Synchronize stable with develop branch (#152)

Synchronize stable with develop branch

.devcontainer/devcontainer.Dockerfile

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+# 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
+

.devcontainer/devcontainer.json

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+{
+    "name": "pdc_devcontainer",
+    "dockerFile": "devcontainer.Dockerfile",
+    "forwardPorts": [
+        3000
+    ],
+    "postCreateCommand": ".devcontainer/post-create.sh",
+    "postStartCommand": ".devcontainer/post-start.sh"
+}

.devcontainer/post-create.sh

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+#!/bin/bash

.devcontainer/post-start.sh

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+#!/bin/bash
+
+
+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

.docker/base.Dockerfile

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+# 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

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+# 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

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+# Exclude files and directories from the Docker build context
+!/.git/

.github/ISSUE_TEMPLATE/bug_report.md

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+**Bug Report**
+
+A clear and concise description of what the bug is, including module and feature.
+
+**To Reproduce**
+
+How are you building/running PDC?
+
+- version of PDC: [e.g., 0.3, branch, or hash]
+- installed PDC using: [spack, from source]
+- operating system: [name and version]
+- machine: [Are you running on a supercomputer or public cluster?]
+- version of Mercury: [e.g., 1.12.0]
+- name and version of MPI: [e.g., OpenMPI 4.1.1]
+
+What did you use to build PDC (cmake command)?
+
+```bash
+...
+```
+
+What is the running setup you use?
+
+```bash
+...
+```
+
+**Expected Behavior**
+
+A clear and concise description of what you expected to happen.
+
+**Additional Information**
+
+If built from source, include the cmake options you used.
+Add any other information about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

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+**What does this feature solve or improve?**
+
+A clear and concise description of what the problem is.
+Example: I always do the following workflow [...]
+
+**Describe the solution you'd like**
+
+A clear and concise description of what you want to happen.
+Example: It would be fantastic if one could [...]
+
+**Describe alternatives you've considered**
+
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional Information**
+
+Add any other information about the feature request here.

.github/ISSUE_TEMPLATE/install_problem.md

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+**Issue Description**
+
+This is what I have tried so far:
+
+
+```commandline
+...
+```
+
+This is the error I am facing during installation:
+
+```
+...
+```
+
+**Software Environment**
+
+- version of PDC: [e.g. 0.3]
+- installed PDC using: [spack, from source]
+- operating system: [name and version]
+- machine: [Are you running on a supercomputer or public cluster?]
+- version of Mercury: [e.g. 1.12.0]
+- name and version of MPI: [e.g. OpenMPI 4.1.1]
+
+**Additional Information**
+
+Add any other information about the problem here.

.github/ISSUE_TEMPLATE/question.md

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+**Usage Case**
+
+A clear and concise description of what your usage case is.
+
+**Additional Information**
+
+Add any other information about your intended usage, limitation, or questions here.
+
+**Software Environment**
+
+- version of PDC: [e.g. 0.3]
+- installed PDC using: [spack, from source]
+- operating system: [name and version]
+- machine: [Are you running on a supercomputer or public cluster?]
+- version of Mercury: [e.g. 1.12.0]
+- name and version of MPI: [e.g. OpenMPI 4.1.1]

.github/pull_request_template.md

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+# Related Issues / Pull Requests
+
+List all related issues and/or pull requests if there are any.
+
+# Description
+
+Include a brief summary of the proposed changes.
+
+# What changes are proposed in this pull request?
+
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality not to work as expected; for instance, examples in this repository must be updated too)
+- [ ] This change requires a documentation update
+
+# Checklist:
+
+- [ ] My code modifies existing public API, or introduces new public API, and I updated or wrote docstrings
+- [ ] I have commented my code
+- [ ] My code requires documentation updates, and I have made corresponding changes to the documentation
+- [ ] I have added tests that prove my fix is effective or that my feature works
+- [ ] New and existing unit tests pass locally with my changes