Trilinos and PETSc interfaces (#30) and Docker containers (#211)

- Trilinos and PETSc interfaces added by @ktbolt
- created dockerfiles to build Docker containers with pre-compiled Trilinos and PETSc libraries in Ubuntu-20.04 and Ubuntu-22.04
- added test cases for fluid and fsi problems to test Trilinos and PETSc linear solvers and preconditioners
- updated the workflow file test_ubuntu.yml to include PETSc and Trilinos tests for continuous integration (CI)

.github/workflows/test_ubuntu.yml

@@ -0,0 +1,64 @@
+name: test Ubuntu
+on: [push, pull_request]
+jobs:
+ test:
+ strategy:
+ matrix:
+ name: [Ubuntu-20.04, Ubuntu-22.04]
+ include:
+ - name: Ubuntu-20.04
+ version: ubuntu-20.04
+ image: ubuntu20
+ - name: Ubuntu-22.04
+ version: ubuntu-22.04
+ image: ubuntu22
+ runs-on: ${{ matrix.version }}
+ container: dcodoni/lib:${{ matrix.image }}
+ steps:
+ - uses: actions/checkout@v3
+ - name: Build svFSIplus
+ run: |
+ if [ -d "build" ]; then
+ rm -rf "build"
+ fi
+ 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})
@@ -267,24 +296,37 @@ if(ENABLE_UNIT_TEST)
  find_package(Threads REQUIRED)
 
  # install Google Test
+ #if(NOT TARGET gtest_main AND NOT TARGET gtest)
  include(FetchContent)
  FetchContent_Declare(
  googletest
- URL https://github.com/google/googletest/archive/03597a01ee50ed33e9dfd640b249b4be3799d395.zip
+ URL https://github.com/google/googletest/archive/refs/heads/main.zip
+ DOWNLOAD_EXTRACT_TIMESTAMP TRUE
  )
  FetchContent_MakeAvailable(googletest)
+ #endif()
+
  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")
+ set(TEST_SOURCES "../../../tests/unitTests/test.cpp")
  list(REMOVE_ITEM CSRCS "main.cpp")
-
+ list(APPEND CSRCS ${TEST_SOURCES})
+
  # include source files (same as what svFSI does except for main.cpp)
  add_executable(run_all_unit_tests ${CSRCS})
 
+ if(USE_TRILINOS)
+ target_link_libraries(run_all_unit_tests ${Trilinos_LIBRARIES} ${Trilinos_TPL_LIBRARIES})
+ endif()
+
+ if(USE_PETSC)
+ target_link_libraries(run_all_unit_tests ${PETSC_LIBRARY_DIRS})
+ endif()
+
  # libraries
  target_link_libraries(run_all_unit_tests
  ${GLOBAL_LIBRARIES}

Code/Source/svFSI/ComMod.h

@@ -56,6 +56,8 @@
 #include <string>
 #include <vector>
 
+class LinearAlgebra;
+
 /// @brief Fourier coefficients that are used to specify unsteady BCs
 //
 class fcType
@@ -613,7 +615,6 @@ class outputType
  std::string name;
 };
 
-
 /// @brief Linear system of equations solver type
 //
 class lsType
@@ -623,9 +624,6 @@ class lsType
  /// @brief LS solver (IN)
  consts::SolverType LS_type = consts::SolverType::lSolver_NA;
 
- /// @brief Preconditioner (IN)
- consts::PreconditionerType PREC_Type = consts::PreconditionerType::PREC_NONE;
-
  /// @brief Successful solving (OUT)
  bool suc = false;
 
@@ -667,6 +665,9 @@ class lsType
 
  /// @brief Calling duration (OUT)
  double callD = 0.0;
+
+ //@brief Configuration file for linear solvers (Trilinos, PETSc)
+ std::string config;
 };
 
 
@@ -1071,6 +1072,18 @@ class eqType
  /// @brief type of linear solver
  lsType ls;
 
+ /// @brief The type of interface to a numerical linear algebra library.
+ consts::LinearAlgebraType linear_algebra_type;
+
+ /// @brief The type of assembly interface to a numerical linear algebra library.
+ consts::LinearAlgebraType linear_algebra_assembly_type;
+
+ /// @brief The type of preconditioner used by the interface to a numerical linear algebra library.
+ consts::PreconditionerType linear_algebra_preconditioner = consts::PreconditionerType::PREC_FSILS;
+
+ /// @brief Interface to a numerical linear algebra library.
+ LinearAlgebra* linear_algebra = nullptr;
+
  /// @brief FSILS type of linear solver
  fsi_linear_solver::FSILS_lsType FSILS;
 
@@ -1289,23 +1302,6 @@ class ibType
  ibCommType cm;
 };
 
-/// @brief Data type for Trilinos Linear Solver related arrays
-//
-class tlsType
-{
- public:
-
- /// @brief Local to global mapping
- Vector<int> ltg;
-
- /// @brief Factor for Dirichlet BCs
- Array<double> W;
-
- /// @brief Residual
- Array<double> R;
-};
-
-
 /// @brief The ComMod class duplicates the data structures in the Fortran COMMOD module
 /// defined in MOD.f. 
 ///
@@ -1597,9 +1593,6 @@ class ComMod {
  /// @brief IB: Immersed boundary data structure
  ibType ib;
 
- /// @brief Trilinos Linear Solver data type
- tlsType tls;
-
  bool debug_active = false;
 
  Timer timer;