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zhangwei217245houjunnickaruwanggithub-actions[bot]jeanbez
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IDIOMS Update & BULKI v0.1 (#203)
* fix cmake mercury_util not found issue * update for Julia support * fix hdf5.h not found for src/tools * update container config * add libhdf5-dev for Github Actions * update CMake for HDF5 in tools * update logic for finding HDF5 * update * remove use system hdf5 * delete useless find library * update findHDF5 * Feature/dart (#11) Update to avoid fixing compilation issue on src/tools (due to : HDF5 cannot be found) * Use cc on Perlmutter (#161) Dr. Tang fixed a compilation issue in NERSC CI where HDF5 cannot be detected even if the cray-parallel-hdf5 module is loaded on Perlmultter. * update with fixes on tools and llsm example * add gitignore for llsm * update gitignore * Feature/dart (#12) * fix formatting * update clangformat10 * update base dockerfile * Add clang-format10 to docker container. Also fixed clang-format. Add clang-format10 to docker container. Also fixed clang-format. * Fix pdc ls (#154) * pdc import, export, ls compiled successfully * removed requested files * formatting issues * changed install tools * gets checkpoint files * grabbing checkpoint files from within sub-directories, minor comments * Committing clang-format changes * Committing clang-format changes * Fix a few issues with pdc_ls * Committing clang-format changes --------- Co-authored-by: nickaruwang <nickwan0318@gmail.com> Co-authored-by: Nick Wang <66816536+nickaruwang@users.noreply.github.com> Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com> Co-authored-by: Jean Luca Bez <jlbez@lbl.gov> * update documentation * update document update document * sync branch sync branch * no UUID module is required * update document and make UUID an optional package * update docker repo name * updating docker repo name and make UUID optional * Complete support for Docker and Github Codespace (#157) Include support for Docker and Github Codespace so we can run our dev environment with the support of Docker. * SQLite and RocksDB support for KVtags (#165) SQLite and RocksDB support for KVtags * fix round for tag delete * update test * bulki update * BULKI base type worked * BULKI all tests done * new index code * update * update new test * update csv bench * update * update script * adding python scripts for generating large metadata set for LLSM application * update json schema * better json validator * update importer * update code for non-MPI compatibility * update llsm converter * update LLSM data converter * split files * update .gitignore * update * add timing info * update * update tag size * detect object creation failure * update * update object name with date * update for robustness * update * update JMD_DEBUG option * update output for overall output * update inttypes.h * update * update extractor * update inttypes.h * update converter * update importer information * Update getting_started.rst (#184) * Removing gres option for ctest (#182) * Removing gres option for ctest * Removing gres option from scripts * Update check for core --------- Co-authored-by: Hyunju Oh <hjoh16@login15.chn.perlmutter.nersc.gov> Co-authored-by: Jean Luca Bez <jlbez@lbl.gov> * fix issue * fixed search issues * update for infix * update * index persistence still needs improvement * update * enable cache by default (#187) * Removing PDC macro (#189) * Removing gres option for ctest * Removing gres option from scripts * Update check for core * Remove PDC macro * Committing clang-format changes --------- Co-authored-by: Hyunju Oh <hjoh16@login15.chn.perlmutter.nersc.gov> Co-authored-by: Jean Luca Bez <jlbez@lbl.gov> Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com> * update * range query done' * range query local test passed * multi-condition in progress * clean up code * add comments * new benchmark * update * update range query test * update cmake: * update * update * update * update * someta range query * someta range query * someta range query * fix value serialization * update * update double free * update * update * update * fixed pointer issue * rb_tree delete fixed, now need to check index persistence * update * update * update * update * update * update * update * update * update * update * update * update * update * BDCATS fix (#193) * Fix issues with bdcats_batch * Committing clang-format changes --------- Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com> * update * clean up code * update test sh * IDIOMS persistence DONE * update * remove old kvtag benchmarks * update * update * update changes * dart info * update * multi data type for the same key, supported now * Monitoring changes from feature/dart to develop (#18) Major changes: * IDIOMS -> affix-based query benchmark * IDIOMS -> Simulation Test * IDIOMS -> Multi data type supported for the same key * IDIOMS -> Range Query and Exact Query for Numeric Values * IDIOMS -> benchmark for numeric values (exact search and range query) * IDIOMS -> Index Persistence * BULKI -> A data serialization and deserialization mechanism. * fix CMakeLists.txt * update * update format * update BULKI interface order * BULKI API sorted * add idioms ci test * Feature/dart (#20) 1. add documentation about BULKI and IDIOMS query conditions 2. add ci test for IDIOMS 3. optimized BULKI to save space on its metadata fields. * Feature/dart (#22) update version * update * update * update * remove unnecessary .bin file * update * update --------- Co-authored-by: Houjun Tang <htang4@lbl.gov> Co-authored-by: nickaruwang <nickwan0318@gmail.com> Co-authored-by: Nick Wang <66816536+nickaruwang@users.noreply.github.com> Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com> Co-authored-by: Jean Luca Bez <jlbez@lbl.gov> Co-authored-by: Hyunju Oh <oh.693@osu.edu> Co-authored-by: Hyunju Oh <hjoh16@login15.chn.perlmutter.nersc.gov>
