fix develop conflict with stable

.docker/base.Dockerfile

@@ -0,0 +1,90 @@
+# Use Ubuntu Jammy (latest LTS) as the base image
+FROM ubuntu:jammy
+
+# Install necessary tools, MPICH, UUID library and developer files
+RUN apt-get update && apt-get install -y \
+ build-essential \
+ git \
+ mpich \
+ libmpich-dev \
+ uuid \
+ uuid-dev \
+ autoconf \
+ libtool \
+ cmake \
+ cmake-curses-gui \
+ wget \
+ axel \
+ curl \
+ vim \
+ nano \
+ gdb \
+ cgdb \
+ curl \
+ valgrind
+
+# Set WORK_SPACE environment variable and create necessary directories
+ENV WORK_SPACE=/home/codespace
+RUN mkdir -p $WORK_SPACE
+
+# Clone the repositories
+WORKDIR $WORK_SPACE/source
+RUN git clone https://github.com/ofiwg/libfabric.git && \
+ git clone https://github.com/mercury-hpc/mercury.git --recursive
+
+COPY ./ ${WORK_SPACE}/source/pdc
+
+ENV LIBFABRIC_SRC_DIR=$WORK_SPACE/source/libfabric
+ENV MERCURY_SRC_DIR=$WORK_SPACE/source/mercury
+ENV PDC_SRC_DIR=$WORK_SPACE/source/pdc
+ENV LIBFABRIC_DIR=$WORK_SPACE/install/libfabric
+ENV MERCURY_DIR=$WORK_SPACE/install/mercury
+ENV PDC_DIR=$WORK_SPACE/install/pdc
+
+RUN mkdir -p $LIBFABRIC_SRC_DIR \
+ mkdir -p $MERCURY_SRC_DIR \
+ mkdir -p $PDC_SRC_DIR \
+ mkdir -p $LIBFABRIC_DIR \
+ mkdir -p $MERCURY_DIR \
+ mkdir -p $PDC_DIR
+
+
+# Save the environment variables to a file
+RUN echo "export LIBFABRIC_SRC_DIR=$WORK_SPACE/source/libfabric" > $WORK_SPACE/pdc_env.sh && \
+ echo "export MERCURY_SRC_DIR=$WORK_SPACE/source/mercury" >> $WORK_SPACE/pdc_env.sh && \
+ echo "export PDC_SRC_DIR=$WORK_SPACE/source/pdc" >> $WORK_SPACE/pdc_env.sh && \
+ echo "export LIBFABRIC_DIR=$WORK_SPACE/install/libfabric" >> $WORK_SPACE/pdc_env.sh && \
+ echo "export MERCURY_DIR=$WORK_SPACE/install/mercury" >> $WORK_SPACE/pdc_env.sh && \
+ echo "export PDC_DIR=$WORK_SPACE/install/pdc" >> $WORK_SPACE/pdc_env.sh
+
+
+# Build and install libfabric
+WORKDIR $LIBFABRIC_SRC_DIR
+RUN git checkout v1.18.0 && \
+ ./autogen.sh && \
+ ./configure --prefix=$LIBFABRIC_DIR CC=mpicc CFLAG="-O2" && \
+ make clean && \
+ make -j && make install && \
+ make check
+
+ENV LD_LIBRARY_PATH="$LIBFABRIC_DIR/lib:$LD_LIBRARY_PATH"
+ENV PATH="$LIBFABRIC_DIR/include:$LIBFABRIC_DIR/lib:$PATH"
+RUN echo 'export LD_LIBRARY_PATH=$LIBFABRIC_DIR/lib:$LD_LIBRARY_PATH' >> $WORK_SPACE/pdc_env.sh && \
+ echo 'export PATH=$LIBFABRIC_DIR/include:$LIBFABRIC_DIR/lib:$PATH' >> $WORK_SPACE/pdc_env.sh
+
+
+# Build and install Mercury
+WORKDIR $MERCURY_SRC_DIR
+ENV MERCURY_CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=$MERCURY_DIR -DCMAKE_C_COMPILER=mpicc -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=ON -DNA_USE_OFI=ON -DNA_USE_SM=OFF -DNA_OFI_TESTING_PROTOCOL=tcp "
+RUN git checkout v2.2.0 \
+ mkdir -p build 
+WORKDIR ${MERCURY_SRC_DIR}/build
+RUN cmake $MERCURY_CMAKE_FLAGS ../ && \
+ make -j && make install && \
+ ctest
+
+# Set the environment variables
+ENV LD_LIBRARY_PATH="$MERCURY_DIR/lib:$LD_LIBRARY_PATH"
+ENV PATH="$MERCURY_DIR/include:$MERCURY_DIR/lib:$PATH"
+RUN echo 'export LD_LIBRARY_PATH=$MERCURY_DIR/lib:$LD_LIBRARY_PATH' >> $WORK_SPACE/pdc_env.sh \
+ echo 'export PATH=$MERCURY_DIR/include:$MERCURY_DIR/lib:$PATH' >> $WORK_SPACE/pdc_env.sh

