openPMD · ax3l · Apr 11, 2023 · Apr 6, 2023 · Apr 7, 2023 · Apr 7, 2023
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -43,7 +43,6 @@ A clear and concise description of what you expected to happen.
  - machine: [Are you running on a public cluster? It's likely we compute on it as well!]
  - name and version of Python implementation: [e.g. CPython 3.9]
  - version of HDF5: [e.g. 1.12.0]
- - version of ADIOS1: [e.g. 1.13.1]
  - version of ADIOS2: [e.g. 2.7.1]
  - name and version of MPI: [e.g. OpenMPI 4.1.1]
 

diff --git a/.github/ci/sanitizer/clang/Leak.supp b/.github/ci/sanitizer/clang/Leak.supp
@@ -9,9 +9,6 @@ leak:libevent*
 leak:*py*
 # 10 byte memleak in main of "make" 4.1
 leak:/usr/bin/make*
-# ADIOS 1.13.1
-leak:adios_read_bp_open_file
-leak:adios_inq_var
 # ADIOS2
 leak:adios2::core::engine::SstReader::*
 leak:adios2::core::engine::SstWriter::*

diff --git a/...clang14_py311_nompi_h5_ad1_ad2/spack.yaml → ...nvs/clang14_py311_nompi_h5_ad2/spack.yaml b/...clang14_py311_nompi_h5_ad1_ad2/spack.yaml → ...nvs/clang14_py311_nompi_h5_ad2/spack.yaml
@@ -6,15 +6,12 @@
 #
 spack:
   specs:
-  - adios
   - adios2
   - hdf5
 
   packages:
     hdf5:
       variants: ~mpi
-    adios:
-      variants: ~mpi ~zfp ~sz ~lz4 ~blosc
     adios2:
       variants: ~mpi ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:

diff --git a/...vs/clang7_nopy_ompi_h5_ad1_ad2/spack.yaml → ...k-envs/clang7_nopy_ompi_h5_ad2/spack.yaml b/...vs/clang7_nopy_ompi_h5_ad1_ad2/spack.yaml → ...k-envs/clang7_nopy_ompi_h5_ad2/spack.yaml
@@ -6,14 +6,11 @@
 #
 spack:
   specs:
-  - adios
   - adios2
   - hdf5
   - openmpi
 
   packages:
-    adios:
-      variants: ~zfp ~sz ~lz4 ~blosc
     adios2:
       variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:

diff --git a/...opy_ompi_h5_ad1_ad2_bp3_libcpp/spack.yaml → ...clang7_nopy_ompi_h5_ad2_libcpp/spack.yaml b/...opy_ompi_h5_ad1_ad2_bp3_libcpp/spack.yaml → ...clang7_nopy_ompi_h5_ad2_libcpp/spack.yaml
@@ -6,14 +6,11 @@
 #
 spack:
   specs:
-  - adios
   - adios2
   - hdf5
   - openmpi
 
   packages:
-    adios:
-      variants: ~zfp ~sz ~lz4 ~blosc
     adios2:
       variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:

diff --git a/...s/clang8_py38_mpich_h5_ad1_ad2/spack.yaml → ...-envs/clang8_py38_mpich_h5_ad2/spack.yaml b/...s/clang8_py38_mpich_h5_ad1_ad2/spack.yaml → ...-envs/clang8_py38_mpich_h5_ad2/spack.yaml
@@ -6,14 +6,11 @@
 #
 spack:
   specs:
-  - adios
   - adios2@2.7.1
   - hdf5
   - mpich
 
   packages:
-    adios:
-      variants: ~zfp ~sz ~lz4 ~blosc
     adios2:
       variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:

diff --git a/...clangtidy_nopy_ompi_h5_ad1_ad2/spack.yaml → ...nvs/clangtidy_nopy_ompi_h5_ad2/spack.yaml b/...clangtidy_nopy_ompi_h5_ad1_ad2/spack.yaml → ...nvs/clangtidy_nopy_ompi_h5_ad2/spack.yaml
@@ -6,14 +6,11 @@
 #
 spack:
   specs:
-  - adios
   - adios2
   - hdf5
   - openmpi
 
   packages:
-    adios:
-      variants: ~zfp ~sz ~lz4 ~blosc
     adios2:
       variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:

diff --git a/...envs/gcc7_py36_ompi_h5_ad1_ad2/spack.yaml → ...ack-envs/gcc7_py36_ompi_h5_ad2/spack.yaml b/...envs/gcc7_py36_ompi_h5_ad1_ad2/spack.yaml → ...ack-envs/gcc7_py36_ompi_h5_ad2/spack.yaml
@@ -6,14 +6,11 @@
 #
 spack:
   specs:
-  - adios
   - adios2
   - hdf5
   - openmpi
 
