chaubold · jakirkham · Dec 11, 2013 · Dec 11, 2013 · Dec 11, 2013 · Dec 11, 2013
diff --git a/BuildSupport.cmake b/BuildSupport.cmake
@@ -49,11 +49,15 @@ if (NOT EXISTS ${BUILDEM_SRC_DIR})
     file (MAKE_DIRECTORY ${BUILDEM_SRC_DIR})
 endif ()
 
+if (NOT EXISTS /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk)
+	message (FATAL_ERROR "ERROR: XCode and the OSX 10.9 SDK have to be installed. Please install XCode from the AppStore")
+endif ()
+
 if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
     # Important to use FALLBACK variable.
     # https://developer.apple.com/library/mac/#documentation/DeveloperTools/Conceptual/DynamicLibraries/100-Articles/DynamicLibraryUsageGuidelines.html
     set (BUILDEM_LD_LIBRARY_VAR "DYLD_FALLBACK_LIBRARY_PATH")
-    set (BUILDEM_PLATFORM_SPECIFIC_ENV "MACOSX_DEPLOYMENT_TARGET=10.5")
+    set (BUILDEM_PLATFORM_SPECIFIC_ENV "MACOSX_DEPLOYMENT_TARGET=10.9")
     set (BUILDEM_PLATFORM_DYLIB_EXTENSION "dylib")
 else()
     set (BUILDEM_LD_LIBRARY_VAR "LD_LIBRARY_PATH")

diff --git a/FindCplex.cmake b/FindCplex.cmake
@@ -89,6 +89,7 @@ FIND_LIBRARY(CPLEX_LIBRARY
         ${CPLEX_ROOT_DIR}/cplex/lib/x86-64_debian4.0_4.1/static_pic #unix
         ${CPLEX_ROOT_DIR}/cplex/lib/x86-64_sles10_4.1/static_pic #unix 
         ${CPLEX_ROOT_DIR}/cplex/lib/x86-64_osx/static_pic #osx 
+        ${CPLEX_ROOT_DIR}/cplex/lib/x86-64_darwin/static_pic #osx 
   PATHS ENV LIBRARY_PATH #unix
         ENV LD_LIBRARY_PATH #unix
   )
@@ -100,6 +101,7 @@ FIND_LIBRARY(CPLEX_ILOCPLEX_LIBRARY
         ${CPLEX_ROOT_DIR}/cplex/lib/x86-64_debian4.0_4.1/static_pic #unix 
         ${CPLEX_ROOT_DIR}/cplex/lib/x86-64_sles10_4.1/static_pic #unix 
         ${CPLEX_ROOT_DIR}/cplex/lib/x86-64_osx/static_pic #osx 
+        ${CPLEX_ROOT_DIR}/cplex/lib/x86-64_darwin/static_pic #osx 
   PATHS ENV LIBRARY_PATH
         ENV LD_LIBRARY_PATH
   )
@@ -111,6 +113,7 @@ FIND_LIBRARY(CPLEX_CONCERT_LIBRARY
         ${CPLEX_ROOT_DIR}/concert/lib/x86-64_debian4.0_4.1/static_pic #unix 
         ${CPLEX_ROOT_DIR}/concert/lib/x86-64_sles10_4.1/static_pic #unix 
         ${CPLEX_ROOT_DIR}/concert/lib/x86-64_osx/static_pic #osx 
+        ${CPLEX_ROOT_DIR}/concert/lib/x86-64_darwin/static_pic #osx 
   PATHS ENV LIBRARY_PATH
         ENV LD_LIBRARY_PATH
   )
@@ -127,6 +130,7 @@ else()
           HINTS ${CPLEX_ROOT_DIR}/cplex/bin/x86-64_sles10_4.1 #unix 
                 ${CPLEX_ROOT_DIR}/cplex/bin/x86-64_debian4.0_4.1 #unix 
                 ${CPLEX_ROOT_DIR}/cplex/bin/x86-64_osx #osx 
+                ${CPLEX_ROOT_DIR}/cplex/bin/x86-64_darwin #osx 
 	  ENV LIBRARY_PATH
           ENV LD_LIBRARY_PATH
 	  )

