:59 AM
To: David Trudgian
Cc: Berk Geveci; ParaView list
Subject: Re: [Paraview] Volume Rendering 17GB 8.5 billion cell volume

Thanks Dave. Haven' t looked at your email in detail (will do in a moment)
but another thought would be some sort of limit we are hitting on the
indices (MAX_INT or MAX_<TYPE>) being used when dealing with very large
dataset such as yours.

Would it be possible for you to try OpenGL2 backend?

- Aashish

On Thu, Sep 10, 2015 at 10:55 AM, David Trudgian <
david.trudgian at utsouthwestern.edu<mailto:david.trudgian at utsouthwestern.edu>>
wrote:
Berk (and others), thanks for your replies!

> This is pretty awesome. I am assuming that this has something to do
> with things not fitting on the GPU memory or exceeding some texture
> memory limitation. Can you provide some more details?

Sure - thanks for your help.

> * Which version of ParaView are you using?

This is with Paraview 4.3.1

> * It sounds like you have multiple GPUs and multiple nodes. What is
> the setup? Are you running in parallel with MPI?

Have tried in two ways, both are using MPI (OpenMPI/1.8.3 on an InfiniBand
FDR
network):

Setup 1) Paraview 4.3.1 pvserver is running with MPI across multiple
cluster nodes, each with a Tesla K20 GPU. Only up to 4 nodes total, each
one has a single Tesla K20. Have used various numbers of MPI tasks. The
machines are 16 physical cores, with hyper-threading on for 32 logical
cores. 256GB RAM and the Tesla K20 has 5GB.

... when this didn't work we did suspect out of GPU memory. Since we have a
limited number of GPU nodes then decided to try the CPU approach...

Setup 2) Paraview 4.3.1 rebuilt with OSMESA support, to run pvserver on a
larger number of cluster nodes without any GPUs. These are 16 or 24 core
machines with 128/256/384GB RAM. Tried various numbers of nodes (up to 16)
and MPI tasks per node, allowing for OSMESA threading per the docs/graphs
on the Paraview wiki page.

Watching the pvserver processes when running across 16 nodes I wasn't
seeing more than ~2GB RAM usage per process. Across 16 nodes I ran with 8
tasks per node, so at 2GB each this is well under the minimum of 128GB RAM
per node.

> * If you are running parallel with MPI and you have multiple GPUs per
> node, did you setup the DISPLAYs to leverage the GPUs?

As above, only 1 GPU per node, or 0 when switched to the OSMESA approach to
try with across more nodes.

As mentioned before, we can view a smaller version of the data without
issue on both GPU and OSMESA setups. I just opened a 4GB version (approx
25% of full size) using the OSMESA setup on a single node (8 MPI tasks)
without issue. The responsiveness is really great - but the 16GB file is a
no-go even scaling up across 16 nodes. The VTI itself seems fine, as slices
and surface look as expected.

Thanks again for any and all suggestions!

DT

> On Wed, Sep 9, 2015 at 5:00 PM, David Trudgian <
> david.trudgian at utsouthwestern.edu<mailto: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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--
David Trudgian Ph.D.
Computational Scientist, BioHPC
UT Southwestern Medical Center
Dallas, TX 75390-9039
Tel: (214) 648-4833<tel:%28214%29%20648-4833 <%28214%29%20648-4833>>

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

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