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Remove ADIOS1 - Long Live ADIOS2 (#1419)
* Remove ADIOS1 - Long Live ADIOS2 Finally removing the deprecated and end-of-life backend ADIOS1. Long live ADIOS2! 🚀 * Fix forward declaration of ADIOS2IOHandlerImpl in Writable.hpp * Remove mentions of ADIOS1 from Serial testing --------- Co-authored-by: Franz Pöschel <franz.poeschel@gmail.com>
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‎.github/ISSUE_TEMPLATE/bug_report.md‎

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- machine: [Are you running on a public cluster? It's likely we compute on it as well!]
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- name and version of Python implementation: [e.g. CPython 3.9]
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- version of HDF5: [e.g. 1.12.0]
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- version of ADIOS1: [e.g. 1.13.1]
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- version of ADIOS2: [e.g. 2.7.1]
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- name and version of MPI: [e.g. OpenMPI 4.1.1]
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‎.github/ci/sanitizer/clang/Leak.supp‎

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leak:*py*
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# 10 byte memleak in main of "make" 4.1
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leak:/usr/bin/make*
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# ADIOS 1.13.1
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leak:adios_read_bp_open_file
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leak:adios_inq_var
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# ADIOS2
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leak:adios2::core::engine::SstReader::*
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leak:adios2::core::engine::SstWriter::*

.github/ci/spack-envs/clang14_py311_nompi_h5_ad1_ad2/spack.yaml renamed to .github/ci/spack-envs/clang14_py311_nompi_h5_ad2/spack.yaml

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#
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spack:
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specs:
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- adios
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- adios2
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- hdf5
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packages:
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hdf5:
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variants: ~mpi
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adios:
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variants: ~mpi ~zfp ~sz ~lz4 ~blosc
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adios2:
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variants: ~mpi ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
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cmake:

.github/ci/spack-envs/clang7_nopy_ompi_h5_ad1_ad2/spack.yaml renamed to .github/ci/spack-envs/clang7_nopy_ompi_h5_ad2/spack.yaml

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#
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spack:
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specs:
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- adios
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- adios2
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- hdf5
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- openmpi
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packages:
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adios:
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variants: ~zfp ~sz ~lz4 ~blosc
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adios2:
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variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
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cmake:

.github/ci/spack-envs/clang7_nopy_ompi_h5_ad1_ad2_bp3_libcpp/spack.yaml renamed to .github/ci/spack-envs/clang7_nopy_ompi_h5_ad2_libcpp/spack.yaml

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#
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spack:
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specs:
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- adios
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- adios2
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- hdf5
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- openmpi
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packages:
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adios:
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variants: ~zfp ~sz ~lz4 ~blosc
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adios2:
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variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
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cmake:

.github/ci/spack-envs/clang8_py38_mpich_h5_ad1_ad2/spack.yaml renamed to .github/ci/spack-envs/clang8_py38_mpich_h5_ad2/spack.yaml

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#
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spack:
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specs:
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- adios
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- adios2@2.7.1
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- hdf5
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- mpich
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packages:
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adios:
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variants: ~zfp ~sz ~lz4 ~blosc
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adios2:
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variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
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cmake:

.github/ci/spack-envs/clangtidy_nopy_ompi_h5_ad1_ad2/spack.yaml renamed to .github/ci/spack-envs/clangtidy_nopy_ompi_h5_ad2/spack.yaml

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#
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spack:
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specs:
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- adios
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- adios2
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- hdf5
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- openmpi
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packages:
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adios:
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variants: ~zfp ~sz ~lz4 ~blosc
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adios2:
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variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
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cmake:

.github/ci/spack-envs/gcc7_py36_ompi_h5_ad1_ad2/spack.yaml renamed to .github/ci/spack-envs/gcc7_py36_ompi_h5_ad2/spack.yaml

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spack:
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specs:
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- adios
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- adios2
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- hdf5
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- openmpi
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packages:
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adios:
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variants: ~zfp ~sz ~lz4 ~blosc
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cmake:

