kameleon-plus/trunk/kameleon-plus-working/Kameleon-Anaconda.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Installing requirements with anaconda\n",
    "\n",
    "Download and install anaconda (for a lighter version install [miniconda](http://conda.pydata.org/docs/install/quick.html#miniconda-quick-install-requirements))\n",
    "\n",
    "Then, open a terminal and type \n",
    "\n",
    "    conda install boost cmake swig gcc hdf5\n",
    "    conda install -c meznom boost-python \n",
    " \n",
    "Note: meznon's boost-python supports unix and osx users only\n",
    "\n",
    "        \n",
    "### getting cdf3.5 ##\n",
    "\n",
    "Download and install cdf 3.5 from [NASA](http://cdaweb.gsfc.nasa.gov/pub/software/cdf/dist/cdf35_0_2/)\n",
    "\n",
    "### getting HDF5 ##\n",
    "Download and install HDF 5 from [HDFGroup](http://www.hdfgroup.org/HDF5/release/obtain5.html)\n",
    "\n",
    "### searching for packages ##\n",
    "Install anaconda command line client:\n",
    "```\n",
    "conda install anaconda-client\n",
    "```\n",
    "search for package:\n",
    "```\n",
    "anaconda search -t conda <packagename>\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Building Kameleon-plus from source\n",
    "\n",
    "On Yosemite, I've had success building Kameleon with these flags:\n",
    "\n",
    "* -DCMAKE_CXX_FLAGS=\"-std=c++11\" \n",
    "* -DCMAKE_C_COMPILER=/usr/bin/clang \n",
    "* -DCMAKE_CXX_COMPILER=/usr/bin/clang++ \n",
    "* -DBOOST_LIBRARYDIR=/Users/apembrok/anaconda_boost_install/lib \n",
    "* -DBOOST_INCLUDEDIR=/Users/apembrok/anaconda_boost_install/include \n",
    "* -DBoost_NO_SYSTEM_PATHS=ON \n",
    "* -DPYTHON_LIBRARY=/Users/apembrok/anaconda/lib/libpython2.7.dylib \n",
    "* -DPYTHON_INCLUDE_DIR=/Users/apembrok/anaconda/include/python2.7/ \n",
    "* -DPYTHON_EXECUTABLE=/Users/apembrok/anaconda/bin/python2.7 \n",
    "* -DBUILD_JAVA=OFF \n",
    "* -DBUILD_HDF5=OFF \n",
    "* -DCMAKE_INSTALL_PREFIX=/Users/apembrok/anaconda \n",
    "* -DINSTALL_CCMC_PYTHON_MODULE=ON"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working\n"
     ]
    }
   ],
   "source": [
    "cd ~/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "!rm -rf build\n",
    "!mkdir build"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/build\n"
     ]
    }
   ],
   "source": [
    "cd build"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Setting up build using boost \n",
    "\n",
    "From a frech conda environment\n",
    "\n",
    "    conda install -c asherp boost=1.59.0\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-- The C compiler identification is AppleClang 7.0.2.7000181\n",
      "-- The CXX compiler identification is AppleClang 7.0.2.7000181\n",
      "-- Check for working C compiler: /usr/bin/clang\n",
      "-- Check for working C compiler: /usr/bin/clang -- works\n",
      "-- Detecting C compiler ABI info\n",
      "-- Detecting C compiler ABI info - done\n",
      "-- Detecting C compile features\n",
      "-- Detecting C compile features - done\n",
      "-- Check for working CXX compiler: /usr/bin/clang++\n",
      "-- Check for working CXX compiler: /usr/bin/clang++ -- works\n",
      "-- Detecting CXX compiler ABI info\n",
      "-- Detecting CXX compiler ABI info - done\n",
      "-- Detecting CXX compile features\n",
      "-- Detecting CXX compile features - done\n",
      "\n",
      "============= Top level CMakeLists.txt ==============\n",
      "--  Kameleon-plus 6.1.0.0 build for Darwin-14.5.0\n",
      "-- Found PythonInterp: /Users/apembrok/miniconda2/envs/boost-python/bin/python2.7 (found suitable version \"2.7.11\", minimum required is \"2.7\") \n",
      "-- Found PythonLibs: /Users/apembrok/miniconda2/envs/boost-python/lib/libpython2.7.dylib (found suitable version \"2.7.11\", minimum required is \"2.7\") \n",
      "--  Python Interpreter:/Users/apembrok/miniconda2/envs/boost-python/bin/python2.7\n",
      "Getting BOOST....\n",
      "-- Boost version: 1.59.0\n",
      "-- Found the following Boost libraries:\n",
      "--   thread\n",
      "--   program_options\n",
      "--   filesystem\n",
      "--   system\n",
      "--   python\n",
      "--  BOOST_ROOT=\n",
      "--  Boost includes: /Users/apembrok/miniconda2/envs/boost-python/include\n",
      "--  Boost library directory: /Users/apembrok/miniconda2/envs/boost-python/lib\n",
      "--  Link boost: /Users/apembrok/miniconda2/envs/boost-python/lib/libboost_thread.dylib/Users/apembrok/miniconda2/envs/boost-python/lib/libboost_program_options.dylib/Users/apembrok/miniconda2/envs/boost-python/lib/libboost_filesystem.dylib/Users/apembrok/miniconda2/envs/boost-python/lib/libboost_system.dylib/Users/apembrok/miniconda2/envs/boost-python/lib/libboost_python.dylib\n",
      "Getting HDF5...\n",
      "-- Found HDF5: /Users/apembrok/miniconda2/envs/boost-python/lib/libhdf5_cpp.dylib;/Users/apembrok/miniconda2/envs/boost-python/lib/libhdf5.dylib;/Users/apembrok/miniconda2/envs/boost-python/lib/libz.dylib;/usr/lib/libdl.dylib;/usr/lib/libm.dylib (found version \"1.8.14\") \n",
      "--  HDF5 Found: will build Kameleon with HDF 5\n",
      "--  HDF_LIBRARY_DIRS:/Users/apembrok/miniconda2/envs/boost-python/lib\n",
      "--  HDF5 includes:/Users/apembrok/miniconda2/envs/boost-python/include\n",
      "--  HDF5_CXX_LIBRARIES:/Users/apembrok/miniconda2/envs/boost-python/lib/libhdf5_cpp.dylib/Users/apembrok/miniconda2/envs/boost-python/lib/libhdf5.dylib/Users/apembrok/miniconda2/envs/boost-python/lib/libz.dylib/usr/lib/libdl.dylib/usr/lib/libm.dylib\n",
      "--  Will NOT build java wrappers\n",
      "Getting CDF..\n",
      "--  retrieving shared CDF libraries\n",
      "--  Include CDF: /Applications/cdf35_0-dist/include\n",
      "--  link CDF: /Applications/cdf35_0-dist/lib/libcdf.dylib\n",
      "--  CDF Path:/Applications/cdf35_0-dist/lib\n",
      " \n",
      "============ ccmc library(src/ccmc>) ==============\n",
      "--  will build SHARED ccmc library\n",
      "--  will build STATIC ccmc library\n",
      "--  ccmc library output location = /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/libccmc.dylib\n",
      "--  Include boost: /Users/apembrok/miniconda2/envs/boost-python/include\n",
      "--  Boost library directory: /Users/apembrok/miniconda2/envs/boost-python/lib\n",
      "--  Link boost: /Users/apembrok/miniconda2/envs/boost-python/lib/libboost_thread.dylib/Users/apembrok/miniconda2/envs/boost-python/lib/libboost_program_options.dylib/Users/apembrok/miniconda2/envs/boost-python/lib/libboost_filesystem.dylib/Users/apembrok/miniconda2/envs/boost-python/lib/libboost_system.dylib/Users/apembrok/miniconda2/envs/boost-python/lib/libboost_python.dylib\n",
      "--  Include CDF: /Applications/cdf35_0-dist/include\n",
      "--  link CDF: /Applications/cdf35_0-dist/lib/libcdf.dylib\n",
      "--  Include HDF5: /Users/apembrok/miniconda2/envs/boost-python/include\n",
      "--  Link HDF5_LIBRARIES: /Users/apembrok/miniconda2/envs/boost-python/lib/libhdf5_cpp.dylib/Users/apembrok/miniconda2/envs/boost-python/lib/libhdf5.dylib/Users/apembrok/miniconda2/envs/boost-python/lib/libz.dylib/usr/lib/libdl.dylib/usr/lib/libm.dylib\n",
      "--  cmake framework path: \n",
      "--  Python Interpreter:/Users/apembrok/miniconda2/envs/boost-python/bin/python2.7\n",
      "--  boost.python library found, creating embedded readers..\n",
      "\n",
      "=========== pyKameleon(src/ccmc/pyreader) ===========\n",
      "setting up python...\n",
      "-- Found PythonInterp: /Users/apembrok/miniconda2/envs/boost-python/bin/python2.7 (found version \"2.7.11\") \n",
      "--  PYTHON_LIBRARIES:/Users/apembrok/miniconda2/envs/boost-python/lib/libpython2.7.dylib\n",
      "--  PYTHON_INCLUDE_DIRS:/Users/apembrok/miniconda2/envs/boost-python/include/python2.7\n",
      "--  PYTHON_INCLUDE_PATH:/Users/apembrok/miniconda2/envs/boost-python/include/python2.7\n",
      "--  PYTHON_EXECUTABLE:/Users/apembrok/miniconda2/envs/boost-python/bin/python2.7\n",
      "setting up boost.python\n",
      "--  Boost_LIBRARIES:/Users/apembrok/miniconda2/envs/boost-python/lib/libboost_thread.dylib/Users/apembrok/miniconda2/envs/boost-python/lib/libboost_program_options.dylib/Users/apembrok/miniconda2/envs/boost-python/lib/libboost_filesystem.dylib/Users/apembrok/miniconda2/envs/boost-python/lib/libboost_system.dylib/Users/apembrok/miniconda2/envs/boost-python/lib/libboost_python.dylib\n",
      "--  BOOST_INCLUDEDIR:/Users/apembrok/miniconda2/envs/boost-python/include\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/pyreaders/__init__.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/pyreaders/AnalyticModel.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/pyreaders/ARMS.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/pyreaders/Attribute.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/pyreaders/exPyFileReader.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/pyreaders/GeneralPyReader.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/pyreaders/generatePyKameleon.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/pyreaders/PAMHD.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/pyreaders/readPAMHD.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/pyreaders/readRCM.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/pyreaders/testReader.py\n",
