ornladios · philip-davis · Aug 19, 2020 · Aug 19, 2020 · Aug 19, 2020 · Aug 19, 2020
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -15,8 +15,8 @@ defaults: &defaults
         name: Build
         command: bash source/scripts/ci/circle/run.sh build
     - run:
-        name: Test
-        command: bash source/scripts/ci/circle/run.sh test
+        name: Sanitize
+        command: bash source/scripts/ci/circle/run.sh memcheck
 
 version: 2
 
@@ -25,10 +25,10 @@ jobs:
     <<: *defaults
     docker:
       - image: ornladios/adios2:ci-fedora-ubsan
-  #"fedora-asan":
-  #  <<: *defaults
-  #  docker:
-  #    - image: ornladios/adios2:ci-fedora-asan
+  "fedora-asan":
+    <<: *defaults
+    docker:
+      - image: ornladios/adios2:ci-fedora-asan
   "fedora-msan":
     <<: *defaults
     docker:
@@ -43,6 +43,6 @@ workflows:
   sanitizers:
     jobs:
       - "fedora-ubsan"
-      #- "fedora-asan"
+      - "fedora-asan"
       - "fedora-msan"
       - "fedora-tsan"
diff --git a/.github/workflows/build-and-test.yml b/.github/workflows/build-and-test.yml
@@ -13,10 +13,12 @@ on:
 jobs:
   linux:
     runs-on: ubuntu-latest
-    container: ${{ matrix.container }}
-    env:
-      GH_YML_JOBNAME: ${{ matrix.jobname }}
-      GH_YML_OS: Linux
+    container:
+      image: ${{ matrix.container }}
+      options: --shm-size=1g
+      env:
+        GH_YML_JOBNAME: ${{ matrix.jobname }}
+        GH_YML_OS: Linux
 
     strategy:
       fail-fast: false
@@ -25,6 +27,7 @@ jobs:
           el7,
           el7-gnu8-ohpc,
           el7-gnu8-openmpi-ohpc,
+          el7-gnu8-openmpi-ohpc-static,
           suse-pgi,
           suse-pgi-openmpi,
           debian-sid,
@@ -36,10 +39,12 @@ jobs:
           container: ornladios/adios2:ci-el7-gnu8-ohpc
         - jobname: el7-gnu8-openmpi-ohpc
           container: ornladios/adios2:ci-el7-gnu8-openmpi-ohpc
+        - jobname: el7-gnu8-openmpi-ohpc-static
+          container: ornladios/adios2:ci-el7-gnu8-openmpi-ohpc
         - jobname: suse-pgi
-          container: ornladios/adios2:ci-suse-pgi
+          container: ornladios/adios2:ci-suse-nvhpcsdk
         - jobname: suse-pgi-openmpi
-          container: ornladios/adios2:ci-suse-pgi-openmpi
+          container: ornladios/adios2:ci-suse-nvhpcsdk-openmpi
         - jobname: debian-sid
           container: ornladios/adios2:ci-debian-sid
         - jobname: debian-sid-openmpi
@@ -49,7 +54,6 @@ jobs:
     - uses: actions/checkout@v2
       with:
         ref: ${{ github.event.pull_request.head.sha }}
-        entrypoint: /usr/bin/sh -c
     - name: Setup
       run: scripts/ci/gh-actions/linux-setup.sh
     - name: Update
@@ -65,32 +69,24 @@ jobs:
     runs-on: ubuntu-latest
     container:
       image: ${{ matrix.container }}
-      options: --privileged
-    env:
-      GH_YML_JOBNAME: ${{ matrix.jobname }}
-      GH_YML_OS: Linux
+      options: --privileged --shm-size=1g
+      env:
+        GH_YML_JOBNAME: ${{ matrix.jobname }}
+        GH_YML_OS: Linux
 
     strategy:
       fail-fast: false
       matrix:
         jobname: [
           power8-el7-xl,
-          power8-el7-xl-smpi,
-          power8-el7-pgi,
-          power8-el7-pgi-smpi ]
+          power8-el7-xl-smpi ]
         include:
         - jobname: power8-el7-xl
           container: ornladios/adios2:ci-x86_64-power8-el7-xl
           arch: ppc64le
         - jobname: power8-el7-xl-smpi
           container: ornladios/adios2:ci-x86_64-power8-el7-xl-smpi
           arch: ppc64le
-        - jobname: power8-el7-pgi
-          container: ornladios/adios2:ci-x86_64-power8-el7-pgi
-          arch: ppc64le
-        - jobname: power8-el7-pgi-smpi
-          container: ornladios/adios2:ci-x86_64-power8-el7-pgi-smpi
-          arch: ppc64le
 
