Merge remote-tracking branch 'origin/feature-gh-actions' into develop

.github/workflows/ci-github-actions.yaml

@@ -0,0 +1,85 @@
+name: GitHub Actions CI
+
+on: 
+  push:
+    branches: 
+    - stable
+    - develop
+  pull_request:
+    branches: 
+    - develop
+
+jobs:
+
+  linux:
+    runs-on: ubuntu-latest
+    container: ${{ matrix.container }}
+    env:
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      GH_JOBNAME: ${{ matrix.jobname }}
+      GH_OS: Linux
+    strategy:
+      fail-fast: false
+      matrix:
+        jobname: [
+          ubuntu22-gcc,
+          ubuntu22-clang,
+        ]
+        include:
+        - jobname: ubuntu22-gcc
+          container: 
+            image: ghcr.io/philipfackler/xolotl-ci:ubuntu22-dev
+            options: -u root 
+        - jobname: ubuntu22-clang
+          container: 
+            image: ghcr.io/philipfackler/xolotl-ci:ubuntu22-dev
+            options: -u root
+
+    steps:
+    - name: Checkout Action
+      uses: actions/checkout@v1
+
+    - name: Configure
+      run: CI/scripts/run_step.sh configure
+
+    - name: Build
+      run: CI/scripts/run_step.sh build
+
+    - name: Test
+      run: CI/scripts/run_step.sh test
+
+
+  macos:
+    runs-on: macos-latest
+    env:
+      GH_YML_JOBNAME: ${{ matrix.jobname }}
+      GH_YML_OS: macOS
+
+    strategy:
+      fail-fast: false
+      matrix:
+        jobname: [
+          macos1015-xcode11 
+        ]
+
+    steps:
+    - name: Checkout Action
+      uses: actions/checkout@v1
+
+    - name: Setup Dependencies
+      run: |
+        brew install boost open-mpi hdf5-mpi make [email protected]
+        echo "PATH=/opt/homebrew/opt/[email protected]/libexec/bin:$PATH" >> $GITHUB_ENV
+
+    - name: Configure
+      run: |
+        export EXTRA_CMAKE_ARGS='-DXolotl_INCLUDE_RN_TPP_FILES=ON -DXolotl_ENABLE_TIMER_TESTS=OFF'
+        CI/scripts/run_step.sh configure
+      env:
+        PATH: ${{ env.PATH }}
+
+    - name: Build
+      run: CI/scripts/run_step.sh build
+
+    - name: Test
+      run: CI/scripts/run_step.sh test

CI/docker/ubuntu22/Dockerfile

@@ -0,0 +1,34 @@
+FROM ubuntu:22.04
+
+ENV DEBIAN_FRONTEND noninteractive
+
+# Install dependencies
+RUN apt-get update -y
+RUN apt-get upgrade -y
+RUN apt-get install -y \
+        python3 \
+        clang \
+        clang-tidy \
+        g++ \
+        git \
+        gdb \
+        make \
+        cmake \
+        cmake-curses-gui \
+        mpi-default-dev \
+        libblas-dev \
+        liblapack-dev \
+        libhdf5-mpi-dev \
+        libboost-filesystem-dev \
+        libboost-program-options-dev \
+        libboost-test-dev \
+        libboost-log-dev \
+        bzip2 \
+        sudo
+
+RUN useradd -mr -u 10000 builduser
+RUN adduser builduser sudo
+RUN echo "builduser:builduser" | chpasswd
+
+USER builduser
+WORKDIR /home/builduser

CI/scripts/run_step.sh

@@ -0,0 +1,67 @@
+#!/bin/bash
+
+set -e
+
+echo -e "\nCheck gcc and clang compilers\n"
+gcc --version
+clang --version
+
+function run_tests () {
+    cd ${GITHUB_WORKSPACE}/../build
+    ctest --output-on-failure --label-exclude xolotl.tests.system
+    local __xolotl_ret=$?
+    ./test/system/SystemTester -- -t
+    local __xolotl_sys_ret=$?
+    return $((__xolotl_ret + __xolotl_sys_ret))
+}
+
+case "$1" in 
+
+  configure)
+
+    git config --global --add safe.directory ${GITHUB_WORKSPACE}
+
+    case "${GH_JOBNAME}" in
+      *"clang"*)
+        export CC=clang
+        export CXX=clang++
+        export OMPI_CC=clang
+        export OMPI_CXX=clang++
+      ;;
+      *)
+      ;;
+    esac
+
+    cd ${GITHUB_WORKSPACE}/..
+
+    git clone https://gitlab.com/petsc/petsc.git -b v3.21.6 petsc
+    cd petsc
+    bash ${GITHUB_WORKSPACE}/../xolotl/scripts/build_petsc.sh \
+        --prefix=${GITHUB_WORKSPACE}/../install \
+        --skip-pull
+
+    cd ${GITHUB_WORKSPACE}/..
+    mkdir build
+    cd build
+
+    cmake \
+        -DCMAKE_PREFIX_PATH=${GITHUB_WORKSPACE}/../install \
+        ${EXTRA_CMAKE_ARGS} \
+        ${GITHUB_WORKSPACE}
+
+    ;;
+
+  build)
+    cd ${GITHUB_WORKSPACE}/../build
+    make -j4
+    ;;
+
+  test)
+    run_tests
+    ;;
+
+  *)
+    echo " Invalid step" "$1"
+    exit -1
+    ;;
+esac

test/CMakeLists.txt

@@ -12,6 +12,9 @@ get_filename_component(XOLOTL_TEST_DATA_DIR
 )
 set(XOLOTL_BUILD_DIR ${CMAKE_BINARY_DIR})
 