      "-- Found SWIG: /Users/apembrok/miniconda2/envs/boost-python/bin/swig (found version \"3.0.8\") \n",
      "--  SWIG installed. Will attempt to build python and java wrappers.\n",
      "-- Found PythonLibs: /Users/apembrok/miniconda2/envs/boost-python/lib/libpython2.7.dylib (found version \"2.7.11\") \n",
      "--  PythonLibs and python executable found. Will build python wrapper.\n",
      "\n",
      "=========== python wrappers(src/ccmc/wrappers/python) ===========\n",
      " setting up python wrappers..\n",
      "--  SWIG_USE_FILE: /Users/apembrok/miniconda2/envs/boost-python/share/cmake-3.3/Modules/UseSWIG.cmake\n",
      "--  Include HDF5: /Users/apembrok/miniconda2/envs/boost-python/include\n",
      "--  Include boost directories: /Users/apembrok/miniconda2/envs/boost-python/include\n",
      "--  Include CDF: /Applications/cdf35_0-dist/include\n",
      "-- /Users/apembrok/miniconda2/envs/boost-python/bin/python2.7\n",
      "-- will install ccmc module to lib/python2.7/site-packages\n",
      "\n",
      "=========== c wrappers(src/ccmc/wrappers/c) ===========\n",
      "-- initializing c wrappers\n",
      "-- will build SHARED ccmc_wrapper_c library\n",
      "-- will build STATIC ccmc_wrapper_c library\n",
      "\n",
      "========== FORTRAN wrappers(src/ccmc/wrappers/fortran) ==========\n",
      "--  building fortran wrappers\n",
      "\n",
      "============ Top level CMakeLists.txt ============\n",
      "\n",
      "========== c++ examples(src/example/c++) ==========\n",
      "--  building c++ examples\n",
      "--  Include HDF5: /Users/apembrok/miniconda2/envs/boost-python/include\n",
      "--  Include boost directories: /Users/apembrok/miniconda2/envs/boost-python/include\n",
      "--  Include CDF: /Applications/cdf35_0-dist/include\n",
      "-- Include python embedding directory: /Users/apembrok/miniconda2/envs/boost-python/include/python2.7\n",
      "\n",
      "=========== c examples(src/example/c) ===========\n",
      "--  building c examples\n",
      "--  Include HDF5: /Users/apembrok/miniconda2/envs/boost-python/include\n",
      "--  Include boost directories: /Users/apembrok/miniconda2/envs/boost-python/include\n",
      "--  Include CDF: /Applications/cdf35_0-dist/include\n",
      "\n",
      "========== fortran examples(src/example/fortran) ==========\n",
      "--  building FORTRAN examples\n",
      "-- The Fortran compiler identification is GNU 4.8.5\n",
      "-- Checking whether Fortran compiler has -isysroot\n",
      "-- Checking whether Fortran compiler has -isysroot - yes\n",
      "-- Checking whether Fortran compiler supports OSX deployment target flag\n",
      "-- Checking whether Fortran compiler supports OSX deployment target flag - yes\n",
      "-- Check for working Fortran compiler: /Users/apembrok/miniconda2/envs/boost-python/bin/gfortran\n",
      "-- Check for working Fortran compiler: /Users/apembrok/miniconda2/envs/boost-python/bin/gfortran  -- works\n",
      "-- Detecting Fortran compiler ABI info\n",
      "-- Detecting Fortran compiler ABI info - done\n",
      "-- Checking whether /Users/apembrok/miniconda2/envs/boost-python/bin/gfortran supports Fortran 90\n",
      "-- Checking whether /Users/apembrok/miniconda2/envs/boost-python/bin/gfortran supports Fortran 90 -- yes\n",
      "--  Include HDF5: /Users/apembrok/miniconda2/envs/boost-python/include\n",
      "--  Include boost directories: /Users/apembrok/miniconda2/envs/boost-python/include\n",
      "--  Include CDF: /Applications/cdf35_0-dist/include\n",
      "\n",
      "=========== python examples(src/example/python) ===========\n",
      "--  building python examples\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/ARMS_test.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/grid.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/ionosphere_test.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/kameleon_test.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/pyModel_test.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/tracer.py\n",
      "--  Python example files will be kept in: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/bin/ccmc/examples/python\n",
      "--  Using CCMC module install path in scripts: sys.path.append('../../../../lib/python2.7/site-packages/ccmc/')\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/ARMS_test.py\n",
      "--  ... will install to: /Users/apembrok/miniconda2/envs/boost-python/bin/ccmc/examples/python/\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/grid.py\n",
      "--  ... will install to: /Users/apembrok/miniconda2/envs/boost-python/bin/ccmc/examples/python/\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/ionosphere_test.py\n",
      "--  ... will install to: /Users/apembrok/miniconda2/envs/boost-python/bin/ccmc/examples/python/\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/kameleon_test.py\n",
      "--  ... will install to: /Users/apembrok/miniconda2/envs/boost-python/bin/ccmc/examples/python/\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/pyModel_test.py\n",
      "--  ... will install to: /Users/apembrok/miniconda2/envs/boost-python/bin/ccmc/examples/python/\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/tracer.py\n",
      "--  ... will install to: /Users/apembrok/miniconda2/envs/boost-python/bin/ccmc/examples/python/\n",
      "-- Configuring done\n",
      "-- Generating done\n",
      "-- Build files have been written to: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/build\n"
     ]
    }
   ],
   "source": [
    "!rm -f CMakeCache.txt\n",
    "!/Users/apembrok/miniconda2/envs/boost-python/bin/cmake -DCMAKE_SHARED_LINKER_FLAGS=\"-Wl,-undefined,error\" -DCMAKE_CXX_FLAGS=\"-std=c++11 -stdlib=libc++\" -DCMAKE_MACOSX_RPATH=ON -DSWIG_EXECUTABLE=/Users/apembrok/miniconda2/envs/boost-python/bin/swig -DCMAKE_C_COMPILER=/usr/bin/clang -DCMAKE_CXX_COMPILER=/usr/bin/clang++ -DBOOST_LIBRARYDIR=/Users/apembrok/miniconda2/envs/boost-python/lib -DBOOST_INCLUDEDIR=/Users/apembrok/miniconda2/envs/boost-python/include -DBoost_NO_SYSTEM_PATHS=ON -DPYTHON_LIBRARY=/Users/apembrok/miniconda2/envs/boost-python/lib/libpython2.7.dylib -DPYTHON_INCLUDE_DIR=/Users/apembrok/miniconda2/envs/boost-python/include/python2.7 -DPYTHON_EXECUTABLE=/Users/apembrok/miniconda2/envs/boost-python/bin/python2.7 -DBUILD_JAVA=OFF -DBUILD_HDF5=ON -DCMAKE_INSTALL_PREFIX=/Users/apembrok/miniconda2/envs/boost-python -DINSTALL_CCMC_PYTHON_MODULE=ON .."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[35m\u001b[1mScanning dependencies of target ccmc_wrapper_c_static\u001b[0m\n",
      "[  2%] \u001b[0mBuilt target pyKameleon\u001b[0m\n",
      "[  2%] \u001b[32mBuilding CXX object src/ccmc/wrappers/c/CMakeFiles/ccmc_wrapper_c_static.dir/Kameleon_c.cpp.o\u001b[0m\n",
      "[  3%] \u001b[32mBuilding CXX object src/ccmc/wrappers/c/CMakeFiles/ccmc_wrapper_c_static.dir/GeneralFileReader_c.cpp.o\u001b[0m\n",
      "[ 35%] \u001b[0mBuilt target ccmc\u001b[0m\n",
      "[ 68%] \u001b[0mBuilt target ccmc_static\u001b[0m\n",
      "[ 69%] \u001b[0mBuilt target CDFReader\u001b[0m\n",
      "[ 70%] \u001b[0mBuilt target enlil_test\u001b[0m\n",
      "[ 71%] \u001b[0mBuilt target coordinate_transformation_test\u001b[0m\n",
      "[ 72%] \u001b[0mBuilt target _CCMC\u001b[0m\n",
      "[ 73%] \u001b[0mBuilt target adapt3d_test\u001b[0m\n",
      "\u001b[35m\u001b[1mScanning dependencies of target ccmc_wrapper_c\u001b[0m\n",
      "\u001b[35m\u001b[1mScanning dependencies of target mas_test\u001b[0m\n",
      "[ 74%] \u001b[0mBuilt target integrator_prog\u001b[0m\n",
      "\u001b[35m\u001b[1mScanning dependencies of target open_ggcm_test\u001b[0m\n",
      "[ 75%] \u001b[0mBuilt target kameleon_prog\u001b[0m\n",
      "[ 76%] \u001b[0mBuilt target magnetogram_test\u001b[0m\n",
      "[ 77%] \u001b[0mBuilt target lfm_test\u001b[0m\n",
      "\u001b[35m\u001b[1mScanning dependencies of target pyModel_prog\u001b[0m\n",
      "\u001b[35m\u001b[1mScanning dependencies of target swmf_iono_test\u001b[0m\n",
      "\u001b[35m\u001b[1mScanning dependencies of target time_interp\u001b[0m\n",
      "[ 77%] \u001b[32mBuilding CXX object src/example/c++/CMakeFiles/mas_test.dir/mas_test.cpp.o\u001b[0m\n",
      "[ 78%] \u001b[32mBuilding CXX object src/example/c++/CMakeFiles/open_ggcm_test.dir/open_ggcm_test.cpp.o\u001b[0m\n",
      "[ 79%] \u001b[32mBuilding CXX object src/example/c++/CMakeFiles/pyModel_prog.dir/pyModel_prog.cpp.o\u001b[0m\n",
      "[ 80%] \u001b[32mBuilding CXX object src/example/c++/CMakeFiles/swmf_iono_test.dir/swmf_iono_test.cpp.o\u001b[0m\n",