diff --git a/README_openblas.txt b/README_openblas.txt
@@ -0,0 +1,15 @@
+If you are having trouble building OpenBLAS out of the box, you may need to specify your CPU Architecture.
+Common architecture options include SandyBridge and Haswell. Even if your build worked correctly, it may
+not be optimal. The default architecture, if not specified, is Nehalem, which is probably not the ideal
+choice unless using an older computer.
+
+To specify the architecture simply use the TARGET flag. For example, TARGET=SANDYBRIDGE will build for
+the SandyBridge architecture. Similarly, TARGET=HASWELL will target the Haswell (or Crystalwell)
+architecture(s). To do this simply modify the BUILD_COMMAND to include this flag ____after____ the call
+to $(MAKE) as it must be an argument to make. It is recommend the same be done for the INSTALL_COMMAND
+as well.
+
+More information can be found on the OpenBLAS GitHub webpage ( https://github.com/xianyi/OpenBLAS/ ). A list
+of architectures supported can be found here ( https://github.com/xianyi/OpenBLAS/blob/develop/TargetList.txt ).
+Note that at the time of writing this READNME, the list has not been updated in about a year; so, it does not
+list HASWELL even though it is supported by the version we are using.
diff --git a/actdiag.cmake b/actdiag.cmake
@@ -0,0 +1,41 @@
+# Action-based diagramming from a DSL.
+
+if (NOT actdiag_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+include (ExternalProject)
+include (ExternalSource)
+include (BuildSupport)
+
+include (python)
+include (setuptools)
+include (pillow)
+include (funcparserlib)
+
+external_source (actdiag
+    0.5.4
+    actdiag-0.5.4.tar.gz
+    d254a4dbac727ba7bee1b252e530cb3f
+    https://pypi.python.org/packages/source/a/actdiag/)
+
+
+# Download and install actdiag
+message ("Installing ${actdiag_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
+
+ExternalProject_Add(${actdiag_NAME}
+    DEPENDS             ${python_NAME} ${setuptools_NAME} ${pillow_NAME} ${funcparserlib}
+    PREFIX              ${BUILDEM_DIR}
+    URL                 ${actdiag_URL}
+    URL_MD5             ${actdiag_MD5}
+    UPDATE_COMMAND      ""
+    PATCH_COMMAND       ""
+    CONFIGURE_COMMAND   ""
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py build
+    BUILD_IN_SOURCE     1
+    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py install
+)
+
+set_target_properties(${actdiag_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+endif (NOT actdiag_NAME)
diff --git a/ann.cmake b/ann.cmake
@@ -15,8 +15,7 @@ external_source (ann
     1.1.2
     ann_1.1.2.tar.gz
     7ffaacc7ea79ca39d4958a6378071365
-    http://www.cs.umd.edu/~mount/ANN/Files/1.1.2
-    FORCE)
+    http://www.cs.umd.edu/~mount/ANN/Files/1.1.2/)
 
 message ("Installing ${ann_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
 ExternalProject_Add(${ann_NAME}
@@ -32,6 +31,7 @@ ExternalProject_Add(${ann_NAME}
         -DBUILD_SHARED_LIBS=ON
         -DCMAKE_INSTALL_PREFIX=${BUILDEM_DIR}
         -DCMAKE_PREFIX_PATH=${BUILDEM_DIR}
+        -DCMAKE_CXX_FLAGS=${BUILDEM_ADDITIONAL_CXX_FLAGS}
 
 
     BUILD_COMMAND       ${BUILDEM_ENV_STRING} $(MAKE)

diff --git a/backports-ssl_match_hostname.cmake b/backports-ssl_match_hostname.cmake
@@ -0,0 +1,37 @@
+# Provides match_hostname from Python 3 for Python 2.
+# Required by tornado.
+
+if (NOT backports-ssl_match_hostname_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+include (ExternalProject)
+include (ExternalSource)
+include (BuildSupport)
+
+
+include (python)
+
+external_source(backports-ssl_match_hostname
+    3.4.0.2
+    backports.ssl_match_hostname-3.4.0.2.tar.gz
+    788214f20214c64631f0859dc79f23c6
+    https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/)
+
+message ("Installing ${backports-ssl_match_hostname_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
+ExternalProject_Add(${backports-ssl_match_hostname_NAME}
+    DEPENDS             ${python_NAME}
+    PREFIX              ${BUILDEM_DIR}
+    URL                 ${backports-ssl_match_hostname_URL}
+    URL_MD5             ${backports-ssl_match_hostname_MD5}
+    UPDATE_COMMAND      ""
+    PATCH_COMMAND       ""
+    CONFIGURE_COMMAND   ""
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py build
+    BUILD_IN_SOURCE     1
+    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py install
+)
+
+set_target_properties(${backports-ssl_match_hostname_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+endif (NOT backports-ssl_match_hostname_NAME)
diff --git a/blockdiag.cmake b/blockdiag.cmake
@@ -0,0 +1,41 @@
+# Block-based diagramming from a DSL.
+
+if (NOT blockdiag_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+include (ExternalProject)
+include (ExternalSource)
+include (BuildSupport)
+
+include (python)
+include (setuptools)
+include (pillow)
+include (funcparserlib)
+
+external_source (blockdiag
+    1.5.1
+    blockdiag-1.5.1.tar.gz
+    e1bcaf5ae64467f7722ad7883fc06abb
+    https://pypi.python.org/packages/source/b/blockdiag/)
+
+
+# Download and install blockdiag
+message ("Installing ${blockdiag_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
+
+ExternalProject_Add(${blockdiag_NAME}
+    DEPENDS             ${python_NAME} ${setuptools_NAME} ${pillow_NAME} ${funcparserlib}
+    PREFIX              ${BUILDEM_DIR}
+    URL                 ${blockdiag_URL}
+    URL_MD5             ${blockdiag_MD5}
+    UPDATE_COMMAND      ""
+    PATCH_COMMAND       ""
+    CONFIGURE_COMMAND   ""
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py build
+    BUILD_IN_SOURCE     1
+    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py install
+)
+
+set_target_properties(${blockdiag_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+endif (NOT blockdiag_NAME)
diff --git a/blockedarray.cmake b/blockedarray.cmake
@@ -31,6 +31,7 @@ ExternalProject_Add(${blockedarray_NAME}
     PATCH_COMMAND       ""       
     CONFIGURE_COMMAND   ${BUILDEM_ENV_STRING} ${CMAKE_COMMAND}
     	-DCMAKE_BUILD_TYPE=Release
+    	-DCMAKE_CXX_FLAGS=${BUILDEM_ADDITIONAL_CXX_FLAGS}
     	-DCMAKE_INSTALL_PREFIX=${BUILDEM_DIR}
         -DCMAKE_PREFIX_PATH=${BUILDEM_DIR}
         -DPYTHON_EXECUTABLE=${PYTHON_EXE}