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‎.docker/dev_base.Dockerfile

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@@ -4,13 +4,55 @@
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ARG ARCH
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FROM ${ARCH}ubuntu:jammy
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RUN echo "ARCH=${ARCH}" && sleep 3
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ARG ARCH_CODE
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RUN echo "ARCH_CODE=${ARCH_CODE}" && sleep 3
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ENV JULIA_HOME=/opt/julia
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ENV WORK_SPACE=/home/project
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ENV LIBFABRIC_SRC_DIR=$WORK_SPACE/source/libfabric
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ENV LIBFABRIC_DIR=$WORK_SPACE/install/libfabric
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ENV MERCURY_SRC_DIR=$WORK_SPACE/source/mercury
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ENV MERCURY_DIR=$WORK_SPACE/install/mercury
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ENV PDC_SRC_DIR=$WORK_SPACE/source/pdc
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ENV PDC_DIR=$WORK_SPACE/install/pdc
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ENV LD_LIBRARY_PATH="$LIBFABRIC_DIR/lib:$LD_LIBRARY_PATH"
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ENV PATH="$LIBFABRIC_DIR/include:$LIBFABRIC_DIR/lib:$PATH"
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ENV LD_LIBRARY_PATH="$MERCURY_DIR/lib:$LD_LIBRARY_PATH"
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ENV PATH="$MERCURY_DIR/include:$MERCURY_DIR/lib:$PATH"
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ENV MERCURY_CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=$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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ENV CLANG_FORMAT_PATH=$WORK_SPACE/software/clang-format-lint-action/clang-format/clang-format10
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# Install necessary tools, MPICH, UUID library and developer files
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RUN apt-get update && apt-get install -y \
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RUN echo "ARCH=${ARCH}" && echo "ARCH_CODE=${ARCH_CODE}" && sleep 3 && mkdir -p $WORK_SPACE && \
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mkdir -p $WORK_SPACE/software && \
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mkdir -p $WORK_SPACE/source && \
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mkdir -p $WORK_SPACE/install && \
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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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rm -rf $LIBFABRIC_SRC_DIR/* && \
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rm -rf $MERCURY_SRC_DIR/* && \
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rm -rf $PDC_SRC_DIR/* && \
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rm -rf $LIBFABRIC_DIR/* && \
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rm -rf $MERCURY_DIR/* && \
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rm -rf $PDC_DIR/* && \
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echo "export LIBFABRIC_SRC_DIR=$WORK_SPACE/source/libfabric" > $WORK_SPACE/pdc_env.sh && \
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echo "export LIBFABRIC_DIR=$WORK_SPACE/install/libfabric" >> $WORK_SPACE/pdc_env.sh && \
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echo "export MERCURY_SRC_DIR=$WORK_SPACE/source/mercury" >> $WORK_SPACE/pdc_env.sh && \
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echo "export MERCURY_DIR=$WORK_SPACE/install/mercury" >> $WORK_SPACE/pdc_env.sh && \
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echo "export PDC_SRC_DIR=$WORK_SPACE/source/pdc" >> $WORK_SPACE/pdc_env.sh && \
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echo "export PDC_DIR=$WORK_SPACE/install/pdc" >> $WORK_SPACE/pdc_env.sh && \
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echo 'export LD_LIBRARY_PATH=$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' >> $WORK_SPACE/pdc_env.sh && \
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echo 'export LD_LIBRARY_PATH=$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' >> $WORK_SPACE/pdc_env.sh && \
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apt-get update && apt-get install -y \
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build-essential \
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git \
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mpich \
@@ -28,107 +70,47 @@ RUN apt-get update && apt-get install -y \
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wget \