   packages:
-    adios:
-      variants: ~zfp ~sz ~lz4 ~blosc
     adios2:
       variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:

diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -33,7 +33,7 @@ jobs:
       - name: Install Packages
         run: |
           sudo apt-get update
-          sudo apt-get install --yes cmake openmpi-bin libopenmpi-dev libhdf5-openmpi-dev libadios-openmpi-dev
+          sudo apt-get install --yes cmake openmpi-bin libopenmpi-dev libhdf5-openmpi-dev
 
           python -m pip install --upgrade pip
           python -m pip install --upgrade wheel

diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml
@@ -39,14 +39,14 @@ jobs:
         cmake --build build --parallel 2
         ctest --test-dir build --output-on-failure
 
-  clang7_nopy_ompi_h5_ad1_ad2_bp3_libcpp:
+  clang7_nopy_ompi_h5_ad2_libcpp:
     runs-on: ubuntu-20.04
     if: github.event.pull_request.draft == false
     steps:
     - uses: actions/checkout@v3
     - name: Spack Cache
       uses: actions/cache@v3
-      with: {path: /opt/spack, key: clang7_nopy_ompi_h5_ad1_ad2_bp3_libcpp_v2}
+      with: {path: /opt/spack, key: clang7_nopy_ompi_h5_ad2_libcpp_v2}
     - name: Install
       run: |
         sudo apt-get update
@@ -62,15 +62,14 @@ jobs:
         mpiexec --version
         perl --version
         python --version
-        eval $(spack env activate --sh .github/ci/spack-envs/clang7_nopy_ompi_h5_ad1_ad2_bp3_libcpp/)
+        eval $(spack env activate --sh .github/ci/spack-envs/clang7_nopy_ompi_h5_ad2_libcpp/)
         spack install
 
         share/openPMD/download_samples.sh build
         cmake -S . -B build \
           -DopenPMD_USE_PYTHON=OFF \
           -DopenPMD_USE_MPI=ON     \
           -DopenPMD_USE_HDF5=ON    \
-          -DopenPMD_USE_ADIOS1=ON  \
           -DopenPMD_USE_ADIOS2=ON  \
           -DopenPMD_USE_INVASIVE_TESTS=ON \
           -DCMAKE_VERBOSE_MAKEFILE=ON
@@ -79,7 +78,6 @@ jobs:
 
         find . -name *.bp     | xargs -n1 -P1 -I {} rm -rf {}
         find . -name *.bp.dir | xargs -n1 -P1 -I {} rm -rf {}
-        export OPENPMD_BP_BACKEND=ADIOS1
         ctest --test-dir build --output-on-failure
 
   clang7_nopy_ompi_h5_ad2_newLayout:
@@ -98,32 +96,31 @@ jobs:
     - name: Build
       env: {CC: clang-7, CXX: clang++-7, CXXFLAGS: -Werror, OPENPMD2_ADIOS2_SCHEMA: 20210209}
       run: |
-        eval $(spack env activate --sh .github/ci/spack-envs/clang7_nopy_ompi_h5_ad1_ad2/)
+        eval $(spack env activate --sh .github/ci/spack-envs/clang7_nopy_ompi_h5_ad2/)
         spack install
 
         share/openPMD/download_samples.sh build
         cmake -S . -B build \
           -DopenPMD_USE_PYTHON=OFF \
           -DopenPMD_USE_MPI=ON     \
           -DopenPMD_USE_HDF5=ON    \
-          -DopenPMD_USE_ADIOS1=OFF \
           -DopenPMD_USE_ADIOS2=ON  \
           -DopenPMD_USE_INVASIVE_TESTS=ON \
           -DCMAKE_VERBOSE_MAKEFILE=ON
         cmake --build build --parallel 2
         ctest --test-dir build --output-on-failure
 
