[Insight-users] Itk 4 - Multithreading over multiple nodes of linux high performance computer

[Bilal Tahir]

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> 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> 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> 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>
> >> Date: Thursday, October 3, 2013 8:50 AM
> >> To: "insight-users at itk.org" <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
> >>
> >>
> >>
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