Resolving conflict between develop and stable (#173)

* Synchronize stable with develop branch (#152)
* Resolve conflicts

.devcontainer/post-create.sh

@@ -38,4 +38,4 @@ make -j && make install
 export LD_LIBRARY_PATH="$PDC_DIR/lib:$LD_LIBRARY_PATH"
 export PATH="$PDC_DIR/include:$PDC_DIR/lib:$PATH"
 echo 'export LD_LIBRARY_PATH=$PDC_DIR/lib:$LD_LIBRARY_PATH' >> $WORK_SPACE/pdc_env.sh
-echo 'export PATH=$PDC_DIR/include:$PDC_DIR/lib:$PATH' >> $WORK_SPACE/pdc_env.sh
+echo 'export PATH=$PDC_DIR/include:$PDC_DIR/lib:$PATH' >> $WORK_SPACE/pdc_env.sh

.devcontainer/post-start.sh

@@ -3,4 +3,4 @@
 nohup /bin/bash /workspaces/pdc/.devcontainer/post-create.sh 2>&1 > /workspaces/pdc_install.out &
 
 echo "Wait for 10 seconds for the building processes to start."
-sleep 10s
+sleep 10s

.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/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 +1845,12 @@ 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?
+                    }
+                    else {
+#ifdef PDC_DEBUG_OUTPUT
+                        println("[NOT FOUND]");
+#endif
                     }
                 } // End for each kvtag in list
             }     // End for each metadata from hash table entry

src/tools/CMakeLists.txt

@@ -95,4 +95,4 @@ add_library(cjson cjson/cJSON.c)
 foreach(program ${PROGRAMS})
   add_executable(${program} ${program}.c)
   target_link_libraries(${program} pdc cjson ${TOOLS_EXT_LIB})
-endforeach(program)
+endforeach(program)