- Trilinos and PETSc interfaces added by @ktbolt (addresses issue Sim…

…Vascular#30)

- created dockerfiles to build Docker containers with pre-compiled Trilinos and PETSc libraries in Ubuntu-20.04 and Ubuntu-22.04 (addresses issue SimVascular#211)
- 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;