     steps:
     - name: Emulation Setup
@@ -112,3 +108,43 @@ jobs:
       run: scripts/ci/gh-actions/run.sh build
     - name: Test
       run: scripts/ci/gh-actions/run.sh test
+
+  linux_spack:
+    runs-on: ubuntu-latest
+    container:
+      image: ${{ matrix.container }}
+      options: --shm-size=1g
+      env:
+        GH_YML_JOBNAME: ${{ matrix.jobname }}
+        GH_YML_OS: Linux
+
+    strategy:
+      fail-fast: false
+      matrix:
+        jobname: [
+          el7-spack,
+          ubuntu1804-spack ]
+        include:
+        - jobname: el7-spack
+          container: ornladios/adios2:ci-el7-spack
+        - jobname: ubuntu1804-spack
+          container: ornladios/adios2:ci-ubuntu1804-spack
+
+    defaults:
+      run:
+        shell: bash -c "source /opt/spack/share/spack/setup-env.sh && spack env activate adios2-ci && bash {0}"
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        ref: ${{ github.event.pull_request.head.sha }}
+      env:
+        PATH: /opt/spack/var/spack/environments/adios2-ci/.spack-env/view/bin:/usr/bin:/bin
+    - name: Update
+      run: scripts/ci/gh-actions/run.sh update
+    - name: Configure
+      run: scripts/ci/gh-actions/run.sh configure
+    - name: Build
+      run: scripts/ci/gh-actions/run.sh build
+    - name: Test
+      run: scripts/ci/gh-actions/run.sh test
diff --git a/.github/workflows/formatting.yml b/.github/workflows/formatting.yml
@@ -0,0 +1,26 @@
+name: Formatting
+
+on: 
+  push: 
+    branches: 
+    - master 
+    - release* 
+  pull_request: 
+    branches: 
+    - master 
+    - release* 
+
+jobs:
+  format:
+    runs-on: ubuntu-latest
+    container:
+      image: ornladios/adios2:ci-formatting
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        ref: ${{ github.event.pull_request.head.sha }}
+    - name: CXX
+      run: scripts/ci/scripts/run-clang-format.sh
+    - name: Python
+      run: scripts/ci/scripts/run-flake8.sh
diff --git a/.gitlab/gitlab-ci-gitlabdotcom.yml b/.gitlab/gitlab-ci-gitlabdotcom.yml
@@ -0,0 +1,6 @@
+sync-github-prs:
+  tags: linux
+  only:
+    - schedules
+  script:
+    - scripts/ci/scripts/github-prs-to-gitlab.sh ornladios/adios2 code.ornl.gov ecpcitest/adios2
diff --git a/.gitlab/gitlab-ci-olcf.yml b/.gitlab/gitlab-ci-olcf.yml
@@ -1,15 +1,3 @@
-sync-github-prs:
-  tags: [nobatch]
-  only:
-    - schedules
-  variables:
-    GIT_STRATEGY: clone
-  script:
-    - module load python/3.7.0
-    - pip3 install --user PyGithub
-    - module load git
-    - bash scripts/ci/gitlab-ci/pr-sync.sh
-
 .all-steps:
   except:
     - schedules

diff --git a/.travis.yml b/.travis.yml
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -88,14 +88,12 @@ mark_as_advanced(ADIOS2_LIBRARY_SUFFIX ADIOS2_EXECUTABLE_SUFFIX)
 
 # Use meta-compile features if available, otherwise use specific language
 # features
-if(CMAKE_VERSION VERSION_LESS 3.9 OR
-   CMAKE_CXX_COMPILER_ID MATCHES "^(GNU|Intel|Clang|AppleClang|MSVC)$")
+if(CMAKE_CXX_COMPILER_ID MATCHES "^(GNU|Intel|Clang|AppleClang|MSVC)$")
   set(ADIOS2_CXX11_FEATURES cxx_auto_type cxx_nullptr)
 else()
   set(ADIOS2_CXX11_FEATURES cxx_std_11)
 endif()
-if(CMAKE_VERSION VERSION_LESS 3.9 OR
-   CMAKE_C_COMPILER_ID MATCHES "^(GNU|Intel|Clang|AppleClang|MSVC)$")
+if(CMAKE_C_COMPILER_ID MATCHES "^(GNU|Intel|Clang|AppleClang|MSVC)$")
   set(ADIOS2_C99_FEATURES c_restrict)
 else()
   set(ADIOS2_C99_FEATURES c_std_99)
@@ -236,7 +234,7 @@ option(ADIOS2_BUILD_TESTING "Build the ADIOS2 testing tree"
 cmake_dependent_option(ADIOS2_RUN_MPI_MPMD_TESTS
   "Enable the parallel MPMD tests" ON
   "ADIOS2_BUILD_TESTING;ADIOS2_HAVE_MPI" OFF)
-mark_as_advanced(ADIOS2_RUN_MPMD_TESTS)
+mark_as_advanced(ADIOS2_RUN_MPI_MPMD_TESTS)
 
