Dear Matthew,
Thank you for your reply. Yes, I found that the line was determined in linux but not in Mac OSX.
Finally I managed to compile parallelized Eddy. I used clang-omp instead of GCC.
http://clang-omp.github.io/
I'm not sure about the details but some options seem different between GCC and clang, and the latter fitted better in compilation of FSL.
Briefly, my procedures were as follows:
1. Download set up script and complied clang-omp.
https://gist.github.com/palmerc/59115c29aa5703f669fc
2. Setting up include path in ~/.bash_profile (sorry, this site is in Japanese)
http://qiita.com/yasuraok/items/dfe2aa1ebb61f14706bc
3. Compile FSL from source code
This end up with whole package compilation except for ptx2, but it's OK for my purpose.
Hope this will help someone who wants Eddy parallelization in Mac.
Best,
Jun
> 差出人: Matthew Webster <[log in to unmask]>
> 件名: Re: EDDY parallelization
> 日付: 2015年9月28日 23:06:21 JST
>
>
> Hello - the config file used by your platform ( it should be $FSLDIR/config/$FSLMACHTYPE/systemvars.mk ) needs to a line setting PARALLELFLAGS:
>
> PARALLELFLAGS = -fopenmp
>
> Kind Regards
> Matthew
>
>> Dear Matthew, Jester, or anyone familiar to building FSL from source code on OSX,
>>
>> I installed gmake (GNU make ver. 4.1) and succeeded in compiling whole FSL package, except for ptx2. However again the OpenMP lines in Eddy source code were ignored, and it did not parallelize.
>> Judging from that ${FSLDIR}/build file and ${FSLDIR}/config/common/buildproj file call C++ and that C++ is linked to clang++ in OSX, I suspected changing the link to GCC, G++ or (real) C++ might solve the problem. I tried but received the attached error message which compiling Eddy.
>>
>> Could any one tell me where I'm wrong and show me the correct way of compiling Eddy on OSX?
>>
>> Jun
>>
>> 2015/09/17 23:55、Jun Miyata <[log in to unmask]> のメール:
>>
>>> Dear Matthew,
>>>
>>> Thank you very much for your help. I tried to build full FSL package and got error messages for some (please see the attached build log). But at least I seemed to succeed to build EDDY.
>>> I tried this re-built EDDY, but the processing was not parallelized. Could you guess the cause? I prepared in the following way:
>>> 1. installed the latest version of Xcode (ver.5 for Mavericks)
>>> 2. installed the latest command line tools
>>> 3. installed MacPorts
>>> 4. installed gcc5 using MacPorts (I created a link and call of gcc correctly refers to gcc5).
>>>
>>> I think so far it's OK, but I'm not so sure if I correctly installed the libraries necessary for building.
>>> GNU make: I read in a website that the make in Mac is already GNU make.
>>> GNU install: I installed coreutils from MacPorts (actually it's ginstall).
>>> expat : I installed from MacPorts.
>>> libX11: I installed xorg-libX11 through MacPorts.
>>> libGL: OpenGL is already installed in Mac.
>>> zlib: I installed from MacPorts.
>>>
>>> In addition, the environment variable omp_num_threads is not set. Is this critical?
>>>
>>> I really appreciate if I can have a feedback.
>>>
>>> Best,
>>>
>>> Jun
>>>
>>>
>>>> 差出人: Matthew Webster <[log in to unmask]>
>>>> 件名: Re: EDDY parallelization
>>>> 日付: 2015年9月16日 23:51:16 JST
>>>>
>>>>
>>>> Hello,
>>>> As you have upgraded your compiler, you probably need to do a full rebuild of FSL ( please see https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/SourceCode for more information )
>>>>
>>>> Kind Regards
>>>> Matthew
>>>>
>>>>> Dear Jesper and FSL experts,
>>>>>
>>>>> I have managed to install gcc5 on my Mavericks. I tried to build Eddy from the source, but I received error message as attached. Could you find what's wrong? I'm sorry I'm not experienced in building from the source.
>>>>> Best,
>>>>>
>>>>> Jun
>>>>> <error_log.txt>
>>>>
>>>
>>> <build.zip>
>> <make_error_log_gcc.txt>
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