Merge branch 'master' into exlicit_variable_constructor

BobCFD · Feb 11, 2020 · 7bfccfd · 7bfccfd
2 parents 691fd39 + ae35657
commit 7bfccfd
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Showing 7 changed files with 28 additions and 19 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -15,8 +15,11 @@ jobs:
       fail-fast: false
       matrix:
         build-type: [Custom, FullDebug]
+        compiler: [gcc, clang]
     env:
       KRATOS_BUILD_TYPE: ${{ matrix.build-type }}
+      MKLVARS_ARCHITECTURE: intel64
+      MKLVARS_INTERFACE: lp64
 
     container:
       image: oberbichler/kratos-dev:latest
@@ -27,8 +30,6 @@ jobs:
         CCACHE_NODISABLE: true
         CCACHE_MAXSIZE: 500M
         FC: gfortran-7
-        CC: /usr/lib/ccache/gcc
-        CXX: /usr/lib/ccache/g++
 
     steps:
     - uses: actions/checkout@v2
@@ -38,13 +39,23 @@ jobs:
       uses: actions/cache@v1
       with:
         path: ~/.ccache
-        key: ${{ runner.os }}-ccache-${{ github.sha }}
-        restore-keys: ${{ runner.os }}-ccache-
+        key: ${{ runner.os }}-${{ matrix.build-type }}-${{ matrix.compiler }}-ccache-${{ github.sha }}
+        restore-keys: ${{ runner.os }}-${{ matrix.build-type }}-${{ matrix.compiler }}-ccache-
 
     - name: Build
       run: |
-        export MKLVARS_ARCHITECTURE=intel64
-        export MKLVARS_INTERFACE=lp64
+        if [ ${{ matrix.compiler }} = gcc ]; then
+          export CC=/usr/lib/ccache/gcc
+          export CXX=/usr/lib/ccache/g++
+          export KRATOS_CMAKE_OPTIONS_FLAGS="-DUSE_EIGEN_MKL=ON"
+          export KRATOS_CMAKE_CXX_FLAGS="-Wignored-qualifiers -Werror=ignored-qualifiers -Werror=suggest-override -Werror=unused-variable -Werror=misleading-indentation -Werror=return-type -Werror=sign-compare -Werror=unused-but-set-variable -Werror=unused-local-typedefs -Werror=reorder -Werror=maybe-uninitialized -Wno-deprecated-declarations"
+        elif [ ${{ matrix.compiler }} = clang ]; then
+          export CC=clang-9
+          export CXX=clang++-9
+        else
+          echo 'Unsupported compiler: ${{ matrix.compiler }}'
+          exit 1
+        fi
         . /opt/intel/mkl/bin/mklvars.sh
         cp .github/workflows/configure.sh configure.sh
         bash configure.sh
@@ -53,8 +64,6 @@ jobs:
     - name: Running small tests
       if: github.event_name == 'pull_request'
       run: |
-        export MKLVARS_ARCHITECTURE=intel64
-        export MKLVARS_INTERFACE=lp64
         . /opt/intel/mkl/bin/mklvars.sh
         export PYTHONPATH=${PYTHONPATH}:${GITHUB_WORKSPACE}/bin/${{ matrix.build-type }}
         export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${GITHUB_WORKSPACE}/bin/${{ matrix.build-type }}/libs
@@ -63,8 +72,6 @@ jobs:
     - name: Running nightly tests
       if: github.event_name == 'schedule' # this is the nightly build
       run: |
-        export MKLVARS_ARCHITECTURE=intel64
-        export MKLVARS_INTERFACE=lp64
         . /opt/intel/mkl/bin/mklvars.sh
         export PYTHONPATH=${PYTHONPATH}:${GITHUB_WORKSPACE}/bin/${{ matrix.build-type }}
         export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${GITHUB_WORKSPACE}/bin/${{ matrix.build-type }}/libs

diff --git a/.github/workflows/configure.sh b/.github/workflows/configure.sh
@@ -50,13 +50,10 @@ echo "Kratos build type is ${KRATOS_BUILD_TYPE}"
 
