[Insight-users] parallelization

[Bill Lorensen]

Are you sure your HPC facility allows you to get more than one
processor? Have you tried a small example on a local machine with
multiple processors?

Bill

On Fri, Sep 4, 2009 at 11:51 AM, Mauro Maiorca<mauromaiorca at gmail.com> wrote:
> 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
>>>
>>
>