[Insight-users] ITK FFTW vs system FFTW

Simon Rit simon.rit at creatis.insa-lyon.fr
Sun Apr 14 10:20:06 EDT 2013 

Hi,
Thanks for pointing this out. Your solution also works for me and I don't
really have a preference between the two.
Simon


On Sun, Apr 14, 2013 at 2:46 PM, Johnson, Hans J <hans-johnson at uiowa.edu>wrote:

>  Simon,
>
>  This was posted last night into gerrit
> http://review.source.kitware.com/#/c/10850/3.  The patch currently on
> gerrit uses an approach very similar to yours (Based on Brad Lowekamp's
> suggestion I cast the "C" pointer, and leave "C++" pointer alone, and you
> do the opposite).
>
>  If I do not receive a negative feedback, this morning, I will merge it
> yet today.
>
>  Hans
>  From: Simon Rit <simon.rit at creatis.insa-lyon.fr>
> Date: Sunday, April 14, 2013 7:15 AM
> To: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Cc: insight-users <insight-users at itk.org>
> Subject: Re: [Insight-users] ITK FFTW vs system FFTW
>
>    Hi,
> Thanks! A few things. First, going from the latest release to HEAD, I had
> a compilation issue:
> /home/srit/src/itk4/itk/Modules/Filtering/FFT/include/
> itkFFTWHalfHermitianToRealInverseFFTImageFilter.hxx:103:5:   required
> from ‘void itk::FFTWHalfHermitianToRealInverseFFTImageFilter<TInputImage,
> TOutputImage>::BeforeThreadedGenerateData() [with TInputImage = itk::Image<std::complex<double>,
> 3u>; TOutputImage = itk::Image<double, 3u>]’
> /home/srit/src/rtk/rtk/testing/rtkdisplaceddetectortest.cxx:203:1:
> required from here
> /usr/lib/gcc/x86_64-redhat-linux/4.7.2/../../../../include/c++/4.7.2/bits/
> stl_algobase.h:329:8: erreur: incompatible types in assignment of ‘const
> std::complex<double>’ to ‘double [2]’
>
> I fixed it with a pointer cast
> diff --git a/Modules/Filtering/FFT/include/itkFFTWHalfHermitianToRealInve
> rseFFTImageFilter.hxx b/Modules/Filtering/FFT/include/
> itkFFTWHalfHermitianToRealInverseFFTImageFilter.hxx
> index 9338cb1..806d803 100644
> --- a/Modules/Filtering/FFT/include/itkFFTWHalfHermitianToRealInve
> rseFFTImageFilter.hxx
> +++ b/Modules/Filtering/FFT/include/itkFFTWHalfHermitianToRealInve
> rseFFTImageFilter.hxx
> @@ -100,7 +100,7 @@ FFTWHalfHermitianToRealInverseFFTImageFilter<
> TInputImage, TOutputImage >
>                                        !m_CanUseDestructiveAlgorithm );
>    if( !m_CanUseDestructiveAlgorithm )
>      {
> -    itk::algorithm::copy_n(inputPtr->GetBufferPointer(), totalInputSize,
>  in);
> +    itk::algorithm::copy_n((typenameFFTWProxyType::ComplexType*)inputPtr
> ->GetBufferPointer(), totalInputSize,  in);
>      }
>    FFTWProxyType::Execute( plan );
>
> Second, there is a missing parenthesis in the patch:
> /home/srit/src/itk4/lin64-dg/fftwd_configure_step.cmake:36:
> Parse error.  Function missing ending ")".  End of file reached.
>
>  Finally, the patch propagates -O3 but does not fully fix the speed
> issue. After a bit more digging, it turns out that sse2 instructions are
> not automatically activated. One must set FFTW_OPTIMIZATION_CONFIGURATION
> to "--enable-sse2". Shouldn't this be done automatically? Setting it
> fixed the compilation time.
>  Thanks again for your help,
>  Simon
>
>
> On Fri, Apr 12, 2013 at 8:27 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>wrote:
>
>> Hello,
>>
>> I have placed a patch on gerrit for review:
>>
>> http://review.source.kitware.com/#/c/10848/
>>
>> Please let us know if works for you.
>>
>> Brad
>>
>> On Apr 12, 2013, at 12:15 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
>> wrote:
>>
>> > Looking at the cmake build scripts:
>> >
>> >
>> https://github.com/Kitware/ITK/blob/master/CMake/itkExternal_FFTW.cmake#L44
>> >
>> > It looks like CMAKE_C_FLAGS_RELEASE is not getting passed.
>> >
>> > I'll see if I can take this on after lunch.
>> >
>> > Brad
>> >
>> > On Apr 12, 2013, at 11:30 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
>> wrote:
>> >
>> >> I'm not sure it's the reason: I don't expect a two fold improvement
>> >> and the system has the same version installed, 3.3.2. Are we sure that
>> >> the release flags are passed to FFTW? When I looked at the compilation
