ADIOS2 2.6.0+

.github/ISSUE_TEMPLATE/bug_report.md

@@ -41,10 +41,10 @@ A clear and concise description of what you expected to happen.
  - installed openPMD-api via: [conda-forge, spack, pip, from source, module system, ...]
  - operating system: [name and version]
  - 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 3.7]
- - version of HDF5: [e.g. 1.10.1]
+ - name and version of Python implementation: [e.g. CPython 3.8]
+ - version of HDF5: [e.g. 1.12.0]
  - version of ADIOS1: [e.g. 1.13.1]
- - version of ADIOS2: [e.g. 2.5.0]
+ - version of ADIOS2: [e.g. 2.6.0]
  - name and version of MPI: [e.g. OpenMPI 3.1.5]
 
 **Additional context**

.github/ci/spack/packages.yaml

@@ -58,8 +58,12 @@ packages:
   adios:
     variants: ~zfp ~sz ~lz4 ~blosc
   adios2:
-    version: [2.5.0]
-    variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc
+    variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
+    # ~shared is a work-around macOS dylib rpath issue for ADIOS2
+    #   https://github.com/ornladios/ADIOS2/issues/2316
+    #   https://spack.readthedocs.io/en/latest/config_yaml.html
+    # ~bzip2
+    #   Library not loaded: @rpath/libbz2.1.dylib
   python:
     version: [3.5.5, 3.6.3, 3.7.1, 3.7.2, 3.8.0]
     paths:

.travis.yml

@@ -17,6 +17,7 @@ env:
     - SPACK_ROOT: $HOME/.cache/spack
     - PATH: $PATH:$HOME/.cache/spack/bin
     - BUILD_TYPE: "Debug"
+    - [email protected]
     - [email protected]
     - USE_SHARED: ON
 
@@ -196,14 +197,17 @@ jobs:
             $EXTRA_CMAKE_FLAGS
             -DCMAKE_INSTALL_PREFIX=$HOME/openPMD-test-install
             $TRAVIS_BUILD_DIR
-        - make -j 2
+        - make VERBOSE=ON
         # run tests
         #   pybind11: work-around for missing symbols with sanitizers
         #   /usr/local/clang-7.0.0/lib/clang/7.0.0/lib/linux/libclang_rt.asan-x86_64.so
         #   /usr/local/clang-7.0.0/lib/clang/7.0.0/lib/linux/libclang_rt.ubsan_minimal-x86_64.so
         - if [ "$USE_PYTHON" == "ON" ] && [ ! -z ${ASAN_OPTIONS+x} ]; then
             export LD_PRELOAD=/usr/local/clang-7.0.0/lib/clang/7.0.0/lib/linux/libclang_rt.asan-x86_64.so;
           fi
+        - if [ "${TRAVIS_OS_NAME}" = "osx" ]; then
+            otool -l /Users/travis/build/bin/openpmd-ls;
+          fi
         - CTEST_OUTPUT_ON_FAILURE=1 travis_wait make test
         - if [ ! -z ${LD_PRELOAD+x} ]; then
             unset LD_PRELOAD;
@@ -399,12 +403,12 @@ jobs:
       script: *script-cpp-unit
     # GCC 9.3.0
     - <<: *test-cpp-unit
-      name: [email protected] -MPI -PY +H5 +ADIOS1 +ADIOS2@2.5.0
+      name: [email protected] -MPI -PY +H5 +ADIOS1 +ADIOS2@2.6.0
       dist: bionic
       language: python
       python: "3.8"
       env:
-        - CXXSPEC="%[email protected]" USE_MPI=OFF USE_PYTHON=OFF USE_HDF5=ON USE_ADIOS1=ON USE_ADIOS2=ON ADIOS2_VERSION=@2.5.0 USE_SAMPLES=ON
+        - CXXSPEC="%[email protected]" USE_MPI=OFF USE_PYTHON=OFF USE_HDF5=ON USE_ADIOS1=ON USE_ADIOS2=ON ADIOS2_VERSION=@2.6.0 USE_SAMPLES=ON
       compiler: gcc
       addons:
         apt:

