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Synchronize stable with develop branch (#152)
Synchronize stable with develop branch
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‎.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.
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# Use Ubuntu Jammy (latest LTS) as the base image
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FROM ubuntu:jammy
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# Install necessary tools, MPICH, UUID library and developer files
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RUN apt-get update && apt-get install -y \
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build-essential \
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git \
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mpich \
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libmpich-dev \
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uuid \
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uuid-dev \
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autoconf \
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libtool \
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cmake \
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cmake-curses-gui \
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wget \
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axel \
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curl \
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vim \
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nano \
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gdb \
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cgdb \
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curl \
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valgrind
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# Set WORK_SPACE environment variable and create necessary directories
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RUN mkdir -p /workspaces
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ENV WORK_SPACE=/workspaces
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# Clone the repositories
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WORKDIR $WORK_SPACE/source
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RUN git clone https://github.com/ofiwg/libfabric.git && \
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git clone https://github.com/mercury-hpc/mercury.git --recursive
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COPY ./ ${WORK_SPACE}/source/pdc
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ENV LIBFABRIC_SRC_DIR=$WORK_SPACE/source/libfabric
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ENV MERCURY_SRC_DIR=$WORK_SPACE/source/mercury
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ENV PDC_SRC_DIR=$WORK_SPACE/source/pdc
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ENV LIBFABRIC_DIR=$WORK_SPACE/install/libfabric
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ENV MERCURY_DIR=$WORK_SPACE/install/mercury
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ENV PDC_DIR=$WORK_SPACE/install/pdc
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RUN mkdir -p $LIBFABRIC_SRC_DIR && \
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mkdir -p $MERCURY_SRC_DIR && \
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mkdir -p $LIBFABRIC_DIR && \
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mkdir -p $MERCURY_DIR && \
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mkdir -p $PDC_DIR
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# Save the environment variables to a file
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RUN echo "export LIBFABRIC_SRC_DIR=$WORK_SPACE/source/libfabric" > $WORK_SPACE/pdc_env.sh && \
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echo "export MERCURY_SRC_DIR=$WORK_SPACE/source/mercury" >> $WORK_SPACE/pdc_env.sh && \
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echo "export PDC_SRC_DIR=$WORK_SPACE/source/pdc" >> $WORK_SPACE/pdc_env.sh && \
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echo "export LIBFABRIC_DIR=$WORK_SPACE/install/libfabric" >> $WORK_SPACE/pdc_env.sh && \
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echo "export MERCURY_DIR=$WORK_SPACE/install/mercury" >> $WORK_SPACE/pdc_env.sh && \
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echo "export PDC_DIR=$WORK_SPACE/install/pdc" >> $WORK_SPACE/pdc_env.sh
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# Build and install libfabric
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WORKDIR $LIBFABRIC_SRC_DIR
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RUN git checkout v1.18.0 && \
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./autogen.sh && \
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./configure --prefix=$LIBFABRIC_DIR CC=mpicc CFLAG="-O2" && \
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make clean && \
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make -j && make install && \
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make check
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ENV LD_LIBRARY_PATH="$LIBFABRIC_DIR/lib:$LD_LIBRARY_PATH"
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ENV PATH="$LIBFABRIC_DIR/include:$LIBFABRIC_DIR/lib:$PATH"
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RUN echo 'export LD_LIBRARY_PATH=$LIBFABRIC_DIR/lib:$LD_LIBRARY_PATH' >> $WORK_SPACE/pdc_env.sh && \
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echo 'export PATH=$LIBFABRIC_DIR/include:$LIBFABRIC_DIR/lib:$PATH' >> $WORK_SPACE/pdc_env.sh
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# Build and install Mercury
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WORKDIR $MERCURY_SRC_DIR
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ENV MERCURY_CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=$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 "
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RUN git checkout v2.2.0 \
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mkdir -p build
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WORKDIR ${MERCURY_SRC_DIR}/build
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RUN cmake $MERCURY_CMAKE_FLAGS ../ && \
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make -j && make install && \
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ctest
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# Set the environment variables
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ENV LD_LIBRARY_PATH="$MERCURY_DIR/lib:$LD_LIBRARY_PATH"
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ENV PATH="$MERCURY_DIR/include:$MERCURY_DIR/lib:$PATH"
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RUN echo 'export LD_LIBRARY_PATH=$MERCURY_DIR/lib:$LD_LIBRARY_PATH' >> $WORK_SPACE/pdc_env.sh \
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echo 'export PATH=$MERCURY_DIR/include:$MERCURY_DIR/lib:$PATH' >> $WORK_SPACE/pdc_env.sh
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‎.devcontainer/devcontainer.json‎

