Merge pull request #101 from ECP-copa/github_actions

Travis -> GitHub Actions

Author: streeve

.github/workflows/CI.yml

@@ -0,0 +1,162 @@
+name: CI
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+  schedule:
+    - cron:  '0 5 * * *'
+
+jobs:
+  CI:
+    strategy:
+      matrix:
+        distro: ['ubuntu:latest']
+        cxx: ['g++', 'clang++']
+        backend: ['SERIAL', 'OPENMP']
+        cmake_build_type: ['Debug', 'Release']
+        kokkos_ver: ['3.2.01']
+        arborx: ['ArborX', 'NoArborX']
+        nnp: ['ON', 'OFF']
+        layout: ['1']
+        vector: ['1']
+        layout_nnp: ['1']
+        vector_nnp: ['1']
+        include:
+          - distro: 'ubuntu:latest'
+            cxx: 'g++'
+            openmp: 'ON'
+            cmake_build_type: 'Release'
+            kokkos_ver: '3.2.01'
+            arborx: 'NoArborX'
+            nnp: 'OFF'
+            layout: '2'
+            vector: '64'
+            layout_nnp: '1'
+            vector_nnp: '1'
+          - distro: 'ubuntu:latest'
+            cxx: 'g++'
+            openmp: 'ON'
+            cmake_build_type: 'Release'
+            kokkos_ver: '3.2.01'
+            arborx: 'NoArborX'
+            nnp: 'ON'
+            layout: '6'
+            vector: '32'
+            layout_nnp: '3'
+            vector_nnp: '32'
+          - distro: 'ubuntu:latest'
+            cxx: 'g++'
+            openmp: 'ON'
+            cmake_build_type: 'Release'
+            kokkos_ver: '3.2.01'
+            arborx: 'NoArborX'
+            nnp: 'OFF'
+            layout: '6'
+            vector: '"1;8;32;1;8;32"'
+            layout_nnp: '3'
+            vector_nnp: '"32;8;1"'
+    runs-on: ubuntu-20.04
+    container: ghcr.io/ecp-copa/ci-containers/${{ matrix.distro }}
+    steps:
+      - name: Get trail license
+        if: ${{ matrix.cxx == 'icpc' }}
+        run: |
+          mkdir ~/Licenses
+          curl https://dynamicinstaller.intel.com/api/v2/license > ~/Licenses/intel.lic
+      - name: Checkout kokkos
+        uses: actions/checkout@v2.2.0
+        with:
+          repository: kokkos/kokkos
+          ref: ${{ matrix.kokkos_ver }}
+          path: kokkos
+      - name: Build kokkos
+        working-directory: kokkos
+        run: |
+          cmake -B build \
+            -DCMAKE_INSTALL_PREFIX=$HOME/kokkos \
+            -DKokkos_ENABLE_OPENMP=${{ matrix.openmp }} \
+            -DCMAKE_CXX_COMPILER=${{ matrix.cxx }} \
+            -DKokkos_ENABLE_HWLOC=ON \
+            -DCMAKE_BUILD_TYPE=${{ matrix.cmake_build_type }}
+          cmake --build build --parallel 2
+          cmake --install build
+      - name: Checkout arborx
+        if: ${{ matrix.arborx == 'ArborX' }}
+        uses: actions/checkout@v2.2.0
+        with:
+          repository: arborx/ArborX
+          ref: master
+          path: arborx
+      - name: Build arborx
+        if: ${{ matrix.arborx == 'ArborX' }}
+        working-directory: arborx
+        run: |
+          cmake -B build \
+            -DCMAKE_PREFIX_PATH=${HOME}/kokkos \
+            -DCMAKE_INSTALL_PREFIX=$HOME/arborx \
+            -DCMAKE_CXX_COMPILER=${{ matrix.cxx }} \
+            -DCMAKE_BUILD_TYPE=${{ matrix.cmake_build_type }}
+          cmake --build build --parallel 2
+          cmake --install build
+      - name: Checkout Cabana
+        uses: actions/checkout@v2.2.0
+        with:
+          repository: ECP-CoPA/Cabana
+          ref: master
+          path: cabana
+      - name: Build Cabana
+        working-directory: cabana
+        run: |
+          cmake -B build \
+            -DCMAKE_INSTALL_PREFIX=$HOME/Cabana \
+            -DMPIEXEC_MAX_NUMPROCS=2 -DMPIEXEC_PREFLAGS="--oversubscribe" \
+            -DCMAKE_PREFIX_PATH="$HOME/kokkos;$HOME/arborx" \
+            -DCMAKE_CXX_COMPILER=${{ matrix.cxx }} \
+            -DCMAKE_BUILD_TYPE=${{ matrix.cmake_build_type }}
+          cmake --build build --parallel 2
+          cmake --install build
+      - name: Checkout n2p2
+        if: ${{ matrix.nnp == 'ON' }}
+        uses: actions/checkout@v2.2.0
+        with:
+          repository: CompPhysVienna/n2p2
+          ref: v2.0.1
+          path: n2p2
+      - name: Build n2p2
+        if: ${{ matrix.nnp == 'ON' }}
+        working-directory: n2p2/src
+        run: |
+          mkdir -p $HOME/n2p2/include
+          mkdir -p $HOME/n2p2/lib
+          make libnnpif INTERFACES=CabanaMD PROJECT_INCLUDE=$HOME/n2p2/include PROJECT_LIB=$HOME/n2p2/lib
+      - name: Checkout CabanaMD
+        uses: actions/checkout@v2.2.0
+      - name: Build CabanaMD
+        run: |
+          cmake -B build \
+            -DCMAKE_INSTALL_PREFIX=$HOME/CabanaMD \
+            -DMPIEXEC_MAX_NUMPROCS=2 -DMPIEXEC_PREFLAGS="--oversubscribe" \
+            -DCMAKE_CXX_COMPILER=${{ matrix.cxx }} \
+            -DCMAKE_CXX_FLAGS="-Wall -Wextra -pedantic -Werror" \
+            -DCMAKE_PREFIX_PATH="$HOME/Cabana" \
+            -DCabanaMD_ENABLE_TESTING=ON \
+            -DCabanaMD_LAYOUT=${{ matrix.layout }} \
+            -DCabanaMD_VECTORLENGTH=${{ matrix.vector }} \
+            -DCabanaMD_ENABLE_NNP=${{ matrix.nnp }} \
+            -DN2P2_DIR=$HOME/n2p2 \
+            -DCabanaMD_LAYOUT_NNP=${{ matrix.layout_nnp }} \
+            -DCabanaMD_VECTORLENGTH_NNP=${{ matrix.vector_nnp }}
+          cmake --build build --parallel 2
+          CTEST_OUTPUT_ON_FAILURE=1 cmake --build build --target test
+          cmake --install build
+      - name: Format CabanaMD
+        working-directory: build
+        run: |
+          make format
+          git diff --exit-code
+      - name: Upload Report to codecov.io
+        if: ${{ matrix.coverage }}
+        uses: codecov/codecov-action@v1

