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

Matt McCormick matt.mccormick at kitware.com
Thu Oct 3 14:24:28 EDT 2013


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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