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

‎.devcontainer/post-create.sh‎

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#!/bin/bash

‎.devcontainer/post-start.sh‎

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#!/bin/bash
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ln -s /workspaces/pdc /home/codespace/source/pdc
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mkdir -p /workspaces/install
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mkdir -p /workspaces/source
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ln -s $PDC_SRC_DIR /workspaces/source/pdc
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ln -s $PDC_DIR /workspaces/install/pdc
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export PDC_SRC_DIR=/workspaces/source/pdc
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# Build and install PDC
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export PDC_CMAKE_FLAGS="-DBUILD_MPI_TESTING=ON -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=ON -DCMAKE_INSTALL_PREFIX=$PDC_DIR -DPDC_ENABLE_MPI=ON -DMERCURY_DIR=$MERCURY_DIR -DCMAKE_C_COMPILER=mpicc -DMPI_RUN_CMD=mpiexec "
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cd $PDC_SRC_DIR
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rm -rf build && mkdir -p build
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cd ${PDC_SRC_DIR}/build
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cmake $PDC_CMAKE_FLAGS ../ 2>&1 > ./cmake_config.log || echo "ignoring cmake config error and proceed"
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make -j && make install
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# Set the environment variables
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export LD_LIBRARY_PATH="$PDC_DIR/lib:$LD_LIBRARY_PATH"
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export PATH="$PDC_DIR/include:$PDC_DIR/lib:$PATH"
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echo 'export LD_LIBRARY_PATH=$PDC_DIR/lib:$LD_LIBRARY_PATH' >> $WORK_SPACE/pdc_env.sh
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echo 'export PATH=$PDC_DIR/include:$PDC_DIR/lib:$PATH' >> $WORK_SPACE/pdc_env.sh
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cd $PDC_SRC_DIR/build
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# ctest