.travis.yml

@@ -94,9 +94,9 @@ void Binning<t_System>::create_binning( T_X_FLOAT dx_in, T_X_FLOAT dy_in,
         minz = -dz * halo_depth - eps + system->local_mesh_lo_z;
         maxz = dz * halo_depth + eps + system->local_mesh_hi_z;
 
-        T_X_FLOAT delta[3] = {dx, dy, dz};
-        T_X_FLOAT min[3] = {minx, miny, minz};
-        T_X_FLOAT max[3] = {maxx, maxy, maxz};
+        T_X_FLOAT delta[3] = { dx, dy, dz };
+        T_X_FLOAT min[3] = { minx, miny, minz };
+        T_X_FLOAT max[3] = { maxx, maxy, maxz };
 
         system->slice_x();
         auto x = system->x;

src/binning_cabana_impl.h

@@ -100,9 +100,9 @@ void Comm<t_System>::create_domain_decomposition()
 
     for ( int p = 0; p < 6; p++ )
     {
-        neighbors_dist[p] = {proc_rank, proc_neighbors_send[p],
-                             proc_neighbors_recv[p]};
-        neighbors_halo[p] = {proc_neighbors_send[p], proc_neighbors_recv[p]};
+        neighbors_dist[p] = { proc_rank, proc_neighbors_send[p],
+                              proc_neighbors_recv[p] };
+        neighbors_halo[p] = { proc_neighbors_send[p], proc_neighbors_recv[p] };
 
         std::sort( neighbors_halo[p].begin(), neighbors_halo[p].end() );
         auto unique_end =

