SciPy stack support, nanshe dependencies, some changes from upstream

BuildSupport.cmake

@@ -53,7 +53,11 @@ if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
     # Important to use FALLBACK variable.
     # https://developer.apple.com/library/mac/#documentation/DeveloperTools/Conceptual/DynamicLibraries/100-Articles/DynamicLibraryUsageGuidelines.html
     set (BUILDEM_LD_LIBRARY_VAR "DYLD_FALLBACK_LIBRARY_PATH")
-    set (BUILDEM_PLATFORM_SPECIFIC_ENV "MACOSX_DEPLOYMENT_TARGET=10.5")
+    if(${CMAKE_OSX_DEPLOYMENT_TARGET})
+    	set (BUILDEM_PLATFORM_SPECIFIC_ENV "MACOSX_DEPLOYMENT_TARGET=${CMAKE_OSX_DEPLOYMENT_TARGET}")
+    else()
+    	set (BUILDEM_PLATFORM_SPECIFIC_ENV "MACOSX_DEPLOYMENT_TARGET=10.5")
+    endif()
     set (BUILDEM_PLATFORM_DYLIB_EXTENSION "dylib")
 else()
     set (BUILDEM_LD_LIBRARY_VAR "LD_LIBRARY_PATH")
@@ -64,7 +68,7 @@ endif()
 # Initialize environment variables string to use for commands.
 set (BUILDEM_BIN_PATH     ${BUILDEM_BIN_DIR}:$ENV{PATH})
 set (BUILDEM_LIB_PATH     ${BUILDEM_LIB_DIR}:$ENV{${BUILDEM_LD_LIBRARY_VAR}})
-set (BUILDEM_ENV_STRING   env PATH=${BUILDEM_BIN_PATH} ${BUILDEM_LD_LIBRARY_VAR}=${BUILDEM_LIB_PATH} ${BUILDEM_PLATFORM_SPECIFIC_ENV})
+set (BUILDEM_ENV_STRING   env PATH=${BUILDEM_BIN_PATH} ${BUILDEM_LD_LIBRARY_VAR}=${BUILDEM_LIB_PATH} ${BUILDEM_PLATFORM_SPECIFIC_ENV} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER})
 set (BUILDEM_LDFLAGS      "-Wl,-rpath,${BUILDEM_LIB_DIR} -L${BUILDEM_LIB_DIR}")
 
 # All library builds should go to BPD/lib

FindCplex.cmake

@@ -88,7 +88,9 @@ FIND_LIBRARY(CPLEX_LIBRARY
   HINTS ${CPLEX_ROOT_DIR}/cplex/lib/${CPLEX_WIN_PLATFORM} #windows
         ${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_linux/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
   )
@@ -99,7 +101,9 @@ FIND_LIBRARY(CPLEX_ILOCPLEX_LIBRARY
   HINTS ${CPLEX_ROOT_DIR}/cplex/lib/${CPLEX_WIN_PLATFORM} #windows 
         ${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_linux/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
   )
@@ -110,7 +114,9 @@ FIND_LIBRARY(CPLEX_CONCERT_LIBRARY
   HINTS ${CPLEX_ROOT_DIR}/concert/lib/${CPLEX_WIN_PLATFORM} #windows 
         ${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_linux/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
   )
@@ -126,7 +132,9 @@ else()
 	  cplex 
           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_linux #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
 	  )

README.md

@@ -1,4 +1,4 @@
-The BuildEM System
+The BuildEM System [![Picture](https://raw.github.com/janelia-flyem/janelia-flyem.github.com/master/images/jfrc_grey_180x40.png)](http://www.janelia.org)
 ==================
 
