[Insight-users] parallelization

[Mauro Maiorca]

I compile with this:
$ c++ -v
Using built-in specs.
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu
4.3.3-5ubuntu4'
--with-bugurl=file:///usr/share/doc/gcc-4.3/README.Bugs
--enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr
--enable-shared --with-system-zlib --libexecdir=/usr/lib
--without-included-gettext --enable-threads=posix --enable-nls
--with-gxx-include-dir=/usr/include/c++/4.3 --program-suffix=-4.3
--enable-clocale=gnu --enable-libstdcxx-debug --enable-objc-gc
--enable-mpfr --with-tune=generic --enable-checking=release
--build=x86_64-linux-gnu --host=x86_64-linux-gnu
--target=x86_64-linux-gnu
Thread model: posix
gcc version 4.3.3 (Ubuntu 4.3.3-5ubuntu4)

I execute in a High Performance Computing (HPC) facility with linux (I
launch the program using a predefined Portable Batch System script,
where I can choose the number of processors for the task).

cheers,
Mauro


On Sat, Sep 5, 2009 at 1:30 AM, Bill Lorensen<bill.lorensen at gmail.com> wrote:
> What hardware, OS and compiler are you using?
>
> On Fri, Sep 4, 2009 at 7:39 AM, Mauro Maiorca<mauromaiorca at gmail.com> wrote:
>> Hi Dan & list,
>>
>> I'm using
>> MattesMutualInformationImageToImageMetric
>> LinearInterpolateImageFunction
>>
>> thanks for mentioning the IJ, it's an excellent source of info indeed!
>> However, according to the article "Optimizing ITK’s Registration
>> Methods for Multi-processor, Shared-Memory Systems" my code should be
>> optimized.
>> I would be really pleased to see any improvement on a multicore
>> architecture (even because I'm planning to register quite big volumes
>> using MMI).
>>
>> Do you have any other clue/test/whatever to solve the problem?
>>
>>
>> cheers,
>> Mauro
>>
>>
>> On Fri, Sep 4, 2009 at 8:59 PM, Dan Mueller<dan.muel at gmail.com> wrote:
>>> Hi Mauro,
>>>
>>> Please report to the list what registration components you are using.
>>>
>>> ie. Linear Interpolator, Mattes Mutual Information Metric, Regular
>>> Step Gradient Descent.
>>>
>>> Only _some_ components have been optimized for parallelization. For
>>> which, please refer to the IJ article or the Code/Review folder (look
>>> for itkOpt*).
>>>
>>> Hope this helps.
>>>
>>> Cheers, Dan
>>>
>>> 2009/9/4 Mauro Maiorca <mauromaiorca at gmail.com>:
>>>> Thankyou very much Dan, John, and  Michael,
>>>>
>>>> I compiled again ITK with:
>>>> ITK_USE_OPTIMIZED_REGISTRATION_METHODS = ON
>>>> And still the same excecution time!
>>>>
>>>> I sent the task to only one processor (exec time 56'14") , four
>>>> processors (56'57"), and 8 processors (56'16"). Pretty much the same
>>>> time, no matter the number of processors involved in the computation.
>>>>
>>>> I also tried to add this to the ccmake of my application
>>>> CMAKE_CXX_FLAGS   -lpthread
>>>> It doesn't make any (significant) difference at all!
>>>>
>>>> any other clue?
>>>> cheers,
>>>> Mauro
>>>>
>>>>
>>>>
>>>> On Fri, Sep 4, 2009 at 1:10 AM, Dan Mueller<dan.muel at gmail.com> wrote:
>>>>> Hi Mauro,
>>>>>
>>>>> To make use of multiple cores for registration, please set the CMake variable
>>>>>    ITK_USE_OPTIMIZED_REGISTRATION_METHODS = ON
>>>>>
>>>>> This allows some interpolators/metrics to utilize multiple cores. For
>>>>> full details, please see:
>>>>>    http://www.insight-journal.org/browse/publication/172
>>>>>
>>>>> Hope this helps.
>>>>>
>>>>> Regards, Dan
>>>>>
>>>>> 2009/9/3 Mauro Maiorca <mauromaiorca at gmail.com>:
>>>>>> Hello list,
>>>>>>
>>>>>> I'm wondering whether the ITK code is optimized for running on a
>>>>>> multiprocessor machine?
>>>>>> I wrote a program to register 2 images but it is quite slow because of
>>>>>> many resamplings, so I'm running it on a 8 processor architecture ...
>>>>>> but no significant improvements.
>>>>>>
>>>>>> I'm using Itk 3.14 compiled (linux) with the following flags:
>>>>>>
>>>>>>  CMAKE_THREAD_LIBS                -lpthread
>>>>>>  CMAKE_USE_PTHREADS               ON
>>>>>>
>>>>>> any suggestion?
>>>>>>
>>>>>> cheers,
>>>>>> Mauro
>>>>>
>>>>
>>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://www.itk.org/mailman/listinfo/insight-users
>>
>