PETSc and Trilinos interface

.github/workflows/test_ubuntu.yml

@@ -0,0 +1,60 @@
+name: test Ubuntu
+on: [push, pull_request]
+jobs:
+ test:
+ strategy:
+ matrix:
+ os:
+ - name: Ubuntu-20.04
+ version: ubuntu-20.04
+ image: ubuntu20
+ - name: Ubuntu-22.04
+ version: ubuntu-22.04
+ image: ubuntu22
+ runs-on: ${{ matrix.os.version }}
+ container: dcodoni/lib:${{ matrix.os.image }}
+ steps:
+ - uses: actions/checkout@v3
+ - name: Build svFSIplus
+ run: |
+ mkdir build
+ cd build
+ cmake -DENABLE_COVERAGE=ON -DENABLE_ARRAY_INDEX_CHECKING=ON -DENABLE_UNIT_TEST=ON -DSV_USE_TRILINOS:BOOL=ON ..
+ make -j2
+ cd ..
+ - name: Build svFSIplus (PETSc)
+ run: |
+ if [ -d "build-petsc" ]; then
+ rm -rf "build-petsc"
+ fi
+ mkdir build-petsc
+ cd build-petsc
+ cmake -DENABLE_COVERAGE=ON -DENABLE_ARRAY_INDEX_CHECKING=ON -DENABLE_UNIT_TEST=ON -DSV_PETSC_DIR:STRING=/petsc ..
+ make -j2
+ cd ..
+ - name: Run integration tests
+ run: |
+ git config --global --add safe.directory /__w/svFSIplus/svFSIplus
+ git lfs pull
+ cd tests
+ conda run -n svfsiplus pytest -rPv --durations=0
+ - name: Run unit tests
+ run: | 
+ cd build/svFSI-build/Source/svFSI
+ ctest --verbose
+ - name: Generate code coverage
+ run: |
+ cd build/svFSI-build
+ make coverage
+ - name: Save coverage report
+ uses: actions/upload-artifact@v3
+ with:
+ name: coverage_report
+ path: build/svFSI-build/coverage
+ - name: Upload coverage reports to Codecov
+ uses: codecov/codecov-action@v3
+ env:
+ CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+
+

Code/Source/svFSI/CMakeLists.txt

@@ -1,3 +1,27 @@
+# Copyright (c) 2014-2015 The Regents of the University of California.
+# All Rights Reserved.
+#
+# Permission is hereby granted, free of charge, to any person obtaining
+# a copy of this software and associated documentation files (the
+# "Software"), to deal in the Software without restriction, including
+# without limitation the rights to use, copy, modify, merge, publish,
+# distribute, sublicense, and/or sell copies of the Software, and to
+# permit persons to whom the Software is furnished to do so, subject
+# to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included
+# in all copies or substantial portions of the Software.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED True)
@@ -84,11 +108,12 @@ if(NOT "${SV_PETSC_DIR}" STREQUAL "")
  message(" PETSC_LIBRARY_DIRS = ${PETSC_LIBRARY_DIRS}")
  message(" PETSC_INCLUDE_DIRS = ${PETSC_INCLUDE_DIRS}")
 
- # Set PETSc include directory.
+ # Set PETSc include and library directories.
  include_directories(${PETSC_INCLUDE_DIRS})
+ #link_directories(${PETSC_LIBRARY_DIRS})
 
- # Set C++ directive to use PETSc in svFSIplus code.
- ADD_DEFINITIONS(-DWITH_PETSC)
+ # Set C++ directive to use PETSc.
+ ADD_DEFINITIONS(-DUSE_PETSC)
  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -pedantic -std=c99")
 
  set(USE_PETSC 1)
@@ -123,6 +148,10 @@ set(lib ${SV_LIB_SVFSI_NAME})
 set(CSRCS 
  Array3.h Array3.cpp 
  Array.h Array.cpp
+ LinearAlgebra.h LinearAlgebra.cpp
+ FsilsLinearAlgebra.h FsilsLinearAlgebra.cpp
+ PetscLinearAlgebra.h PetscLinearAlgebra.cpp
+ TrilinosLinearAlgebra.h TrilinosLinearAlgebra.cpp
  Tensor4.h Tensor4.cpp
  Vector.h Vector.cpp 
 
@@ -192,12 +221,12 @@ set(CSRCS
 )
 
  # Set PETSc interace code.
- if(USE_PETSC)
- #set(CSRCS ${CSRCS} petsc_linear_solver.c)
- endif()
+ #if(USE_PETSC)
+ # set(CSRCS ${CSRCS} petsc_linear_solver.h petsc_linear_solver.c)
+ #endif()
 
 if(USE_TRILINOS)
- set(CSRCS ${CSRCS} trilinos_linear_solver.cpp)
+ #set(CSRCS ${CSRCS} trilinos_linear_solver.cpp)
 
  # trilinos directories and libraries
  include_directories(${Trilinos_TPL_INCLUDE_DIRS})
@@ -260,56 +289,4 @@ if(ENABLE_COVERAGE)
  WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
 endif()
 
-# unit tests and Google Test
-if(ENABLE_UNIT_TEST)
-
- # link pthread on ubuntu20
- find_package(Threads REQUIRED)
-
- # install Google Test
- include(FetchContent)
- FetchContent_Declare(
- googletest
- URL https://github.com/google/googletest/archive/03597a01ee50ed33e9dfd640b249b4be3799d395.zip
- )
- FetchContent_MakeAvailable(googletest)
- enable_testing()
- include(GoogleTest)
-
- # add test.cpp for unit test
-
- # remove the main.cpp and add test.cpp
- list(APPEND CSRCS "../../../tests/unitTests/test.cpp")
- list(REMOVE_ITEM CSRCS "main.cpp")
-
- # include source files (same as what svFSI does except for main.cpp)
- add_executable(run_all_unit_tests ${CSRCS})
-
- # libraries
- target_link_libraries(run_all_unit_tests
- ${GLOBAL_LIBRARIES}
- ${INTELRUNTIME_LIBRARIES}
- ${ZLIB_LIBRARY}
- ${BLAS_LIBRARIES}
- ${LAPACK_LIBRARIES}
- ${METIS_SVFSI_LIBRARY_NAME}
- ${PARMETIS_SVFSI_LIBRARY_NAME}
- ${TETGEN_LIBRARY_NAME}
- ${TINYXML_LIBRARY_NAME}
- ${SV_LIB_SVFSILS_NAME}${SV_MPI_NAME_EXT}
- ${VTK_LIBRARIES}
- )
-
- # link Google Test
- target_link_libraries(
- run_all_unit_tests
- gtest
- GTest::gtest_main 
- pthread # link pthread on ubuntu20
- )
-
- # gtest_discover_tests(runUnitTest)
- add_test(NAME all_unit_tests COMMAND run_all_unit_tests)
-
-endif()