 include(CTest)
 set(BUILD_TESTING ${ADIOS2_BUILD_TESTING})

diff --git a/CTestCustom.cmake.in b/CTestCustom.cmake.in
@@ -13,6 +13,9 @@ list(APPEND CTEST_CUSTOM_WARNING_EXCEPTION
   "warning: Using '.*' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking"
   "PGC.*compilation completed with warnings"
   "Warning: stand-alone `data16' prefix"
+  "Warning: Type mismatch between actual argument.*"
+  "Warning: Rank mismatch between actual argument.*"
+  "zfp/types.h.*typedef"
 )
 list(APPEND CTEST_CUSTOM_COVERAGE_EXCLUDE
   ".*/thirdparty/.*"

diff --git a/ReadMe.md b/ReadMe.md
@@ -12,50 +12,59 @@
 [![Coverity Scan Build Status](https://scan.coverity.com/projects/11116/badge.svg)](https://scan.coverity.com/projects/ornladios-adios2)
 
 
-# ADIOS 2 : The Adaptable Input Output System version 2
-This is ADIOS 2 : The Adaptable Input/Output (I/O) System, ADIOS 2 is developed as part of the United States Department of Energy's Exascale Computing Program.
+# ADIOS2 : The Adaptable Input Output System version 2
 
-ADIOS 2 is a framework designed for scientific data I/O to publish and subscribe (put/get) data when and where required. 
+This is ADIOS2: The Adaptable Input/Output (I/O) System.
 
-ADIOS 2 transports data as groups of self-describing variables and attributes across different media types (such as files, wide-area-networks, and remote direct memory access) using a common application programming interface for all transport modes. ADIOS 2 can be used on supercomputers, cloud systems, and personal computers.
+ADIOS2 is developed as part of the United States Department of Energy's Exascale Computing Project.
+It is a framework for scientific data I/O to publish and subscribe to data when and where required.
 
-ADIOS 2 focuses on:
+ADIOS2 transports data as groups of self-describing variables and attributes across different media types (such as files, wide-area-networks, and remote direct memory access) using a common application programming interface for all transport modes.
+ADIOS2 can be used on supercomputers, cloud systems, and personal computers.
+
+ADIOS2 focuses on:
 
 1. **Performance** I/O scalability in high performance computing (HPC) applications.
 2. **Adaptability** unified interfaces to allow for several modes of transport (files, memory-to-memory)  
 3. **Ease of Use** two-level application programming interface (APIs)
-    * Full APIs for HPC applications: C++11, Fortran 90, C 99, Python 2 and 3 
-    * Simplified High-Level APIs for data analysis: Python 2 and 3, C++11, Matlab  
-    
-In addition, ADIOS 2 APIs are based on:
+* Full APIs for HPC applications: C++11, Fortran 90, C 99, Python 2 and 3
+* Simplified High-Level APIs for data analysis: Python 2 and 3, C++11, Matlab
+
+In addition, ADIOS2 APIs are based on:
 
-* **MPI** ADIOS 2 is MPI-based, it can be used in non-MPI serial code. Non-MPI 100% serial build is optional.
+* **MPI** Although ADIOS2 is MPI-based, it can also be used in non-MPI serial code.
 
-* **Data Groups** ADIOS 2 favors a deferred/prefetch/grouped variables transport mode by default to maximize data-per-request ratios. Sync mode, one variable at a time, is treated as the special case.
+* **Data Groups** ADIOS2 favors a deferred/prefetch/grouped variables transport mode by default to maximize data-per-request ratios.
+Sync mode, one variable at a time, is treated as the special case.
 
-* **Data Steps** ADIOS 2 follows the actual production/consumption of data using an I/O “steps” abstraction removing the need to manage extra indexing information.
+* **Data Steps** ADIOS2 follows the actual production/consumption of data using an I/O “steps” abstraction removing the need to manage extra indexing information.
 
