Adding cmake based build system (tested under Linux and Mac OSX)

CMakeLists.txt

@@ -0,0 +1,166 @@
+# cmake compatibility issues
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+# project name
+PROJECT(FourierConvolutionCUDALib CXX)
+if(NOT(${CMAKE_VERSION} VERSION_LESS "3.0.0"))
+cmake_policy(SET CMP0042 NEW)
+endif()
+
+if(${CMAKE_VERSION} VERSION_GREATER "3.1")
+cmake_policy(SET CMP0054 NEW)
+endif()
+
+
+# version number
+SET (FOURIERCONVOLUTIONCUDALIB_NAME "CUDA FOURIER CONVOLUTION LIBRARY")
+SET (FOURIERCONVOLUTIONCUDALIB_CODENAME "${PROJECT_NAME}")
+SET (FOURIERCONVOLUTIONCUDALIB_COPYRIGHT_YEARS "2013")
+SET (FOURIERCONVOLUTIONCUDALIB_VERSION_MAJOR 2)
+SET (FOURIERCONVOLUTIONCUDALIB_VERSION_MINOR 5)
+SET (FOURIERCONVOLUTIONCUDALIB_VERSION_PATCH 0)
+SET (FOURIERCONVOLUTIONCUDALIB_VERSION_TYPE SNAPSHOT)
+SET (FOURIERCONVOLUTIONCUDALIB_VERSION_STRING "${FOURIERCONVOLUTIONCUDALIB_VERSION_MAJOR}.${FOURIERCONVOLUTIONCUDALIB_VERSION_MINOR}.${FOURIERCONVOLUTIONCUDALIB_VERSION_PATCH}-${CMAKE_BUILD_TYPE}")
+SET (FOURIERCONVOLUTIONCUDALIB_VERSION "${FOURIERCONVOLUTIONCUDALIB_VERSION_MAJOR}.${FOURIERCONVOLUTIONCUDALIB_VERSION_MINOR}.${FOURIERCONVOLUTIONCUDALIB_VERSION_PATCH}")
+SET (FOURIERCONVOLUTIONCUDALIB_VENDOR_ID "mpi cbg")
+SET (FOURIERCONVOLUTIONCUDALIB_VENDOR_NAME "Max Planck Institute of Molecular Cell Biology and Genetics ")
+SET (FOURIERCONVOLUTIONCUDALIB_VENDOR_URL "www.mpi-cbg.de")
+SET (FOURIERCONVOLUTIONCUDALIB_ID "${FOURIERCONVOLUTIONCUDALIB_VENDOR_ID}.${PROJECT_NAME}")
+
+# trying to setup paths so this package can be picked up
+set(INSTALL_LIB_DIR lib CACHE PATH "Installation directory for libraries")
+set(INSTALL_INCLUDE_DIR include CACHE PATH "Installation directory for header files")
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE "Release" CACHE STRING
+      "Choose the type of build, options are: Debug Release
+RelWithDebInfo MinSizeRel."
+      FORCE)
+endif(NOT CMAKE_BUILD_TYPE)
+MESSAGE(">> Setting up ${CMAKE_BUILD_TYPE} build")
+
+# shared path is architecture independent for now, TODO extend this to lib/bin/include
+IF(UNIX)
+  IF(APPLE)
+    set(INSTALL_SHARE_DIR ${PROJECT_NAME}.app/Contents/Resources/ CACHE PATH "Installation directory for shared files")
+    #the following was tested with OSX 10.8.5 and Xcode 5.0.2
+    #seems to me that under apple the rpath is not stripped automatically when doing the install
+    #under linux it is
+    SET(CMAKE_SKIP_RPATH ON)
+  ELSE(APPLE)