‎.github/workflows/codeql.yml‎

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- name: Install Packages
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run: |
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sudo apt-get update
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sudo apt-get install --yes cmake openmpi-bin libopenmpi-dev libhdf5-openmpi-dev libadios-openmpi-dev
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sudo apt-get install --yes cmake openmpi-bin libopenmpi-dev libhdf5-openmpi-dev
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python -m pip install --upgrade pip
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python -m pip install --upgrade wheel

‎.github/workflows/linux.yml‎

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cmake --build build --parallel 2
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ctest --test-dir build --output-on-failure
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clang7_nopy_ompi_h5_ad1_ad2_bp3_libcpp:
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clang7_nopy_ompi_h5_ad2_libcpp:
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if: github.event.pull_request.draft == false
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- uses: actions/checkout@v3
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- name: Spack Cache
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uses: actions/cache@v3
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with: {path: /opt/spack, key: clang7_nopy_ompi_h5_ad1_ad2_bp3_libcpp_v2}
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with: {path: /opt/spack, key: clang7_nopy_ompi_h5_ad2_libcpp_v2}
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- name: Install
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mpiexec --version
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eval $(spack env activate --sh .github/ci/spack-envs/clang7_nopy_ompi_h5_ad1_ad2_bp3_libcpp/)
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eval $(spack env activate --sh .github/ci/spack-envs/clang7_nopy_ompi_h5_ad2_libcpp/)
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spack install
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share/openPMD/download_samples.sh build
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cmake -S . -B build \
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-DopenPMD_USE_PYTHON=OFF \
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-DopenPMD_USE_MPI=ON \
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-DopenPMD_USE_HDF5=ON \
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-DopenPMD_USE_ADIOS1=ON \
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-DopenPMD_USE_ADIOS2=ON \
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-DopenPMD_USE_INVASIVE_TESTS=ON \
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-DCMAKE_VERBOSE_MAKEFILE=ON
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find . -name *.bp | xargs -n1 -P1 -I {} rm -rf {}
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find . -name *.bp.dir | xargs -n1 -P1 -I {} rm -rf {}
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export OPENPMD_BP_BACKEND=ADIOS1
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ctest --test-dir build --output-on-failure
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clang7_nopy_ompi_h5_ad2_newLayout:
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eval $(spack env activate --sh .github/ci/spack-envs/clang7_nopy_ompi_h5_ad1_ad2/)
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eval $(spack env activate --sh .github/ci/spack-envs/clang7_nopy_ompi_h5_ad2/)
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spack install
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share/openPMD/download_samples.sh build
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cmake -S . -B build \
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-DopenPMD_USE_PYTHON=OFF \
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-DopenPMD_USE_MPI=ON \
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-DopenPMD_USE_HDF5=ON \
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-DopenPMD_USE_ADIOS1=OFF \
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-DopenPMD_USE_ADIOS2=ON \
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-DopenPMD_USE_INVASIVE_TESTS=ON \
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-DCMAKE_VERBOSE_MAKEFILE=ON
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cmake --build build --parallel 2
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ctest --test-dir build --output-on-failure
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# TODO
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# clang7_py36_nompi_h5_ad1_ad2_libstdc++
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# clang7_py36_nompi_h5_ad2_libstdc++
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clang14_py311_nompi_h5_ad1_ad2:
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clang14_py311_nompi_h5_ad2:
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with: {path: /opt/spack, key: clang14_py311_nompi_h5_ad2_v2 }
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eval $(spack env activate --sh .github/ci/spack-envs/clang14_py311_nompi_h5_ad1_ad2/)
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eval $(spack env activate --sh .github/ci/spack-envs/clang14_py311_nompi_h5_ad2/)
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spack install