 The [buildem](https://github.com/janelia-flyem/buildem) repo is a modular CMake-based system that leverages [CMake's ExternalProject](http://www.kitware.com/media/html/BuildingExternalProjectsWithCMake2.8.html) to simplify and automate a complex build process.  Its goal is to allow *simple*, *modular* specification of software dependencies and automate the download, patch, configure, build, and install process.  Initially, we are focused on Linux (and occasionally MacOS X) support for the modules, but we hope to integrate patches from Windows users as needed.
@@ -311,8 +311,8 @@ To build on the cluster, login to a compute node and set the environment variabl
 
 ```bash
 export FLYEMCLUSTER=/groups/flyem/proj/builds/cluster
-export PATH=/usr/local/cmake-2.8.8/bin:/usr/local/git-1.8.1/bin:$FLYEMCLUSTER/bin:$PATH
-export LD_LIBRARY_PATH=$FLYEMCLUSTER/lib:$LD_LIBRARY_PATH
+export PATH=/usr/local/gcc/bin:/usr/local/cmake-2.8.8/bin:/usr/local/git-1.8.1/bin:$FLYEMCLUSTER/bin:$PATH
+export LD_LIBRARY_PATH=/usr/local/gcc/lib64:$FLYEMCLUSTER/lib:$LD_LIBRARY_PATH
 export PYTHONPATH=$FLYEMCLUSTER/lib/python2.7:$FLYEMCLUSTER/lib/python2.7/site-packages:$FLYEMCLUSTER/lib
 ```
 

armadillo.cmake

@@ -0,0 +1,48 @@
+#
+# Install armadillo from source
+#
+
+if (NOT armadillo_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+include (ExternalProject)
+include (ExternalSource)
+include (BuildSupport)
+include (PatchSupport)
+
+include (blas)
+
+
+external_source (armadillo
+    4.000.2
+    armadillo-4.000.2.tar.gz
+    b2891c7b59b96337c154c5d961fd40fb
+    http://downloads.sourceforge.net/project/arma
+    "FORCE"
+    )
+
+message ("Installing ${armadillo_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
+ExternalProject_Add(${armadillo_NAME}
+    DEPENDS             ${lapack_NAME} ${blas_NAME}
+    PREFIX              ${BUILDEM_DIR}
+    URL                 ${armadillo_URL}
+    URL_MD5             ${armadillo_MD5}
+    UPDATE_COMMAND      ""
+    PATCH_COMMAND       ${BUILDEM_ENV_STRING} ${PATCH_EXE}
+    	${armadillo_SRC_DIR}/include/armadillo_bits/config.hpp
+        ${PATCH_DIR}/armadillo.patch
+
+
+    CONFIGURE_COMMAND   ${BUILDEM_ENV_STRING} ${CMAKE_COMMAND} ${armadillo_SRC_DIR} 
+        -DBUILD_SHARED_LIBS=ON
+        -DCMAKE_INSTALL_PREFIX=${BUILDEM_DIR}
+        -DCMAKE_PREFIX_PATH=${BUILDEM_DIR}
+
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} make
+    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} make install
+)
+
+set_target_properties(${armadillo_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+endif (NOT armadillo_NAME)

blas.cmake

@@ -1,7 +1,7 @@
 
 # select the desired blas implementation
 IF(NOT DEFINED WITH_ATLAS)
-    SET(WITH_ATLAS "OFF")
+    SET(WITH_ATLAS 1)
 ENDIF()
 SET(WITH_ATLAS ${WITH_ATLAS}
     CACHE BOOL "Use ATLAS (WITH_ATLAS=1) or openBLAS (WITH_ATLAS=0) ?"

boost.cmake

@@ -17,18 +17,20 @@ 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_55_0
+    boost_1_55_0.tar.gz
+    93780777cfbf999a600f62883bd54b17 
+    http://sourceforge.net/projects/boost/files/boost/1.55.0/)
 
 set (boost_LIBS ${BUILDEM_LIB_DIR}/libboost_thread.${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}
                 ${BUILDEM_LIB_DIR}/libboost_unit_test_framework.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
                 ${BUILDEM_LIB_DIR}/libboost_filesystem.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
-                ${BUILDEM_LIB_DIR}/libboost_chrono.${BUILDEM_PLATFORM_DYLIB_EXTENSION} )
+                ${BUILDEM_LIB_DIR}/libboost_chrono.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+                ${BUILDEM_LIB_DIR}/libboost_random.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+                ${BUILDEM_LIB_DIR}/libboost_atomic.${BUILDEM_PLATFORM_DYLIB_EXTENSION} )
 
