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

[Matt McCormick]

Hi Bilal,

Welcome to the ITK community!  Your contributions are welcome and appreciated.

The community is in the process of updating the Software Guide.  The
built version on Sourceforge is more up-to-date, or it can be built
from here:

  http://itk.org/gitweb?p=ITKSoftwareGuide.git

The contribution process for the Software Guide is the same as ITK.

Thanks,
Matt

On Thu, Oct 3, 2013 at 6:18 PM, Bilal Tahir
<bilalahmedtahir at googlemail.com> 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> 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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