      "[ 81%] \u001b[32mBuilding CXX object src/example/c++/CMakeFiles/time_interp.dir/time_interp.cpp.o\u001b[0m\n",
      "[ 81%] \u001b[32mBuilding CXX object src/ccmc/wrappers/c/CMakeFiles/ccmc_wrapper_c.dir/GeneralFileReader_c.cpp.o\u001b[0m\n",
      "\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/wrappers/c/GeneralFileReader_c.cpp:74:8: \u001b[0m\u001b[0;1;31merror: \u001b[0m\u001b[1m\n",
      "      no member named 'var_str' in namespace 'std'\u001b[0m\n",
      "        std:: var_str = variable;\n",
      "\u001b[0;1;32m        ~~~~~ ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/wrappers/c/GeneralFileReader_c.cpp:78:59: \u001b[0m\u001b[0;1;31merror: \u001b[0m\u001b[1m\n",
      "      use of undeclared identifier 'var_str'\u001b[0m\n",
      "  ...std::vector<float>* vData = (*iter).second->getVariable(var_str);\n",
      "\u001b[0;1;32m                                                             ^\n",
      "\u001b[0m2 errors generated.\n",
      "make[2]: *** [src/ccmc/wrappers/c/CMakeFiles/ccmc_wrapper_c_static.dir/GeneralFileReader_c.cpp.o] Error 1\n",
      "make[2]: *** Waiting for unfinished jobs....\n",
      "\u001b[35m\u001b[1mScanning dependencies of target tracer_prog\u001b[0m\n",
      "make[1]: *** [src/ccmc/wrappers/c/CMakeFiles/ccmc_wrapper_c_static.dir/all] Error 2\n",
      "make[1]: *** Waiting for unfinished jobs....\n",
      "[ 82%] \u001b[32mBuilding CXX object src/ccmc/wrappers/c/CMakeFiles/ccmc_wrapper_c.dir/Kameleon_c.cpp.o\u001b[0m\n",
      "[ 83%] \u001b[32mBuilding CXX object src/example/c++/CMakeFiles/tracer_prog.dir/tracer_prog.cpp.o\u001b[0m\n",
      "\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/wrappers/c/GeneralFileReader_c.cpp:74:8: \u001b[0m\u001b[0;1;31merror: \u001b[0m\u001b[1m\n",
      "      no member named 'var_str' in namespace 'std'\u001b[0m\n",
      "        std:: var_str = variable;\n",
      "\u001b[0;1;32m        ~~~~~ ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/wrappers/c/GeneralFileReader_c.cpp:78:59: \u001b[0m\u001b[0;1;31merror: \u001b[0m\u001b[1m\n",
      "      use of undeclared identifier 'var_str'\u001b[0m\n",
      "  ...std::vector<float>* vData = (*iter).second->getVariable(var_str);\n",
      "\u001b[0;1;32m                                                             ^\n",
      "\u001b[0m2 errors generated.\n",
      "make[2]: *** [src/ccmc/wrappers/c/CMakeFiles/ccmc_wrapper_c.dir/GeneralFileReader_c.cpp.o] Error 1\n",
      "make[2]: *** Waiting for unfinished jobs....\n",
      "[ 83%] \u001b[32m\u001b[1mLinking CXX executable ../../../../bin/ccmc/examples/c++/open_ggcm_test\u001b[0m\n",
      "[ 84%] \u001b[32m\u001b[1mLinking CXX executable ../../../../bin/ccmc/examples/c++/mas_test\u001b[0m\n",
      "[ 84%] \u001b[32m\u001b[1mLinking CXX executable ../../../../bin/ccmc/examples/c++/swmf_iono_test\u001b[0m\n",
      "[ 84%] \u001b[0mBuilt target open_ggcm_test\u001b[0m\n",
      "[ 84%] \u001b[0mBuilt target mas_test\u001b[0m\n",
      "[ 84%] \u001b[0mBuilt target swmf_iono_test\u001b[0m\n",
      "[ 84%] \u001b[32m\u001b[1mLinking CXX executable ../../../../bin/ccmc/examples/c++/time_interp\u001b[0m\n",
      "[ 84%] \u001b[32m\u001b[1mLinking CXX executable ../../../../bin/ccmc/examples/c++/pyModel_prog\u001b[0m\n",
      "[ 84%] \u001b[0mBuilt target time_interp\u001b[0m\n",
      "[ 84%] \u001b[0mBuilt target pyModel_prog\u001b[0m\n",
      "make[1]: *** [src/ccmc/wrappers/c/CMakeFiles/ccmc_wrapper_c.dir/all] Error 2\n",
      "[ 85%] \u001b[32m\u001b[1mLinking CXX executable ../../../../bin/ccmc/examples/c++/tracer_prog\u001b[0m\n",
      "[ 85%] \u001b[0mBuilt target tracer_prog\u001b[0m\n",
      "make: *** [all] Error 2\n"
     ]
    }
   ],
   "source": [
    "!make -j8"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "kameleon <filename> variable c0 c1 c2\r\n",
      "\tAdapt3D, OpenGGCM, BATSRUS: x y z\r\n",
      "\tENLIL, MAS: r theta(latitude) phi(longitude)\r\n"
     ]
    }
   ],
   "source": [
    "!../bin/ccmc/examples/c++/kameleon_prog"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "../bin/ccmc/examples/c++/kameleon_prog:\r\n",
      "\t@rpath/libccmc.6.1.0.0.dylib (compatibility version 6.1.0, current version 0.0.0)\r\n",
      "\t/Applications/cdf35_0-dist/lib/libcdf.dylib (compatibility version 0.0.0, current version 0.0.0)\r\n",
      "\t@rpath/libhdf5_cpp.9.dylib (compatibility version 10.0.0, current version 10.0.0)\r\n",
      "\t@rpath/libhdf5.9.dylib (compatibility version 10.0.0, current version 10.0.0)\r\n",
      "\t@rpath/libz.1.dylib (compatibility version 1.0.0, current version 1.2.8)\r\n",
      "\t/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1213.0.0)\r\n",
      "\t@rpath/pyKameleon.so (compatibility version 0.0.0, current version 0.0.0)\r\n",
      "\t@rpath/libboost_thread.dylib (compatibility version 0.0.0, current version 0.0.0)\r\n",
      "\t@rpath/libboost_program_options.dylib (compatibility version 0.0.0, current version 0.0.0)\r\n",
      "\t@rpath/libboost_filesystem.dylib (compatibility version 0.0.0, current version 0.0.0)\r\n",
      "\t@rpath/libboost_system.dylib (compatibility version 0.0.0, current version 0.0.0)\r\n",
      "\t@rpath/libboost_python.dylib (compatibility version 0.0.0, current version 0.0.0)\r\n",
      "\tlibpython2.7.dylib (compatibility version 2.7.0, current version 2.7.0)\r\n",
      "\t/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0)\r\n"
     ]
    }
   ],
   "source": [
    "!otool -L ../bin/ccmc/examples/c++/kameleon_prog"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Build from my custom anaconda build"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "============= Top level CMakeLists.txt ==============\n",
      "--  Kameleon-plus 6.1.0.0 build for Darwin-14.5.0\n",
      "-- Found PythonInterp: /Users/apembrok/anaconda/bin/python2.7 (found suitable version \"2.7.10\", minimum required is \"2.7\") \n",
      "-- Found PythonLibs: /Users/apembrok/anaconda/lib/libpython2.7.dylib (found suitable version \"2.7.10\", minimum required is \"2.7\") \n",
      "--  Python Interpreter:/Users/apembrok/anaconda/bin/python2.7\n",
      "Getting BOOST....\n",
      "-- Boost version: 1.57.0\n",
      "-- Found the following Boost libraries:\n",
      "--   thread\n",
      "--   program_options\n",
      "--   filesystem\n",
      "--   system\n",
      "--   python\n",
      "--  BOOST_ROOT=\n",
      "--  Boost includes: /Users/apembrok/anaconda_boost_install/include\n",
      "--  Boost library directory: /Users/apembrok/anaconda_boost_install/lib\n",
      "--  Link boost: /Users/apembrok/anaconda_boost_install/lib/libboost_thread.dylib/Users/apembrok/anaconda_boost_install/lib/libboost_program_options.dylib/Users/apembrok/anaconda_boost_install/lib/libboost_filesystem.dylib/Users/apembrok/anaconda_boost_install/lib/libboost_system.dylib/Users/apembrok/anaconda_boost_install/lib/libboost_python.dylib\n",
      " Will NOT build Kameleon with HDF5.\n",
      "--  Will NOT build java wrappers\n",
      "Getting CDF..\n",
      "--  retrieving shared CDF libraries\n",
      "--  Include CDF: /Applications/cdf35_0-dist/include\n",
      "--  link CDF: /Applications/cdf35_0-dist/lib/libcdf.dylib\n",
      "--  CDF Path:/Applications/cdf35_0-dist/lib\n",
      " \n",
      "============ ccmc library(src/ccmc>) ==============\n",
      "--  ignoring HDF5FileReader.cpp  HDF5FileReader.h\n",
      "--  will build SHARED ccmc library\n",
      "--  will build STATIC ccmc library\n",
      "--  ccmc library output location = /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/libccmc.dylib\n",
      "--  Include boost: /Users/apembrok/anaconda_boost_install/include\n",
      "--  Boost library directory: /Users/apembrok/anaconda_boost_install/lib\n",
      "--  Link boost: /Users/apembrok/anaconda_boost_install/lib/libboost_thread.dylib/Users/apembrok/anaconda_boost_install/lib/libboost_program_options.dylib/Users/apembrok/anaconda_boost_install/lib/libboost_filesystem.dylib/Users/apembrok/anaconda_boost_install/lib/libboost_system.dylib/Users/apembrok/anaconda_boost_install/lib/libboost_python.dylib\n",
      "--  Include CDF: /Applications/cdf35_0-dist/include\n",
      "--  link CDF: /Applications/cdf35_0-dist/lib/libcdf.dylib\n",
      "--  cmake framework path: \n",
      "--  Python Interpreter:/Users/apembrok/anaconda/bin/python2.7\n",
      "--  boost.python library found, creating embedded readers..\n",
      "\n",
      "=========== pyKameleon(src/ccmc/pyreader) ===========\n",
      "setting up python...\n",
      "-- Found PythonInterp: /Users/apembrok/anaconda/bin/python2.7 (found version \"2.7.10\") \n",
      "--  PYTHON_LIBRARIES:/Users/apembrok/anaconda/lib/libpython2.7.dylib\n",
      "--  PYTHON_INCLUDE_DIRS:/Users/apembrok/anaconda/include/python2.7\n",
      "--  PYTHON_INCLUDE_PATH:/Users/apembrok/anaconda/include/python2.7\n",
      "--  PYTHON_EXECUTABLE:/Users/apembrok/anaconda/bin/python2.7\n",
      "setting up boost.python\n",