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axel \
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curl \
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bc \
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vim \
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nano \
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gdb \
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cgdb \
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curl \
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valgrind \
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python3
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# Install Oh My Bash
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RUN bash -c "$(curl -fsSL https://raw.githubusercontent.com/ohmybash/oh-my-bash/master/tools/install.sh)" && \
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sed -i 's/OSH_THEME="font"/OSH_THEME="powerline-multiline"/g' ~/.bashrc
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# Install Julia
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RUN echo "https://julialang-s3.julialang.org/bin/linux/aarch64/1.6/julia-1.6.7-linux-aarch64.tar.gz" > /julia_url_arm64v8.txt && \
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echo "https://julialang-s3.julialang.org/bin/linux/x64/1.6/julia-1.6.7-linux-x86_64.tar.gz" > /julia_url_amd64.txt
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RUN echo $(cat /julia_url_${ARCH_CODE}.txt) && sleep 3
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RUN mkdir -p /opt/julia && wget -O - $(cat /julia_url_${ARCH_CODE}.txt) | tar -xz -C /opt/julia --strip-components=1 && \
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ln -s /opt/julia/bin/julia /usr/local/bin/julia
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RUN rm -rf /tmp/julia_url_*.txt
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ENV JULIA_HOME=/opt/julia
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# Install Rust
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RUN curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
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RUN echo 'source $HOME/.cargo/env' >> ~/.bashrc
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# Set WORK_SPACE environment variable and create necessary directories
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ENV WORK_SPACE=/home/project
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RUN mkdir -p $WORK_SPACE
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# Install clang-format repo
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RUN mkdir -p $WORK_SPACE/software
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RUN cd $WORK_SPACE/software && git clone https://github.com/DoozyX/clang-format-lint-action.git
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ENV CLANG_FORMAT_PATH=$WORK_SPACE/software/clang-format-lint-action/clang-format/clang-format10
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# Clone the repositories
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WORKDIR $WORK_SPACE/source
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RUN git clone https://github.com/ofiwg/libfabric.git && \
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git clone https://github.com/mercury-hpc/mercury.git --recursive
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ENV LIBFABRIC_SRC_DIR=$WORK_SPACE/source/libfabric
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ENV LIBFABRIC_DIR=$WORK_SPACE/install/libfabric
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ENV MERCURY_SRC_DIR=$WORK_SPACE/source/mercury
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ENV MERCURY_DIR=$WORK_SPACE/install/mercury
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ENV PDC_SRC_DIR=$WORK_SPACE/source/pdc
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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" > $WORK_SPACE/pdc_env.sh && \
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echo "export LIBFABRIC_DIR=$WORK_SPACE/install/libfabric" >> $WORK_SPACE/pdc_env.sh && \
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echo "export MERCURY_SRC_DIR=$WORK_SPACE/source/mercury" >> $WORK_SPACE/pdc_env.sh && \
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echo "export MERCURY_DIR=$WORK_SPACE/install/mercury" >> $WORK_SPACE/pdc_env.sh && \
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echo "export PDC_SRC_DIR=$WORK_SPACE/source/pdc" >> $WORK_SPACE/pdc_env.sh && \
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echo "export PDC_DIR=$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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python3 && \
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cd $WORK_SPACE/software && \
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bash -c "$(curl -fsSL https://raw.githubusercontent.com/ohmybash/oh-my-bash/master/tools/install.sh)" && \
83+
sed -i 's/OSH_THEME="font"/OSH_THEME="powerline-multiline"/g' ~/.bashrc && \
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echo "https://julialang-s3.julialang.org/bin/linux/aarch64/1.6/julia-1.6.7-linux-aarch64.tar.gz" > $WORK_SPACE/software/julia_url_arm64v8.txt && \
85+
echo "https://julialang-s3.julialang.org/bin/linux/x64/1.6/julia-1.6.7-linux-x86_64.tar.gz" > $WORK_SPACE/software/julia_url_amd64.txt && \
