CUDA pipeline for computing APR

CMakeLists.txt

@@ -6,7 +6,7 @@ project(APR DESCRIPTION "Adaptive Particle Representation library")
 
 message(STATUS "CMAKE VERSION ${CMAKE_VERSION}")
 
-set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
 if(POLICY CMP0135)
@@ -171,17 +171,17 @@ if(WIN32)
 
 
 else()
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++14 ")
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++17 ")
 
     if(CMAKE_COMPILER_IS_GNUCC)
-        set(CMAKE_CXX_FLAGS_RELEASE "-O4 -ffast-math")
+        set(CMAKE_CXX_FLAGS_RELEASE "-O4")
         set(CMAKE_CXX_FLAGS_DEBUG "-O0 -g  -Wall -pedantic")
         set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Bdynamic")
         if(NOT WIN32)
             set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -ldl -lz")
         endif()
     elseif (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
-        set(CMAKE_CXX_FLAGS_RELEASE "-O3 -ffast-math")
+        set(CMAKE_CXX_FLAGS_RELEASE "-O3")
         set(CMAKE_CXX_FLAGS_DEBUG "-O0 -g  -Wall -pedantic")
         set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lz")
     endif()
@@ -209,10 +209,11 @@ set_property(TARGET aprObjLib PROPERTY POSITION_INDEPENDENT_CODE ON)
 
 if(APR_USE_CUDA)
     message(STATUS "APR: Building CUDA for APR")
-    set(CMAKE_CUDA_STANDARD 14)
+    set(CMAKE_CUDA_COMPILER "/usr/local/cuda/bin/nvcc")
+    set(CMAKE_CUDA_STANDARD 17)
     set(CMAKE_CUDA_RUNTIME_LIBRARY "Static")
-    set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} --default-stream per-thread -Xptxas -v -DAPR_USE_CUDA")
-    set(CMAKE_CUDA_FLAGS_RELEASE "-O3 --use_fast_math") # -lineinfo for profiling
+    set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -rdc=true --fmad=false --default-stream per-thread -Wno-deprecated-gpu-targets -Xptxas -v -DAPR_USE_CUDA")
+    set(CMAKE_CUDA_FLAGS_RELEASE "-O3") # -lineinfo for profiling
     set(CMAKE_CUDA_FLAGS_DEBUG "-O0 -g -G")
     if(APR_BENCHMARK)
         set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -DAPR_BENCHMARK")
@@ -226,6 +227,7 @@ if(APR_USE_CUDA)
             src/algorithm/LocalIntensityScale.cu
             src/algorithm/OVPC.cu
             src/data_structures/APR/access/GPUAccess.cu
+            src/data_structures/APR/access/LinearAccessCuda.cu
             src/numerics/miscCuda.cu
             src/numerics/APRDownsampleGPU.cu
             src/numerics/PixelNumericsGPU.cu
@@ -241,6 +243,7 @@ if(APR_BUILD_STATIC_LIB)
     # generate static library used as a intermediate step in generating fat lib
     set(STATIC_TARGET_NAME staticLib)
     add_library(${STATIC_TARGET_NAME} STATIC $<TARGET_OBJECTS:aprObjLib> ${APR_CUDA_SOURCE_FILES})
+    set_property(TARGET ${STATIC_TARGET_NAME} PROPERTY CUDA_ARCHITECTURES OFF)
     target_compile_features(${STATIC_TARGET_NAME} PUBLIC cxx_std_14)
     set_target_properties(${STATIC_TARGET_NAME} PROPERTIES OUTPUT_NAME ${LIBRARY_NAME})
     set_target_properties(${STATIC_TARGET_NAME} PROPERTIES CUDA_SEPARABLE_COMPILATION OFF)
@@ -262,7 +265,7 @@ if(APR_BUILD_SHARED_LIB)
 # generate fat shared library
     set(SHARED_TARGET_NAME sharedLib)
     add_library(${SHARED_TARGET_NAME} SHARED $<TARGET_OBJECTS:aprObjLib> ${APR_CUDA_SOURCE_FILES})
-
+    set_property(TARGET ${SHARED_TARGET_NAME} PROPERTY CUDA_ARCHITECTURES OFF)
     target_include_directories(${SHARED_TARGET_NAME} PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/src> $<BUILD_INTERFACE:${PROJECT_BINARY_DIR}>)
     set_target_properties(${SHARED_TARGET_NAME} PROPERTIES OUTPUT_NAME ${LIBRARY_NAME})
     set_target_properties(${SHARED_TARGET_NAME} PROPERTIES LIBRARY_OUTPUT_NAME ${LIBRARY_NAME})

examples/CMakeLists.txt

@@ -1,5 +1,6 @@
 macro(buildTarget TARGET)
     add_executable(${TARGET} ${TARGET}.cpp)
+    set_property(TARGET ${TARGET} PROPERTY CUDA_SEPARABLE_COMPILATION ON)
     target_link_libraries(${TARGET} ${HDF5_LIBRARIES} ${TIFF_LIBRARIES} ${APR_BUILD_LIBRARY} Threads::Threads ${OPENMP_LINK})
 endmacro(buildTarget)
 

examples/Example_get_apr.cpp

@@ -48,7 +48,7 @@ int runAPR(cmdLineOptions options) {
     //the apr datastructure
     APR apr;
 
-    APRConverter<float> aprConverter;
+    APRConverter<uint16_t> aprConverter;
 
     //read in the command line options into the parameters file
     aprConverter.par.Ip_th = options.Ip_th;

examples/Example_get_apr.h

@@ -30,7 +30,7 @@ struct cmdLineOptions{
     bool auto_parameters = false;
 
     float Ip_th = 0;
-    float lambda = -1;
+    float lambda = 3.0;
     float sigma_th = 0;
     float rel_error = 0.1;
     float grad_th = 1;