merged with master

janelia-flyem · Sep 17, 2013 · 18c07f5 · 18c07f5
2 parents 8fd9e02 + fbcfc75
commit 18c07f5
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Showing 12 changed files with 62 additions and 142 deletions.
diff --git a/BuildSupport.cmake b/BuildSupport.cmake
@@ -15,9 +15,12 @@ if (NOT BUILDEM_ENV_STRING)
 
 
 if (NOT BUILDEM_DIR)
-    message (FATAL_ERROR "ERROR: FlyEM build directory (for all downloads & builds) should be specified via -DBUILDEM_DIR=<path> on cmake command line.")
+    message (FATAL_ERROR "ERROR: BuildEM build directory (for all downloads & builds) should be specified via -DBUILDEM_DIR=<path> on cmake command line.")
 endif ()
 
+if (NOT BUILDEM_REPO_DIR)
+    message (FATAL_ERROR "ERROR: BUILDEM_REPO_DIR must be specified via your application's CMakeLists.txt file, and must be set to ${BUILDEM_DIR}/src/buildem.")
+endif ()
 
 # Make sure the main directories for FlyEM build directory are already 
 # created so paths won't error out.

diff --git a/CMakeLists.txt b/CMakeLists.txt
diff --git a/ExternalSource.cmake b/ExternalSource.cmake
@@ -99,14 +99,26 @@ macro (external_source ABBREV SRC_VERSION FILENAME MD5)
 endmacro (external_source)
 
 # Define macro to set a number of variables per external git repo
+# Note: Besides these named args, this macro accepts the following optional args:
+#  OVERRIDE_NAME - Used to override the <package>_NAME and <package>_SRC_DIR variables set by this macro
 macro (external_git_repo ABBREV SRC_VERSION URL)
+	# Check for extra (optional) macro args.
+	set (extra_macro_args ${ARGN})
+	list(LENGTH extra_macro_args num_extra_args)
 
     # RELEASE builds are by default
     if (NOT ${ABBREV}_BUILD)
         set (${ABBREV}_BUILD "RELEASE")
     endif ()
 
+	# By default, package NAME and SRC_DIR are <package>-git
     set (external_source_name  ${ABBREV}-git)
+
+    # First optional macro arg overrides package NAME and SRC_DIR
+    if (${num_extra_args} GREATER 0)
+    	list(GET extra_macro_args 0 external_source_name)
+    endif ()
+
     message ("Setting external_git_repo: ${external_source_name}")
 
     # Append this external source name to our list of dependencies

diff --git a/README.md b/README.md
@@ -25,7 +25,6 @@ Buildem is predicated on some basic assertions:
 * Developer attention should be minimized since developer time is very expensive compared to freely available computer time.
 * Disk space is cheap and plentiful.
 * Each application build process should be easily specified and automated.
-* Required components should be easily shared on network drives among networked computers that can share software, i.e., the computers have compatible operating systems, because intranets have excellent bandwidth.
 * Required components can be automatically built from source, and CMake is a sufficiently flexible and cross-platform tool on which to base our system.
 * Builds of all components should be specific to OS, compiler, and compiler version to minimize conflicts in [ABI](http://en.wikipedia.org/wiki/Application_binary_interface), and we are not sure that pre-compiled components (e.g., RPMs) are available for all target machines/compilers.
 * Third-party pre-built packages, like Enthought Python Distribution, are not viable due to licensing costs for cluster operation as well as inability to easily adapt to new dependencies.

diff --git a/golang.cmake b/golang.cmake
@@ -11,9 +11,9 @@ include (ExternalSource)
 include (BuildSupport)
 
 external_source (golang
-    1.1
-    go1.1.src.tar.gz
-    4933f6a2f3ec1ffb01b42fd88de03851
+    1.1.2
+    go1.1.2.src.tar.gz
+    705feb2246c8ddaf820d7e171f1430c5
     http://go.googlecode.com/files)
 
 message ("Installing ${golang_NAME} into build area: ${BUILDEM_DIR} ...")