diff --git a/boost.cmake b/boost.cmake
@@ -17,12 +17,13 @@ set (boost_INCLUDE_DIR  ${BUILDEM_INCLUDE_DIR}/boost)
 include_directories (${boost_INCLUDE_DIR})
 
 external_source (boost
-    1_51_0
-    boost_1_51_0.tar.gz
-    6a1f32d902203ac70fbec78af95b3cf8
-    http://downloads.sourceforge.net/project/boost/boost/1.51.0)
+    1_56_0
+    boost_1_56_0.tar.bz2
+    a744cf167b05d72335f27c88115f211d
+    http://hivelocity.dl.sourceforge.net/project/boost/boost/1.56.0)
 
-set (boost_LIBS ${BUILDEM_LIB_DIR}/libboost_thread.${BUILDEM_PLATFORM_DYLIB_EXTENSION} 
+set (boost_LIBS ${BUILDEM_LIB_DIR}/libboost_container.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+                ${BUILDEM_LIB_DIR}/libboost_thread.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
                 ${BUILDEM_LIB_DIR}/libboost_system.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
                 ${BUILDEM_LIB_DIR}/libboost_program_options.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
                 ${BUILDEM_LIB_DIR}/libboost_python.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
@@ -42,18 +43,18 @@ ExternalProject_Add(${boost_NAME}
     UPDATE_COMMAND      ""
     PATCH_COMMAND       ""
     CONFIGURE_COMMAND   ${BUILDEM_ENV_STRING} ./bootstrap.sh 
-        --with-libraries=date_time,filesystem,python,regex,serialization,system,test,thread,program_options,chrono
+        --with-libraries=container,date_time,filesystem,python,regex,serialization,system,test,thread,program_options,chrono
         --with-python=${PYTHON_EXE} 
         --prefix=${BUILDEM_DIR}
-        LDFLAGS=${BUILDEM_LDFLAGS}
-        CPPFLAGS=-I${BUILDEM_DIR}/include
-    BUILD_COMMAND       ${BUILDEM_ENV_STRING} ./b2 
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} ./b2
+    	cxxflags="${BUILDEM_ADDITIONAL_CXX_FLAGS}" linkflags="${BUILDEM_ADDITIONAL_CXX_FLAGS}"
         --layout=tagged
         -sNO_BZIP2=1 
         -sZLIB_INCLUDE=${BUILDEM_DIR}/include 
         -sZLIB_SOURCE=${zlib_SRC_DIR} install
     BUILD_IN_SOURCE     1
-    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} ./b2 
+    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} ./b2
+    	cxxflags="${BUILDEM_ADDITIONAL_CXX_FLAGS}" linkflags="${BUILDEM_ADDITIONAL_CXX_FLAGS}"
         -sNO_BZIP2=1 
         -sZLIB_INCLUDE=${BUILDEM_DIR}/include 
         -sZLIB_SOURCE=${zlib_SRC_DIR} install