+    set(INSTALL_SHARE_DIR lib/CMake/${PROJECT_NAME} CACHE PATH "Installation directory for shared files")
+  ENDIF(APPLE)
+ELSE(UNIX)
+  IF(WIN32 AND NOT CYGWIN)
+    set(INSTALL_SHARE_DIR CMake CACHE PATH "Installation directory for shared files")
+  ELSE()
+    MESSAGE(FATAL_ERROR ">> UNKNOWN ARCHITECTURE .. unable to set share dir")
+  ENDIF()
+ENDIF(UNIX)
+
+# Make relative paths absolute (needed later on)
+foreach(p LIB INCLUDE SHARE)
+  set(var INSTALL_${p}_DIR)
+  if(NOT IS_ABSOLUTE "${${var}}")
+    set(${var} "${CMAKE_INSTALL_PREFIX}/${${var}}")
+  endif()
+endforeach()
+
+#########################################################################################################
+## CUDA related
+# project options
+OPTION(INCLUDE_CUDA "Set to OFF to not search for CUDA" ON)
+# find project dependencies
+# find cuda
+IF(INCLUDE_CUDA)
+    FIND_PACKAGE(CUDA)
+    IF(CUDA_FOUND)
+	SET(CUDA_VERBOSE_BUILD ON)
+
+	set(CUDA_NVCC_FLAGS -gencode arch=compute_10,code=sm_10;-gencode arch=compute_20,code=sm_20)
+	SET(CUDA_HOST_COMPILER "${CMAKE_CXX_COMPILER}")
+	IF(APPLE)
+	  IF(${CUDA_HOST_COMPILER} MATCHES "/usr/bin/.*cc" OR EXISTS "/usr/bin/llvm-g++")
+	    MESSAGE(">> adapting CUDA_HOST_COMPILER (${CUDA_HOST_COMPILER}) to match a CUDA supported compiler (/usr/bin/llvm-g++-4.2)")
+	    SET(CUDA_HOST_COMPILER "/usr/bin/llvm-g++")
+	    SET(CMAKE_CXX_COMPILER ${CUDA_HOST_COMPILER})
+	    SET(CMAKE_C_COMPILER "/usr/bin/llvm-gcc")
+	    SET(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -stdlib=libstdc++")
+
+	    SET(CUDA_PROPAGATE_HOST_FLAGS OFF)
+	  ELSE()
+	    MESSAGE(WARNING ">> unknown CUDA_HOST_COMPILER (${CUDA_HOST_COMPILER}) or /usr/bin/llvm-g++-4.2 does not exist, cuda host compiler remains set to default")
+	  ENDIF()
+	ENDIF(APPLE)
+	IF("${CUDA_VERSION}" VERSION_GREATER "5" OR "${CUDA_VERSION}" VERSION_EQUAL "5")
+	  MESSAGE(">> compiling for Compute Capability 2.x, 3.0 and 3.5 only ")
+          set(CUDA_NVCC_FLAGS "-gencode arch=compute_20,code=sm_20;-gencode arch=compute_30,code=sm_30;-gencode arch=compute_35,code=sm_35")
+	ELSE()
+	  MESSAGE(">> CUDA less than version 5.0 detected, compiling for Compute Capability 2.x only ")
+          set(CUDA_NVCC_FLAGS "-gencode arch=compute_20,code=sm_20;-gencode arch=compute_10,code=sm_10")
+	ENDIF()
+	set(CUDA_NVCC_FLAGS_RELEASE ${CUDA_NVCC_FLAGS_RELEASE};-O2;--use_fast_math)
+	set(CUDA_NVCC_FLAGS_DEBUG ${CUDA_NVCC_FLAGS_DEBUG};-g;-G)
+    ELSE(CUDA_FOUND)
