Merge remote-tracking branch 'polysolve/main' into slim

polyfem · Aug 20, 2024 · c2921f1 · c2921f1
2 parents e7e41ad + 0cd21ba
commit c2921f1
Show file tree

Hide file tree

Showing 12 changed files with 152 additions and 115 deletions.
diff --git a/.github/workflows/continuous.yml b/.github/workflows/continuous.yml
@@ -29,7 +29,7 @@ jobs:
             name: Linux
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v1
+        uses: actions/checkout@v4.1.6
         with:
           fetch-depth: 10
 
@@ -53,7 +53,7 @@ jobs:
 
       - name: Cache Build
         id: cache-build
-        uses: actions/cache@v2
+        uses: actions/cache@v4.0.2
         with:
           path: ${{ env.CACHE_PATH }}
           key: ${{ runner.os }}-${{ matrix.config }}-cache-${{ github.sha }}
@@ -92,7 +92,7 @@ jobs:
         config: [Debug, Release]
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v1
+        uses: actions/checkout@v4.1.6
         with:
           fetch-depth: 10
 
@@ -105,7 +105,7 @@ jobs:
 
       - name: Cache build
         id: cache-build
-        uses: actions/cache@v2
+        uses: actions/cache@v4.0.2
         with:
           path: ${{ env.appdata }}\Mozilla\sccache
           key: ${{ runner.os }}-${{ matrix.config }}-cache-${{ github.sha }}

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
@@ -23,7 +23,7 @@ jobs:
             name: Linux
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v1
+        uses: actions/checkout@v4.1.6
         with:
           fetch-depth: 10
 
@@ -41,7 +41,7 @@ jobs:
 
       - name: Cache Build
         id: cache-build
-        uses: actions/cache@v3
+        uses: actions/cache@v4.0.2
         with:
           path: ${{ env.CACHE_PATH }}
           key: ${{ runner.os }}-Release-${{ matrix.threading }}-cache-${{ github.sha }}
@@ -72,7 +72,9 @@ jobs:
           lcov --remove coverage.info '/usr/*' "${HOME}"'/.cache/*' '*tests/*.cpp' '*tests/*.h' --output-file coverage.info
 
       - name: Upload Coverage
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:
             flags: polysolve # optional
             files: coverage.info

diff --git a/cmake/recipes/jse.cmake b/cmake/recipes/jse.cmake
@@ -8,4 +8,4 @@ endif()
 message(STATUS "Third-party: creating target 'jse::jse'")
 
 include(CPM)
-CPMAddPackage("gh:geometryprocessing/json-spec-engine#49f1a30f8c2912814916ec3d6108a649b23cb243")
+CPMAddPackage("gh:geometryprocessing/json-spec-engine#11d028ebf54c3665e1a7c25d8ac622a8cb851223")
diff --git a/cmake/recipes/mkl.cmake b/cmake/recipes/mkl.cmake
@@ -34,8 +34,8 @@ set_property(CACHE MKL_LINKING PROPERTY STRINGS ${MKL_LINKINK_CHOICES})
 message(STATUS "MKL linking strategy: ${MKL_LINKING}")
 
 # MKL version
-set(MKL_VERSION "2021.3.0" CACHE STRING "MKL version to use (2020.4 or 2021.3.0)")
-set(MKL_VERSION_CHOICES 2020.4 2021.3.0)
+set(MKL_VERSION "2022.2.1" CACHE STRING "MKL version to use (2022.2.1)")
+set(MKL_VERSION_CHOICES 2022.2.1)
 set_property(CACHE MKL_VERSION PROPERTY STRINGS ${MKL_VERSION_CHOICES})
 message(STATUS "MKL version: ${MKL_VERSION}")
 
@@ -78,66 +78,34 @@ elseif(UNIX)
     set(MKL_PLATFORM linux-64)
 endif()
 