diff --git a/ilastik-gui.cmake b/ilastik-gui.cmake
@@ -42,11 +42,12 @@ configure_file(${TEMPLATE_DIR}/ilastik_script.template ${BUILDEM_DIR}/bin/ilasti
 set(LAUNCH_ILASTIK ilastik/tests/test_applets/pixelClassification/testPixelClassificationGui.py)
 configure_file(${TEMPLATE_DIR}/ilastik_script.template ${BUILDEM_DIR}/bin/ilastik_gui_test @ONLY)
 
-# Run the gui test script
-ExternalProject_add_step(${ilastik_NAME} test_ilastik_gui
-    DEPENDEES   install_gui_test
+# Run the gui test script after the ilastik-gui target is built
+add_custom_command (
+    TARGET     ${ilastik-gui_NAME}
+    POST_BUILD
     COMMAND     ${BUILDEM_ENV_STRING} ${BUILDEM_DIR}/bin/ilastik_gui_test
-    COMMENT     "Ran ilastik gui test"
+    COMMENT     "Running ilastik gui test"
 )
 
 endif (NOT ilastik-gui_NAME)

diff --git a/ilastik.cmake b/ilastik.cmake
@@ -41,9 +41,8 @@ SET(ILASTIK_VERSION ${ILASTIK_VERSION}
 
 external_git_repo (ilastik
     ${ILASTIK_VERSION}
-    http://github.com/janelia-flyem/flyem-ilastik)
-set(ilastik_NAME ilastik)
-set(ilastik_SRC_DIR "${BUILDEM_DIR}/src/${ilastik_NAME}")
+    http://github.com/janelia-flyem/flyem-ilastik
+    ilastik)
 set(lazyflow_SRC_DIR "${ilastik_SRC_DIR}/lazyflow")
 
 if("${ILASTIK_VERSION}" STREQUAL "master")

diff --git a/lemon.cmake b/lemon.cmake
@@ -11,33 +11,11 @@ include (ExternalSource)
 include (BuildSupport)
 include (PatchSupport)
 
-## FIXME: v1.2.3 of lemon doesn't compile under clang.
-## From their issue tracker (#449), it looks like the next release (v1.3) will fix this.
-## For now, this means that we MUST use gcc for this package.
-## As soon as v1.3 is ready, we should try to upgrade.
-#
-#set (CMAKE_C_COMPILER /usr/bin/gcc)
-#set (CMAKE_CXX_COMPILER /usr/bin/g++)
-
-# This is the snapshot of the lemon commit we are using, but we are using a 
-#  github-hosted tarball to avoid requiring CMake-2.8.10
-#
-## CMake 2.8.10 is required because we want to use ExternalProject_Add with a hg repo.
-#CMAKE_MINIMUM_REQUIRED(VERSION 2.8.10)
-#
-#message ("FIXME: Using a tag from the lemon mainline hg repo instead of a release.")
-#message ("       The tests in this version don't pass.")
-#message ("       As soon as lemon-1.3 is released, switch to it (and uncomment the test step)!")
-#external_git_repo (lemon
-#    473c71baff72
-#    http://lemon.cs.elte.hu/hg/lemon-main)
-
-# Using special cached tarball.  See note above.
 external_source (lemon
-  1.2.3
-  lemon-1.2.3.tar.gz
-  750251a77be450ddddedab14e5163afb
-  http://lemon.cs.elte.hu/pub/sources)
+    1.2.4
+	lemon-1.2.4.tar.gz
+	fd89e8bf5035b02e2622a48ac7fe0641
+    http://lemon.cs.elte.hu/pub/sources)
 
 message ("Installing ${lemon_NAME} into FlyEM build area: ${BUILDEM_DIR} ...")
 ExternalProject_Add(${lemon_NAME}
@@ -46,7 +24,12 @@ ExternalProject_Add(${lemon_NAME}
     URL_MD5             ${lemon_MD5}
     UPDATE_COMMAND      ""
     PATCH_COMMAND       ${BUILDEM_ENV_STRING} ${PATCH_EXE}
-    	${lemon_SRC_DIR}/lemon/CMakeLists.txt ${PATCH_DIR}/lemon.patch
+        # This patch fixes a build error that clang detects.
+        # (Already fixed in lemon trunk, but not in the tarball release.)
+    	${lemon_SRC_DIR}/lemon/graph_to_eps.h ${PATCH_DIR}/lemon.patch
+    	# Apparently one test file is missing from the release.
+    	# This patch removes it from CMakeLists.txt
+        ${lemon_SRC_DIR}/test/CMakeLists.txt ${PATCH_DIR}/lemon-test.patch
 
