[Insight-developers] [Insight-users] Coda ITK

Fri Feb 13 15:43:53 EST 2009

My lab currently makes heavy use of acceleration on the Cell, and we are
looking to do more with CUDA (hopefully OpenCL as it matures).  Our take is
that accelerated code works best next to, and not inside ITK.  For instance,
run an ITK pipeline, grab the output into some CUDA code, process using
CUDA, then back into ITK.  This paradigm works quite well, though you'll
have to manage the pipeline updates manually.

This way ITK is used for what it's best at, and CUDA/OpenCL is used for what
it's best at.

$0.02,
-dan

On 2/12/09 2:19 PM, "Hua-Mei Chen" <huameichen0523 at gmail.com> wrote:

> I have seen several discussions on this issue before in this emailing list.
> 
My impression is that it is not possible or very difficult to combine CUDA
> 
and ITK for now. All I can say is that CUDA indeed is able to give you a
> 
significant speedup, but it strongly depends on the quality of your CUDA
> 
codes.

Chen

----- Original Message ----- 
From: "Marcel Weiss"
> <mweiss at cbs.mpg.de>
To: "Hua-Mei Chen" <huameichen0523 at gmail.com>
Cc:
> <insight-users at itk.org>; <insight-developers at itk.org>
Sent: Thursday, February
> 12, 2009 11:06 AM
Subject: Re: [Insight-developers] [Insight-users] Cuda
> ITK

As we ordered a new number crunching machine including a NVIDIA Tesla TM
> 
C1060 and we are planning to use it for the fast processing of our
> 
high-resolition 3D images, I´d be interested in some more statements and
> 
experiences on CUDA (pure and/or with ITK).

Would you suggest planning and
> programming new code or adjusting existing 
code?
I´m sure there is a tradeoff
> between man power needed and speed-up gained 
...

Marcel
> Weiss
Dipl.-Inf.(FH)
PhD student
Department of Neurophysics
Max Planck
> Institute for Human Cognitive and Brain Sciences

----- Original Message
> -----
From: "Hua-Mei Chen" <huameichen0523 at gmail.com>
To: "Dan Mueller"
> <dan.muel at gmail.com>, "Gaëtan Lehmann" 
<gaetan.lehmann at jouy.inra.fr>, "Badri
> Roysam" <roysam at ecse.rpi.edu>
Cc: "ITK Users" <insight-users at itk.org>, "ITK
> Developers" 
<insight-developers at itk.org>
Sent: Thursday, February 12, 2009
> 5:21:11 PM GMT +01:00 Amsterdam / Berlin / 
Bern / Rome / Stockholm /
> Vienna
Subject: Re: [Insight-developers] [Insight-users]  Cuda ITK

Well, we
> wrote some PURE CUDA code for our mutual information based
non-rigid
> registration. It did give us a significant (> 100 times for some
routines)
> speedup. But I have no idea how to use it with ITK.

Chen

----- Original
> Message ----- 
From: "Badri Roysam" <roysam at ecse.rpi.edu>
To: "Dan Mueller"
> <dan.muel at gmail.com>; "Gaëtan Lehmann"
<gaetan.lehmann at jouy.inra.fr>
Cc: "ITK
> Users" <insight-users at itk.org>; "ITK
> Developers"
<insight-developers at itk.org>
Sent: Thursday, February 12, 2009
> 8:50 AM
Subject: Re: [Insight-users] [Insight-developers] Cuda ITK

We
> invested heavily in GPUs and CUDA in my lab a couple of years ago.
> Our
practical
experience has been that these things don't work quite as we had
> imagined
from the
advertising. In other words, when we compiled our vessel
> segmentation codes
on CUDA,
we found no speedup (in some case, it was slower
> than optimized compilation
on the CPU.
It took a lot of work to get speedup
> over serial code. You have to rethink
your
code to suit a streaming
> architecture, and spend time working out the data
flows carefully.
Overall, we
> learned that the effort involved in building
"GPU versions" of existing
> routines is
manpower intensive. I am interested to know what others'
> experience has
been.