CHANGELOG.rst

@@ -53,6 +53,7 @@ Other
 """""
 
 - CMake: require version 3.12.0+ #755
+- ADIOS2: require version 2.6.0+ #754
 - separate header for export macros #704
 - rename ``AccessType``/``Access_Type`` to ``Access`` #740 #743 #744
 - CI:

CMakeLists.txt

@@ -232,14 +232,14 @@ endif()
 
 # external library: ADIOS2 (optional)
 if(openPMD_USE_ADIOS2 STREQUAL AUTO)
-    find_package(ADIOS2 2.5.0 CONFIG)
+    find_package(ADIOS2 2.6.0 CONFIG)
     if(ADIOS2_FOUND)
         set(openPMD_HAVE_ADIOS2 TRUE)
     else()
         set(openPMD_HAVE_ADIOS2 FALSE)
     endif()
 elseif(openPMD_USE_ADIOS2)
-    find_package(ADIOS2 2.5.0 REQUIRED CONFIG)
+    find_package(ADIOS2 2.6.0 REQUIRED CONFIG)
     set(openPMD_HAVE_ADIOS2 TRUE)
 else()
     set(openPMD_HAVE_ADIOS2 FALSE)
@@ -516,7 +516,11 @@ endif()
 
 # ADIOS2 Backend
 if(openPMD_HAVE_ADIOS2)
-    target_link_libraries(openPMD PUBLIC adios2::adios2)
+    if(openPMD_HAVE_MPI)
+        target_link_libraries(openPMD PUBLIC adios2::cxx11_mpi)
+    else()
+        target_link_libraries(openPMD PUBLIC adios2::cxx11)
+    endif()
 endif()
 
 # Runtime parameter and API status checks ("asserts")

Dockerfile

@@ -64,7 +64,7 @@ RUN        curl -sLo adios-1.13.1.tar.gz http://users.nccs.gov/~pnorbert/adios-1
            && make \
            && make install
 
-RUN        curl -sLo adios2-2.5.0.tar.gz https://github.com/ornladios/ADIOS2/archive/v2.5.0.tar.gz \
+RUN        curl -sLo adios2-2.6.0.tar.gz https://github.com/ornladios/ADIOS2/archive/v2.6.0.tar.gz \
            && file adios2*.tar.gz \
            && tar -xzf adios2*.tar.gz \
            && rm adios2*.tar.gz \

README.md

@@ -112,7 +112,7 @@ I/O backends:
 * [JSON](https://en.wikipedia.org/wiki/JSON)
 * [HDF5](https://support.hdfgroup.org/HDF5) 1.8.13+ (optional)
 * [ADIOS1](https://www.olcf.ornl.gov/center-projects/adios) 1.13.1+ (optional)
-* [ADIOS2](https://github.com/ornladios/ADIOS2) 2.5.0+ (optional)
+* [ADIOS2](https://github.com/ornladios/ADIOS2) 2.6.0+ (optional)
 
 while those can be built either with or without:
 * MPI 2.1+, e.g. OpenMPI 1.6.5+ or MPICH2

docs/source/dev/dependencies.rst

@@ -28,7 +28,7 @@ Optional: I/O backends
 * `JSON <https://en.wikipedia.org/wiki/JSON>`_
 * `HDF5 <https://support.hdfgroup.org/HDF5>`_ 1.8.13+
 * `ADIOS1 <https://www.olcf.ornl.gov/center-projects/adios>`_ 1.13.1+
-* `ADIOS2 <https://github.com/ornladios/ADIOS2>`_ 2.5.0+
+* `ADIOS2 <https://github.com/ornladios/ADIOS2>`_ 2.6.0+
 
 while those can be build either with or without: