[Insight-users] ITK FFTW vs system FFTW
Johnson, Hans J
hans-johnson at uiowa.edu
Sun Apr 14 10:42:30 EDT 2013
Merged! Thanks for the review Brad.
Hans
From: Simon Rit <simon.rit at creatis.insa-lyon.fr<mailto:simon.rit at creatis.insa-lyon.fr>>
Date: Sunday, April 14, 2013 9:20 AM
To: Hans Johnson <hans-johnson at uiowa.edu<mailto:hans-johnson at uiowa.edu>>
Cc: Bradley Lowekamp <blowekamp at mail.nih.gov<mailto:blowekamp at mail.nih.gov>>, Matt McCormick <matt.mccormick at kitware.com<mailto:matt.mccormick at kitware.com>>, insight-users <insight-users at itk.org<mailto:insight-users at itk.org>>
Subject: Re: [Insight-users] ITK FFTW vs system FFTW
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<mailto: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<mailto:simon.rit at creatis.insa-lyon.fr>>
Date: Sunday, April 14, 2013 7:15 AM
To: Bradley Lowekamp <blowekamp at mail.nih.gov<mailto:blowekamp at mail.nih.gov>>
Cc: insight-users <insight-users at itk.org<mailto: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/itkFFTWHalfHermitianToRealInverseFFTImageFilter.hxx b/Modules/Filtering/FFT/include/itkFFTWHalfHermitianToRealInverseFFTImageFilter.hxx
index 9338cb1..806d803 100644
--- a/Modules/Filtering/FFT/include/itkFFTWHalfHermitianToRealInverseFFTImageFilter.hxx
+++ b/Modules/Filtering/FFT/include/itkFFTWHalfHermitianToRealInverseFFTImageFilter.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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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
>>>>>> _____________________________________
>>>>>> Powered by www.kitware.com<http://www.kitware.com>
>>>>>>
>>>>>> Visit other Kitware open-source projects at
>>>>>> http://www.kitware.com/opensource/opensource.html
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>>>>>> http://www.kitware.com/products/protraining.php
>>>>>>
>>>>>> Please keep messages on-topic and check the ITK FAQ at:
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>>>>>>
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>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
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>>>
>>>
>>>
>>>
>>> --
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>> _____________________________________
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>> Visit other Kitware open-source projects at
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