      "--  Boost_LIBRARIES:/Users/apembrok/anaconda_boost_install/lib/libboost_thread.dylib/Users/apembrok/anaconda_boost_install/lib/libboost_program_options.dylib/Users/apembrok/anaconda_boost_install/lib/libboost_filesystem.dylib/Users/apembrok/anaconda_boost_install/lib/libboost_system.dylib/Users/apembrok/anaconda_boost_install/lib/libboost_python.dylib\n",
      "--  BOOST_INCLUDEDIR:/Users/apembrok/anaconda_boost_install/include\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/pyreaders/__init__.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/pyreaders/AnalyticModel.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/pyreaders/ARMS.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/pyreaders/Attribute.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/pyreaders/exPyFileReader.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/pyreaders/GeneralPyReader.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/pyreaders/generatePyKameleon.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/pyreaders/PAMHD.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/pyreaders/readPAMHD.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/pyreaders/readRCM.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/pyreaders/testReader.py\n",
      "-- Found SWIG: /Users/apembrok/anaconda/bin/swig (found version \"3.0.2\") \n",
      "--  SWIG installed. Will attempt to build python and java wrappers.\n",
      "-- Found PythonLibs: /Users/apembrok/anaconda/lib/libpython2.7.dylib (found version \"2.7.10\") \n",
      "--  PythonLibs and python executable found. Will build python wrapper.\n",
      "\n",
      "=========== python wrappers(src/ccmc/wrappers/python) ===========\n",
      " setting up python wrappers..\n",
      "--  SWIG_USE_FILE: /Users/apembrok/anaconda/share/cmake-3.3/Modules/UseSWIG.cmake\n",
      "--  Include boost directories: /Users/apembrok/anaconda_boost_install/include\n",
      "--  Include CDF: /Applications/cdf35_0-dist/include\n",
      "-- /Users/apembrok/anaconda/bin/python2.7\n",
      "-- will install ccmc module to lib/python2.7/site-packages\n",
      "\n",
      "=========== c wrappers(src/ccmc/wrappers/c) ===========\n",
      "-- initializing c wrappers\n",
      "-- will build SHARED ccmc_wrapper_c library\n",
      "-- will build STATIC ccmc_wrapper_c library\n",
      "\n",
      "========== FORTRAN wrappers(src/ccmc/wrappers/fortran) ==========\n",
      "--  building fortran wrappers\n",
      "\n",
      "============ Top level CMakeLists.txt ============\n",
      "\n",
      "========== c++ examples(src/example/c++) ==========\n",
      "--  building c++ examples\n",
      "--  Include boost directories: /Users/apembrok/anaconda_boost_install/include\n",
      "--  Include CDF: /Applications/cdf35_0-dist/include\n",
      "-- Include python embedding directory: /Users/apembrok/anaconda/include/python2.7\n",
      "\n",
      "=========== c examples(src/example/c) ===========\n",
      "--  building c examples\n",
      "--  Include boost directories: /Users/apembrok/anaconda_boost_install/include\n",
      "--  Include CDF: /Applications/cdf35_0-dist/include\n",
      "\n",
      "========== fortran examples(src/example/fortran) ==========\n",
      "--  building FORTRAN examples\n",
      "-- Checking whether Fortran compiler has -isysroot\n",
      "-- Checking whether Fortran compiler has -isysroot - yes\n",
      "-- Checking whether Fortran compiler supports OSX deployment target flag\n",
      "-- Checking whether Fortran compiler supports OSX deployment target flag - yes\n",
      "--  Include boost directories: /Users/apembrok/anaconda_boost_install/include\n",
      "--  Include CDF: /Applications/cdf35_0-dist/include\n",
      "\n",
      "=========== python examples(src/example/python) ===========\n",
      "--  building python examples\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/ARMS_test.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/grid.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/ionosphere_test.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/kameleon_test.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/pyModel_test.py\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/tracer.py\n",
      "--  Python example files will be kept in: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/bin/ccmc/examples/python\n",
      "--  Using CCMC module install path in scripts: sys.path.append('../../../../lib/python2.7/site-packages/ccmc/')\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/ARMS_test.py\n",
      "--  ... will install to: /Users/apembrok/anaconda/bin/ccmc/examples/python/\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/grid.py\n",
      "--  ... will install to: /Users/apembrok/anaconda/bin/ccmc/examples/python/\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/ionosphere_test.py\n",
      "--  ... will install to: /Users/apembrok/anaconda/bin/ccmc/examples/python/\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/kameleon_test.py\n",
      "--  ... will install to: /Users/apembrok/anaconda/bin/ccmc/examples/python/\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/pyModel_test.py\n",
      "--  ... will install to: /Users/apembrok/anaconda/bin/ccmc/examples/python/\n",
      "--  Process file: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/example/python/tracer.py\n",
      "--  ... will install to: /Users/apembrok/anaconda/bin/ccmc/examples/python/\n",
      "-- Configuring done\n",
      "CMake Warning (dev):\n",
      "  Policy CMP0042 is not set: MACOSX_RPATH is enabled by default.  Run \"cmake\n",
      "  --help-policy CMP0042\" for policy details.  Use the cmake_policy command to\n",
      "  set the policy and suppress this warning.\n",
      "\n",
      "  MACOSX_RPATH is not specified for the following targets:\n",
      "\n",
      "   ccmc\n",
      "   ccmc_wrapper_c\n",
      "   ccmc_wrapper_fortran\n",
      "   pyKameleon\n",
      "\n",
      "This warning is for project developers.  Use -Wno-dev to suppress it.\n",
      "\n",
      "-- Generating done\n",
      "-- Build files have been written to: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/build\n"
     ]
    }
   ],
   "source": [
    "!rm -f CMakeCache.txt\n",
    "!cmake -DCMAKE_CXX_FLAGS=\"-std=c++11\" -DCMAKE_C_COMPILER=/usr/bin/clang -DCMAKE_CXX_COMPILER=/usr/bin/clang++ -DBOOST_LIBRARYDIR=/Users/apembrok/anaconda_boost_install/lib -DBOOST_INCLUDEDIR=/Users/apembrok/anaconda_boost_install/include -DBoost_NO_SYSTEM_PATHS=ON -DPYTHON_LIBRARY=/Users/apembrok/anaconda/lib/libpython2.7.dylib -DPYTHON_INCLUDE_DIR=/Users/apembrok/anaconda/include/python2.7/ -DPYTHON_EXECUTABLE=/Users/apembrok/anaconda/bin/python2.7 -DBUILD_JAVA=OFF -DBUILD_HDF5=OFF -DCMAKE_INSTALL_PREFIX=/Users/apembrok/anaconda -DINSTALL_CCMC_PYTHON_MODULE=ON .."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[  0%] \u001b[32mBuilding CXX object src/ccmc/pyreaders/CMakeFiles/pyKameleon.dir/__/Attribute.cpp.o\u001b[0m\n",
      "[  2%] \u001b[32mBuilding CXX object src/ccmc/pyreaders/CMakeFiles/pyKameleon.dir/__/FileReader.cpp.o\u001b[0m\n",
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      "[ 82%] \u001b[32mBuilding CXX object src/ccmc/CMakeFiles/ccmc.dir/OpenGGCMInterpolator.cpp.o\u001b[0m\n",
      "[ 82%] \u001b[32mBuilding CXX object src/ccmc/CMakeFiles/ccmc.dir/Point3f.cpp.o\u001b[0m\n",
      "[ 85%] \u001b[32mBuilding CXX object src/ccmc/CMakeFiles/ccmc.dir/PythonInterpolator.cpp.o\u001b[0m\n",
      "[ 85%] \u001b[32mBuilding CXX object src/ccmc/CMakeFiles/ccmc.dir/PythonModel.cpp.o\u001b[0m\n",
      "[ 88%] \u001b[32mBuilding CXX object src/ccmc/CMakeFiles/ccmc.dir/Shue.cpp.o\u001b[0m\n",
      "[ 88%] \u001b[32mBuilding CXX object src/ccmc/CMakeFiles/ccmc.dir/SWMFIono.cpp.o\u001b[0m\n",
      "[ 91%] \u001b[32mBuilding CXX object src/ccmc/CMakeFiles/ccmc.dir/SWMFIonoInterpolator.cpp.o\u001b[0m\n",
      "[ 91%] \u001b[32mBuilding CXX object src/ccmc/CMakeFiles/ccmc.dir/TimeInterpolator.cpp.o\u001b[0m\n",
      "[ 94%] \u001b[32mBuilding CXX object src/ccmc/CMakeFiles/ccmc.dir/Tracer.cpp.o\u001b[0m\n",
      "[ 94%] \u001b[32mBuilding C object src/ccmc/CMakeFiles/ccmc.dir/cxform-auto.c.o\u001b[0m\n",
      "[ 97%] \u001b[32mBuilding C object src/ccmc/CMakeFiles/ccmc.dir/cxform-manual.c.o\u001b[0m\n",
      "\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/cxform-manual.c:357:21: \u001b[0m\u001b[0;1;35mwarning: \u001b[0m\u001b[1m\n",
      "      implicit conversion from 'double' to 'int' changes value from 29619.4 to\n",
      "      29619 [-Wliteral-conversion]\u001b[0m\n",
      "                 -29775, -29692, -29619.4, -29554.63, -29496.5, 11.4};\n",
      "\u001b[0;1;32m                                  ^~~~~~~\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/cxform-manual.c:357:31: \u001b[0m\u001b[0;1;35mwarning: \u001b[0m\u001b[1m\n",
      "      implicit conversion from 'double' to 'int' changes value from 29554.63 to\n",