.docker/local.Dockerfile

@@ -0,0 +1,29 @@
+# Note: Run `docker build -f .docker/Dockerfile -t pdc:latest .` from the root directory of the repository to build the docker image.
+
+# Use Ubuntu Jammy (latest LTS) as the base image
+FROM zhangwei217245/pdc_dev_base:latest
+
+# Build and install PDC
+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 "
+
+
+WORKDIR $PDC_SRC_DIR
+RUN rm -rf build && \
+ mkdir -p build
+
+# COPY ../ ${PDC_SRC_DIR}
+# RUN ls -l $PDC_SRC_DIR
+
+WORKDIR ${PDC_SRC_DIR}/build
+RUN cmake $PDC_CMAKE_FLAGS ../ 2>&1 > ./cmake_config.log || echo "ignoring cmake config error and proceed" && \
+ make -j && make install
+
+# Set the environment variables
+ENV LD_LIBRARY_PATH="$PDC_DIR/lib:$LD_LIBRARY_PATH"
+ENV PATH="$PDC_DIR/include:$PDC_DIR/lib:$PATH"
+RUN echo 'export LD_LIBRARY_PATH=$PDC_DIR/lib:$LD_LIBRARY_PATH' >> $WORK_SPACE/pdc_env.sh && \
+ echo 'export PATH=$PDC_DIR/include:$PDC_DIR/lib:$PATH' >> $WORK_SPACE/pdc_env.sh
+
+
+# WORKDIR $PDC_SRC_DIR/build
+# RUN ctest

.docker/local.Dockerfile.dockerignore

@@ -0,0 +1,2 @@
+# Exclude files and directories from the Docker build context
+!/.git/

src/server/CMakeLists.txt

@@ -1,72 +1,4 @@
-find_package(MERCURY REQUIRED)
 
