Feature/dart (#12)

Author: zhangwei217245

.docker/dev_base.Dockerfile

@@ -17,6 +17,8 @@ RUN apt-get update && apt-get install -y \
     libmpich-dev \
     libhdf5-dev \
     libhdf5-mpich-dev \
+    libtiff5 \
+    libtiff5-dev \
     uuid \
     uuid-dev \
     autoconf \

examples/llsm/.gitignore

@@ -0,0 +1 @@
+build

examples/llsm/CMakeLists.txt

@@ -0,0 +1,96 @@
+cmake_minimum_required (VERSION 2.8.12)
+
+# Setup cmake policies.
+foreach(p
+    CMP0012
+    CMP0013
+    CMP0014
+    CMP0022 # CMake 2.8.12
+    CMP0025 # CMake 3.0
+    CMP0053 # CMake 3.1
+    CMP0054 # CMake 3.1
+    CMP0074 # CMake 3.12
+    CMP0075 # CMake 3.12
+    CMP0083 # CMake 3.14
+    CMP0093 # CMake 3.15
+  )
+  if(POLICY ${p})
+    cmake_policy(SET ${p} NEW)
+  endif()
+endforeach()
+
+project(PDC_LLSM_EXAM C)
+
+set(LLSM_EXT_INCLUDE_DIRS "")
+set(LLSM_EXT_LIBRARIES "")
+
+
+
+set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build." FORCE)
+
+find_package(PDC REQUIRED)
+if(PDC_FOUND)
+    #message(STATUS "PDC include directory: ${PDC_INCLUDE_DIR}")
+  set(LLSM_EXT_INCLUDE_DIRS ${PDC_INCLUDE_DIR}
+    ${LLSM_EXT_INCLUDE_DIRS}
+    )
+  set(LLSM_EXT_LIBRARIES pdc ${LLSM_EXT_LIBRARIES})
+endif()
+
+option(USE_SYSTEM_MPI "Use system-installed OpenMP." ON)
+if(USE_SYSTEM_MPI)
+  find_package(MPI)
+  if(MPI_FOUND)
+    add_definitions(-DLLSM_ENABLE_MPI=1)
+    SET(CMAKE_C_COMPILER ${MPI_C_COMPILER})
+    SET(CMAKE_CXX_COMPILER ${MPI_CXX_COMPILER})
+    set(LLSM_EXT_INCLUDE_DIRS ${MPI_C_INCLUDE_PATH}
+      ${LLSM_EXT_INCLUDE_DIRS}
+      )
+    set(LLSM_EXT_LIBRARIES ${MPI_C_LIBRARIES} ${LLSM_EXT_LIBRARIES})
+  endif()
+endif()
+
+option(USE_SYSTEM_OPENMP "Use system-installed OpenMP." ON)
+if(USE_SYSTEM_OPENMP)
+  find_package(OpenMP REQUIRED)
+  if(OPENMP_FOUND)
+      add_definitions(-DENABLE_OPENMP=1)
+      set(ENABLE_OPENMP 1)
+      set(OPENMP_LIBRARIES "${OpenMP_C_LIBRARIES}")
+      set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fopenmp")
+  else()
+      message(FATAL_ERROR "OpenMP not found")
+  endif()
+endif()
+
+include_directories(
+  ${LLSM_EXT_INCLUDE_DIRS}
+)
+
+
+# Find LibTIFF
+option(USE_LIB_TIFF "Enable LibTiff." ON)
+if(USE_LIB_TIFF)
+  find_package(TIFF REQUIRED)
+  if(TIFF_FOUND)
+    set(LLSM_LIB_SOURCE 
+      llsm_aux/parallelReadTiff.c
+      llsm_aux/csvReader.c
+      llsm_aux/pdc_list.c
+    )
+    # Add the LibTIFF include directory to the include path
+    include_directories(${TIFF_INCLUDE_DIRS})
+    add_library(llsm_tiff ${LLSM_LIB_SOURCE})
+    target_compile_options(llsm_tiff PRIVATE ${OpenMP_C_FLAGS})
+    target_link_libraries(llsm_tiff PUBLIC ${OpenMP_C_LIBRARIES})
+    target_link_libraries(llsm_tiff PUBLIC ${TIFF_LIBRARIES})
+    target_include_directories(llsm_tiff PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/llsm)
+
+    add_executable(llsm_importer llsm_importer.c)
+    target_link_libraries(llsm_importer ${PDC_EXT_LIB_DEPENDENCIES} pdc ${TIFF_LIBRARIES} llsm_tiff ${LLSM_EXT_LIBRARIES})
+    target_include_directories(llsm_importer PUBLIC ${LLSM_EXT_INCLUDE_DIRS})
+  else()
+    message(WARNING "LibTiff not found, ignore building the executables which requires LibTiff support.")
+  endif()
+endif()

tools/LLSM_IMPORTER.md renamed to examples/llsm/LLSM_IMPORTER.md

@@ -1,7 +1,8 @@
 #include "parallelReadTiff.h"
 #include "tiffio.h"
+#include "inttypes.h"
 
-#define ENABLE_OPENMP
+// #define ENABLE_OPENMP
 
 #ifdef ENABLE_OPENMP
 #include "omp.h"
@@ -50,7 +51,7 @@ readTiffParallelBak(uint64_t x, uint64_t y, uint64_t z, const char *fileName, vo
 
             int counter = 0;
             while (!TIFFSetDirectory(tif, (uint64_t)dir) && counter < 3) {
-                printf("Thread %d: File \"%s\" Directory \"%d\" failed to open. Try %d\n", w, fileName, dir,
+                printf("Thread %d: File \"%s\" Directory \"%"PRId64"\" failed to open. Try %d\n", w, fileName, dir,
                        counter + 1);
                 counter++;
             }
@@ -344,7 +345,7 @@ readTiffParallel2DBak(uint64_t x, uint64_t y, uint64_t z, const char *fileName,
 
             int counter = 0;
             while (!TIFFSetDirectory(tif, (uint64_t)0) && counter < 3) {
-                printf("Thread %d: File \"%s\" Directory \"%d\" failed to open. Try %d\n", w, fileName, dir,
+                printf("Thread %d: File \"%s\" Directory \"%"PRId64"\" failed to open. Try %d\n", w, fileName, dir,
                        counter + 1);
                 counter++;
             }