+        MESSAGE(FATAL_ERROR ">> CUDA not found. Exiting ...")
+    ENDIF(CUDA_FOUND)
+
+	IF(WIN32)
+		IF(${CUDA_VERSION} VERSION_GREATER "7" OR ${CUDA_VERSION} VERSION_EQUAL "7")
+			IF(${CMAKE_SIZEOF_VOID_P} EQUAL 4)
+				message(FATAL_ERROR ">> CUDA version 7 or higher does not support 32bit builds on Windows (found CMAKE_SIZEOF_VOID_P ${CMAKE_SIZEOF_VOID_P})")
+			ELSE()
+				message(">> [Windows] 64bit build detected, size of void pointer ${CMAKE_SIZEOF_VOID_P}")
+			ENDIF()
+
+		ENDIF()
+		SET(CUDA_ATTACH_VS_BUILD_RULE_TO_CUDA_FILE OFF)
+
+	ENDIF(WIN32)
+ENDIF(INCLUDE_CUDA)
+
+
+# add subdirectories
+ADD_SUBDIRECTORY(src)
+
+FIND_PACKAGE (Boost 1.42 COMPONENTS system filesystem unit_test_framework thread QUIET)
+IF(Boost_FOUND)
+ADD_SUBDIRECTORY(tests)
+enable_testing()
+include("CTestLists.txt")
+ELSE()
+MESSAGE(">> Boost libraries not found, skipping building setting up tests")
+ENDIF()
+
+# Export the package for use from the build-tree
+# (this registers the build-tree with a global CMake-registry)
+#              v = binary    v = library
+
+export(PACKAGE ${PROJECT_NAME})
+
+# Create the fourierconvolutioncudalib-config.cmake and fourierconvolutioncudalib-config-version files
+file(RELATIVE_PATH REL_INCLUDE_DIR "${INSTALL_SHARE_DIR}"
+   "${INSTALL_INCLUDE_DIR}")
+# ... for the build tree
+set(CONF_INCLUDE_DIRS "${PROJECT_SOURCE_DIR}" "${PROJECT_BINARY_DIR}")
+configure_file(fourierconvolutioncudalib-config.cmake.in
+  "${PROJECT_BINARY_DIR}/fourierconvolutioncudalib-config.cmake" @ONLY)
+# ... for the install tree
+set(CONF_INCLUDE_DIRS "\${FOURIERCONVOLUTIONCUDALIB}/${REL_INCLUDE_DIR}")
+configure_file(fourierconvolutioncudalib-config.cmake.in
+  "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/fourierconvolutioncudalib-config.cmake" @ONLY)
+# ... for both
+configure_file(fourierconvolutioncudalib-config-version.cmake.in
+  "${PROJECT_BINARY_DIR}/fourierconvolutioncudalib-config-version.cmake" @ONLY)
+
+# Install the fourierconvolutioncudalib-config.cmake and fourierconvolutioncudalib-config-version.cmake
+install(FILES
+  "${PROJECT_BINARY_DIR}/${CMAKE_FILES_DIRECTORY}/fourierconvolutioncudalib-config.cmake"
+  "${PROJECT_BINARY_DIR}/fourierconvolutioncudalib-config-version.cmake"
+  DESTINATION "${INSTALL_SHARE_DIR}" COMPONENT dev)
+
+# Install the export set for use with the install-tree 
+install(EXPORT fourierconvolutioncudalib-targets 
+  DESTINATION "${INSTALL_SHARE_DIR}" COMPONENT dev)
+
+
+

