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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 It is badly out of date and incomplete, so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.<br>
<br>
Tim<br>
<br>
<div class="moz-cite-prefix">On 13-10-03 02:18 PM, Bilal Tahir
wrote:<br>
</div>
<blockquote
cite="mid:CAE2VRov38T01GfDBwi=HL68sWA187iVCxQiEZFW_n6d-zk945g@mail.gmail.com"
type="cite">
<p dir="ltr">Dear Matt, </p>
<p dir="ltr">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. </p>
<p dir="ltr">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? </p>
<p dir="ltr">All the best </p>
<p dir="ltr">Bilal Tahir, <br>
Weston Park Hospital / University of Sheffield</p>
<div class="gmail_quote">On 3 Oct 2013 17:07, "Matt McCormick"
<<a moz-do-not-send="true"
href="mailto:matt.mccormick@kitware.com">matt.mccormick@kitware.com</a>>
wrote:<br type="attribution">
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Bilal,<br>
<br>
We have started to merge these patches, and we will continue
to merge<br>
them in the coming weeks. Instruction for downloading the Git
version<br>
can be found here:<br>
<br>
<a moz-do-not-send="true"
href="http://www.itk.org/Wiki/ITK/Git/Download"
target="_blank">http://www.itk.org/Wiki/ITK/Git/Download</a><br>
<br>
To get involved in the patch review and development, it would
be good<br>
to join the code review hangouts announced on the ITK Bar Camp
G+<br>
Community:<br>
<br>
<a moz-do-not-send="true"
href="https://plus.google.com/communities/111375098792764998322/stream/a1cf9df1-06f5-4abd-9142-bd8149f6b191"
target="_blank">https://plus.google.com/communities/111375098792764998322/stream/a1cf9df1-06f5-4abd-9142-bd8149f6b191</a><br>
<br>
Thanks,<br>
Matt<br>
<br>
On Thu, Oct 3, 2013 at 2:21 PM, Bilal Tahir<br>
<<a moz-do-not-send="true"
href="mailto:bilalahmedtahir@googlemail.com">bilalahmedtahir@googlemail.com</a>>
wrote:<br>
> Dear Hans,<br>
><br>
> Many thanks for your reply. I would like to try your
patches for<br>
> antsRegistration to see if it speeds up my pipelines
using the SyN<br>
> algorithm. I am new to the process of applying patches so
any guidance on<br>
> what steps are required would be greatly appreciated.<br>
><br>
> Best wishes<br>
><br>
> Bilal<br>
><br>
> On 3 Oct 2013 14:58, "Johnson, Hans J" <<a
moz-do-not-send="true" href="mailto:hans-johnson@uiowa.edu">hans-johnson@uiowa.edu</a>>
wrote:<br>
>><br>
>> Bilal,<br>
>><br>
>> Unfortunately the answer is that you can not take
advantage of multiple<br>
>> nodes or OpenMP. The reality is that in many cases
ITK does not efficiently<br>
>> take advantage of the parallelism that is available
in modern multi-core<br>
>> computers. My experience is that it often scales
well to 4 processors, but<br>
>> rarely takes full advantage of the resources for 16
processors. This is an<br>
>> ongoing area of improvement.<br>
>><br>
>> Of particular interest is the antsRegistration
example. I have been<br>
>> working on improving the performance of this tool in
these patch sets<br>
>> <a moz-do-not-send="true"
href="http://review.source.kitware.com/#/q/status:open+project:ITK+branch:master+topic:RemoveFalseSharing,n,z"
target="_blank">http://review.source.kitware.com/#/q/status:open+project:ITK+branch:master+topic:RemoveFalseSharing,n,z</a><br>
>><br>
>> In some cases I have been able to improve the
perforce by 70x by<br>
>> identifying the ways to better utilize the existing
threads. It is my<br>
>> belief that you would benefit more from helping
improve the utilization of<br>
>> the existing threads than to try to add more threads
across different<br>
>> platforms.<br>
>><br>
>> Regards,<br>
>> Hans<br>
>><br>
>> From: Bilal Tahir <<a moz-do-not-send="true"
href="mailto:bilalahmedtahir@googlemail.com">bilalahmedtahir@googlemail.com</a>><br>
>> Date: Thursday, October 3, 2013 8:50 AM<br>
>> To: "<a moz-do-not-send="true"
href="mailto:insight-users@itk.org">insight-users@itk.org</a>"
<<a moz-do-not-send="true"
href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>
>> Subject: [Insight-users] Itk 4 - Multithreading over
multiple nodes of<br>
>> linux high performance computer<br>
>><br>
>> Dear ITK community,<br>
>><br>
>> This is my first email on this mail base so please
bear with me.<br>
>><br>
>> My query is regarding multithreading over multiple
cores. In our high<br>
>> performance Linux Sun Grid Engine, we have 16 CPUs
per node. Currently I use<br>
>> image registration software based on ITK 4 (e.g. ants
Registration,<br>
>> Elastix) and set the environment variable<br>
>> ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS and openMP
options in my bash scripts<br>
>> to 16.<br>
>><br>
>> However, some of our Linux administrators suggested
to run parallel across<br>
>> multiple nodes to increase the total number of CPUs.
Is this possible with<br>
>> ITK 4 and does it require something like the MPI
framework? Without some<br>
>> form of message passing I would imagine it will be
difficult to envisage<br>
>> taking advantage of multiple nodes from a single
program. I heard there were<br>
>> some discussions about MPI implementations of ITK 4
but nothing has<br>
>> materialised yet.<br>
>><br>
>> Could anyone shed any light as to whether it is
feasible to run ITK 4 over<br>
>> several nodes and how to go about doing this?<br>
>><br>
>> Best wishes<br>
>><br>
>> Bilal<br>
>><br>
>><br>
>><br>
>> ________________________________<br>
>> Notice: This UI Health Care e-mail (including
attachments) is covered by<br>
>> the Electronic Communications Privacy Act, 18 U.S.C.
2510-2521, is<br>
>> confidential and may be legally privileged. If you
are not the intended<br>
>> recipient, you are hereby notified that any
retention, dissemination,<br>
>> distribution, or copying of this communication is
strictly prohibited.<br>
>> Please reply to the sender that you have received the
message in error, then<br>
>> delete it. Thank you.<br>
>> ________________________________<br>
><br>
><br>
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<br>
<pre class="moz-signature" cols="72">--
Tim Allman, Ph.D.
35 Margaret Street,
Guelph Ontario N1E 5R6
Canada
</pre>
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