Merge pull request #3753 from vicentebolea/add-mgard-to-ci

ci: add mgard dependency to spack builds
ornladios · Aug 17, 2023 · c8d87b0 · c8d87b0
2 parents 2f78f24 + 41ed053
commit c8d87b0
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Showing 20 changed files with 101 additions and 82 deletions.
diff --git a/.github/workflows/everything.yml b/.github/workflows/everything.yml
@@ -108,7 +108,7 @@ jobs:
 
     runs-on: ubuntu-20.04
     container:
-      image: ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-${{ matrix.compiler }}
+      image: ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-tmp-${{ matrix.compiler }}
       options: --shm-size=1g
       env:
         GH_YML_JOBNAME: ${{ matrix.os }}-${{ matrix.compiler }}${{ matrix.shared == 'static' && '-static' || ''}}-${{ matrix.parallel }}

diff --git a/.shellcheck_exclude_paths b/.shellcheck_exclude_paths
@@ -2,7 +2,6 @@ scripts/ci/circle/postCDashStatus.sh
 scripts/ci/circle/run.sh
 scripts/ci/gh-actions/check-branch-name.sh
 scripts/ci/gh-actions/get-changed-files.sh
-scripts/ci/gh-actions/linux-setup.sh
 scripts/ci/gh-actions/macos-setup.sh
 scripts/ci/gh-actions/run.sh
 scripts/ci/scripts/github-prs-to-gitlab.sh

diff --git a/bindings/CXX11/CMakeLists.txt b/bindings/CXX11/CMakeLists.txt
@@ -24,7 +24,7 @@ add_library(adios2_cxx11
 
 set_property(TARGET adios2_cxx11 PROPERTY EXPORT_NAME cxx11)
 set_property(TARGET adios2_cxx11 PROPERTY OUTPUT_NAME adios2${ADIOS2_LIBRARY_SUFFIX}_cxx11)
-target_link_libraries(adios2_cxx11 PRIVATE adios2_core adios2::thirdparty::pugixml)
+target_link_libraries(adios2_cxx11 PRIVATE adios2_core)
 target_compile_features(adios2_cxx11 INTERFACE ${ADIOS2_CXX11_FEATURES})
 
 target_include_directories(adios2_cxx11

diff --git a/scripts/ci/cmake/ci-ubuntu20.04-clang10-ompi.cmake b/scripts/ci/cmake/ci-ubuntu20.04-clang10-ompi.cmake
@@ -12,8 +12,8 @@ execute_process(
   OUTPUT_STRIP_TRAILING_WHITESPACE)
 
 set(dashboard_cache "
-ADIOS2_USE_BZip2:BOOL=ON
 ADIOS2_USE_Blosc:BOOL=ON
+ADIOS2_USE_BZip2:BOOL=ON
 ADIOS2_USE_DataMan:BOOL=ON
 ADIOS2_USE_Fortran:BOOL=ON
 ADIOS2_USE_HDF5:BOOL=ON

diff --git a/scripts/ci/cmake/ci-ubuntu20.04-clang10-serial.cmake b/scripts/ci/cmake/ci-ubuntu20.04-clang10-serial.cmake
@@ -8,8 +8,8 @@ execute_process(
   OUTPUT_STRIP_TRAILING_WHITESPACE)
 
 set(dashboard_cache "
-ADIOS2_USE_BZip2:BOOL=ON
 ADIOS2_USE_Blosc:BOOL=ON
+ADIOS2_USE_BZip2:BOOL=ON
 ADIOS2_USE_DataMan:BOOL=ON
 ADIOS2_USE_Fortran:BOOL=ON
 ADIOS2_USE_HDF5:BOOL=ON

diff --git a/scripts/ci/cmake/ci-ubuntu20.04-clang6-ompi.cmake b/scripts/ci/cmake/ci-ubuntu20.04-clang6-ompi.cmake
@@ -12,11 +12,12 @@ execute_process(
   OUTPUT_STRIP_TRAILING_WHITESPACE)
 
 set(dashboard_cache "
-ADIOS2_USE_BZip2:BOOL=ON
 ADIOS2_USE_Blosc:BOOL=ON
+ADIOS2_USE_BZip2:BOOL=ON
 ADIOS2_USE_DataMan:BOOL=ON
 ADIOS2_USE_Fortran:BOOL=ON
 ADIOS2_USE_HDF5:BOOL=ON
+ADIOS2_USE_MGARD:BOOL=OFF
 ADIOS2_USE_MPI:BOOL=ON
 ADIOS2_USE_Python:BOOL=ON
 ADIOS2_USE_SZ:BOOL=ON
@@ -37,6 +38,9 @@ MPIEXEC_EXTRA_FLAGS:STRING=--allow-run-as-root --oversubscribe
 MPIEXEC_MAX_NUMPROCS:STRING=${N2CPUS}
 ")
 