      "      29554 [-Wliteral-conversion]\u001b[0m\n",
      "                 -29775, -29692, -29619.4, -29554.63, -29496.5, 11.4};\n",
      "\u001b[0;1;32m                                            ^~~~~~~~\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/cxform-manual.c:357:42: \u001b[0m\u001b[0;1;35mwarning: \u001b[0m\u001b[1m\n",
      "      implicit conversion from 'double' to 'int' changes value from 29496.5 to\n",
      "      29496 [-Wliteral-conversion]\u001b[0m\n",
      "                 -29775, -29692, -29619.4, -29554.63, -29496.5, 11.4};\n",
      "\u001b[0;1;32m                                                       ^~~~~~~\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/cxform-manual.c:357:51: \u001b[0m\u001b[0;1;35mwarning: \u001b[0m\u001b[1m\n",
      "      implicit conversion from 'double' to 'int' changes value from 11.4 to 11\n",
      "      [-Wliteral-conversion]\u001b[0m\n",
      "                 -29775, -29692, -29619.4, -29554.63, -29496.5, 11.4};\n",
      "\u001b[0;1;32m                                                                ^~~~\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/cxform-manual.c:368:21: \u001b[0m\u001b[0;1;35mwarning: \u001b[0m\u001b[1m\n",
      "      implicit conversion from 'double' to 'int' changes value from 1728.2 to\n",
      "      1728 [-Wliteral-conversion]\u001b[0m\n",
      "                 -1848,  -1784,  -1728.2,  -1669.05,  -1585.9,   16.7};\n",
      "\u001b[0;1;32m                                  ^~~~~~\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/cxform-manual.c:368:31: \u001b[0m\u001b[0;1;35mwarning: \u001b[0m\u001b[1m\n",
      "      implicit conversion from 'double' to 'int' changes value from 1669.05 to\n",
      "      1669 [-Wliteral-conversion]\u001b[0m\n",
      "                 -1848,  -1784,  -1728.2,  -1669.05,  -1585.9,   16.7};\n",
      "\u001b[0;1;32m                                            ^~~~~~~\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/cxform-manual.c:368:42: \u001b[0m\u001b[0;1;35mwarning: \u001b[0m\u001b[1m\n",
      "      implicit conversion from 'double' to 'int' changes value from 1585.9 to\n",
      "      1585 [-Wliteral-conversion]\u001b[0m\n",
      "                 -1848,  -1784,  -1728.2,  -1669.05,  -1585.9,   16.7};\n",
      "\u001b[0;1;32m                                                       ^~~~~~\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/cxform-manual.c:368:52: \u001b[0m\u001b[0;1;35mwarning: \u001b[0m\u001b[1m\n",
      "      implicit conversion from 'double' to 'int' changes value from 16.7 to 16\n",
      "      [-Wliteral-conversion]\u001b[0m\n",
      "                 -1848,  -1784,  -1728.2,  -1669.05,  -1585.9,   16.7};\n",
      "\u001b[0;1;32m                                                                 ^~~~\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/cxform-manual.c:379:20: \u001b[0m\u001b[0;1;35mwarning: \u001b[0m\u001b[1m\n",
      "      implicit conversion from 'double' to 'int' changes value from 5186.1 to\n",
      "      5186 [-Wliteral-conversion]\u001b[0m\n",
      "                 5406,   5306,   5186.1,   5077.99,   4945.1,  -28.8};\n",
      "\u001b[0;1;32m                                 ^~~~~~\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/cxform-manual.c:379:30: \u001b[0m\u001b[0;1;35mwarning: \u001b[0m\u001b[1m\n",
      "      implicit conversion from 'double' to 'int' changes value from 5077.99 to\n",
      "      5077 [-Wliteral-conversion]\u001b[0m\n",
      "                 5406,   5306,   5186.1,   5077.99,   4945.1,  -28.8};\n",
      "\u001b[0;1;32m                                           ^~~~~~~\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/cxform-manual.c:379:41: \u001b[0m\u001b[0;1;35mwarning: \u001b[0m\u001b[1m\n",
      "      implicit conversion from 'double' to 'int' changes value from 4945.1 to\n",
      "      4945 [-Wliteral-conversion]\u001b[0m\n",
      "                 5406,   5306,   5186.1,   5077.99,   4945.1,  -28.8};\n",
      "\u001b[0;1;32m                                                      ^~~~~~\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/cxform-manual.c:379:51: \u001b[0m\u001b[0;1;35mwarning: \u001b[0m\u001b[1m\n",
      "      implicit conversion from 'double' to 'int' changes value from 28.8 to 28\n",
      "      [-Wliteral-conversion]\u001b[0m\n",
      "                 5406,   5306,   5186.1,   5077.99,   4945.1,  -28.8};\n",
      "\u001b[0;1;32m                                                                ^~~~\n",
      "\u001b[0m12 warnings generated.\n",
      "[ 97%] \u001b[32m\u001b[1mLinking CXX shared library ../../../lib/ccmc/libccmc.dylib\u001b[0m\n",
      "[ 97%] \u001b[0mBuilt target ccmc\u001b[0m\n",
      "[ 97%] \u001b[34m\u001b[1mSwig source\u001b[0m\n",
      "/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/cdf.h:1612: Warning 305: Bad constant value (ignored).\n",
      "/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/cdf.h:1615: Warning 305: Bad constant value (ignored).\n",
      "/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/Polyhedron.h:60: Warning 314: 'lambda' is a python keyword, renaming to '_lambda'\n",
      "/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/Polyhedron.h:60: Warning 314: 'lambda' is a python keyword, renaming to '_lambda'\n",
      "/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/Point3f.h:10: Warning 503: Can't wrap 'operator <<' unless renamed to a valid identifier.\n",
      "/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/Attribute.h:44: Warning 503: Can't wrap 'operator <<' unless renamed to a valid identifier.\n",
      "/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/Vector.h:37: Warning 509: Overloaded method ccmc::Vector< float >::dot(ccmc::Vector< float > *,ccmc::Vector< float > *) effectively ignored,\n",
      "/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/Vector.h:36: Warning 509: as it is shadowed by ccmc::Vector< float >::dot(ccmc::Vector< float > &,ccmc::Vector< float > &).\n",
      "/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/Vector.h:39: Warning 509: Overloaded method ccmc::Vector< float >::cross(ccmc::Vector< float > *,ccmc::Vector< float > *) effectively ignored,\n",
      "/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/Vector.h:38: Warning 509: as it is shadowed by ccmc::Vector< float >::cross(ccmc::Vector< float > &,ccmc::Vector< float > &).\n",
      "/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/Vector.h:43: Warning 509: Overloaded method ccmc::Vector< float >::norm(ccmc::Vector< float > *) effectively ignored,\n",
      "/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/Vector.h:42: Warning 509: as it is shadowed by ccmc::Vector< float >::norm(ccmc::Vector< float > &).\n",
      "/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/Vector.h:44: Warning 509: Overloaded method ccmc::Vector< float >::norm() effectively ignored,\n",
      "/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/src/ccmc/Vector.h:42: Warning 509: as it is shadowed by ccmc::Vector< float >::norm(ccmc::Vector< float > &).\n",
      "\u001b[35m\u001b[1mScanning dependencies of target _CCMC\u001b[0m\n",
      "[100%] \u001b[32mBuilding CXX object src/ccmc/wrappers/python/CMakeFiles/_CCMC.dir/__/__/__/__/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx.o\u001b[0m\n",
      "\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:4657:9: \u001b[0m\u001b[0;1;35mwarning: \u001b[0m\u001b[1m\n",
      "      destination for this 'memset' call is a pointer to dynamic class\n",
      "      'Point<float>'; vtable pointer will be overwritten\n",
      "      [-Wdynamic-class-memaccess]\u001b[0m\n",
      "        memset(v_def,0,sizeof(Type));\n",
      "\u001b[0;1;32m        ~~~~~~ ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:4682:62: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of member function 'swig::traits_as<ccmc::Point<float>,\n",
      "      swig::pointer_category>::as' requested here\u001b[0m\n",
      "    return traits_as<Type, typename traits<Type>::category>::as(obj, te);\n",
      "\u001b[0;1;32m                                                             ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:5245:15: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of function template specialization\n",
      "      'swig::as<ccmc::Point<float> >' requested here\u001b[0m\n",
      "        return swig::as<T>(item, true);\n",
      "\u001b[0;1;32m                     ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:5514:42: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of member function\n",
      "      'swig::SwigPySequence_Ref<ccmc::Point<float> >::operator Point' requested\n",
      "      here\u001b[0m\n",
      "      seq->insert(seq->end(),(value_type)(*it));\n",