CTestLists.txt

@@ -0,0 +1,10 @@
+# include(BoostTestTargets)
+# add_boost_test(Independent
+#  SOURCES
+#  test_Independent.cpp
+#  TESTS
+#  Independent_suite)
+
+
+add_test(NAME gpu_convolve COMMAND test_gpu_convolve)
+

README.md

@@ -3,11 +3,58 @@ FourierConvolutionCUDALib
 
 Implementation of 3d non-separable convolution using CUDA & FFT Convolution, originally implemented by Fernando Amat for our Nature Methods paper (http://www.nature.com/nmeth/journal/v11/n6/full/nmeth.2929.html).
 
-To compile it under Linux/Mac/Windows I suggest NSight. Clone this repository into your cuda-workspace directory. Then make a new shared library project with the same name as the directory.
+Windows Build Instructions
+--------------------------
+
+To compile it under Windows, NSight available from the CUDA SDK is suggested. Clone this repository into your cuda-workspace directory. Then make a new shared library project with the same name as the directory.
 
 Under Project > Properties > Build > Settings > Tool Settings > NVCC Linker add -lcufft and -lcuda to the command line pattern so that it looks like this:
 
 ${COMMAND} ${FLAGS} -lcufft -lcuda ${OUTPUT_FLAG} ${OUTPUT_PREFIX} ${OUTPUT} ${INPUTS}
 
 Now build the .so/.dll library and put it into the Fiji directory.
 
+The cmake build system is also supported under Windows 7 64bit now!
+
+```bash
+$ cd X:\path\to\repo
+$ mkdir build
+$ cd build
+$ cmake.exe -G "Visual Studio 12 2013 Win64" -DCMAKE_INSTALL_PREFIX=C:/msys64/home/steinbac/ftmp -DBOOST_LIBRARYDIR=C:/boost_1_58_0/msvc-12-x86_64/lib64-msvc-12.0 -DBOOST_ROOT=C:/boost_1_58_0/msvc-12-x86_64 ..
+$ cmake.exe --build . --target ALL_BUILD --config Release
+$ ctest.exe -C Release #(optional) the above builds in Release mode
+$ cmake.exe --build . --target install --config Release
+```
+
+OSX/Linux Build Instructions
+----------------------------
+
+First, make sure that CUDA must be available through `PATH`, `LD_LIBRARY_PATH` or equivalent. The build system is based on cmake, so please install this at any version higher or equal than 2.8.
+
+```bash
+$ cd /path/to/repo
+$ mkdir build
+$ cd build
+$ cmake -DCMAKE_INSTALL_PREFIX=/directory/of/your/choice .. #default is /usr/lib/ or /usr/lib64 depending on your OS
+$ make
+$ ctest #(optional) in case you'd like to make sure the library does what it should on your system
+$ make install
+```
+
+
+Dependencies
+------------
+
+The unit tests that come with the library require boost (version 1.42 or higher) to be available to the cmake build system. If cmake is unable to detect them, try:
+
+```
+$ cmake -DCMAKE_INSTALL_PREFIX=/directory/of/your/choice -DBOOST_ROOT=/path/to/boost/root .. #default is /usr/lib/ or /usr/lib64 depending on your OS
+```
+
+Here, ```/path/to/boost/root``` should contain the boost libraries and the boost headers.
+
+
+How to get Help
+===============
+
+In case something does not work, do not hesitate to open a ticket on our github page: https://github.com/StephanPreibisch/FourierConvolutionCUDALib

fourierconvolutioncudalib-config-version.cmake.in

@@ -0,0 +1,11 @@
+set(PACKAGE_VERSION "@FOURIERCONVOLUTIONCUDALIB_VERSION@")
+
+# Check whether the requested PACKAGE_FIND_VERSION is compatible
+if("${PACKAGE_VERSION}" VERSION_LESS "${PACKAGE_FIND_VERSION}")
+  set(PACKAGE_VERSION_COMPATIBLE FALSE)
+else()
+  set(PACKAGE_VERSION_COMPATIBLE TRUE)
+  if ("${PACKAGE_VERSION}" VERSION_EQUAL "${PACKAGE_FIND_VERSION}")
+    set(PACKAGE_VERSION_EXACT TRUE)
+  endif()
+endif()

