[Insight-users] ITK FFTW vs system FFTW

Fri Apr 12 14:27:23 EDT 2013

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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>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> --
>>>>> Unpaid intern in BillsBasement at noware dot com
>>> 
>>> 
>>> 
>>> 
>>> --
>>> Unpaid intern in BillsBasement at noware dot com
>> _____________________________________
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>> 
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> 
> _____________________________________
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> 
> Visit other Kitware open-source projects at
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> 
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> 
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