 # Add layout=tagged param to first boost install to explicitly create -mt libraries
 # some libraries require.  TODO: Possibly shore up all library find paths to only
@@ -42,7 +44,7 @@ ExternalProject_Add(${boost_NAME}
     UPDATE_COMMAND      ""
     PATCH_COMMAND       ""
     CONFIGURE_COMMAND   ${BUILDEM_ENV_STRING} ./bootstrap.sh 
-        --with-libraries=date_time,filesystem,python,regex,serialization,system,test,thread,program_options,chrono
+        --with-libraries=date_time,filesystem,python,regex,serialization,system,test,thread,program_options,chrono,atomic,random
         --with-python=${PYTHON_EXE} 
         --prefix=${BUILDEM_DIR}
         LDFLAGS=${BUILDEM_LDFLAGS}
@@ -59,6 +61,14 @@ ExternalProject_Add(${boost_NAME}
         -sZLIB_SOURCE=${zlib_SRC_DIR} install
 )
 
+if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin" AND "${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
+    ExternalProject_Add_Step(${boost_NAME} osx-gcc-fix-config
+       COMMAND bash ${PATCH_DIR}/boost-osx-gcc-fix-config.sh ${boost_SRC_DIR} ${CMAKE_CXX_COMPILER}
+       DEPENDERS configure
+       DEPENDEES patch
+    )
+endif()
+
 set_target_properties(${boost_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
 
 endif (NOT boost_NAME)

boost1550.cmake

@@ -0,0 +1,64 @@
+#
+# Install boost1550 libraries from source
+#
+
+if (NOT boost1550_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+include (ExternalProject)
+include (BuildSupport)
+include (ExternalSource)
+
+include (python)
+include (zlib)
+
+set (boost_INCLUDE_DIR  ${BUILDEM_INCLUDE_DIR}/boost)
+include_directories (${boost_INCLUDE_DIR})
+
+external_source (boost1550
+    1_55_0
+    boost_1_55_0.tar.gz
+    93780777cfbf999a600f62883bd54b17 
+    http://sourceforge.net/projects/boost/files/boost/1.55.0/)
+
+set (boost_LIBS ${BUILDEM_LIB_DIR}/libboost_thread.${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}
+                ${BUILDEM_LIB_DIR}/libboost_unit_test_framework.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+                ${BUILDEM_LIB_DIR}/libboost_filesystem.${BUILDEM_PLATFORM_DYLIB_EXTENSION}
+                ${BUILDEM_LIB_DIR}/libboost_chrono.${BUILDEM_PLATFORM_DYLIB_EXTENSION} )
+
+# Add layout=tagged param to first boost1550 install to explicitly create -mt libraries
+# some libraries require.  TODO: Possibly shore up all library find paths to only
+# allow use of built libs.
+message ("Installing ${boost1550_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
+ExternalProject_Add(${boost1550_NAME}
+    DEPENDS             ${python_NAME} ${zlib_NAME}
+    PREFIX              ${BUILDEM_DIR}
+    URL                 ${boost1550_URL}
+    URL_MD5             ${boost1550_MD5}
+    UPDATE_COMMAND      ""
+    PATCH_COMMAND       ""
+    CONFIGURE_COMMAND   ${BUILDEM_ENV_STRING} ./bootstrap.sh 
+        --with-libraries=date_time,filesystem,python,regex,serialization,system,test,thread,program_options,chrono
+        --with-python=${PYTHON_EXE} 
+        --prefix=${BUILDEM_DIR}
+        LDFLAGS=${BUILDEM_LDFLAGS}
+        CPPFLAGS=-I${BUILDEM_DIR}/include
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} ./b2 
+        --layout=tagged
+        -sNO_BZIP2=1 
+        -sZLIB_INCLUDE=${BUILDEM_DIR}/include 
+        -sZLIB_SOURCE=${zlib_SRC_DIR} install
+    BUILD_IN_SOURCE     1
+    INSTALL_COMMAND     ${BUILDEM_ENV_STRING} ./b2 
+        -sNO_BZIP2=1 
+        -sZLIB_INCLUDE=${BUILDEM_DIR}/include 
+        -sZLIB_SOURCE=${zlib_SRC_DIR} install
+)
+
+set_target_properties(${boost1550_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+endif (NOT boost1550_NAME)

