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

[Bilal Tahir]

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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