 # TODO
-#  clang7_py36_nompi_h5_ad1_ad2_libstdc++
+#  clang7_py36_nompi_h5_ad2_libstdc++
 
-  clang14_py311_nompi_h5_ad1_ad2:
+  clang14_py311_nompi_h5_ad2:
     runs-on: ubuntu-22.04
     if: github.event.pull_request.draft == false
     steps:
     - uses: actions/checkout@v3
     - name: Spack Cache
       uses: actions/cache@v3
-      with: {path: /opt/spack, key: clang14_py311_nompi_h5_ad1_ad2_v2 }
+      with: {path: /opt/spack, key: clang14_py311_nompi_h5_ad2_v2 }
     - name: Install
       run: |
         sudo apt update
@@ -135,15 +132,14 @@ jobs:
     - name: Build
       env: {CC: clang-14, CXX: clang++-14, CXXFLAGS: -Werror}
       run: |
-        eval $(spack env activate --sh .github/ci/spack-envs/clang14_py311_nompi_h5_ad1_ad2/)
+        eval $(spack env activate --sh .github/ci/spack-envs/clang14_py311_nompi_h5_ad2/)
         spack install
 
         share/openPMD/download_samples.sh build
         cmake -S . -B build \
           -DopenPMD_USE_PYTHON=ON \
           -DopenPMD_USE_MPI=OFF   \
           -DopenPMD_USE_HDF5=ON   \
-          -DopenPMD_USE_ADIOS1=ON \
           -DopenPMD_USE_ADIOS2=ON \
           -DopenPMD_USE_INVASIVE_TESTS=ON \
           -DCMAKE_VERBOSE_MAKEFILE=ON     \
@@ -152,14 +148,14 @@ jobs:
         ctest --test-dir build --output-on-failure
 
   # ADIOS2 v2.7.1
-  clang8_py38_mpich_h5_ad1_ad2_newLayout:
+  clang8_py38_mpich_h5_ad2_newLayout:
     runs-on: ubuntu-20.04
     if: github.event.pull_request.draft == false
     steps:
     - uses: actions/checkout@v3
     - name: Spack Cache
       uses: actions/cache@v3
-      with: {path: /opt/spack, key: clang8_py38_mpich_h5_ad1_ad2_newLayout_v2 }
+      with: {path: /opt/spack, key: clang8_py38_mpich_h5_ad2_newLayout_v2 }
     - name: Install
       run: |
         sudo apt-get update
@@ -172,43 +168,42 @@ jobs:
         mpiexec --version
         perl --version
         python --version
-        eval $(spack env activate --sh .github/ci/spack-envs/clang8_py38_mpich_h5_ad1_ad2/)
+        eval $(spack env activate --sh .github/ci/spack-envs/clang8_py38_mpich_h5_ad2/)
         spack install
 
         share/openPMD/download_samples.sh build
         cmake -S . -B build \
           -DopenPMD_USE_PYTHON=OFF \
           -DopenPMD_USE_MPI=ON     \
           -DopenPMD_USE_HDF5=ON    \
-          -DopenPMD_USE_ADIOS1=ON  \
           -DopenPMD_USE_ADIOS2=ON  \
           -DopenPMD_USE_INVASIVE_TESTS=ON
         cmake --build build --parallel 2
         ctest --test-dir build --output-on-failure
 
 # TODO: (old Travis-CI coverage)
-#  clang10_py38_ompi_h5_1-10-6_ad1_ad2_release
+#  clang10_py38_ompi_h5_1-10-6_ad2_release
 #  ..._h5coll with OPENPMD_HDF5_INDEPENDENT: OFF
 
 # TODO: (old Travis-CI coverage)
-#  gcc-4.9.4_nopy_nompi_h5_ad1_ad2
-#  gcc-4.9.4_nopy_ompi_h5_ad1_ad2
-#  gcc-9.3.0_nopy_nompi_h5_ad1_ad2-2.6.0
-#  gcc-7.4.0_nopy_ompi_h5_ad1_h5coll
-#  gcc-6.5.0_py35_nompi_h5_ad1-1.13.1
-#  gcc-8.1.0_py37_nompi_h5_ad1_static
+#  gcc-4.9.4_nopy_nompi_h5_ad2
+#  gcc-4.9.4_nopy_ompi_h5_ad2
+#  gcc-9.3.0_nopy_nompi_h5_ad2-2.6.0
+#  gcc-7.4.0_nopy_ompi_h5_h5coll
+#  gcc-6.5.0_py35_nompi_h5-1.13.1
+#  gcc-8.1.0_py37_nompi_h5_static
 #  gcc-6.5.0_py36_nompi_h5-1.8.13
 #  gcc-4.8.5_py35_nompi_h5
-#  gcc-7.4.0_py_ompi_h5_ad1_ad2_coveralls
+#  gcc-7.4.0_py_ompi_h5_ad2_coveralls
 