+# We have a dedicated build for this setup without MPI
+set(CTEST_TEST_ARGS EXCLUDE ".Serial$")
+
 set(CTEST_CMAKE_GENERATOR "Ninja")
 list(APPEND CTEST_UPDATE_NOTES_FILES "${CMAKE_CURRENT_LIST_FILE}")
 include(${CMAKE_CURRENT_LIST_DIR}/ci-common.cmake)
diff --git a/scripts/ci/cmake/ci-ubuntu20.04-clang6-serial.cmake b/scripts/ci/cmake/ci-ubuntu20.04-clang6-serial.cmake
@@ -8,11 +8,12 @@ execute_process(
   OUTPUT_STRIP_TRAILING_WHITESPACE)
 
 set(dashboard_cache "
-ADIOS2_USE_BZip2:BOOL=ON
 ADIOS2_USE_Blosc:BOOL=ON
+ADIOS2_USE_BZip2:BOOL=ON
 ADIOS2_USE_DataMan:BOOL=ON
 ADIOS2_USE_Fortran:BOOL=ON
 ADIOS2_USE_HDF5:BOOL=ON
+ADIOS2_USE_MGARD:BOOL=OFF
 ADIOS2_USE_MPI:BOOL=OFF
 ADIOS2_USE_Python:BOOL=ON
 ADIOS2_USE_SZ:BOOL=ON

diff --git a/scripts/ci/cmake/ci-ubuntu20.04-gcc10-mpich.cmake b/scripts/ci/cmake/ci-ubuntu20.04-gcc10-mpich.cmake
@@ -37,7 +37,7 @@ MPIEXEC_MAX_NUMPROCS:STRING=${N2CPUS}
 ")
 
 set(CTEST_TEST_ARGS
-  EXCLUDE "Engine.BPEngineTest.SzComplex.MPI|Engine.BPEngineTest.ZfpComplex.MPI")
+  EXCLUDE "Engine.BPEngineTest.SzComplex.MPI|Engine.BPEngineTest.ZfpComplex.MPI|.Serial$")
 
 set(CTEST_CMAKE_GENERATOR "Ninja")
 list(APPEND CTEST_UPDATE_NOTES_FILES "${CMAKE_CURRENT_LIST_FILE}")

diff --git a/scripts/ci/cmake/ci-ubuntu20.04-gcc10-ompi.cmake b/scripts/ci/cmake/ci-ubuntu20.04-gcc10-ompi.cmake
@@ -37,6 +37,9 @@ MPIEXEC_EXTRA_FLAGS:STRING=--allow-run-as-root --oversubscribe
 MPIEXEC_MAX_NUMPROCS:STRING=${N2CPUS}
 ")
 
+# We have a dedicated build for this setup without MPI
+set(CTEST_TEST_ARGS EXCLUDE ".Serial$")
+
 set(CTEST_CMAKE_GENERATOR "Ninja")
 list(APPEND CTEST_UPDATE_NOTES_FILES "${CMAKE_CURRENT_LIST_FILE}")
 include(${CMAKE_CURRENT_LIST_DIR}/ci-common.cmake)
diff --git a/scripts/ci/gh-actions/linux-setup.sh b/scripts/ci/gh-actions/linux-setup.sh
@@ -5,7 +5,8 @@ set -ex
 export CI_ROOT_DIR="${GITHUB_WORKSPACE}/.."
 export CI_SOURCE_DIR="${GITHUB_WORKSPACE}/source"
 
-declare -r local_scripts_dir="$(dirname -- $0)/config"
+local_scripts_dir="$(dirname -- "$0")/config"
+readonly local_scripts_dir
 
 echo "**********Install dependencies Begin**********"
 