fourierconvolutioncudalib-config.cmake.in

@@ -0,0 +1,33 @@
+# - Config file for the FooBar package
+# It defines the following variables
+#  FOURIERCONVOLUTIONCUDALIB_INCLUDE_DIRS - include directories for fourierconvolutioncudalib
+#  FOURIERCONVOLUTIONCUDALIB_LIBRARIES    - libraries to link against
+#  FOURIERCONVOLUTIONCUDALIB_EXECUTABLE   - the bar executable
+
+# Compute paths
+get_filename_component(FOURIERCONVOLUTIONCUDALIB_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
+
+
+# Our library dependencies (contains definitions for IMPORTED targets)
+include("${FOURIERCONVOLUTIONCUDALIB_CMAKE_DIR}/fourierconvolutioncudalib-targets.cmake")
+
+# These are IMPORTED targets created by fourierconvolutioncudalib-targets.cmake
+IF(UNIX)
+  IF(APPLE)
+    get_filename_component(FOURIERCONVOLUTIONCUDALIB_INCLUDE_DIRS "${FOURIERCONVOLUTIONCUDALIB_CMAKE_DIR}/../../include" ABSOLUTE)
+    get_filename_component(FOURIERCONVOLUTIONCUDALIB_LIB_DIRS "${FOURIERCONVOLUTIONCUDALIB_CMAKE_DIR}/../../lib" ABSOLUTE)
+    get_filename_component(FOURIERCONVOLUTIONCUDALIB_BIN_DIRS "${FOURIERCONVOLUTIONCUDALIB_CMAKE_DIR}/../../bin" ABSOLUTE)
+    ELSE(APPLE)
+    get_filename_component(FOURIERCONVOLUTIONCUDALIB_INCLUDE_DIRS "${FOURIERCONVOLUTIONCUDALIB_CMAKE_DIR}/../../../include" ABSOLUTE)
+    get_filename_component(FOURIERCONVOLUTIONCUDALIB_LIB_DIRS "${FOURIERCONVOLUTIONCUDALIB_CMAKE_DIR}/../../../lib" ABSOLUTE)
+    get_filename_component(FOURIERCONVOLUTIONCUDALIB_BIN_DIRS "${FOURIERCONVOLUTIONCUDALIB_CMAKE_DIR}/../../../bin" ABSOLUTE)
+  ENDIF(APPLE)
+ENDIF(UNIX)
+
+set(FOURIERCONVOLUTIONCUDALIB_LIBRARIES  "${FOURIERCONVOLUTIONCUDALIB_LIB_DIRS}/libFourierConvolutionCUDALib.so")
+
+set(FOURIERCONVOLUTIONCUDALIB_VERSION  "@FOURIERCONVOLUTIONCUDALIB_VERSION@")
+set(FOURIERCONVOLUTIONCUDALIB_VERSION_MAJOR  "@FOURIERCONVOLUTIONCUDALIB_VERSION_MAJOR@")
+set(FOURIERCONVOLUTIONCUDALIB_VERSION_MINOR  "@FOURIERCONVOLUTIONCUDALIB_VERSION_MINOR@")
+set(FOURIERCONVOLUTIONCUDALIB_VERSION_PATCH  "@FOURIERCONVOLUTIONCUDALIB_VERSION_PATCH@")
+set(FOURIERCONVOLUTIONCUDALIB_BUILD_TYPE  "@CMAKE_BUILD_TYPE@")

