Feature/dart (#11)

Update to avoid fixing compilation issue on src/tools (due to : HDF5 cannot be found)

Author: zhangwei217245

.devcontainer/post-create.sh

@@ -24,7 +24,7 @@ mkdir -p /workspaces/install/pdc
 ln -s /workspaces/install/pdc $(dirname $PDC_SRC_DIR)
 
 # Build and install PDC
-export PDC_CMAKE_FLAGS="-DBUILD_MPI_TESTING=ON -DBUILD_SHARED_LIBS=ON -DUSE_SYSTEM_HDF5=OFF -DBUILD_TESTING=ON -DCMAKE_INSTALL_PREFIX=$PDC_DIR -DPDC_ENABLE_MPI=ON -DMERCURY_DIR=$MERCURY_DIR -DCMAKE_C_COMPILER=mpicc -DMPI_RUN_CMD=mpiexec "
+export PDC_CMAKE_FLAGS="-DBUILD_MPI_TESTING=ON -DBUILD_SHARED_LIBS=ON -DBUILD_TOOLS=OFF -DBUILD_TESTING=ON -DCMAKE_INSTALL_PREFIX=$PDC_DIR -DPDC_ENABLE_MPI=ON -DMERCURY_DIR=$MERCURY_DIR -DCMAKE_C_COMPILER=mpicc -DMPI_RUN_CMD=mpiexec "
 
 cd $PDC_SRC_DIR
 rm -rf build && mkdir -p build

.docker/dev_base.Dockerfile

@@ -123,6 +123,6 @@ RUN echo 'export LD_LIBRARY_PATH=$MERCURY_DIR/lib:$LD_LIBRARY_PATH' >> $WORK_SPA
     echo 'export PATH=$MERCURY_DIR/include:$MERCURY_DIR/lib:$PATH' >> $WORK_SPACE/pdc_env.sh
 
 
-ENV PDC_CMAKE_FLAGS="-DBUILD_MPI_TESTING=ON -DBUILD_SHARED_LIBS=ON -DUSE_SYSTEM_HDF5=OFF -DBUILD_TESTING=ON -DCMAKE_INSTALL_PREFIX=$PDC_DIR -DPDC_ENABLE_MPI=ON -DMERCURY_DIR=$MERCURY_DIR -DCMAKE_C_COMPILER=mpicc -DMPI_RUN_CMD=mpiexec "
+ENV PDC_CMAKE_FLAGS="-DBUILD_MPI_TESTING=ON -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=ON -DCMAKE_INSTALL_PREFIX=$PDC_DIR -DPDC_ENABLE_MPI=ON -DMERCURY_DIR=$MERCURY_DIR -DCMAKE_C_COMPILER=mpicc -DMPI_RUN_CMD=mpiexec "
 
 ENTRYPOINT [ "/workspaces/pdc/.devcontainer/post-attach.sh" ]

CMakeLists.txt

@@ -322,45 +322,6 @@ if(PDC_USE_CRAY_DRC)
   endif()
 endif()
 
-#-----------------------------------------------------------------------------
-# Find HDF5
-#-----------------------------------------------------------------------------
-#HDF5
-option(USE_SYSTEM_HDF5 "Use system-installed HDF5." ON)
-  if(USE_SYSTEM_HDF5)
-  find_package(HDF5 NO_MODULE NAMES hdf5 COMPONENTS C shared)
-  if(HDF5_FOUND)
-    set(HDF5_C_SHARED_LIBRARY hdf5-shared)
-#    if(NOT TARGET ${HDF5_C_SHARED_LIBRARY})
-#      message(FATAL_ERROR "Could not find hdf5 shared target, please make "
-#"sure that HDF5 has ben compiled with shared libraries enabled.")
-#    endif()
-    set(PDC_EXT_INCLUDE_DEPENDENCIES
-        ${PDC_EXT_INCLUDE_DEPENDENCIES}
-        ${HDF5_INCLUDE_DIR}
-      )
-    set(PDC_EXT_LIB_DEPENDENCIES
-      ${PDC_EXT_LIB_DEPENDENCIES}
-      ${HDF5_C_SHARED_LIBRARY}
-    )
-  else()
-    # Allow for HDF5 autotools builds
-    find_package(HDF5 MODULE REQUIRED)
-    if(HDF5_FOUND)
-      set(PDC_EXT_INCLUDE_DEPENDENCIES
-        ${PDC_EXT_INCLUDE_DEPENDENCIES}
-        ${HDF5_INCLUDE_DIRS}
-      )
-      set(PDC_EXT_LIB_DEPENDENCIES
-        ${PDC_EXT_LIB_DEPENDENCIES}
-        ${HDF5_LIBRARIES}
-      )
-    else()
-      message(FATAL_ERROR "Could not find HDF5, please check HDF5_DIR.")
-    endif()
-  endif()
-endif()
-
 #-----------------------------------------------------------------------------
 # DART Suffix Tree mode
 #-----------------------------------------------------------------------------
@@ -688,5 +649,4 @@ add_custom_target(format
   | xargs -0 clang-format -i -style=file && echo "... done"
   COMMENT "clang-format all source codes"
   VERBATIM 
-)
-
+)

src/tests/CMakeLists.txt

@@ -30,9 +30,8 @@ if(UUID_FOUND)
 endif(UUID_FOUND)
 
 # *************************************************
-# * Find MERCURY
+# *  MERCURY
 # *************************************************
-# Mercury
 find_package(MERCURY REQUIRED)
 if(MERCURY_FOUND)
   set(TEST_EXT_INCLUDE_DIRS ${MERCURY_INCLUDE_DIRS}
@@ -136,6 +135,13 @@ set(PROGRAMS
   query_data
   )
 
+# TODO: Check if import_vpic.c is needed. If yes, we have to add the following :
+# if (HDF5_FOUND) 
+#   set(TEST_EXT_LIB ${HDF5_LIBRARIES} ${TEST_EXT_LIB})
+#   set(TEST_EXT_INCLUDE_DIRS ${HDF5_INCLUDE_DIRS} ${TEST_EXT_INCLUDE_DIRS})
+# else ()
+#   message(FATAL_ERROR "Could not find HDF5, please make sure that HDF5 has been compiled with shared libraries enabled.")
+# endif()
 
 
 foreach(program ${PROGRAMS})
@@ -212,12 +218,6 @@ foreach(script ${SCRIPTS})
 endforeach(script)
 
 
-# *******************************************
-# Add the HDF5 library for pdc-neon
-# *******************************************
-FIND_LIBRARY(HDF5_LIBRARY NAMES hdf5_debug PATHS $ENV{HOME}/lib)
-
-
 # *******************************************
 # Create a transform library which contains:
 #  1. compression/depression functions

src/tools/CMakeLists.txt

@@ -12,35 +12,22 @@ include_directories(
   $ENV{HOME}/include
 )
 
-set(EXT_LIB "")
-set(EXT_INCLUDE_DIRS "")
-
-# *************************************************
-# * Find MERCURY
-# *************************************************
-# Mercury
-find_package(MERCURY REQUIRED)
-if(MERCURY_FOUND)
-  set(EXT_INCLUDE_DIRS ${MERCURY_INCLUDE_DIRS}
-    ${EXT_INCLUDE_DIRS}
-    )
-  set(EXT_LIB ${MERCURY_LIBRARIES} ${EXT_LIB})
-endif()
-include_directories(${EXT_INCLUDE_DIRS})
-
 set(PROGRAMS
   pdc_import
   pdc_export
   pdc_ls
   )
 
 add_library(cjson cjson/cJSON.c)
-set(EXT_LIB cjson ${EXT_LIB})
 
 foreach(program ${PROGRAMS})
   add_executable(${program} ${program}.c)
-  target_link_libraries(${program} pdc pdc_commons ${EXT_LIB})
+  target_link_libraries(${program} pdc)
+  target_link_libraries(${program} cjson)
 endforeach(program)
 
 
-
+# *******************************************
+# Add the HDF5 library for pdc-neon
+# *******************************************
+FIND_LIBRARY(HDF5_LIBRARY NAMES hdf5_debug PATHS $ENV{HOME}/lib)