@@ -18,15 +19,3 @@ find "$local_scripts_dir" -type f -name '*.sh' -perm /a=x -exec ./{} \;
 find "$local_scripts_dir" -type f -name '*.cmake' -exec cmake --trace -VV -P {} \;
 
 echo "**********Install dependencies End**********"
-
-SETUP_SCRIPT=${CI_SOURCE_DIR}/scripts/ci/setup/ci-${GH_YML_JOBNAME}.sh
-
-if [ -x "${SETUP_SCRIPT}" ]
-then
-  echo "**********Setup Begin**********"
-  echo "${SETUP_SCRIPT}"
-  "${SETUP_SCRIPT}"
-  echo "**********Setup End**********"
-fi
-
-exit 0
diff --git a/scripts/ci/gh-actions/run.sh b/scripts/ci/gh-actions/run.sh
@@ -28,6 +28,7 @@ then
 else
   export CI_BUILD_NAME="${GITHUB_REF_NAME}_${GH_YML_JOBNAME}"
 fi
+
 if [[ "${GH_YML_BASE_OS}" =~ "Windows" ]]
 then
   export CI_ROOT_DIR="${GITHUB_WORKSPACE//\\//}"
@@ -75,24 +76,14 @@ then
   export OMPI_MCA_btl_base_warn_component_unused=0
   export OMPI_MCA_btl_vader_single_copy_mechanism=none
 
-  # Force only shared mem backends
-  export OMPI_MCA_btl="self,vader"
-
-  # Workaround for open-mpi/ompi#7516
-  export OMPI_MCA_gds=hash
-
-  # Workaround for open-mpi/ompi#5798
-  export OMPI_MCA_btl_vader_backing_directory="/tmp"
-
   # Enable overscription in OpenMPI
   export OMPI_MCA_rmaps_base_oversubscribe=1
   export OMPI_MCA_hwloc_base_binding_policy=none
+fi
 
-  # Disable OpenMPI rsh launching
-  export OMPI_MCA_plm_rsh_agent=false
-
-  # Disable cuda warnings
-  export OMPI_MCA_opal_warn_on_missing_libcuda=0
+if [[ "${GH_YML_MATRIX_PARALLEL}" =~ ompi ]]
+then
+  export HYDRA_LAUNCHER=fork
 fi
 
 # Make sure staging tests use localhost

diff --git a/scripts/ci/images/Dockerfile.ci-spack-ubuntu20.04-base b/scripts/ci/images/Dockerfile.ci-spack-ubuntu20.04-base
@@ -1,43 +1,60 @@
 # vim: ft=dockerfile
-FROM ecpe4s/ubuntu20.04:23.02
+FROM ecpe4s/ubuntu20.04:23.05
 
 COPY packages.yaml /etc/spack/packages.yaml
-COPY specs.yaml /tmp/specs.yaml
 
+# Install Base specs
 RUN . /spack/share/spack/setup-env.sh && \
     export ADIOS_SPEC_NO_MPI="adios2~mpi" && \
-    export ADIOS_SPEC_OPENMPI="adios2+mpi^openmpi@4.1.4" && \
-    export ADIOS_SPEC_MPICH="adios2+mpi^mpich device=ch3 netmod=tcp" && \
-    spack env create adios2-ci-serial /tmp/specs.yaml && \
+    export ADIOS_SPEC_OPENMPI="adios2+mpi^openmpi" && \
+    export ADIOS_SPEC_MPICH="adios2+mpi^mpich" && \
+    spack config add "config:checksum:false" && \
+    spack config add "config:build_jobs:$(nproc)" && \
+    spack config add "concretizer:unify:false" && \
+    spack env create adios2-ci-serial && \
     spack -e adios2-ci-serial add ${ADIOS_SPEC_NO_MPI} && \
     spack -e adios2-ci-serial concretize && \
     spack -e adios2-ci-serial install \
       --include-build-deps \
       --no-check-signature \
       --fail-fast \
-      --only dependencies \
-      -j$(grep -c '^processor' /proc/cpuinfo) && \
-    spack env create adios2-ci-ompi /tmp/specs.yaml && \
+      --only dependencies && \
+    spack env create adios2-ci-ompi && \
     spack -e adios2-ci-ompi add ${ADIOS_SPEC_OPENMPI} && \
     spack -e adios2-ci-ompi concretize && \
     spack -e adios2-ci-ompi install \
       --include-build-deps \
       --no-check-signature \
       --fail-fast \
-      --only dependencies \
-      -j$(grep -c '^processor' /proc/cpuinfo) && \
-    spack env create adios2-ci-mpich /tmp/specs.yaml && \
+      --only dependencies && \
+    spack env create adios2-ci-mpich && \
     spack -e adios2-ci-mpich add ${ADIOS_SPEC_MPICH} && \
     spack -e adios2-ci-mpich concretize && \
     spack -e adios2-ci-mpich install \
       --include-build-deps \
       --no-check-signature \
       --fail-fast \
-      --only dependencies \
-      -j$(grep -c '^processor' /proc/cpuinfo) && \
+      --only dependencies && \
     spack clean -a && \
     echo "source /spack/share/spack/setup-env.sh" >> /etc/profile.d/zz-spack.sh
 