-* **Data Engines** ADIOS 2 Engine abstraction allows for reusing the APIs for different transport modes removing the need for drastic code changes.
+* **Data Engines** ADIOS2 Engine abstraction allows for reusing the APIs for different transport modes removing the need for drastic code changes.
 
 ## Documentation
-Please find [The ADIOS 2 User Guide at readthedocs](https://adios2.readthedocs.io)
 
+Documentation is hosted at [readthedocs](https://adios2.readthedocs.io).
+
+## Citing
+
+If you find ADIOS2 useful, please cite our [SoftwareX paper](https://doi.org/10.1016/j.softx.2020.100561), which also gives a high-level overview to the motivation and goals of ADIOS; complementing the documentation.
 
 ## Getting ADIOS2
 
-* From source: [Install ADIOS 2 documentation](https://adios2.readthedocs.io/en/latest/setting_up/setting_up.html#) requires CMake v3.6 or above. For a cmake configuration example see [scripts/runconf/runconf.sh](https://github.com/ornladios/ADIOS2/blob/master/scripts/runconf/runconf.sh)
+* From source: [Install ADIOS2 documentation](https://adios2.readthedocs.io/en/latest/setting_up/setting_up.html#).
+For a `cmake` configuration example see [scripts/runconf/runconf.sh](https://github.com/ornladios/ADIOS2/blob/master/scripts/runconf/runconf.sh)
 
 
 * Conda packages: 
-    * [https://anaconda.org/williamfgc](https://anaconda.org/williamfgc)
-    * [https://anaconda.org/conda-forge/adios2](https://anaconda.org/conda-forge/adios2)
+* [https://anaconda.org/williamfgc](https://anaconda.org/williamfgc)
+* [https://anaconda.org/conda-forge/adios2](https://anaconda.org/conda-forge/adios2)
 
 
 * Spack: [adios2 package](https://spack.readthedocs.io/en/latest/package_list.html#adios2)
 
 
 * Docker images: 
-    * Ubuntu 18.04: under [scripts/docker/images/ubuntu18.04/Dockerfile](https://github.com/ornladios/ADIOS2/tree/master/scripts/docker/images/ubuntu18.04/Dockerfile)
+* Ubuntu 18.04: under [scripts/docker/images/ubuntu18.04/Dockerfile](https://github.com/ornladios/ADIOS2/tree/master/scripts/docker/images/ubuntu18.04/Dockerfile)
 
 
 Once ADIOS 2 is installed refer to: 
@@ -71,15 +80,15 @@ Once ADIOS 2 is installed refer to:
 
 ## Reporting Bugs
 
-If you found a bug, please open an [issue on ADIOS2 github repository](https://github.com/ornladios/ADIOS2/issues)
+If you find a bug, please open an [issue on ADIOS2 github repository](https://github.com/ornladios/ADIOS2/issues)
 
 ## Contributing
 
-We invite the community to contribute, see [Contributor's Guide to ADIOS 2](Contributing.md) for instructions on how to contribute. ADIOS 2 will always be free and open-source.
+See the [Contributor's Guide to ADIOS 2](Contributing.md) for instructions on how to contribute.
 
 ## License
-ADIOS >= 2.0 is licensed under the Apache License v2.0.  See the accompanying
-[Copyright.txt](Copyright.txt) for more details.
+ADIOS2 is licensed under the Apache License v2.0.
+See the accompanying [Copyright.txt](Copyright.txt) for more details.
 
 
 ## Directory layout
@@ -92,7 +101,7 @@ ADIOS >= 2.0 is licensed under the Apache License v2.0.  See the accompanying
 * scripts - Project maintenance and development scripts
 
 * source - Internal source code for private components 
-    * adios2 - source directory for the ADIOS2 library to be installed under install-dir/lib/libadios2.  
-    * utils  - source directory for the binary utilities, to be installed under install-dir/bin 
+* adios2 - source directory for the ADIOS2 library to be installed under install-dir/lib/libadios2.
+* utils  - source directory for the binary utilities, to be installed under install-dir/bin
 
 * testing - Tests using [gtest](https://github.com/google/googletest)
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -13,8 +13,10 @@ resources:
   containers:
   - container: el7-intel-ohpc
     image: ornladios/adios2:ci-el7-intel-ohpc
+    options: --shm-size=1g
   - container: el7-intel-openmpi-ohpc
     image: ornladios/adios2:ci-el7-intel-openmpi-ohpc
+    options: --shm-size=1g
 
 jobs:
 - job: windows