cplex-shared.cmake

@@ -25,9 +25,15 @@ set(CPLEX_ILOCPLEX_LIBRARY CPLEX_ILOCPLEX_LIBRARY-NOTFOUND)
 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 "")
+    if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+    	set(SHARED_CPLEX_COMPILE_FLAGS "-fpic -stdlib=libstdc++")
+    	set(SHARED_CPLEX_LINK_FLAGS_1 "-Wl,-all_load")
+    	set(SHARED_CPLEX_LINK_FLAGS_2 "-stdlib=libstdc++")
+    else()
+    	set(SHARED_CPLEX_COMPILE_FLAGS "-fpic")
+    	set(SHARED_CPLEX_LINK_FLAGS_1 "-Wl,-all_load")
+    	set(SHARED_CPLEX_LINK_FLAGS_2 "")
+    endif()
 else()
     set(SHARED_CPLEX_COMPILE_FLAGS "-shared -fpic")
     set(SHARED_CPLEX_LINK_FLAGS_1 "-Wl,-whole-archive")

cppnetlib.cmake

@@ -0,0 +1,43 @@
+#
+# Install cppnetlib library from source
+#
+
+if (NOT cppnetlib_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8.6)
+
+include (ExternalProject)
+include (ExternalSource)
+include (BuildSupport)
+include (PatchSupport)
+
+include (boost)
+
+external_source (cppnetlib
+    0.11.0
+    cpp-netlib-0.11.0.tar.gz
+    6fba4f2f64f19af9f172fd60ad8e76ab 
+    http://commondatastorage.googleapis.com/cpp-netlib-downloads/0.11.0/
+    )
+
+# set libs properly
+set (CPPNETLIB_LIBRARIES ${BUILDEM_DIR}/lib64/libcppnetlib-client-connections.a ${BUILDEM_DIR}/lib64/libcppnetlib-server-parsers.a ${BUILDEM_DIR}/lib64/libcppnetlib-uri.a)
+
+message ("Installing ${cppnetlib_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
+ExternalProject_Add(${cppnetlib_NAME}
+    DEPENDS                 ${boost_NAME}
+    PREFIX                  ${BUILDEM_DIR}
+    URL                     ${cppnetlib_URL}
+    URL_MD5                 ${cppnetlib_MD5}
+    UPDATE_COMMAND          ""
+    PATCH_COMMAND           ""
+    CONFIGURE_COMMAND       ${BUILDEM_ENV_STRING} ${CMAKE_COMMAND} ${cppnetlib_SRC_DIR} 
+        -DCMAKE_INSTALL_PREFIX=${BUILDEM_DIR}
+        -DCMAKE_PREFIX_PATH=${BUILDEM_DIR}
+        BUILD_COMMAND           ${BUILDEM_ENV_STRING} $(MAKE)
+    INSTALL_COMMAND         ${BUILDEM_ENV_STRING} $(MAKE) install
+)
+
+set_target_properties(${cppnetlib_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+endif (NOT cppnetlib_NAME)

dlib.cmake

@@ -12,10 +12,10 @@ include (BuildSupport)
 include (PatchSupport)
 
 external_source (dlib
-    18.3
-    dlib-18.3.tar.bz2
-    1ad26ec7bddccf8a605e1edfd0620c65
-    http://downloads.sourceforge.net/project/dclib/dlib/v18.3
+    18.10
+    dlib-18.10.tar.bz2
+    ede77c5a1fb8c249b13987728424be74
+    http://downloads.sourceforge.net/project/dclib/dlib/v18.10
     FORCE)
 
 message ("Installing ${dlib_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")

drmaa-python.cmake

@@ -0,0 +1,40 @@
+#
+# Install drmaa-python library from source
+#
+
+if (NOT drmaa-python_NAME)
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+include (ExternalProject)
+include (ExternalSource)
+include (BuildSupport)
+
+include (python)
+include (setuptools)
+
+external_source (drmaa-python
+    0.5
+    drmaa-0.5.tar.gz
+    04c7fa199a86ccf20d3b91c8705cb8be 
+    http://drmaa-python.googlecode.com/files/
+    )
+
+message ("Installing ${drmaa-python_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
+ExternalProject_Add(${drmaa-python_NAME}
+    DEPENDS             ${python_NAME} ${setuptools_NAME}
+    PREFIX              ${BUILDEM_DIR}
+    URL                 ${drmaa-python_URL}
+    URL_MD5             ${drmaa-python_MD5}
+    UPDATE_COMMAND      ""
+    PATCH_COMMAND       ""
+    CONFIGURE_COMMAND   ""
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py install
+    BUILD_IN_SOURCE     1
+    TEST_COMMAND        ""
+    INSTALL_COMMAND     ""
+)
+
+set_target_properties(${drmaa-python_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)
+
+endif (NOT drmaa-python_NAME)