      "\u001b[0;1;32m                                         ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:5536:6: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of function template specialization\n",
      "      'swig::assign<swig::SwigPySequence_Cont<ccmc::Point<float> >,\n",
      "      std::__1::vector<ccmc::Point<float>,\n",
      "      std::__1::allocator<ccmc::Point<float> > > >' requested here\u001b[0m\n",
      "            assign(swigpyseq, pseq);\n",
      "\u001b[0;1;32m            ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:5590:47: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of member function\n",
      "      'swig::traits_asptr_stdseq<std::__1::vector<ccmc::Point<float>,\n",
      "      std::__1::allocator<ccmc::Point<float> > >, ccmc::Point<float> >::asptr'\n",
      "      requested here\u001b[0m\n",
      "        return traits_asptr_stdseq<std::vector<T> >::asptr(obj, vec);\n",
      "\u001b[0;1;32m                                                     ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:4574:32: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of member function\n",
      "      'swig::traits_asptr<std::__1::vector<ccmc::Point<float>,\n",
      "      std::__1::allocator<ccmc::Point<float> > > >::asptr' requested here\u001b[0m\n",
      "    return traits_asptr<Type>::asptr(obj, vptr);\n",
      "\u001b[0;1;32m                               ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:29960:18: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of function template specialization\n",
      "      'swig::asptr<std::__1::vector<ccmc::Point<float>,\n",
      "      std::__1::allocator<ccmc::Point<float> > > >' requested here\u001b[0m\n",
      "    res4 = swig::asptr(obj3, &ptr);\n",
      "\u001b[0;1;32m                 ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:4657:9: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      explicitly cast the pointer to silence this warning\u001b[0m\n",
      "        memset(v_def,0,sizeof(Type));\n",
      "\u001b[0;1;32m               ^\n",
      "\u001b[0m\u001b[0;32m               (void*)\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:4657:9: \u001b[0m\u001b[0;1;35mwarning: \u001b[0m\u001b[1m\n",
      "      destination for this 'memset' call is a pointer to dynamic class\n",
      "      'Vector<float>'; vtable pointer will be overwritten\n",
      "      [-Wdynamic-class-memaccess]\u001b[0m\n",
      "        memset(v_def,0,sizeof(Type));\n",
      "\u001b[0;1;32m        ~~~~~~ ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:4682:62: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of member function 'swig::traits_as<ccmc::Vector<float>,\n",
      "      swig::pointer_category>::as' requested here\u001b[0m\n",
      "    return traits_as<Type, typename traits<Type>::category>::as(obj, te);\n",
      "\u001b[0;1;32m                                                             ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:5245:15: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of function template specialization\n",
      "      'swig::as<ccmc::Vector<float> >' requested here\u001b[0m\n",
      "        return swig::as<T>(item, true);\n",
      "\u001b[0;1;32m                     ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:5514:42: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of member function\n",
      "      'swig::SwigPySequence_Ref<ccmc::Vector<float> >::operator Vector'\n",
      "      requested here\u001b[0m\n",
      "      seq->insert(seq->end(),(value_type)(*it));\n",
      "\u001b[0;1;32m                                         ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:5536:6: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of function template specialization\n",
      "      'swig::assign<swig::SwigPySequence_Cont<ccmc::Vector<float> >,\n",
      "      std::__1::vector<ccmc::Vector<float>,\n",
      "      std::__1::allocator<ccmc::Vector<float> > > >' requested here\u001b[0m\n",
      "            assign(swigpyseq, pseq);\n",
      "\u001b[0;1;32m            ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:5590:47: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of member function\n",
      "      'swig::traits_asptr_stdseq<std::__1::vector<ccmc::Vector<float>,\n",
      "      std::__1::allocator<ccmc::Vector<float> > >, ccmc::Vector<float> >::asptr'\n",
      "      requested here\u001b[0m\n",
      "        return traits_asptr_stdseq<std::vector<T> >::asptr(obj, vec);\n",
      "\u001b[0;1;32m                                                     ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:4574:32: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of member function\n",
      "      'swig::traits_asptr<std::__1::vector<ccmc::Vector<float>,\n",
      "      std::__1::allocator<ccmc::Vector<float> > > >::asptr' requested here\u001b[0m\n",
      "    return traits_asptr<Type>::asptr(obj, vptr);\n",
      "\u001b[0;1;32m                               ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:34538:18: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of function template specialization\n",
      "      'swig::asptr<std::__1::vector<ccmc::Vector<float>,\n",
      "      std::__1::allocator<ccmc::Vector<float> > > >' requested here\u001b[0m\n",
      "    res4 = swig::asptr(obj3, &ptr);\n",
      "\u001b[0;1;32m                 ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:4657:9: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      explicitly cast the pointer to silence this warning\u001b[0m\n",
      "        memset(v_def,0,sizeof(Type));\n",
      "\u001b[0;1;32m               ^\n",
      "\u001b[0m\u001b[0;32m               (void*)\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:4657:9: \u001b[0m\u001b[0;1;35mwarning: \u001b[0m\u001b[1m\n",
      "      destination for this 'memset' call is a pointer to dynamic class\n",
      "      'Point3f'; vtable pointer will be overwritten [-Wdynamic-class-memaccess]\u001b[0m\n",
      "        memset(v_def,0,sizeof(Type));\n",
      "\u001b[0;1;32m        ~~~~~~ ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:4682:62: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of member function 'swig::traits_as<ccmc::Point3f,\n",
      "      swig::pointer_category>::as' requested here\u001b[0m\n",
      "    return traits_as<Type, typename traits<Type>::category>::as(obj, te);\n",
      "\u001b[0;1;32m                                                             ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:5245:15: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of function template specialization\n",
      "      'swig::as<ccmc::Point3f>' requested here\u001b[0m\n",
      "        return swig::as<T>(item, true);\n",
      "\u001b[0;1;32m                     ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:5514:42: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of member function\n",
      "      'swig::SwigPySequence_Ref<ccmc::Point3f>::operator Point3f' requested here\u001b[0m\n",
      "      seq->insert(seq->end(),(value_type)(*it));\n",
      "\u001b[0;1;32m                                         ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:5536:6: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of function template specialization\n",
      "      'swig::assign<swig::SwigPySequence_Cont<ccmc::Point3f>,\n",
      "      std::__1::vector<ccmc::Point3f, std::__1::allocator<ccmc::Point3f> > >'\n",
      "      requested here\u001b[0m\n",
      "            assign(swigpyseq, pseq);\n",
      "\u001b[0;1;32m            ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:5590:47: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of member function\n",
      "      'swig::traits_asptr_stdseq<std::__1::vector<ccmc::Point3f,\n",
      "      std::__1::allocator<ccmc::Point3f> >, ccmc::Point3f>::asptr' requested\n",
      "      here\u001b[0m\n",
      "        return traits_asptr_stdseq<std::vector<T> >::asptr(obj, vec);\n",
      "\u001b[0;1;32m                                                     ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:4574:32: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of member function\n",
      "      'swig::traits_asptr<std::__1::vector<ccmc::Point3f,\n",
      "      std::__1::allocator<ccmc::Point3f> > >::asptr' requested here\u001b[0m\n",
      "    return traits_asptr<Type>::asptr(obj, vptr);\n",
      "\u001b[0;1;32m                               ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:36498:18: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of function template specialization\n",
      "      'swig::asptr<std::__1::vector<ccmc::Point3f,\n",
      "      std::__1::allocator<ccmc::Point3f> > >' requested here\u001b[0m\n",
      "    res4 = swig::asptr(obj3, &ptr);\n",
      "\u001b[0;1;32m                 ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:4657:9: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      explicitly cast the pointer to silence this warning\u001b[0m\n",