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echo $(cat $WORK_SPACE/software/julia_url_${ARCH_CODE}.txt) && sleep 3 && \
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mkdir -p /opt/julia && wget -O - $(cat $WORK_SPACE/software/julia_url_${ARCH_CODE}.txt) | tar -xz -C /opt/julia --strip-components=1 && \
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ln -s /opt/julia/bin/julia /usr/local/bin/julia && \
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rm -rf $WORK_SPACE/software/julia_url_*.txt && \
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curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y && \
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echo 'source $HOME/.cargo/env' >> ~/.bashrc && \
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git clone https://github.com/DoozyX/clang-format-lint-action.git && \
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git clone https://github.com/ofiwg/libfabric.git ${LIBFABRIC_SRC_DIR} && \
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git clone https://github.com/mercury-hpc/mercury.git --recursive ${MERCURY_SRC_DIR} && \
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cd $LIBFABRIC_SRC_DIR && \
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git checkout v1.18.0 && \
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./autogen.sh && \
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./configure --prefix=$LIBFABRIC_DIR CC=mpicc CFLAG="-O2" && \
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make clean && \
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make -j 8 && 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
117-
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 \
120-
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 check && \
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cd $MERCURY_SRC_DIR && \
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git checkout v2.2.0 && \
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mkdir -p build && \
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cd ${MERCURY_SRC_DIR}/build && \
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cmake $MERCURY_CMAKE_FLAGS ../ && \
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make -j 16 && make install && \
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ctest
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# Set the environment variables
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ENV LD_LIBRARY_PATH="$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' >> $WORK_SPACE/pdc_env.sh
131-
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ctest && \
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apt-get autoremove -y && \
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apt-get clean && \
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rm -rf /var/lib/apt/lists/* && \
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rm -rf /tmp/* && \
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rm -rf /var/tmp/*
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133115
ENV PDC_CMAKE_FLAGS="-DBUILD_MPI_TESTING=ON -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=ON -DCMAKE_INSTALL_PREFIX=$PDC_DIR -DPDC_ENABLE_MPI=ON -DMERCURY_DIR=$MERCURY_DIR -DCMAKE_C_COMPILER=mpicc -DMPI_RUN_CMD=mpiexec "
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‎.gitignore

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@@ -19,3 +19,9 @@ build
1919

2020
# ignore docs build dir
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docs/build
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# ignore venv
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**/*venv
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# ignore .zed
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.zed

‎CMakeLists.txt

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Original file line numberDiff line numberDiff line change
@@ -198,6 +198,9 @@ if(SUPPRESS_IGNORABLE_WARNINGS)
198198
set(SUPPRESSED_LIST "-Wno-deprecated-non-prototype" ${SUPPRESSED_LIST})
199199
else()
200200
set(SUPPRESSED_LIST "-Wno-maybe-uninitialized" ${SUPPRESSED_LIST})
201+
set(SUPPRESSED_LIST "-Wno-alloc-size-larger-than" ${SUPPRESSED_LIST})
202+
# set(SUPPRESSED_LIST "-Wno-use-after-free" ${SUPPRESSED_LIST})
203+
set(SUPPRESSED_LIST "-Wno-stringop-truncation" ${SUPPRESSED_LIST})
201204
endif()
202205
set(SUPPRESSED_LIST "-Wno-sign-compare" ${SUPPRESSED_LIST})
203206
set(SUPPRESSED_LIST "-Wno-format" ${SUPPRESSED_LIST})
@@ -207,6 +210,8 @@ if(SUPPRESS_IGNORABLE_WARNINGS)
207210
set(SUPPRESSED_LIST "-Wno-unused-function" ${SUPPRESSED_LIST})
208211
set(SUPPRESSED_LIST "-Wno-unused-result" ${SUPPRESSED_LIST})
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set(SUPPRESSED_LIST "-Wno-unused-but-set-variable" ${SUPPRESSED_LIST})
213+
set(SUPPRESSED_LIST "-Wno-inline" ${SUPPRESSED_LIST})
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set(SUPPRESSED_LIST "-Wno-array-bounds" ${SUPPRESSED_LIST})
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211216
if(CMAKE_C_COMPILER_ID MATCHES "GNU|Clang")
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add_compile_options(${SUPPRESSED_LIST})

‎benchmark/idioms/CMakeLists.txt

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@@ -0,0 +1,68 @@
1+
cmake_minimum_required (VERSION 2.8.12)
