[Insight-users] Itk 4 - Multithreading over multiple nodes of linux high performance computer
Tim Allman
dr.tim.allman at gmail.com
Thu Oct 3 18:17:36 EDT 2013
Don't buy the hard copy. It is badly out of date and incomplete, so much
so that I always refer to the pdf version. Kitware really shouldn't be
selling this anymore.
Tim
On 13-10-03 02:18 PM, Bilal Tahir wrote:
>
> Dear Matt,
>
> Many thanks for this. It will be an honour to contribute to ITK. So
> far, I have mostly been using precompiled binaries of software based
> on ITK but I would like to delve deeper into what ITK can offer for my
> applications. In particular, for my radiotherapy based applications as
> I am a radiotherapy physicist.
>
> I was going to have my institution order a hard copy of the ITK
> Version 2.4 software guide but I found a very recent pdf version for
> ITK 4.4 on sourceforge so I guess that is the correct document that I
> should be working with to get up to speed?
>
> All the best
>
> Bilal Tahir,
> Weston Park Hospital / University of Sheffield
>
> On 3 Oct 2013 17:07, "Matt McCormick" <matt.mccormick at kitware.com
> <mailto:matt.mccormick at kitware.com>> wrote:
>
> Hi Bilal,
>
> We have started to merge these patches, and we will continue to merge
> them in the coming weeks. Instruction for downloading the Git version
> can be found here:
>
> http://www.itk.org/Wiki/ITK/Git/Download
>
> To get involved in the patch review and development, it would be good
> to join the code review hangouts announced on the ITK Bar Camp G+
> Community:
>
> https://plus.google.com/communities/111375098792764998322/stream/a1cf9df1-06f5-4abd-9142-bd8149f6b191
>
> Thanks,
> Matt
>
> On Thu, Oct 3, 2013 at 2:21 PM, Bilal Tahir
> <bilalahmedtahir at googlemail.com
> <mailto:bilalahmedtahir at googlemail.com>> wrote:
> > Dear Hans,
> >
> > Many thanks for your reply. I would like to try your patches for
> > antsRegistration to see if it speeds up my pipelines using the SyN
> > algorithm. I am new to the process of applying patches so any
> guidance on
> > what steps are required would be greatly appreciated.
> >
> > Best wishes
> >
> > Bilal
> >
> > On 3 Oct 2013 14:58, "Johnson, Hans J" <hans-johnson at uiowa.edu
> <mailto:hans-johnson at uiowa.edu>> wrote:
> >>
> >> Bilal,
> >>
> >> Unfortunately the answer is that you can not take advantage of
> multiple
> >> nodes or OpenMP. The reality is that in many cases ITK does
> not efficiently
> >> take advantage of the parallelism that is available in modern
> multi-core
> >> computers. My experience is that it often scales well to 4
> processors, but
> >> rarely takes full advantage of the resources for 16 processors.
> This is an
> >> ongoing area of improvement.
> >>
> >> Of particular interest is the antsRegistration example. I have been
> >> working on improving the performance of this tool in these
> patch sets
> >>
> http://review.source.kitware.com/#/q/status:open+project:ITK+branch:master+topic:RemoveFalseSharing,n,z
> >>
> >> In some cases I have been able to improve the perforce by 70x by
> >> identifying the ways to better utilize the existing threads.
> It is my
> >> belief that you would benefit more from helping improve the
> utilization of
> >> the existing threads than to try to add more threads across
> different
> >> platforms.
> >>
> >> Regards,
> >> Hans
> >>
> >> From: Bilal Tahir <bilalahmedtahir at googlemail.com
> <mailto:bilalahmedtahir at googlemail.com>>
> >> Date: Thursday, October 3, 2013 8:50 AM
> >> To: "insight-users at itk.org <mailto:insight-users at itk.org>"
> <insight-users at itk.org <mailto:insight-users at itk.org>>
> >> Subject: [Insight-users] Itk 4 - Multithreading over multiple
> nodes of
> >> linux high performance computer
> >>
> >> Dear ITK community,
> >>
> >> This is my first email on this mail base so please bear with me.
> >>
> >> My query is regarding multithreading over multiple cores. In
> our high
> >> performance Linux Sun Grid Engine, we have 16 CPUs per node.
> Currently I use
> >> image registration software based on ITK 4 (e.g. ants Registration,
> >> Elastix) and set the environment variable
> >> ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS and openMP options in my
> bash scripts
> >> to 16.
> >>
> >> However, some of our Linux administrators suggested to run
> parallel across
> >> multiple nodes to increase the total number of CPUs. Is this
> possible with
> >> ITK 4 and does it require something like the MPI framework?
> Without some
> >> form of message passing I would imagine it will be difficult to
> envisage
> >> taking advantage of multiple nodes from a single program. I
> heard there were
> >> some discussions about MPI implementations of ITK 4 but nothing has
> >> materialised yet.
> >>
> >> Could anyone shed any light as to whether it is feasible to run
> ITK 4 over
> >> several nodes and how to go about doing this?
> >>
> >> Best wishes
> >>
> >> Bilal
> >>
> >>
> >>
> >> ________________________________
> >> Notice: This UI Health Care e-mail (including attachments) is
> covered by
> >> the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is
> >> confidential and may be legally privileged. If you are not the
> intended
> >> recipient, you are hereby notified that any retention,
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> >> distribution, or copying of this communication is strictly
> prohibited.
> >> Please reply to the sender that you have received the message
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> >> delete it. Thank you.
> >> ________________________________
> >
> >
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>
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--
Tim Allman, Ph.D.
35 Margaret Street,
Guelph Ontario N1E 5R6
Canada
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