      "        memset(v_def,0,sizeof(Type));\n",
      "\u001b[0;1;32m               ^\n",
      "\u001b[0m\u001b[0;32m               (void*)\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:4657:9: \u001b[0m\u001b[0;1;35mwarning: \u001b[0m\u001b[1m\n",
      "      destination for this 'memset' call is a pointer to class containing a\n",
      "      dynamic class 'Point3f'; vtable pointer will be overwritten\n",
      "      [-Wdynamic-class-memaccess]\u001b[0m\n",
      "        memset(v_def,0,sizeof(Type));\n",
      "\u001b[0;1;32m        ~~~~~~ ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:4682:62: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of member function 'swig::traits_as<ccmc::Fieldline,\n",
      "      swig::pointer_category>::as' requested here\u001b[0m\n",
      "    return traits_as<Type, typename traits<Type>::category>::as(obj, te);\n",
      "\u001b[0;1;32m                                                             ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:5245:15: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of function template specialization\n",
      "      'swig::as<ccmc::Fieldline>' requested here\u001b[0m\n",
      "        return swig::as<T>(item, true);\n",
      "\u001b[0;1;32m                     ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:5514:42: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of member function\n",
      "      'swig::SwigPySequence_Ref<ccmc::Fieldline>::operator Fieldline' requested\n",
      "      here\u001b[0m\n",
      "      seq->insert(seq->end(),(value_type)(*it));\n",
      "\u001b[0;1;32m                                         ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:5536:6: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of function template specialization\n",
      "      'swig::assign<swig::SwigPySequence_Cont<ccmc::Fieldline>,\n",
      "      std::__1::vector<ccmc::Fieldline, std::__1::allocator<ccmc::Fieldline> >\n",
      "      >' requested here\u001b[0m\n",
      "            assign(swigpyseq, pseq);\n",
      "\u001b[0;1;32m            ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:5590:47: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of member function\n",
      "      'swig::traits_asptr_stdseq<std::__1::vector<ccmc::Fieldline,\n",
      "      std::__1::allocator<ccmc::Fieldline> >, ccmc::Fieldline>::asptr' requested\n",
      "      here\u001b[0m\n",
      "        return traits_asptr_stdseq<std::vector<T> >::asptr(obj, vec);\n",
      "\u001b[0;1;32m                                                     ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:4574:32: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of member function\n",
      "      'swig::traits_asptr<std::__1::vector<ccmc::Fieldline,\n",
      "      std::__1::allocator<ccmc::Fieldline> > >::asptr' requested here\u001b[0m\n",
      "    return traits_asptr<Type>::asptr(obj, vptr);\n",
      "\u001b[0;1;32m                               ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:42412:18: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      in instantiation of function template specialization\n",
      "      'swig::asptr<std::__1::vector<ccmc::Fieldline,\n",
      "      std::__1::allocator<ccmc::Fieldline> > >' requested here\u001b[0m\n",
      "    res4 = swig::asptr(obj3, &ptr);\n",
      "\u001b[0;1;32m                 ^\n",
      "\u001b[0m\u001b[1m/Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC/ccmcPYTHON_wrap.cxx:4657:9: \u001b[0m\u001b[0;1;30mnote: \u001b[0m\n",
      "      explicitly cast the pointer to silence this warning\u001b[0m\n",
      "        memset(v_def,0,sizeof(Type));\n",
      "\u001b[0;1;32m               ^\n",
      "\u001b[0m\u001b[0;32m               (void*)\n",
      "\u001b[0m4 warnings generated.\n",
      "[100%] \u001b[32m\u001b[1mLinking CXX shared module ../../../../../lib/ccmc/python/CCMC/_CCMC.so\u001b[0m\n",
      "[100%] \u001b[0mBuilt target _CCMC\u001b[0m\n"
     ]
    }
   ],
   "source": [
    "!make clean\n",
    "\n",
    "!make -j8 _CCMC"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Check that new coordinate conversion methods are available"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "../lib/ccmc/python/CCMC/_CCMC.so:\r\n",
      "\tlibpython2.7.dylib (compatibility version 2.7.0, current version 2.7.0)\r\n",
      "\t@rpath/libccmc.6.1.0.0.dylib (compatibility version 6.1.0, current version 0.0.0)\r\n",
      "\t/Applications/cdf35_0-dist/lib/libcdf.dylib (compatibility version 0.0.0, current version 0.0.0)\r\n",
      "\t@rpath/pyKameleon.so (compatibility version 0.0.0, current version 0.0.0)\r\n",
      "\t@rpath/libboost_thread.dylib (compatibility version 0.0.0, current version 0.0.0)\r\n",
      "\t@rpath/libboost_program_options.dylib (compatibility version 0.0.0, current version 0.0.0)\r\n",
      "\t@rpath/libboost_filesystem.dylib (compatibility version 0.0.0, current version 0.0.0)\r\n",
      "\t@rpath/libboost_system.dylib (compatibility version 0.0.0, current version 0.0.0)\r\n",
      "\t@rpath/libboost_python.dylib (compatibility version 0.0.0, current version 0.0.0)\r\n",
      "\t/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0)\r\n",
      "\t/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1213.0.0)\r\n"
     ]
    }
   ],
   "source": [
    "!otool -L ../lib/ccmc/python/CCMC/_CCMC.so"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['',\n",
       " '/Users/apembrok/miniconda2/lib/python2.7/site-packages/CCMC-6.0.0.1-py2.7.egg',\n",
       " '/Users/apembrok/miniconda2/lib/python27.zip',\n",
       " '/Users/apembrok/miniconda2/lib/python2.7',\n",
       " '/Users/apembrok/miniconda2/lib/python2.7/plat-darwin',\n",
       " '/Users/apembrok/miniconda2/lib/python2.7/plat-mac',\n",
       " '/Users/apembrok/miniconda2/lib/python2.7/plat-mac/lib-scriptpackages',\n",
       " '/Users/apembrok/miniconda2/lib/python2.7/lib-tk',\n",
       " '/Users/apembrok/miniconda2/lib/python2.7/lib-old',\n",
       " '/Users/apembrok/miniconda2/lib/python2.7/lib-dynload',\n",
       " '/Users/apembrok/miniconda2/lib/python2.7/site-packages/setuptools-20.2.2-py2.7.egg',\n",
       " '/Users/apembrok/miniconda2/lib/python2.7/site-packages',\n",
       " '/Users/apembrok/miniconda2/lib/python2.7/site-packages/IPython/extensions',\n",
       " '/Users/apembrok/.ipython']"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sys.path"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "SyntaxError",
     "evalue": "invalid syntax (<ipython-input-18-030b5a1507ba>, line 3)",
     "output_type": "error",
     "traceback": [
      "\u001b[0;36m  File \u001b[0;32m\"<ipython-input-18-030b5a1507ba>\"\u001b[0;36m, line \u001b[0;32m3\u001b[0m\n\u001b[0;31m    from /Users/apembrok/git/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC import _CCMC as ccmc\u001b[0m\n\u001b[0m         ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n"
     ]
    }
   ],
   "source": [
    "import sys\n",
    "sys.path.append('/Users/apembrok/git/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/')\n",
    "from /Users/apembrok/git/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/lib/ccmc/python/CCMC import _CCMC as ccmc"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<method 'getPreferredCoordinates' of 'CCMC.KameleonInterpolator' objects>\n",
      "<method 'setPreferredCoordinates' of 'CCMC.KameleonInterpolator' objects>\n",
      "<method 'convertCoordinates' of 'CCMC.KameleonInterpolator' objects>\n"
     ]
    }
   ],
   "source": [
    "print ccmc.KameleonInterpolator.getPreferredCoordinates\n",
    "print ccmc.KameleonInterpolator.setPreferredCoordinates\n",
    "print ccmc.KameleonInterpolator.convertCoordinates"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Check that kameleon_prog compiles\n",
    "kameleon_prog is a simple program that interpolates a given variable onto a user's input position, assuming the user knows the coordinate system of the unerlying model."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[  5%] \u001b[0mBuilt target pyKameleon\u001b[0m\n",
      "[ 97%] \u001b[0mBuilt target ccmc\u001b[0m\n",
      "\u001b[35m\u001b[1mScanning dependencies of target kameleon_prog\u001b[0m\n",
      "[ 97%] \u001b[32mBuilding CXX object src/example/c++/CMakeFiles/kameleon_prog.dir/kameleon_prog.cpp.o\u001b[0m\n",
      "[100%] \u001b[32m\u001b[1mLinking CXX executable ../../../../bin/examples/c++/kameleon_prog\u001b[0m\n",
      "[100%] \u001b[0mBuilt target kameleon_prog\u001b[0m\n"
     ]
    }
   ],
   "source": [
    "!make -j8 kameleon_prog"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "main: opened file: /Users/apembrok/Work/DeVore/ARMS_Peter.ini with status: 0\n",
      "main: kameleon file was opened successfully\n",
      "Warning: No standard position information available. Set standard_grid_target attribute\n",