2+
3+
# Setup cmake policies.
4+
foreach(p
5+
CMP0012
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CMP0013
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CMP0014
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CMP0022 # CMake 2.8.12
9+
CMP0025 # CMake 3.0
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CMP0053 # CMake 3.1
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CMP0054 # CMake 3.1
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CMP0074 # CMake 3.12
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CMP0075 # CMake 3.12
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CMP0083 # CMake 3.14
15+
CMP0093 # CMake 3.15
16+
)
17+
if(POLICY ${p})
18+
cmake_policy(SET ${p} NEW)
19+
endif()
20+
endforeach()
21+
22+
project(METADATA_JSON_LOADER C)
23+
24+
set(JMD_LDR_EXT_INCLUDE_DIRS "")
25+
set(JMD_LDR_EXT_LIBRARIES "")
26+
27+
set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build." FORCE)
28+
# set(JMD_DEBUG ON CACHE BOOL "Enable debug mode.")
29+
option(JMD_DEBUG_MODE "Enable debug mode." ON)
30+
if(JMD_DEBUG_MODE)
31+
add_definitions(-DJMD_DEBUG=1)
32+
endif()
33+
34+
option(USE_SYSTEM_MPI "Use system-installed MPI." ON)
35+
if(USE_SYSTEM_MPI)
36+
find_package(MPI)
37+
if(MPI_FOUND)
38+
add_definitions(-DJMD_LDR_ENABLE_MPI=1)
39+
SET(CMAKE_C_COMPILER ${MPI_C_COMPILER})
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SET(CMAKE_CXX_COMPILER ${MPI_CXX_COMPILER})
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set(JMD_LDR_EXT_INCLUDE_DIRS ${MPI_C_INCLUDE_PATH}
42+
${JMD_LDR_EXT_INCLUDE_DIRS}
43+
)
44+
set(JMD_LDR_EXT_LIBRARIES ${MPI_C_LIBRARIES} ${JMD_LDR_EXT_LIBRARIES})
45+
endif()
46+
endif()
47+
48+
find_package(PDC REQUIRED)
49+
if(PDC_FOUND)
50+
#message(STATUS "PDC include directory: ${PDC_INCLUDE_DIR}")
51+
set(JMD_LDR_EXT_INCLUDE_DIRS ${PDC_INCLUDE_DIR}
52+
${JMD_LDR_EXT_INCLUDE_DIRS}
53+
)
54+
set(JMD_LDR_EXT_LIBRARIES pdc ${JMD_LDR_EXT_LIBRARIES})
55+
endif()
56+
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add_library(cjson cjson/cJSON.c)
59+
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add_executable(metadata_json_loader
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metadata_json_loader.c
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metadata_json_processor.h
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metadata_json_printer.c
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metadata_json_printer.h
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metadata_json_importer.c
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metadata_json_importer.h)
67+
target_link_libraries(metadata_json_loader ${PDC_EXT_LIB_DEPENDENCIES} pdc cjson ${JMD_LDR_EXT_LIBRARIES})
68+
target_include_directories(metadata_json_loader PUBLIC ${PDC_EXT_INCLUDE_DEPENDENCIES} ${JMD_LDR_EXT_INCLUDE_DIRS})

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