-if(PDC_ENABLE_FASTBIT)
- add_definitions(-DENABLE_FASTBIT=1)
- find_path(FASTBIT_INCLUDE_DIR fastbit/iapi.h)
- find_library(FASTBIT_LIBRARY fastbit $ENV{HOME}/cori/fastbit-2.0.3/install)
-endif()
-
-if(PDC_ENABLE_ROCKSDB)
- add_definitions(-DENABLE_ROCKSDB=1)
- find_path(ROCKSDB_INCLUDE_DIR include/db.h)
- find_library(ROCKSDB_LIBRARY rocksdb 8.1.1< REQUIRED)
-endif()
-
-if(PDC_ENABLE_SQLITE3)
- add_definitions(-DENABLE_SQLITE3=1)
- find_package(SQLite3 3.31.0 REQUIRED)
-endif()
-
-include_directories(
- ${PDC_COMMON_INCLUDE_DIRS}
- ${PDC_INCLUDES_BUILD_TIME}
- ${PROJECT_SOURCE_DIR}
- ${PROJECT_BINARY_DIR}
- ${CMAKE_CURRENT_SOURCE_DIR}
- ${CMAKE_CURRENT_BINARY_DIR}
- ${PDC_SOURCE_DIR}/src/server/include
- ${PDC_SOURCE_DIR}/src/server/pdc_server_region
- ${PDC_SOURCE_DIR}/src/server/pdc_server_region/include
- ${PDC_SOURCE_DIR}/src/server/pdc_server_analysis/include
- ${PDC_SOURCE_DIR}/src/server/dablooms
- ${PDC_SOURCE_DIR}/src/api/include
- ${PDC_SOURCE_DIR}/src/api/pdc_obj/include
- ${PDC_SOURCE_DIR}/src/api/pdc_region/include
- ${PDC_SOURCE_DIR}/src/api/pdc_query/include
- ${PDC_SOURCE_DIR}/src/api/pdc_transform/include
- ${PDC_SOURCE_DIR}/src/api/pdc_analysis/include
- ${PDC_SOURCE_DIR}/src/api/profiling/include
- ${PDC_SOURCE_DIR}/src/utils/include
- ${MERCURY_INCLUDE_DIR}
- ${FASTBIT_INCLUDE_DIR}
- ${ROCKSDB_INCLUDE_DIR}
-)
-
-add_definitions( -DIS_PDC_SERVER=1 )
-add_definitions( -DPDC_LUSTRE_TOTAL_OST=${PDC_LUSTRE_TOTAL_OST} )
-if(PDC_ENABLE_TIMING)
- add_definitions(-DPDC_TIMING=1)
-endif()
-
-
-add_library(pdc_server_lib
- pdc_server.c
- pdc_server_metadata_index.c
- pdc_server_metadata.c
- pdc_client_server_common.c
- dablooms/pdc_dablooms.c
- dablooms/pdc_murmur.c
- pdc_hash-table.c
- ${PDC_SOURCE_DIR}/src/server/pdc_server_analysis/pdc_server_analysis.c
- ${PDC_SOURCE_DIR}/src/server/pdc_server_region/pdc_server_data.c
- ${PDC_SOURCE_DIR}/src/server/pdc_server_region/pdc_server_region_cache.c
- ${PDC_SOURCE_DIR}/src/server/pdc_server_region/pdc_server_region_transfer.c
- ${PDC_SOURCE_DIR}/src/server/pdc_server_region/pdc_server_region_transfer_metadata_query.c
- ${PDC_SOURCE_DIR}/src/utils/pdc_region_utils.c
- ${PDC_SOURCE_DIR}/src/api/pdc_analysis/pdc_analysis_common.c
- ${PDC_SOURCE_DIR}/src/api/pdc_transform/pdc_transforms_common.c
- ${PDC_SOURCE_DIR}/src/api/pdc_analysis/pdc_hist_pkg.c
-)
 if(PDC_ENABLE_FASTBIT)
  message(STATUS "Enabled fastbit")
  target_link_libraries(pdc_server_lib ${MERCURY_LIBRARY} ${PDC_COMMONS_LIBRARIES} -lm -ldl ${PDC_EXT_LIB_DEPENDENCIES} ${FASTBIT_LIBRARY}/libfastbit.so)
@@ -80,27 +12,4 @@ elseif(PDC_ENABLE_SQLITE3)
  target_link_libraries(pdc_server_lib ${MERCURY_LIBRARY} ${PDC_COMMONS_LIBRARIES} -lm -ldl ${PDC_EXT_LIB_DEPENDENCIES} SQLite::SQLite3)
 else()
  target_link_libraries(pdc_server_lib ${MERCURY_LIBRARY} ${PDC_COMMONS_LIBRARIES} -lm -ldl ${PDC_EXT_LIB_DEPENDENCIES})
-endif()
-
-add_executable(pdc_server.exe
- pdc_server_main.c
-)
-target_link_libraries(pdc_server.exe pdc_server_lib)
-
-
-add_executable(pdc_server_metadata_index_test
- pdc_server_metadata_index_test.c
-)
-target_link_libraries(pdc_server_metadata_index_test pdc_server_lib)
-
-
-if(NOT ${PDC_INSTALL_BIN_DIR} MATCHES ${PROJECT_BINARY_DIR}/bin)
-install(
- TARGETS
- pdc_server.exe
- pdc_server_lib
- LIBRARY DESTINATION ${PDC_INSTALL_LIB_DIR}
- ARCHIVE DESTINATION ${PDC_INSTALL_LIB_DIR}
- RUNTIME DESTINATION ${PDC_INSTALL_BIN_DIR}
-)
-endif()
+endif()

src/server/pdc_server.c

@@ -2384,4 +2384,4 @@ server_run(int argc, char *argv[])
  MPI_Finalize();
 #endif
  return 0;
-}
+}

src/server/pdc_server_metadata.c

@@ -1845,7 +1845,7 @@ PDC_Server_query_kvtag_someta(pdc_kvtag_t *in, uint32_t *n_meta, uint64_t **obj_
  *obj_ids = (void *)realloc(*obj_ids, alloc_size * sizeof(uint64_t));
  }
  (*obj_ids)[iter++] = elt->obj_id;
- break;
+ // break; // FIXME: shall we break here? or continue to check other kvtags?
  }
  } // End for each kvtag in list
  } // End for each metadata from hash table entry