NAMICExternalProjects

A superbuild infrastructure to build all superbuild structures

Ash nazg durbatulûk, 
ash nazg gimbatul,
Ash nazg thrakatulûk 
agh burzum-ishi krimpatul.
                - Sauron, the Abhorred

This project acts as a template to model building all other SuperBuild projects around.

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Directory layout

NAMICExternalProjects/

• CMakeLists.txt

  A file that acts as a top level switch, it runs the building of pre-requisite ExternalProjects defined in SuperBuild.cmake (where ${MyProject} is last ExternalProject to be built). This file is processed by CMake 2 times: the first time processes SuperBuild.cmake and the second time processes ${MyProject}.cmake

• Common.cmake

  Included in SuperBuild.cmake and ${MYProject}.cmake for common conditional compilation options to be set. These options must be passed to all ExternalProjects (including ${MYProject})

• SuperBuild.cmake

  Infrastructure to build all the pre-requisite packages where ${MYProject} is the last one listed

• ${MYProject}.cmake

  Standard cmake build instructions for ${MYProject}

• SuperBuild/

  A directory full of External_${extProjName}.cmake files defining how to build external dependencies.

• CMake/

  A directory of support files.

Build Instruction

1. Install Anaconda Python Environment: https://www.continuum.io/downloads

   (Nipype/BRAINS Auto Workup dependes on python 2.7v)

   $ ${conda_dir}/conda create --name namicAnacondaEnv python=2.7
   export ${conda_dir}:PATH # Add conda build on your PATH. 
   source activate namicAnacondaEnv
   

2. Install SimpleITK Against above Anaconda Python Environment: http://www.itk.org/Wiki/SimpleITK/GettingStarted

   $ conda install -c https://conda.binstar.org/simpleitk SimpleITK
   

3. Install NiPype against above Anaconda Python Environment: http://nipy.org/nipype/users/install.html

   $ pip install nipype
   

   Please check out following if you encounter any issues at this stage.

   BLAS/LAPACK for OSX:

   See https://www.continuum.io/blog/developer/mkl-optimizations-anaconda for blas/lapack if not installed.

   $ pip install mkl
   

   Scipy Issue for Mac/Linux:

   Failed building wheel for scipy

   $ conda install numpy 
   $ conda install scipy
   $ pip install nipype
   

   If that does not work try:

   Scipy Issue for Linux:

   Failed building wheel for scipy

   See http://stackoverflow.com/questions/24353267/build-wheel-for-a-package-like-scipy-lacking-dependency-declaration

   $ pip wheel numpy
   $ pip install nipype
   

4. TBB Build: https://www.threadingbuildingblocks.org/download

   Download source code

    $ cd "tbb44_20151115oss"
    $ make
    $ mv macos_intel64_clang_cc4.2.1_os10.10.4_release/ ../lib
    
    $ cd Namic_build_Dir
    $ cmake -DCMAKE_CXX_STANDARD:STRING=11 -DTBB_ROOT:PATH=/Shared/sinapse/scratch/eunyokim/src/tbb44_20151115oss  ../NAMICExternalProjects  -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.9
   

5. Build Namic against all above:

$ git clone https://github.com/BRAINSia/NAMICExternalProjects.git
$ mkdir ${build_dir_name}
$ cd ${build_dir_name}
$ ccmake ../NAMICExternalProjects
$ make

6. Additional Package Installation for BRAINS Auto Workup:

$pip install docopt
$pip install pydas
$pip install joblib
$pip install dipy
$pip install future
$pip install ipython
$pip install simplejson

7. Deactivate Anaconda environment when finished:

$ source deactivate