Badri Roysam
Professor, Department of Electrical,
> Computer and Systems Engineering
Associate Director, NSF Center for Subsurface
> Sensing & Imaging Systems
(CenSSIS ERC)
Co-Director, Rensselaer Center for
> Open Source Software
Rensselaer Polytechnic Institute
110 8th Street, Troy,
> New York 12180-3590, USA.
Office(JEC 7010): 518-276-8067, Assistant:
> 518-276-8525, Lab(JEC 6308):
518-276-8207, Fax: 518-276-8715
Email:
> roysam at ecse.rpi.edu, Web: http://www.ecse.rpi.edu/~roysam

----- Original
> Message -----
From: Dan Mueller [mailto:dan.muel at gmail.com]
To: Gaëtan Lehmann
> [mailto:gaetan.lehmann at jouy.inra.fr]
Cc: ITK Users
> [mailto:insight-users at itk.org], ITK
> Developers
[mailto:insight-developers at itk.org]
Subject: Re: [Insight-users]
> [Insight-developers] Cuda ITK

> Hi Gaetan,
>
> I too have been following the
> closely development of the GPGPU field
>
> http://en.wikipedia.org/wiki/Gpgpu
> and waiting for ITK to jump on board
> (unfortunately I have had little
> spare time to spearhead this myself).
>
> I
> remember speaking to Luis at a t-con last year about ITK+CUDA and he
>
> mentioned one of outcomes of the project was discovering that CUDA is
> not
> (yet) very portable (i.e. code that works on one NVIDIA card, does
> not
> necessarily work on another).
>
> If ITK is going to be GPGPU-enabled, then
> perhaps the OpenCL standard
> will provide more portability:
>
> http://en.wikipedia.org/wiki/OpenCL
>
> Obviously OpenCL is still new (version
> 1.0 approved December 8, 2008),
> but I imagine we'll start seeing supporting
> hardware soon
>     http://www.nvidia.com/object/io_1228825271885.html
>
>
> http://news.softpedia.com/news/AMD-Takes-Up-OpenCL-1-0-Puts-More-Effort-on-ATI
> -Stream-SDK-99578.shtml
> and maybe even Intel's Larrabee
>
> http://www.hpcwire.com/blogs/OpenCL_On_the_Fast_Track_33608199.html
>
> (I
> don't think NVIDIA or ATI has to date officially announced a chip
> with
> OpenCL support...I'd be happy to be proved wrong...)
>
> Because much of this
> is still speculative, it doesn't really factor
> into your discussion about
> what hardware to buy today... Just a
> warning: while CUDA is the pioneer, it
> may not be be around to see the
> real action.
>
> Cheers, Dan
>
> 2009/2/11
> Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>:
> >
> > Hi,
> >
> > We are
> currently thinking to buy a few powerful workstations to run ITK
> > in
> > my
> lab.
> > I heard of nvidia's tesla cards, and I see that some experiments
> has
> > been
> > made to use them in ITK.
> >
> >
> http://www.na-mic.org/Wiki/images/f/f9/Itk-gpu-meeting-Fall2007.ppt
> >
> > Is
> there any update since fall 2007?
> >
> > Regards,
> >
> > Gaëtan
> >
> >
> >
> --
> > Gaëtan Lehmann
> > Biologie du Développement et de la Reproduction
> >
> INRA de Jouy-en-Josas (France)
> > tel: +33 1 34 65 29 66    fax: 01 34 65 29
> 09
> > http://voxel.jouy.inra.fr  http://www.mandriva.org
> >
> http://www.itk.org  http://www.clavier-dvorak.org
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit
> other Kitware open-source projects at
>
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages
> on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
>
> Follow this link to subscribe/unsubscribe:
>
> http://www.itk.org/mailman/listinfo/insight-users
>
__________________________
> ___________
Powered by www.kitware.com

Visit other Kitware open-source
> projects at
http://www.kitware.com/opensource/opensource.html

Please keep
> messages on-topic and check the ITK FAQ
> at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to
> subscribe/unsubscribe:
http://www.itk.org/mailman/listinfo/insight-users

____
> ___________________________________________
Powered by www.kitware.com

Visit
> other Kitware open-source projects at
> 
http://www.kitware.com/opensource/opensource.html

Please keep messages
> on-topic and check the ITK FAQ at: 
http://www.itk.org/Wiki/ITK_FAQ

Follow
> this link to 
> subscribe/unsubscribe:
http://www.itk.org/mailman/listinfo/insight-developers
> 

_____________________________________
Powered by www.kitware.com

Visit
> other Kitware open-source projects
> at
http://www.kitware.com/opensource/opensource.html

Please keep messages
> on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ

Follow
> this link to 
> subscribe/unsubscribe:
http://www.itk.org/mailman/listinfo/insight-users