Update CMake File, cleanup, add WITH_CUDA and WITH_OPENMP defines, add fftw3 float lib

CMakeLists.txt

 CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
 PROJECT( BioEM )
 
+SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
+SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}")
+
 FIND_PACKAGE(CUDA)
 
-    SET( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -march=native -fopenmp -fweb -mfpmath=sse -frename-registers -minline-all-stringops -ftracer -funroll-loops -fpeel-loops -fprefetch-loop-arrays -ffast-math -ggdb" )
+FIND_PACKAGE(PkgConfig REQUIRED)
+
+PKG_CHECK_MODULES(FFTW fftw3 REQUIRED)
+INCLUDE_DIRECTORIES(${FFTW_INCLUDE_DIRS})
+
+FIND_PACKAGE(Boost 1.54 REQUIRED)
+INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
 
+FIND_PACKAGE(OpenMP)
+IF(OPENMP_FOUND)
+	SET( CMAKE_CXX_FLAGS ${OpenMP_CXX_FLAGS})
+	ADD_DEFINITIONS(-DWITH_OPENMP)
+ENDIF()
+
+SET( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -march=native -fopenmp -fweb -mfpmath=sse -frename-registers -minline-all-stringops -ftracer -funroll-loops -fpeel-loops -fprefetch-loop-arrays -ffast-math -ggdb" )
 SET( CUDA_NVCC_FLAGS "${CUDA_NVCC_FLAGS};-gencode arch=compute_35,code=sm_35;--use_fast_math;-ftz=true;-O4;-Xptxas -O4" )
 
 INCLUDE_DIRECTORIES( include $HOME/usr/include )
 
+IF(CUDA_FOUND)
+	ADD_DEFINITIONS(-DWITH_CUDA)
 	CUDA_ADD_EXECUTABLE( bioEM bioem.cpp  main.cpp  map.cpp  model.cpp  param.cpp cmodules/timer.cpp bioem_cuda.cu )
+ELSE()
+	ADD_EXECUTABLE( bioEM bioem.cpp  main.cpp  map.cpp  model.cpp  param.cpp cmodules/timer.cpp )
+ENDIF()
+TARGET_LINK_LIBRARIES(bioEM -L${FFTW_LIBDIR} -lfftw3 -lfftw3f)
+TARGET_LINK_LIBRARIES(bioEM -L${Boost_LIBRARY_DIRS} -lboost_program_options)
 
 SET( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++0x -Wall -Wno-vla -Wno-unused-result -pedantic" )
 
-    TARGET_LINK_LIBRARIES( bioEM -lfftw3 -fopenmp -lboost_program_options )
-
+message(STATUS "FFTW library: ${FFTW_LIBDIR}")
+message(STATUS "Boost directory: ${Boost_LIBRARY_DIRS}")
+message(STATUS "FFTW includedir: ${FFTW_INCLUDEDIR}")
 
+#get_cmake_property(_variableNames VARIABLES)
+#foreach (_variableName ${_variableNames})
+#message(STATUS "${_variableName}=${${_variableName}}")
+#endforeach()

main.cpp

@@ -32,11 +32,13 @@ int main(int argc, char* argv[])
     HighResTimer timer;
 
     bioem* bio;
+#ifdef WITH_CUDA
     if (getenv("GPU") && atoi(getenv("GPU")))
     {
 		bio = bioem_cuda_create();
     }
     else
+#endif
     {
         bio = new bioem;
 	}