 # Configure
 cmake -H"${KRATOS_SOURCE}" -B"${KRATOS_BUILD}/${KRATOS_BUILD_TYPE}" \
+${KRATOS_CMAKE_OPTIONS_FLAGS} \
 -DUSE_MPI=ON \
 -DPYBIND11_PYTHON_VERSION="3.6" \
--DCMAKE_CXX_FLAGS="-O0 -fopenmp -Wall \
--Wignored-qualifiers -Werror=ignored-qualifiers -Werror=suggest-override -Werror=unused-variable \
--Werror=misleading-indentation -Werror=return-type \
--Werror=sign-compare -Werror=unused-but-set-variable \
--Werror=unused-local-typedefs -Werror=reorder -Werror=maybe-uninitialized -Wno-deprecated-declarations" \
+-DCMAKE_CXX_FLAGS="${KRATOS_CMAKE_CXX_FLAGS} -std=c++11 -O0 -fopenmp -Wall" \
 -DTRILINOS_INCLUDE_DIR="/usr/include/trilinos" \
 -DTRILINOS_LIBRARY_DIR="/usr/lib/x86_64-linux-gnu" \
 -DTRILINOS_LIBRARY_PREFIX="trilinos_" \
@@ -69,8 +66,7 @@ cmake -H"${KRATOS_SOURCE}" -B"${KRATOS_BUILD}/${KRATOS_BUILD_TYPE}" \
 -DMMG_LIBRARY="/usr/local/lib/libmmg.so"            \
 -DMMG2D_LIBRARY="/usr/local/lib/libmmg2d.so"        \
 -DMMG3D_LIBRARY="/usr/local/lib/libmmg3d.so"        \
--DMMGS_LIBRARY="/usr/local/lib/libmmgs.so"          \
--DUSE_EIGEN_MKL=ON
+-DMMGS_LIBRARY="/usr/local/lib/libmmgs.so"
 
 # Buid
 cmake --build "${KRATOS_BUILD}/${KRATOS_BUILD_TYPE}" --target all_unity    -- -j1

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,5 +1,6 @@
 project (KratosMultiphysics)
 cmake_minimum_required (VERSION 2.8.6)
+set (CMAKE_CXX_STANDARD 11)
 
 # Setting some policies
 # No recursive dereferencing

diff --git a/applications/DEMApplication/custom_strategies/strategies/explicit_solver_strategy.cpp b/applications/DEMApplication/custom_strategies/strategies/explicit_solver_strategy.cpp
@@ -705,6 +705,8 @@ namespace Kratos {
         ProcessInfo& r_fem_process_info = r_fem_model_part.GetProcessInfo();
         ConditionsArrayType& pConditions = r_fem_model_part.GetCommunicator().LocalMesh().Conditions();
 
+        RebuildListOfSphericParticles<SphericParticle>(r_model_part.GetCommunicator().LocalMesh().Elements(), mListOfSphericParticles);
+
         SetNormalRadiiOnAllParticles(*mpDem_model_part);
 
         #pragma omp parallel

diff --git a/applications/EigenSolversApplication/CMakeLists.txt b/applications/EigenSolversApplication/CMakeLists.txt
@@ -67,6 +67,8 @@ if( USE_EIGEN_MKL MATCHES ON )
         find_library(MKL_RT_LIB mkl_rt)
         message( "mkl_rt.lib found at: ${MKL_RT_LIB}")
         target_link_libraries( KratosEigenSolversCore PUBLIC ${MKL_RT_LIB} )
+    elseif( ${CMAKE_CXX_COMPILER_ID} MATCHES Clang )
+        message( FATAL_ERROR "Clang does not yet support MKL" )
     else( ${CMAKE_SYSTEM_NAME} MATCHES "Windows" )
         target_link_libraries( KratosEigenSolversCore PUBLIC mkl_rt )
     endif( ${CMAKE_SYSTEM_NAME} MATCHES "Windows" )

diff --git a/kratos/python/add_utilities_to_python.cpp b/kratos/python/add_utilities_to_python.cpp
@@ -39,14 +39,12 @@
 
 // #include "utilities/signed_distance_calculator_bin_based.h"
 #include "utilities/timer.h"
-
 #include "utilities/binbased_fast_point_locator.h"
 #include "utilities/binbased_fast_point_locator_conditions.h"
 #include "utilities/binbased_nodes_in_element_locator.h"
 #include "utilities/embedded_skin_utility.h"
 #include "utilities/geometry_tester.h"
 #include "utilities/cutting_utility.h"
-
 #include "utilities/python_function_callback_utility.h"
 #include "utilities/interval_utility.h"
 #include "utilities/table_stream_utility.h"

diff --git a/kratos/utilities/read_materials_utility.h b/kratos/utilities/read_materials_utility.h
@@ -102,6 +102,9 @@ class KRATOS_API(KRATOS_CORE) ReadMaterialsUtility
      */
     ReadMaterialsUtility(const std::string& rParametersName, Model& rModel);
 
+    /// Destructor.
+    virtual ~ReadMaterialsUtility() {}
+
     ///@}
     ///@name Operators
     ///@{