+option(Xolotl_ENABLE_TIMER_TESTS "Include tests for accurate timing" ON)
+set(XOLOTL_ENABLE_TIMER_TESTS ${Xolotl_ENABLE_TIMER_TESTS})
+
 execute_process(COMMAND
     ${CMAKE_COMMAND} -E make_directory ${XOLOTL_BINARY_INCLUDE_DIR}/xolotl/test
 )

test/config.h.in

@@ -5,3 +5,5 @@
 #define XOLOTL_BUILD_DIR @XOLOTL_BUILD_DIR@
 
 #define XOLOTL_TEST_DATA_DIR @XOLOTL_TEST_DATA_DIR@
+
+#cmakedefine XOLOTL_ENABLE_TIMER_TESTS

test/perf/CMakeLists.txt

@@ -4,14 +4,19 @@ list(APPEND tests
     dummy/DummyEventCounterTester.cpp
     dummy/DummyHardwareCounterTester.cpp
     dummy/DummyTimerTester.cpp
-    os/OSTimerTester.cpp
 )
 
+if(Xolotl_ENABLE_TIMER_TESTS)
+    list(APPEND tests os/OSTimerTester.cpp)
+endif()
+
 if(PAPI_FOUND)
     list(APPEND tests
         papi/PAPIHardwareCounterTester.cpp
-        papi/PAPITimerTester.cpp
     )
+    if(Xolotl_ENABLE_TIMER_TESTS)
+        list(APPEND tests papi/PAPITimerTester.cpp)
+    endif()
 endif(PAPI_FOUND)
 
 if(CMAKE_BUILD_TYPE MATCHES "^Debug$")

test/perf/PerfHandlerTester.cpp

@@ -14,6 +14,7 @@
 #include <xolotl/perf/IPerfHandler.h>
 #include <xolotl/perf/PerfObjStatistics.h>
 #include <xolotl/test/MPITestUtils.h>
+#include <xolotl/test/config.h>
 
 using namespace xolotl;
 
@@ -122,10 +123,12 @@ BOOST_AUTO_TEST_CASE(aggregateStats)
 			BOOST_REQUIRE_EQUAL(timerStatsObj.name, "testTimer");
 			BOOST_REQUIRE_EQUAL(
 				timerStatsObj.processCount, (unsigned int)cwSize);
+#ifdef XOLOTL_ENABLE_TIMER_TESTS
 			BOOST_REQUIRE_CLOSE(timerStatsObj.average, nTimedSeconds, 0.03);
 			BOOST_REQUIRE_CLOSE(timerStatsObj.min, nTimedSeconds, 0.03);
 			BOOST_REQUIRE_CLOSE(timerStatsObj.max, nTimedSeconds, 0.03);
 			BOOST_REQUIRE_SMALL(timerStatsObj.stdev, 0.001);
+#endif
 
 			// Next check counts.  We can compute exactly what the values
 			// should be.

xolotl/core/include/xolotl/core/flux/FluxHandler.h

@@ -162,7 +162,7 @@ class FluxHandler : public IFluxHandler
 	/**
 	 * \see IFluxHandler.h
 	 */
-	virtual void
+	void
 	computeIncidentFlux(double currentTime, Kokkos::View<const double*>,
 		Kokkos::View<double*> updatedConcOffset, int xi,
 		int surfacePos) override;
@@ -230,17 +230,17 @@ class FluxHandler : public IFluxHandler
 	/**
 	 * \see IFluxHandler.h
 	 */
-	virtual void
-	setFissionYield(double yield)
+	void
+	setFissionYield(double yield) override
 	{
 		return;
 	}
 
 	/**
 	 * \see IFluxHandler.h
 	 */
-	virtual std::vector<std::pair<IdType, double>>
-	getImplantedFlux(std::vector<IdType> map)
+	std::vector<std::pair<IdType, double>>
+	getImplantedFlux(std::vector<IdType> map) override
 	{
 		return std::vector<std::pair<IdType, double>>();
 	}

xolotl/core/include/xolotl/core/flux/FuelFitFluxHandler.h

@@ -242,8 +242,8 @@ class FuelFitFluxHandler : public FluxHandler
 	/**
 	 * \see IFluxHandler.h
 	 */
-	virtual void
-	setFissionYield(double yield)
+	void
+	setFissionYield(double yield) override
 	{
 		xeYield = yield;
 	}