diff --git a/bottleneck.cmake b/bottleneck.cmake
@@ -0,0 +1,41 @@
+# Provides functions to deal with nan in NumPy arrays efficiently.
+#
+# Required by pandas.
+
+
+if (NOT bottleneck_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+include (ExternalProject)
+include (ExternalSource)
+include (BuildSupport)
+include (TemplateSupport)
+
+include (python)
+include (numpy)
+include (scipy)
+include (nose)
+
+external_git_repo(bottleneck
+	v0.7.0 #4042977fa716f127a2074de011b9ef84caf2e965
+	https://github.com/kwgoodman/bottleneck)
+
+message ("Installing ${bottleneck_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
+ExternalProject_Add(${bottleneck_NAME}
+    DEPENDS             ${python_NAME} ${numpy_NAME} ${scipy_NAME} ${nose_NAME}
+    PREFIX              ${BUILDEM_DIR}
+    GIT_REPOSITORY	${bottleneck_URL}
+    GIT_TAG             ${bottleneck_TAG}
+    UPDATE_COMMAND      ""
+    PATCH_COMMAND       ""
+    CONFIGURE_COMMAND   ""
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py build
+    BUILD_IN_SOURCE     1
+    TEST_COMMAND        ""
+    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py install
+)
+
+set_target_properties(${bottleneck_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+endif (NOT bottleneck_NAME)
diff --git a/chatty.cmake b/chatty.cmake
@@ -33,6 +33,7 @@ ExternalProject_Add(${chatty_NAME}
     	-DCMAKE_BUILD_TYPE=Release
     	-DCMAKE_INSTALL_PREFIX=${BUILDEM_DIR}
         -DCMAKE_PREFIX_PATH=${BUILDEM_DIR}
+        -DCMAKE_CXX_FLAGS=${BUILDEM_ADDITIONAL_CXX_FLAGS}
         -DPYTHON_EXECUTABLE=${PYTHON_EXE}
         -DPYTHON_INCLUDE_DIR=${PYTHON_PREFIX}/include/python2.7
         "-DPYTHON_LIBRARY=${PYTHON_PREFIX}/lib/libpython2.7.${BUILDEM_PLATFORM_DYLIB_EXTENSION}"

diff --git a/cloud_sptheme.cmake b/cloud_sptheme.cmake
@@ -0,0 +1,40 @@
+#
+# Install cloud_sptheme from source. Provides theme for Sphinx.
+#
+
+if (NOT cloud_sptheme_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+include (ExternalProject)
+include (ExternalSource)
+include (BuildSupport)
+include (TemplateSupport)
+
+include (python)
+include (sphinx)
+
+external_source (cloud_sptheme
+    1.6
+    cloud_sptheme-1.6.tar.gz
+    23d5fce0b87836d9f29573d6ee6a9bc1
+    https://pypi.python.org/packages/source/c/cloud_sptheme/)
+
+message ("Installing ${cloud_sptheme_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
+ExternalProject_Add(${cloud_sptheme_NAME}
+    DEPENDS             ${python_NAME} ${sphinx_NAME}
+    PREFIX              ${BUILDEM_DIR}
+    URL                 ${cloud_sptheme_URL}
+    URL_MD5             ${cloud_sptheme_MD5}
+    UPDATE_COMMAND      ""
+    PATCH_COMMAND       ""
+    CONFIGURE_COMMAND   ""
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py build
+    BUILD_IN_SOURCE     1
+    TEST_COMMAND        ""
+    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py install
+)
+
+set_target_properties(${cloud_sptheme_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+endif (NOT cloud_sptheme_NAME)
diff --git a/cplex-shared.cmake b/cplex-shared.cmake
@@ -27,7 +27,7 @@ find_package( Cplex REQUIRED )
 if (APPLE)
     set(SHARED_CPLEX_COMPILE_FLAGS "-fpic -stdlib=libstdc++")
     set(SHARED_CPLEX_LINK_FLAGS_1 "-Wl,-all_load")
-    set(SHARED_CPLEX_LINK_FLAGS_2 "")
+    set(SHARED_CPLEX_LINK_FLAGS_2 "-stdlib=libstdc++")
 else()
     set(SHARED_CPLEX_COMPILE_FLAGS "-shared -fpic")
     set(SHARED_CPLEX_LINK_FLAGS_1 "-Wl,-whole-archive")

diff --git a/cylemon.cmake b/cylemon.cmake
@@ -32,7 +32,7 @@ ExternalProject_Add(${cylemon_NAME}
     GIT_TAG             ${cylemon_TAG}
     UPDATE_COMMAND      ""
     CONFIGURE_COMMAND   ""
-    BUILD_COMMAND       ${BUILDEM_ENV_STRING} ${PYTHON_EXE} 
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} env "CPPFLAGS=${BUILDEM_ADDITIONAL_CXX_FLAGS}" "LDFLAGS=${BUILDEM_ADDITIONAL_CXX_FLAGS}" ${PYTHON_EXE} 
     	setup.py --no-extra-includes ${cylemon_SPECIAL_SETUP} build build_ext -I${BUILDEM_INCLUDE_DIR} -L${BUILDEM_LIB_DIR}
     BUILD_IN_SOURCE     1
     INSTALL_COMMAND     ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py install