+# Install deps
+RUN pip install shyaml
+COPY specs.yaml /tmp/specs.yaml
+RUN . /spack/share/spack/setup-env.sh && \
+    spack env create adios2-ci-deps /tmp/specs.yaml && \
+    spack -e adios2-ci-deps install \
+      --no-check-signature \
+      --include-build-deps \
+      --fail-fast && \
+    spack -e adios2-ci-serial add $(shyaml get-values spack.specs < /tmp/specs.yaml) && \
+    spack -e adios2-ci-serial concretize && \
+    spack -e adios2-ci-ompi add $(shyaml get-values spack.specs < /tmp/specs.yaml) && \
+    spack -e adios2-ci-ompi concretize && \
+    spack -e adios2-ci-mpich add $(shyaml get-values spack.specs < /tmp/specs.yaml) && \
+    spack -e adios2-ci-mpich concretize && \
+    spack clean -a
+
 ### Other missing packages (compared to el8 base):
 RUN apt-get update && apt-get install -y \
     ccache \

diff --git a/scripts/ci/images/Dockerfile.ci-spack-ubuntu20.04-clang b/scripts/ci/images/Dockerfile.ci-spack-ubuntu20.04-clang
@@ -1,6 +1,7 @@
-FROM ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-base
+FROM ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-tmp-base
 ARG CLANG_VERSION=10
 
 RUN apt-get update && apt-get install -y \
-    clang-${CLANG_VERSION} && \
+    clang-${CLANG_VERSION} \
+    libomp-dev && \
     rm -rf /var/lib/apt/lists/*
diff --git a/scripts/ci/images/Dockerfile.ci-spack-ubuntu20.04-gcc b/scripts/ci/images/Dockerfile.ci-spack-ubuntu20.04-gcc
@@ -1,4 +1,4 @@
-FROM ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-base
+FROM ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-tmp-base
 ARG GCC_VERSION=8
 
 RUN apt-get update && apt-get install -y \

diff --git a/scripts/ci/images/Dockerfile.ci-spack-ubuntu20.04-intel b/scripts/ci/images/Dockerfile.ci-spack-ubuntu20.04-intel
@@ -1,4 +1,4 @@
-FROM ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-base
+FROM ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-tmp-base
 
 RUN wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB | gpg --dearmor | tee /usr/share/keyrings/oneapi-archive-keyring.gpg && \
     echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | tee /etc/apt/sources.list.d/oneAPI.list && \

diff --git a/scripts/ci/images/build-ubuntu.sh b/scripts/ci/images/build-ubuntu.sh
@@ -3,25 +3,25 @@
 set -ex
 
 # Build the base image
-docker build --rm -f ./Dockerfile.ci-spack-ubuntu20.04-base -t ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-base .
+docker build --rm -f ./Dockerfile.ci-spack-ubuntu20.04-base -t ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-tmp-base .
 
 # Which is also the gcc11 image
-docker tag ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-base ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-gcc11
+docker tag ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-tmp-base ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-tmp-gcc11
 
 # Build the gcc8, gcc9, and gcc10 images
-docker build --rm --build-arg GCC_VERSION=8 -f ./Dockerfile.ci-spack-ubuntu20.04-gcc -t ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-gcc8 .
-docker build --rm --build-arg GCC_VERSION=9 -f ./Dockerfile.ci-spack-ubuntu20.04-gcc -t ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-gcc9 .
-docker build --rm --build-arg GCC_VERSION=10 -f ./Dockerfile.ci-spack-ubuntu20.04-gcc -t ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-gcc10 .
+docker build --rm --build-arg GCC_VERSION=8 -f ./Dockerfile.ci-spack-ubuntu20.04-gcc -t ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-tmp-gcc8 .
+docker build --rm --build-arg GCC_VERSION=9 -f ./Dockerfile.ci-spack-ubuntu20.04-gcc -t ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-tmp-gcc9 .
+docker build --rm --build-arg GCC_VERSION=10 -f ./Dockerfile.ci-spack-ubuntu20.04-gcc -t ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-tmp-gcc10 .
 