-  gcc7_py36_pd_dd_ompi_h5_ad1_ad2:
+  gcc7_py36_pd_dd_ompi_h5_ad2:
     runs-on: ubuntu-20.04
     if: github.event.pull_request.draft == false
     steps:
     - uses: actions/checkout@v3
     - name: Spack Cache
       uses: actions/cache@v3
-      with: {path: /opt/spack, key: gcc7_py36_ompi_h5_ad1_ad2_v2 }
+      with: {path: /opt/spack, key: gcc7_py36_ompi_h5_ad2_v2 }
     - name: Install
       run: |
         sudo apt-get update
@@ -223,15 +218,14 @@ jobs:
     - name: Build
       env: {CC: gcc-7, CXX: g++-7, CXXFLAGS: -Werror}
       run: |
-        eval $(spack env activate --sh .github/ci/spack-envs/gcc7_py36_ompi_h5_ad1_ad2/)
+        eval $(spack env activate --sh .github/ci/spack-envs/gcc7_py36_ompi_h5_ad2/)
         spack install
 
         share/openPMD/download_samples.sh build
         cmake -S . -B build \
           -DopenPMD_USE_PYTHON=ON \
           -DopenPMD_USE_MPI=ON    \
           -DopenPMD_USE_HDF5=ON   \
-          -DopenPMD_USE_ADIOS1=ON \
           -DopenPMD_USE_ADIOS2=ON \
           -DopenPMD_USE_INVASIVE_TESTS=ON
         cmake --build build --parallel 2
@@ -245,7 +239,7 @@ jobs:
     - name: Install
       run: |
         sudo apt-get update
-        sudo apt-get install g++ libopenmpi-dev libhdf5-openmpi-dev libadios-dev python3 python3-numpy python3-mpi4py python3-pandas
+        sudo apt-get install g++ libopenmpi-dev libhdf5-openmpi-dev python3 python3-numpy python3-mpi4py python3-pandas
 #       TODO ADIOS2
     - name: Build
       env: {CXXFLAGS: -Werror, PKG_CONFIG_PATH: /usr/lib/x86_64-linux-gnu/pkgconfig}
@@ -313,7 +307,6 @@ jobs:
           -DopenPMD_USE_PYTHON=ON \
           -DopenPMD_USE_MPI=ON    \
           -DopenPMD_USE_HDF5=ON   \
-          -DopenPMD_USE_ADIOS1=ON \
           -DopenPMD_USE_ADIOS2=ON \
           -DopenPMD_USE_INVASIVE_TESTS=ON
         cmake --build build --parallel 2

diff --git a/.github/workflows/macos.yml b/.github/workflows/macos.yml
@@ -8,7 +8,7 @@ concurrency:
 
 jobs:
 # TODO: (old Travis-CI coverage)
-#  appleclang9_py37_nompi_h5_ad1
+#  appleclang9_py37_nompi_h5
 #  appleclang10_py37_h5_ad2_libcpp
 #  appleclang11_nopy_nompi_h5_ad2
 
@@ -43,7 +43,7 @@ jobs:
         cmake --build build --parallel 3
         ctest --test-dir build --verbose
 
-  appleclang12_py_ad1:
+  appleclang12_py:
     runs-on: macos-10.15
     # next: macOS-11
     if: github.event.pull_request.draft == false
@@ -54,13 +54,6 @@ jobs:
       run: |
         set +e
         python3 -m pip install -U numpy pandas
-
-        curl -Lo adios-1.13.1.tar.gz http://users.nccs.gov/~pnorbert/adios-1.13.1.tar.gz
-        tar -xzf adios-1.13.1.tar.gz
-        cd adios-1.13.1/
-        CFLAGS="-fPIC" ./configure --enable-static --enable-shared --prefix=/usr/local --without-mpi --disable-fortran
-        make -j 3
-        make install
         set -e
     - name: Build
       env: {CXXFLAGS: -Werror -DTOML11_DISABLE_STD_FILESYSTEM, MACOSX_DEPLOYMENT_TARGET: 10.14}
@@ -73,7 +66,6 @@ jobs:
           -DopenPMD_USE_PYTHON=ON  \
           -DopenPMD_USE_MPI=OFF    \
           -DopenPMD_USE_HDF5=OFF   \
-          -DopenPMD_USE_ADIOS1=ON \
           -DopenPMD_USE_ADIOS2=OFF \
           -DopenPMD_USE_INVASIVE_TESTS=ON
         cmake --build build --parallel 3
-Original file line number
+Diff line change
@@ Expand Up / @@ -6,14 +6,11 @@ @@
     #
     spack:
       specs:
-      - adios
       - adios2
       - hdf5
       - openmpi
       packages:
-        adios:
-          variants: ~zfp ~sz ~lz4 ~blosc
         adios2:
           variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
         cmake:
@@ Expand Down @@