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cmake -S . -B build \
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-DopenPMD_USE_HDF5=ON \
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-DopenPMD_USE_ADIOS1=ON \
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-DopenPMD_USE_ADIOS2=ON \
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-DopenPMD_USE_INVASIVE_TESTS=ON \
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-DCMAKE_VERBOSE_MAKEFILE=ON \
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# ADIOS2 v2.7.1
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clang8_py38_mpich_h5_ad1_ad2_newLayout:
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clang8_py38_mpich_h5_ad2_newLayout:
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with: {path: /opt/spack, key: clang8_py38_mpich_h5_ad1_ad2_newLayout_v2 }
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with: {path: /opt/spack, key: clang8_py38_mpich_h5_ad2_newLayout_v2 }
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eval $(spack env activate --sh .github/ci/spack-envs/clang8_py38_mpich_h5_ad1_ad2/)
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eval $(spack env activate --sh .github/ci/spack-envs/clang8_py38_mpich_h5_ad2/)
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spack install
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-DopenPMD_USE_MPI=ON \
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-DopenPMD_USE_HDF5=ON \
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-DopenPMD_USE_ADIOS1=ON \
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cmake --build build --parallel 2
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# clang10_py38_ompi_h5_1-10-6_ad1_ad2_release
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# clang10_py38_ompi_h5_1-10-6_ad2_release
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# ..._h5coll with OPENPMD_HDF5_INDEPENDENT: OFF
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# TODO: (old Travis-CI coverage)
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# gcc-4.9.4_nopy_nompi_h5_ad1_ad2
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# gcc-4.9.4_nopy_ompi_h5_ad1_ad2
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# gcc-9.3.0_nopy_nompi_h5_ad1_ad2-2.6.0
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# gcc-7.4.0_nopy_ompi_h5_ad1_h5coll
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# gcc-6.5.0_py35_nompi_h5_ad1-1.13.1
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# gcc-8.1.0_py37_nompi_h5_ad1_static
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# gcc-4.9.4_nopy_nompi_h5_ad2
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# gcc-4.9.4_nopy_ompi_h5_ad2
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# gcc-9.3.0_nopy_nompi_h5_ad2-2.6.0
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# gcc-7.4.0_nopy_ompi_h5_h5coll
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# gcc-6.5.0_py35_nompi_h5-1.13.1
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# gcc-8.1.0_py37_nompi_h5_static
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# gcc-6.5.0_py36_nompi_h5-1.8.13
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# gcc-4.8.5_py35_nompi_h5
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# gcc-7.4.0_py_ompi_h5_ad1_ad2_coveralls
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# gcc-7.4.0_py_ompi_h5_ad2_coveralls
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gcc7_py36_pd_dd_ompi_h5_ad1_ad2:
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gcc7_py36_pd_dd_ompi_h5_ad2:
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with: {path: /opt/spack, key: gcc7_py36_ompi_h5_ad1_ad2_v2 }
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with: {path: /opt/spack, key: gcc7_py36_ompi_h5_ad2_v2 }
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eval $(spack env activate --sh .github/ci/spack-envs/gcc7_py36_ompi_h5_ad1_ad2/)
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eval $(spack env activate --sh .github/ci/spack-envs/gcc7_py36_ompi_h5_ad2/)
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spack install
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share/openPMD/download_samples.sh build
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-DopenPMD_USE_PYTHON=ON \
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-DopenPMD_USE_MPI=ON \
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-DopenPMD_USE_HDF5=ON \
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-DopenPMD_USE_ADIOS1=ON \
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sudo apt-get install g++ libopenmpi-dev libhdf5-openmpi-dev python3 python3-numpy python3-mpi4py python3-pandas
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- name: Build
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env: {CXXFLAGS: -Werror, PKG_CONFIG_PATH: /usr/lib/x86_64-linux-gnu/pkgconfig}
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-DopenPMD_USE_PYTHON=ON \
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-DopenPMD_USE_MPI=ON \
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-DopenPMD_USE_HDF5=ON \
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-DopenPMD_USE_ADIOS1=ON \
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-DopenPMD_USE_ADIOS2=ON \
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-DopenPMD_USE_INVASIVE_TESTS=ON
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cmake --build build --parallel 2

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