 # Build the clang6 and clang10 images
-docker build --rm --build-arg CLANG_VERSION=6.0 -f ./Dockerfile.ci-spack-ubuntu20.04-clang -t ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-clang6 .
-docker build --rm --build-arg CLANG_VERSION=10 -f ./Dockerfile.ci-spack-ubuntu20.04-clang -t ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-clang10 .
+docker build --rm --build-arg CLANG_VERSION=6.0 -f ./Dockerfile.ci-spack-ubuntu20.04-clang -t ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-tmp-clang6 .
+docker build --rm --build-arg CLANG_VERSION=10 -f ./Dockerfile.ci-spack-ubuntu20.04-clang -t ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-tmp-clang10 .
 
 # Push images to github container registry
-docker push ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-base
-docker push ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-gcc8
-docker push ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-gcc9
-docker push ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-gcc10
-docker push ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-gcc11
-docker push ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-clang6
-docker push ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-clang10
+docker push ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-tmp-base
+docker push ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-tmp-gcc8
+docker push ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-tmp-gcc9
+docker push ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-tmp-gcc10
+docker push ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-tmp-gcc11
+docker push ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-tmp-clang6
+docker push ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-tmp-clang10
diff --git a/scripts/ci/images/packages.yaml b/scripts/ci/images/packages.yaml
@@ -2,6 +2,8 @@ packages:
   all:
     target: [haswell]
   adios2:
-    require: +blosc+bzip2+zfp+sz+png+sst+dataman+ssc+hdf5+python+fortran
-  cmake:
-    version: [3.24]
+    require: '+blosc+bzip2+zfp+sz+png+sst+dataman+ssc+hdf5+python+fortran'
+  mpich:
+    require: 'device=ch3 netmod=tcp'
+  openmpi:
+    require: '@4.1'
diff --git a/scripts/ci/images/specs.yaml b/scripts/ci/images/specs.yaml
@@ -1,6 +1,5 @@
 spack:
   view: true
-  config:
-    checksum: false
-  concretizer:
-    unify: false
+  specs:
+    # https://github.com/ornladios/ADIOS2/issues/3754
+    - mgard@2023-01-10
diff --git a/source/adios2/toolkit/remote/CMakeLists.txt b/source/adios2/toolkit/remote/CMakeLists.txt
@@ -5,15 +5,17 @@
 
 add_executable(remote_server ./remote_server.cpp remote_common.cpp)
 
-target_link_libraries(remote_server
-		      PUBLIC EVPath::EVPath
-                      PUBLIC adios2_core adios2sys
-                      PRIVATE adios2::thirdparty::pugixml $<$<PLATFORM_ID:Windows>:shlwapi>)
-target_include_directories(remote_server PRIVATE ${PROJECT_BINARY_DIR})
+target_link_libraries(remote_server PUBLIC EVPath::EVPath adios2_core adios2sys
+  PRIVATE $<$<PLATFORM_ID:Windows>:shlwapi>)
+
+get_property(pugixml_headers_path
+  TARGET pugixml
+  PROPERTY INTERFACE_INCLUDE_DIRECTORIES
+)
+
+target_include_directories(remote_server PRIVATE ${PROJECT_BINARY_DIR} ${pugixml_headers_path})
 
 set_property(TARGET remote_server PROPERTY OUTPUT_NAME remote_server${ADIOS2_EXECUTABLE_SUFFIX})
 install(TARGETS remote_server EXPORT adios2
   RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} COMPONENT adios2_tools-runtime
 )
-
-
diff --git a/source/utils/CMakeLists.txt b/source/utils/CMakeLists.txt
@@ -13,8 +13,19 @@ configure_file(
 add_executable(bpls ./bpls/bpls.cpp)
 target_link_libraries(bpls
                       PUBLIC adios2_core adios2sys
-                      PRIVATE adios2::thirdparty::pugixml $<$<PLATFORM_ID:Windows>:shlwapi>)
-target_include_directories(bpls PRIVATE ${PROJECT_BINARY_DIR} ${PROJECT_SOURCE_DIR}/bindings/C)
+                      PRIVATE $<$<PLATFORM_ID:Windows>:shlwapi>)
+
+get_property(pugixml_headers_path
+  TARGET pugixml
+  PROPERTY INTERFACE_INCLUDE_DIRECTORIES
+)
+
+target_include_directories(bpls PRIVATE
+  ${PROJECT_BINARY_DIR}
+  ${PROJECT_SOURCE_DIR}/bindings/C
+  ${pugixml_headers_path}
+)
+
 set_property(TARGET bpls PROPERTY OUTPUT_NAME bpls${ADIOS2_EXECUTABLE_SUFFIX})
 install(TARGETS bpls EXPORT adios2
   RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} COMPONENT adios2_tools-runtime