      "starting interpolations\n",
      "Interpolator::convertCoordinates called\n",
      "value: -0.0867515\n",
      "deleting interpolator\n",
      "Kameleon::close() calling model's close\n"
     ]
    }
   ],
   "source": [
    "!../bin/examples/c++/kameleon_prog /Users/apembrok/Work/DeVore/ARMS_Peter.ini Magnetic_Field_X 1.1 0 0"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Packaging a distribution with CPack\n",
    "\n",
    "You can distribute the kameleon binaries by running the following command in your build directory:\n",
    "\n",
    "    cpack --config CPackConfig.cmake"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPack: Create package using TGZ\n",
      "CPack: Install projects\n",
      "CPack: - Run preinstall target for: Kameleon\n",
      "CPack: - Install project: Kameleon\n",
      "CPack: Create package\n",
      "CPack: - package: /Users/apembrok/git/ccmc/ccmc-software/kameleon-plus/trunk/kameleon-plus-working/build/CCMC.tar.gz generated.\n"
     ]
    }
   ],
   "source": [
    "!cpack --config CPackConfig.cmake"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Errors you might see"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Error: Could not find platform independent libraries ... No module named site\n",
    "\n",
    "If you encounter this error:\n",
    "\n",
    "    Could not find platform independent libraries <prefix>\n",
    "    Could not find platform dependent libraries <exec_prefix>\n",
    "    Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]\n",
    "    ImportError: No module named site\n",
    "    \n",
    "It may be that the compiler flags are wrong or that the wrong python executable is invoked by GeneralFileReader. Make sure cmake is passed \"-std=c++11\". Also, make sure boost is built with c++11 support: running otool on a boost library should list ```libc++.1.dylib``` (which supports c++11) instead of, say, ```libstdc++.6.dylib``` (which does not)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Error: Undefined symbols for architecture x86_64: \"boost::python::objects::function_object ..etc\n",
    "\n",
    "Solution: reinstall boost with clang and pointing to anaconda's python. Jump to solution [here](http://localhost:8888/notebooks/Kameleon-Anaconda.ipynb#Building-with-clang,-anaconda,-and-c++11-support)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Building with clang, anaconda, and c++11 support\n",
    "\n",
    "After compilation with clang and pointing to anaconda's python and rebuilt boost, we get errors like this:\n",
    "```\n",
    "dyld: Symbol not found: __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEED1Ev\n",
    "  Referenced from: /Users/apembrok/anaconda_boost_install/lib/libboost_system.dylib\n",
    "  Expected in: /usr/lib/libstdc++.6.dylib\n",
    " in /Users/apembrok/anaconda_boost_install/lib/libboost_system.dylib\n",
    "```\n",
    "It seems that I had rebuilt boost without c++11 support, according to [this](http://stackoverflow.com/questions/16358957/os-x-10-6sdk-compatible-with-10-5-leopard-system-znkst13bad-exception4whatev) guy. To include c++11 support, I'm following instructions [here](http://hnrkptrsn.github.io/2013/02/26/c11-and-boost-setup-guide/)\n",
    "\n",
    "Similar instructions may be found [here](https://github.com/beniz/libcmaes/wiki/Building-libcmaes-on-Mac-OSX#building-with-anaconda-python) and [here](http://darkmatter.ps.uci.edu/wiki/AnacondaGalSim) (rebuilding with clang and c++11 explicitly)\n",
    "\n",
    "#### Download boost 1.57.0 and unpack\n",
    "```\n",
    "mkdir $HOME/anaconda_boost_install    \n",
    "wget http://sourceforge.net/projects/boost/files/boost/1.57.0/boost_1_57_0.tar.bz2/download\n",
    "mv download boost_1_57_0.tar.bz2\n",
    "tar xvjf boost_1_57_0.tar.bz2\n",
    "cd boost_1_57_0\n",
    "```\n",
    "#### Install\n",
    "```\n",
    "./bootstrap.sh --with-toolset=clang --prefix=/Users/apembrok/anaconda_boost_install/ --with-python=/Users/apembrok/anaconda/bin/python2.7\n",
    "./b2 clean\n",
    "./b2 toolset=clang cxxflags=\"-std=c++11 -stdlib=libc++\" linkflags=\"-stdlib=libc++\" --prefix=/usr/local -j 10 define=BOOST_SYSTEM_NO_DEPRECATED stage release -a\n",
    "./b2 install toolset=clang cxxflags=\"-std=c++11 -stdlib=libc++\" linkflags=\"-stdlib=libc++\" --prefix=/Users/apembrok/anaconda_boost_install/ -a\n",
    "```\n",
    "\"-a\" should build everything, including boost-python\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## \"Fixing\" anaconda's install names\n",
    "\n",
    "You may see ```library not found errors``` after compiling Kameleon executables linked to anaconda libraries. The reason is that anaconda doesn't include the full path to the library in the library itself. If running otool -L on libboost_python.dylib looks like this:\n",
    "\n",
    "\t@rpath/./libboost_python.dylib (compatibility version 0.0.0, current version 0.0.0)\n",
    "\n",
    "You may need to use install name tool on anaconda/lib/libpython2.7.dylib, as well as the following boost libraries libpython2.7.dylib\n",
    "\n",
    "* libboost_thread.dylib \n",
    "* libboost_program_options.dylib \n",
    "* libboost_filesystem.dylib \n",
    "* libboost_system.dylib\n",
    "* libboost_python.dylib\n",
    "* libboost_python-mt.dylib\n",
    "\n",
    "Example:\n",
    "\n",
    "    install_name_tool -id /Users/apembrok/anaconda/lib/libboost_python.dylib /Users/apembrok/anaconda/lib/libboost_python.dylib\n",
    "    \n",
    "    install_name_tool -id /Users/apembrok/anaconda_boost_install/lib/libpython2.7.dylib /Users/apembrok/anaconda/lib/libpython2.7.dylib\n",
    "    \n",
    "After running install_name_tool, check that the full path to each library is included in the name according to otool -L"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/apembrok/anaconda/lib/libboost_python.dylib:\r\n",
      "\t/Users/apembrok/anaconda/lib/libboost_python.dylib (compatibility version 0.0.0, current version 0.0.0)\r\n",
      "\t@rpath/libpython2.7.dylib (compatibility version 2.7.0, current version 2.7.0)\r\n",
      "\t/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 19.0.0)\r\n",
      "\t/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 159.1.0)\r\n"
     ]
    }
   ],
   "source": [
    "!otool -L /Users/apembrok/anaconda/lib/libboost_python.dylib"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "!install_name_tool -id /Users/apembrok/anaconda/lib/libpython2.7.dylib /Users/apembrok/anaconda/lib/libpython2.7.dylib"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Consider using these compiler flags\n",
    "Here's a description of the flags recommended for different platforms http://stackoverflow.com/a/19774902\n",
    "\n",
    "#### gcc-5 support c++ 11\n",
    "Getting gcc-5 for Linux-64 and OS-X 64\n",
    "\n",
    "    conda install -c salford_systems gcc-5 libgcc-5\n",
    "\n",
    "#### Compiler flags"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-I/Users/apembrok/anaconda/include/python2.7 -I/Users/apembrok/anaconda/include/python2.7 -fno-strict-aliasing -I/Users/apembrok/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes\r\n"
     ]
    }
   ],
   "source": [
    "!python-config --cflags"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "compile with c++11\n",
    "\n",
    "    cmake -DCMAKE_CXX_FLAGS=\"-std=c++11\" .."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Linker Flags"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-lpython2.7 -ldl -framework CoreFoundation -u _PyMac_Error\r\n"
     ]
    }
   ],
   "source": [
    "!python-config --ldflags "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# More on c++11 flags\n",
    "\n",
    "Taken from http://stackoverflow.com/questions/19774778/when-is-it-necessary-to-use-use-the-flag-stdlib-libstdc\n",
    "\n",
    "**On Linux**: In general, all commonly available linux distributions will use libstdc++ by default. If you want to compile c++11 code here, use one of:\n",
    "\n",
    "* g++ -std=c++11 input.cxx -o a.out\n",
    "* g++ -std=gnu++11 input.cxx -o a.out\n",
    "\n",
    "**On OS X before Mavericks**: libstdc++ was the default. You could use libc++ (which included c++11 library support) by passing -stdlib=libc++. If you want to compile c++11 code here, use one of:\n",
    "\n",
    "* g++ -std=c++11 -stdlib=libc++ input.cxx -o a.out\n",
    "* g++ -std=gnu++11 -stdlib=libc++ input.cxx -o a.out\n",
    "* clang++ -std=c++11 -stdlib=libc++ input.cxx -o a.out\n",
    "* clang++ -std=gnu++11 -stdlib=libc++ input.cxx -o a.out\n",
    "\n",
    "**On OS X since Mavericks**: libc++ is the default. You can use libstdc++ (which does not include c++11 library support) by passing -stdlib=libstdc++\n",
    "\n",
    "* clang++ -std=c++11 input.cxx -o a.out\n",
    "* clang++ -std=gnu++11 input.cxx -o a.out"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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