src/comm_mpi_impl.h

@@ -56,8 +56,8 @@ std::vector<std::string> split( const std::string &line )
 {
     // Split line on spaces and tabs
     std::regex re( "[ \r\t\n]" );
-    std::sregex_token_iterator first{line.begin(), line.end(), re, -1}, last;
-    std::vector<std::string> words{first, last};
+    std::sregex_token_iterator first{ line.begin(), line.end(), re, -1 }, last;
+    std::vector<std::string> words{ first, last };
     // Remove empty
     words.erase(
         std::remove_if( words.begin(), words.end(),
@@ -497,8 +497,8 @@ void InputFile<t_System>::create_lattice( Comm<t_System> *comm )
     T_X_FLOAT max_x = lattice_constant * lattice_nx;
     T_X_FLOAT max_y = lattice_constant * lattice_ny;
     T_X_FLOAT max_z = lattice_constant * lattice_nz;
-    std::array<T_X_FLOAT, 3> global_low = {0.0, 0.0, 0.0};
-    std::array<T_X_FLOAT, 3> global_high = {max_x, max_y, max_z};
+    std::array<T_X_FLOAT, 3> global_low = { 0.0, 0.0, 0.0 };
+    std::array<T_X_FLOAT, 3> global_high = { max_x, max_y, max_z };
     system->create_domain( global_low, global_high );
     s = *system;
 
@@ -723,7 +723,7 @@ void InputFile<t_System>::create_lattice( Comm<t_System> *comm )
     for ( T_INT i = 0; i < system->N_local; i++ )
     {
         LAMMPS_RandomVelocityGeom random;
-        double x_i[3] = {h_x( i, 0 ), h_x( i, 1 ), h_x( i, 2 )};
+        double x_i[3] = { h_x( i, 0 ), h_x( i, 1 ), h_x( i, 2 ) };
         random.reset( temperature_seed, x_i );
 
         T_FLOAT mass_i = h_mass( h_type( i ) );

src/inputFile_impl.h

@@ -44,10 +44,10 @@ class NeighborVerlet : public Neighbor<t_System>
     {
         T_INT N_local = system->N_local;
 
-        double grid_min[3] = {system->ghost_mesh_lo_x, system->ghost_mesh_lo_y,
-                              system->ghost_mesh_lo_z};
-        double grid_max[3] = {system->ghost_mesh_hi_x, system->ghost_mesh_hi_y,
-                              system->ghost_mesh_hi_z};
+        double grid_min[3] = { system->ghost_mesh_lo_x, system->ghost_mesh_lo_y,
+                               system->ghost_mesh_lo_z };
+        double grid_max[3] = { system->ghost_mesh_hi_x, system->ghost_mesh_hi_y,
+                               system->ghost_mesh_hi_z };
 
         system->slice_x();
         auto x = system->x;

src/neighbor_types/neighbor_verlet.h

@@ -141,7 +141,7 @@ class SystemCommon
         global_mesh_z = global_mesh->extent( 2 );
 
         // Create the global grid.
-        std::array<bool, 3> is_periodic = {true, true, true};
+        std::array<bool, 3> is_periodic = { true, true, true };
         auto global_grid = Cajita::createGlobalGrid(
             MPI_COMM_WORLD, global_mesh, is_periodic, partitioner );
 

src/system.h

@@ -43,8 +43,8 @@ t_System createParticles( const int num_particle, const int num_ghost,
     system.N_local = num_particle - num_ghost;
     system.N_ghost = num_ghost;
 
-    system.create_domain( {box_min, box_min, box_min},
-                          {box_max, box_max, box_max} );
+    system.create_domain( { box_min, box_min, box_min },
+                          { box_max, box_max, box_max } );
 
     system.slice_integrate();
     auto x = system.x;
@@ -112,10 +112,11 @@ void testIntegratorReversibility( int steps )
     system.slice_v();
     auto v = system.v;
     Kokkos::RangePolicy<TEST_EXECSPACE> exec_policy( 0, num_particle );
-    Kokkos::parallel_for( exec_policy, KOKKOS_LAMBDA( const int p ) {
-        for ( int d = 0; d < 3; ++d )
-            v( p, d ) *= -1.0;
-    } );
+    Kokkos::parallel_for(
+        exec_policy, KOKKOS_LAMBDA( const int p ) {
+            for ( int d = 0; d < 3; ++d )
+                v( p, d ) *= -1.0;
+        } );
 
     // Integrate back
     for ( int s = 0; s < steps; ++s )