Synchronize stable with develop branch

.devcontainer/devcontainer.Dockerfile

@@ -1,95 +1,8 @@
 # Note: Run `docker build -f .devcontainer/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 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
-RUN mkdir -p /workspaces
-ENV WORK_SPACE=/workspaces
-
-
-# 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 $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
+# FROM ubuntu:jammy
+FROM hpcio/pdc-dev-base:latest
 
+RUN rm -rf $PDC_SRC_DIR && \
+    rm -rf $PDC_DIR

.devcontainer/devcontainer.json

@@ -5,5 +5,63 @@
         3000
     ],
     "postCreateCommand": ".devcontainer/post-create.sh",
-    "postStartCommand": ".devcontainer/post-start.sh"
+    "postStartCommand": ".devcontainer/post-start.sh",
+    "postAttachCommand": ".devcontainer/post-attach.sh",
+    "customizations": {
+        "vscode": {
+            "extensions": [
+                "1YiB.rust-bundle",
+                "batisteo.vscode-django",
+                "ChrisChinchilla.vscode-pandoc",
+                "DamianKoper.gdb-debug",
+                "donjayamanne.python-environment-manager",
+                "donjayamanne.python-extension-pack",
+                "dustypomerleau.rust-syntax",
+                "eamodio.gitlens",
+                "formulahendry.code-runner",
+                "GitHub.copilot",
+                "GitHub.copilot-chat",
+                "JScearcy.rust-doc-viewer",
+                "julialang.language-julia",
+                "KevinRose.vsc-python-indent",
+                "lextudio.iis",
+                "lextudio.restructuredtext",
+                "lextudio.restructuredtext-pack",
+                "ms-azuretools.vscode-docker",
+                "ms-python.python",
+                "ms-python.vscode-pylance",
+                "ms-toolsai.jupyter",
+                "ms-toolsai.jupyter-keymap",
+                "ms-toolsai.jupyter-renderers",
+                "ms-toolsai.vscode-jupyter-cell-tags",
+                "ms-toolsai.vscode-jupyter-slideshow",
+                "ms-vscode.cmake-tools",
+                "ms-vscode.cpptools",
+                "ms-vscode.cpptools-extension-pack",
+                "ms-vscode.cpptools-themes",
+                "njpwerner.autodocstring",
+                "PolyMeilex.rust-targets",
+                "rogalmic.bash-debug",
+                "rust-lang.rust-analyzer",
+                "serayuzgur.crates",
+                "shakram02.bash-beautify",
+                "shd101wyy.markdown-preview-enhanced",
+                "Swellaby.rust-pack",
+                "tamasfe.even-better-toml",
+                "trond-snekvik.simple-rst",
+                "twxs.cmake",
+                "VisualStudioExptTeam.intellicode-api-usage-examples",
+                "VisualStudioExptTeam.vscodeintellicode",
+                "wholroyd.jinja",
+                "xaver.clang-format",
+                "yzane.markdown-pdf",
+                "yzhang.markdown-all-in-one",
+                "ZhangYue.rust-mod-generator"
+            ],
+            "settings": {
+                "C_Cpp.clang_format_path": "/home/project/software/clang-format-lint-action/clang-format/clang-format10",
+                "terminal.integrated.scrollback": 10000
+            }
+        }
+    }
 }

.devcontainer/post-attach.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+
+WORK_SPACE_INITIALIZED_FILE=/workspaces/.workspace_initialized
+
+if ! [ -f $WORK_SPACE_INITIALIZED_FILE ]; then
+    /bin/bash /workspaces/pdc/.devcontainer/post-start.sh
+    watch -t -n 5 'echo "Press Ctrl+C when there is no building processes."; echo "Number of initial PDC building processes:"; ps -ef | grep make | grep -v -c grep'
+else
+    echo "Welcome Back!"
+fi
+
+/bin/bash

.devcontainer/post-create.sh

@@ -1 +1,41 @@
 #!/bin/bash
+
+
+WORK_SPACE_INITIALIZED_FILE=/workspaces/.workspace_initialized
+
+if ! [ -f $WORK_SPACE_INITIALIZED_FILE ]; then
+    touch $WORK_SPACE_INITIALIZED_FILE
+    echo "First time to create workspace, start to install PDC"
+else
+    echo "Workspace already initialized, skip the installation"
+    exit 0
+fi
+
+rm -rf $PDC_SRC_DIR
+rm -rf $PDC_DIR
+
+
+ln -s /workspaces/pdc $(dirname $PDC_SRC_DIR)
+
+mkdir -p /workspaces/source
+ln -s $PDC_SRC_DIR /workspaces/source/pdc
+
+mkdir -p /workspaces/install/pdc
+ln -s /workspaces/install/pdc $(dirname $PDC_SRC_DIR)
+
+# Build and install PDC
+export PDC_CMAKE_FLAGS="-DBUILD_MPI_TESTING=ON -DBUILD_SHARED_LIBS=ON -DBUILD_TOOLS=OFF -DBUILD_TESTING=ON -DCMAKE_INSTALL_PREFIX=$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
+
+
+cd ${PDC_SRC_DIR}/build
+cmake $PDC_CMAKE_FLAGS ../ 2>&1 > ./cmake_config.log || echo "ignoring cmake config error and proceed"
+make -j && make install
+
+# Set the environment variables
+export LD_LIBRARY_PATH="$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

.devcontainer/post-start.sh

@@ -1,31 +1,6 @@
 #!/bin/bash
 
+nohup /bin/bash /workspaces/pdc/.devcontainer/post-create.sh 2>&1 > /workspaces/pdc_install.out &
 
-ln -s /workspaces/pdc /home/codespace/source/pdc 
-mkdir -p /workspaces/install
-mkdir -p /workspaces/source
-ln -s $PDC_SRC_DIR /workspaces/source/pdc
-ln -s $PDC_DIR  /workspaces/install/pdc
-
-export PDC_SRC_DIR=/workspaces/source/pdc
-
-# Build and install PDC
-export PDC_CMAKE_FLAGS="-DBUILD_MPI_TESTING=ON -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=ON -DCMAKE_INSTALL_PREFIX=$PDC_DIR -DPDC_ENABLE_MPI=ON -DMERCURY_DIR=$MERCURY_DIR -DCMAKE_C_COMPILER=mpicc -DMPI_RUN_CMD=mpiexec "
-
-cd $PDC_SRC_DIR
-rm -rf build && mkdir -p build
-
-
-cd ${PDC_SRC_DIR}/build
-cmake $PDC_CMAKE_FLAGS ../ 2>&1 > ./cmake_config.log || echo "ignoring cmake config error and proceed"
-make -j && make install
-
-# Set the environment variables
-export LD_LIBRARY_PATH="$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
-
-
-cd $PDC_SRC_DIR/build
-# ctest
+echo "Wait for 10 seconds for the building processes to start."
+sleep 10s

.docker/dev.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/dev.Dockerfile.dockerignore

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