>> >> log, I don't see -O3, here is an excerpt:
>> >>
>> >> /bin/sh ../libtool --tag=CC   --mode=compile /usr/bin/cc -std=gnu99
>> >> -DHAVE_CONFIG_H -I.
>> >> -I/home/srit/src/itk4/lin64-dg/fftwd/src/fftwd/kernel -I..
>> >> -I/home/srit/src/itk4/lin64-dg/fftwd/src/fftwd/simd
>> >> -Wno-uninitialized -Wno-unused-parameter -Wall -Wcast-align
>> >> -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch
>> >> -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused
>> >> -Wwrite-strings -funit-at-a-time -Wno-strict-overflow  -MT
>> >> cpy2d-pair.lo -MD -MP -MF .deps/cpy2d-pair.Tpo -c -o cpy2d-pair.lo
>> >> /home/srit/src/itk4/lin64-dg/fftwd/src/fftwd/kernel/cpy2d-pair.c
>> >> libtool: compile:  /usr/bin/cc -std=gnu99 -DHAVE_CONFIG_H -I.
>> >> -I/home/srit/src/itk4/lin64-dg/fftwd/src/fftwd/kernel -I..
>> >> -I/home/srit/src/itk4/lin64-dg/fftwd/src/fftwd/simd -Wno-uninitialized
>> >> -Wno-unused-parameter -Wall -Wcast-align -Wdisabled-optimization
>> >> -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral
>> >> -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time
>> >> -Wno-strict-overflow -MT cpy2d-pair.lo -MD -MP -MF
>> >> .deps/cpy2d-pair.Tpo -c
>> >> /home/srit/src/itk4/lin64-dg/fftwd/src/fftwd/kernel/cpy2d-pair.c -o
>> >> cpy2d-pair.o
>> >> mv -f .deps/cpy2d-pair.Tpo .deps/cpy2d-pair.Plo
>> >> /bin/sh ../libtool --tag=CC   --mode=compile /usr/bin/cc -std=gnu99
>> >> -DHAVE_CONFIG_H -I.
>> >> -I/home/srit/src/itk4/lin64-dg/fftwd/src/fftwd/kernel -I..
>> >> -I/home/srit/src/itk4/lin64-dg/fftwd/src/fftwd/simd
>> >> -Wno-uninitialized -Wno-unused-parameter -Wall -Wcast-align
>> >> -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch
>> >> -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused
>> >> -Wwrite-strings -funit-at-a-time -Wno-strict-overflow  -MT cpy2d.lo
>> >> -MD -MP -MF .deps/cpy2d.Tpo -c -o cpy2d.lo
>> >> /home/srit/src/itk4/lin64-dg/fftwd/src/fftwd/kernel/cpy2d.c
>> >> libtool: compile:  /usr/bin/cc -std=gnu99 -DHAVE_CONFIG_H -I.
>> >> -I/home/srit/src/itk4/lin64-dg/fftwd/src/fftwd/kernel -I..
>> >> -I/home/srit/src/itk4/lin64-dg/fftwd/src/fftwd/simd -Wno-uninitialized
>> >> -Wno-unused-parameter -Wall -Wcast-align -Wdisabled-optimization
>> >> -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral
>> >> -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time
>> >> -Wno-strict-overflow -MT cpy2d.lo -MD -MP -MF .deps/cpy2d.Tpo -c
>> >> /home/srit/src/itk4/lin64-dg/fftwd/src/fftwd/kernel/cpy2d.c -o cpy2d.o
>> >> mv -f .deps/cpy2d.Tpo .deps/cpy2d.Plo
>> >>
>> >>
>> >> On Fri, Apr 12, 2013 at 5:21 PM, Bill Lorensen <
>> bill.lorensen at gmail.com> wrote:
>> >>> Looks like the fftw folks have made some efficiency improvements.
>> >>>
>> >>>
>> >>>
>> >>> On Fri, Apr 12, 2013 at 11:18 AM, Simon Rit <
>> simon.rit at creatis.insa-lyon.fr>
>> >>> wrote:
>> >>>>
>> >>>> I should have mentioned it: yes, it is!
>> >>>>
>> >>>> On Fri, Apr 12, 2013 at 5:16 PM, Bill Lorensen <
>> bill.lorensen at gmail.com>
>> >>>> wrote:
>> >>>>> Is your ITK built Release?
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>> On Fri, Apr 12, 2013 at 11:13 AM, Simon Rit
>> >>>>> <simon.rit at creatis.insa-lyon.fr>
>> >>>>> wrote:
>> >>>>>>
>> >>>>>> Hi,
>> >>>>>> We have recently observed on a fedora distribution that FFTW is two
>> >>>>>> times slower when one uses the ITK compilation
>> >>>>>> (USE_SYSTEM_FFTW:BOOL=OFF, default) than when one uses the system
>> fftw
>> >>>>>> (USE_SYSTEM_FFTW:BOOL=ON).
>> >>>>>>
>> >>>>>> We have looked for an explanation in the flags (the Fedora flags
>> are
>> >>>>>> available here
>> >>>>>> http://pkgs.fedoraproject.org/cgit/fftw.git/tree/fftw.spec)
>> >>>>>> but we have not managed to figure it out. Would someone happen to
>> have
>> >>>>>> an explanation and solution?
>> >>>>>>
>> >>>>>> Thanks in advance,
>> >>>>>> Simon
>> >>>>>> _____________________________________
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>> >>>>>
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>> >>>
>> >>>
>> >>>
>> >>>
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