     CONFIGURE_COMMAND   ${BUILDEM_ENV_STRING} ${CMAKE_COMMAND} ${lemon_SRC_DIR} 
         -DBUILD_SHARED_LIBS=ON
@@ -62,9 +45,7 @@ ExternalProject_Add(${lemon_NAME}
 
     BUILD_COMMAND       ${BUILDEM_ENV_STRING} make
     INSTALL_COMMAND     ${BUILDEM_ENV_STRING} make install
-
-    # Sadly, the tests do not pass in this version that we are pulling.
-    #TEST_COMMAND        ${BUILDEM_ENV_STRING} make check
+    TEST_COMMAND        ${BUILDEM_ENV_STRING} make check
 )
 
 set_target_properties(${lemon_NAME} PROPERTIES EXCLUDE_FROM_ALL ON)

diff --git a/patches/lemon-test.patch b/patches/lemon-test.patch
@@ -0,0 +1,11 @@
+--- test/CMakeLists.txt	2013-08-26 15:10:22.000000000 -0400
++++ test/CMakeLists.txt.patched	2013-08-26 15:10:15.000000000 -0400
+@@ -13,7 +13,7 @@
+
+ SET(TESTS
+   adaptors_test
+-  arc_look_up_test
++  #arc_look_up_test
+   bellman_ford_test
+   bfs_test
+   circulation_test
diff --git a/patches/lemon.patch b/patches/lemon.patch
@@ -1,10 +1,10 @@
---- lemon/CMakeLists.txt	2013-02-20 15:19:54.068061699 -0500
-+++ lemon/CMakeLists.txt.patched	2013-02-20 15:20:39.467490359 -0500
-@@ -57,6 +57,7 @@
- INSTALL(
-   TARGETS lemon
-   ARCHIVE DESTINATION lib
-+  LIBRARY DESTINATION lib
-   COMPONENT library
- )
+--- lemon/graph_to_eps.h	2013-08-10 06:25:53.000000000 -0400
++++ lemon/graph_to_eps.h.patched	2013-08-26 15:01:35.000000000 -0400
+@@ -222,7 +222,6 @@
+   using T::_title;
+   using T::_copyright;
 
+-  using T::NodeTextColorType;
+   using T::CUST_COL;
+   using T::DIST_COL;
+   using T::DIST_BW;
diff --git a/vigra.cmake b/vigra.cmake
@@ -34,8 +34,6 @@ external_git_repo (vigra
     ${VIGRA_VERSION}
     http://github.com/ukoethe/vigra)
 
-#set(vigra_NAME vigra)
-
 if("${VIGRA_VERSION}" STREQUAL "master")
     set(VIGRA_UPDATE_COMMAND git checkout master && git pull)
 else()

diff --git a/vtk.cmake b/vtk.cmake
@@ -55,7 +55,11 @@ ExternalProject_Add(${vtk_NAME}
 	-DVTK_USE_TK=OFF
 	# NETCDF caused weird errors in vtk's xml
 	-DVTK_USE_SYSTEM_LIBXML2=ON
-    BUILD_COMMAND       ${BUILDEM_ENV_STRING} make
+	# We want vtk to be built in parallel if possible.
+	# Therefore we use $(MAKE) instead of 'make', which somehow enables sub-make files to use the jobserver correctly.
+	# See: http://stackoverflow.com/questions/2942465/cmake-and-parallel-building-with-make-jn
+	# And: http://www.cmake.org/pipermail/cmake/2011-April/043720.html
+    BUILD_COMMAND       ${BUILDEM_ENV_STRING} $(MAKE)
     #TEST_COMMAND        ${BUILDEM_ENV_STRING} make check
     INSTALL_COMMAND     ${BUILDEM_ENV_STRING} make install
 )