src/CMakeLists.txt

@@ -0,0 +1,39 @@
+# include directories
+# src directory
+INCLUDE_DIRECTORIES(.)
+
+# build and link
+FIND_PACKAGE(CUDA QUIET)
+CUDA_ADD_LIBRARY(${PROJECT_NAME} convolution3Dfft.cu standardCUDAfunctions.cu SHARED)
+CUDA_ADD_LIBRARY(${PROJECT_NAME}_static convolution3Dfft.cu standardCUDAfunctions.cu)
+CUDA_ADD_CUFFT_TO_TARGET(${PROJECT_NAME})
+CUDA_ADD_CUFFT_TO_TARGET(${PROJECT_NAME}_static)
+
+IF(WIN32)
+IF(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
+include (GenerateExportHeader)
+GENERATE_EXPORT_HEADER( ${PROJECT_NAME}
+			BASE_NAME ${PROJECT_NAME}
+            EXPORT_MACRO_NAME ${PROJECT_NAME}_EXPORT
+            EXPORT_FILE_NAME ${PROJECT_NAME}_Export.h
+            STATIC_DEFINE ${PROJECT_NAME}_BUILT_AS_STATIC
+)
+set_target_properties(${PROJECT_NAME}_static PROPERTIES COMPILE_FLAGS "-D${PROJECT_NAME}_BUILT_AS_STATIC")
+INCLUDE_DIRECTORIES(${PROJECT_BINARY_DIR}/src)
+ENDIF()
+ENDIF()
+
+TARGET_LINK_LIBRARIES(${PROJECT_NAME}_static ${CUDA_CUDA_LIBRARY})
+TARGET_LINK_LIBRARIES(${PROJECT_NAME} ${CUDA_CUDA_LIBRARY})
+
+SET_TARGET_PROPERTIES(${PROJECT_NAME} PROPERTIES PUBLIC_HEADER "${PROJECT_SOURCE_DIR}/src/convolution3Dfft.h;${PROJECT_NAME}_Export.h") 
+SET_TARGET_PROPERTIES(${PROJECT_NAME}_static PROPERTIES PUBLIC_HEADER "${PROJECT_SOURCE_DIR}/src/convolution3Dfft.h;${PROJECT_NAME}_Export.h") 
+
+INSTALL(TARGETS ${PROJECT_NAME} ${PROJECT_NAME}_static
+  EXPORT fourierconvolutioncudalib-targets 
+  LIBRARY DESTINATION ${INSTALL_LIB_DIR}
+  ARCHIVE DESTINATION ${INSTALL_LIB_DIR}
+  PUBLIC_HEADER DESTINATION ${INSTALL_INCLUDE_DIR}
+  )
+
+

src/FourierConvolutionCUDALib_Export.h

@@ -0,0 +1,41 @@
+
+#ifndef FourierConvolutionCUDALib_EXPORT_H
+#define FourierConvolutionCUDALib_EXPORT_H
+
+#ifdef FourierConvolutionCUDALib_BUILT_AS_STATIC
+#  define FourierConvolutionCUDALib_EXPORT
+#  define FOURIERCONVOLUTIONCUDALIB_NO_EXPORT
+#else
+#  ifndef FourierConvolutionCUDALib_EXPORT
+#    ifdef FourierConvolutionCUDALib_EXPORTS
+        /* We are building this library */
+#      define FourierConvolutionCUDALib_EXPORT __declspec(dllexport)
+#    else
+        /* We are using this library */
+#      define FourierConvolutionCUDALib_EXPORT __declspec(dllimport)
+#    endif
+#  endif
+
+#  ifndef FOURIERCONVOLUTIONCUDALIB_NO_EXPORT
+#    define FOURIERCONVOLUTIONCUDALIB_NO_EXPORT 
+#  endif
+#endif
+
+#ifndef FOURIERCONVOLUTIONCUDALIB_DEPRECATED
+#  define FOURIERCONVOLUTIONCUDALIB_DEPRECATED __declspec(deprecated)
+#endif
+
+#ifndef FOURIERCONVOLUTIONCUDALIB_DEPRECATED_EXPORT
+#  define FOURIERCONVOLUTIONCUDALIB_DEPRECATED_EXPORT FourierConvolutionCUDALib_EXPORT FOURIERCONVOLUTIONCUDALIB_DEPRECATED
+#endif
+
+#ifndef FOURIERCONVOLUTIONCUDALIB_DEPRECATED_NO_EXPORT
+#  define FOURIERCONVOLUTIONCUDALIB_DEPRECATED_NO_EXPORT FOURIERCONVOLUTIONCUDALIB_NO_EXPORT FOURIERCONVOLUTIONCUDALIB_DEPRECATED
+#endif
+
+#define DEFINE_NO_DEPRECATED 0
+#if DEFINE_NO_DEPRECATED
+# define FOURIERCONVOLUTIONCUDALIB_NO_DEPRECATED
+#endif
+
+#endif