‎.docker/base.Dockerfile‎

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# Use Ubuntu Jammy (latest LTS) as the base image
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FROM ubuntu:jammy
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# Install necessary tools, MPICH, UUID library and developer files
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RUN apt-get update && apt-get install -y \
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build-essential \
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git \
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mpich \
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libmpich-dev \
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uuid \
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uuid-dev \
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autoconf \
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libtool \
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cmake \
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cmake-curses-gui \
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wget \
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axel \
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curl \
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vim \
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nano \
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gdb \
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cgdb \
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curl \
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valgrind
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# Set WORK_SPACE environment variable and create necessary directories
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ENV WORK_SPACE=/home/codespace
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RUN mkdir -p $WORK_SPACE
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# Clone the repositories
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WORKDIR $WORK_SPACE/source
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RUN git clone https://github.com/ofiwg/libfabric.git && \
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git clone https://github.com/mercury-hpc/mercury.git --recursive
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COPY ./ ${WORK_SPACE}/source/pdc
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ENV LIBFABRIC_SRC_DIR=$WORK_SPACE/source/libfabric
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ENV MERCURY_SRC_DIR=$WORK_SPACE/source/mercury
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ENV PDC_SRC_DIR=$WORK_SPACE/source/pdc
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ENV LIBFABRIC_DIR=$WORK_SPACE/install/libfabric
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ENV MERCURY_DIR=$WORK_SPACE/install/mercury
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ENV PDC_DIR=$WORK_SPACE/install/pdc
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RUN mkdir -p $LIBFABRIC_SRC_DIR \
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mkdir -p $MERCURY_SRC_DIR \
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mkdir -p $PDC_SRC_DIR \
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mkdir -p $LIBFABRIC_DIR \
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mkdir -p $MERCURY_DIR \
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mkdir -p $PDC_DIR
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# Save the environment variables to a file
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RUN echo "export LIBFABRIC_SRC_DIR=$WORK_SPACE/source/libfabric" > $WORK_SPACE/pdc_env.sh && \
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echo "export MERCURY_SRC_DIR=$WORK_SPACE/source/mercury" >> $WORK_SPACE/pdc_env.sh && \
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echo "export PDC_SRC_DIR=$WORK_SPACE/source/pdc" >> $WORK_SPACE/pdc_env.sh && \
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echo "export LIBFABRIC_DIR=$WORK_SPACE/install/libfabric" >> $WORK_SPACE/pdc_env.sh && \
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echo "export MERCURY_DIR=$WORK_SPACE/install/mercury" >> $WORK_SPACE/pdc_env.sh && \
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echo "export PDC_DIR=$WORK_SPACE/install/pdc" >> $WORK_SPACE/pdc_env.sh
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# Build and install libfabric
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WORKDIR $LIBFABRIC_SRC_DIR
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RUN git checkout v1.18.0 && \
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./autogen.sh && \
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./configure --prefix=$LIBFABRIC_DIR CC=mpicc CFLAG="-O2" && \
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make clean && \
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make -j && make install && \
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make check
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ENV LD_LIBRARY_PATH="$LIBFABRIC_DIR/lib:$LD_LIBRARY_PATH"
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ENV PATH="$LIBFABRIC_DIR/include:$LIBFABRIC_DIR/lib:$PATH"
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RUN echo 'export LD_LIBRARY_PATH=$LIBFABRIC_DIR/lib:$LD_LIBRARY_PATH' >> $WORK_SPACE/pdc_env.sh && \
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echo 'export PATH=$LIBFABRIC_DIR/include:$LIBFABRIC_DIR/lib:$PATH' >> $WORK_SPACE/pdc_env.sh
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# Build and install Mercury
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WORKDIR $MERCURY_SRC_DIR
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ENV MERCURY_CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=$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 "
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RUN git checkout v2.2.0 \
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mkdir -p build
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WORKDIR ${MERCURY_SRC_DIR}/build
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RUN cmake $MERCURY_CMAKE_FLAGS ../ && \
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make -j && make install && \
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ctest
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# Set the environment variables
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ENV LD_LIBRARY_PATH="$MERCURY_DIR/lib:$LD_LIBRARY_PATH"
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ENV PATH="$MERCURY_DIR/include:$MERCURY_DIR/lib:$PATH"
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RUN echo 'export LD_LIBRARY_PATH=$MERCURY_DIR/lib:$LD_LIBRARY_PATH' >> $WORK_SPACE/pdc_env.sh \
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echo 'export PATH=$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.
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# Use Ubuntu Jammy (latest LTS) as the base image
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FROM zhangwei217245/pdc_dev_base:latest
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# Build and install PDC
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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 "
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WORKDIR $PDC_SRC_DIR
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RUN rm -rf build && \
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mkdir -p build
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# COPY ../ ${PDC_SRC_DIR}
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# RUN ls -l $PDC_SRC_DIR
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WORKDIR ${PDC_SRC_DIR}/build
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RUN cmake $PDC_CMAKE_FLAGS ../ 2>&1 > ./cmake_config.log || echo "ignoring cmake config error and proceed" && \
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make -j && make install
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# Set the environment variables
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ENV LD_LIBRARY_PATH="$PDC_DIR/lib:$LD_LIBRARY_PATH"
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ENV PATH="$PDC_DIR/include:$PDC_DIR/lib:$PATH"
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RUN echo 'export LD_LIBRARY_PATH=$PDC_DIR/lib:$LD_LIBRARY_PATH' >> $WORK_SPACE/pdc_env.sh && \
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echo 'export PATH=$PDC_DIR/include:$PDC_DIR/lib:$PATH' >> $WORK_SPACE/pdc_env.sh
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# WORKDIR $PDC_SRC_DIR/build
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# RUN ctest

‎.docker/local.Dockerfile.dockerignore‎

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

‎.github/ISSUE_TEMPLATE/bug_report.md‎

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**Bug Report**
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A clear and concise description of what the bug is, including module and feature.
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**To Reproduce**
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How are you building/running PDC?
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- version of PDC: [e.g., 0.3, branch, or hash]
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- installed PDC using: [spack, from source]
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- operating system: [name and version]
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- machine: [Are you running on a supercomputer or public cluster?]
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- version of Mercury: [e.g., 1.12.0]
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- name and version of MPI: [e.g., OpenMPI 4.1.1]
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What did you use to build PDC (cmake command)?
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```bash
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...
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```
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What is the running setup you use?
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```bash
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...
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```
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**Expected Behavior**
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A clear and concise description of what you expected to happen.
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**Additional Information**
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If built from source, include the cmake options you used.
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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?**
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A clear and concise description of what the problem is.
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Example: I always do the following workflow [...]
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**Describe the solution you'd like**
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A clear and concise description of what you want to happen.
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Example: It would be fantastic if one could [...]
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**Describe alternatives you've considered**
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A clear and concise description of any alternative solutions or features you've considered.
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**Additional Information**
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Add any other information about the feature request here.

‎.github/ISSUE_TEMPLATE/install_problem.md‎

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

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