-if(MKL_VERSION VERSION_EQUAL 2020.4)
-    # To compute the md5 checksums for each lib, use the following bash script (replace the target version number):
-    # for f in mkl mkl-include mkl-static mkl-devel; do for os in linux osx win; do cat <(printf "$f-$os-64-md5") <(conda search --override-channel --channel intel $f=2020.4 --platform $os-64 -i | grep md5 | cut -d : -f 2); done; done
-    set(mkl-linux-64-md5 f85891f97a04c7b2fbf619d1b903d7f5)
-    set(mkl-osx-64-md5 735d7f93c7fbcffe658f1ccf67418cb3)
-    set(mkl-win-64-md5 37ade09cace5cd73053b16574a3ee3c3)
-    set(mkl-include-linux-64-md5 8b2bf0e42bd95dd700d9877add1ca6de)
-    set(mkl-include-osx-64-md5 26043328553952cdb064c5aab8b50c78)
-    set(mkl-include-win-64-md5 87e9a73a6e6757a8ed0dbc87d50d7f60)
-    set(mkl-static-linux-64-md5 9f589a1508fb083c3e73427db459ca4c)
-    set(mkl-static-osx-64-md5 2f9e1b8b6d6b0903e81a573084e4494f)
-    set(mkl-static-win-64-md5 5ae780c06edd0be62966c6d8ab47d5fb)
-    set(mkl-devel-linux-64-md5 b571698ef237c0e61abe15b7d300f157)
-    set(mkl-devel-osx-64-md5 ee58da0463676d910eeab9aec0470f0e)
-    set(mkl-devel-win-64-md5 8a7736b81b9bc2d5c044b88d6ac8af6e)
-
-    # To compute file names, we use the following bash script:
-    # for f in mkl mkl-include mkl-static mkl-devel; do for os in linux osx win; do cat <(printf "$f-$os-64-file") <(conda search --override-channel --channel intel $f=2020.4 --platform $os-64 -i | grep file | cut -d : -f 2); done; done
-    set(mkl-linux-64-file mkl-2020.4-intel_304.tar.bz2)
-    set(mkl-osx-64-file mkl-2020.4-intel_301.tar.bz2)
-    set(mkl-win-64-file mkl-2020.4-intel_311.tar.bz2)
-    set(mkl-include-linux-64-file mkl-include-2020.4-intel_304.tar.bz2)
-    set(mkl-include-osx-64-file mkl-include-2020.4-intel_301.tar.bz2)
-    set(mkl-include-win-64-file mkl-include-2020.4-intel_311.tar.bz2)
-    set(mkl-static-linux-64-file mkl-static-2020.4-intel_304.tar.bz2)
-    set(mkl-static-osx-64-file mkl-static-2020.4-intel_301.tar.bz2)
-    set(mkl-static-win-64-file mkl-static-2020.4-intel_311.tar.bz2)
-    set(mkl-devel-linux-64-file mkl-devel-2020.4-intel_304.tar.bz2)
-    set(mkl-devel-osx-64-file mkl-devel-2020.4-intel_301.tar.bz2)
-    set(mkl-devel-win-64-file mkl-devel-2020.4-intel_311.tar.bz2)
-elseif(MKL_VERSION VERSION_EQUAL 2021.3.0)
+if(MKL_VERSION VERSION_EQUAL 2022.2.1)
     # To compute the md5 checksums for each lib, use the following bash script (replace the target version number):
     # for f in mkl mkl-include mkl-static mkl-devel; do for os in linux osx win; do cat <(printf "$f-$os-64-md5") <(conda search --override-channel --channel intel $f=2021.3.0 --platform $os-64 -i | grep md5 | cut -d : -f 2); done; done
-    set(mkl-linux-64-md5 2501643729c00b24fddb9530b339aea7)
-    set(mkl-osx-64-md5 d6129ae9dfba58671667a65c160d0776)
-    set(mkl-win-64-md5 264213ea4c5cb6b6d81ea97f59e757ab)
-    set(mkl-include-linux-64-md5 70b4f9a53401a3d11ce27d7ddb0e2511)
-    set(mkl-include-osx-64-md5 6da50c06992b78c4127a1881d39c1804)
-    set(mkl-include-win-64-md5 28d785eb22d28512d4e40e5890a817dc)
-    set(mkl-static-linux-64-md5 1469ad60a34269d4d0c5666bc131b82a)
-    set(mkl-static-osx-64-md5 4a099581ba95cc50bb538598b26389e4)
-    set(mkl-static-win-64-md5 69aef10428893314bc486e81397e1b25)
-    set(mkl-devel-linux-64-md5 2432ad963e3f7e4619ffc7f896178fbe)
-    set(mkl-devel-osx-64-md5 61b84a60715a3855a2097a3b619a00c8)
-    set(mkl-devel-win-64-md5 6128dee67d2b20ff534cf54757f623e0)
+    # set(mkl-linux-64-md5 2501643729c00b24fddb9530b339aea7)
+    # set(mkl-win-64-md5 264213ea4c5cb6b6d81ea97f59e757ab)
+
+    # set(mkl-include-linux-64-md5 70b4f9a53401a3d11ce27d7ddb0e2511)
+    # set(mkl-include-win-64-md5 28d785eb22d28512d4e40e5890a817dc)
+
+    # set(mkl-static-linux-64-md5 1469ad60a34269d4d0c5666bc131b82a)
+    # set(mkl-static-win-64-md5 69aef10428893314bc486e81397e1b25)
+
+    # set(mkl-devel-linux-64-md5 2432ad963e3f7e4619ffc7f896178fbe)
+    # set(mkl-devel-win-64-md5 6128dee67d2b20ff534cf54757f623e0)
 
     # To compute file names, we use the following bash script:
     # for f in mkl mkl-include mkl-static mkl-devel; do for os in linux osx win; do cat <(printf "$f-$os-64-file") <(conda search --override-channel --channel intel $f=2021.3.0 --platform $os-64 -i | grep file | cut -d : -f 2); done; done
-    set(mkl-linux-64-file mkl-2021.3.0-intel_520.tar.bz2)
-    set(mkl-osx-64-file mkl-2021.3.0-intel_517.tar.bz2)
-    set(mkl-win-64-file mkl-2021.3.0-intel_524.tar.bz2)
-    set(mkl-include-linux-64-file mkl-include-2021.3.0-intel_520.tar.bz2)
-    set(mkl-include-osx-64-file mkl-include-2021.3.0-intel_517.tar.bz2)
-    set(mkl-include-win-64-file mkl-include-2021.3.0-intel_524.tar.bz2)
-    set(mkl-static-linux-64-file mkl-static-2021.3.0-intel_520.tar.bz2)
-    set(mkl-static-osx-64-file mkl-static-2021.3.0-intel_517.tar.bz2)
-    set(mkl-static-win-64-file mkl-static-2021.3.0-intel_524.tar.bz2)
-    set(mkl-devel-linux-64-file mkl-devel-2021.3.0-intel_520.tar.bz2)
-    set(mkl-devel-osx-64-file mkl-devel-2021.3.0-intel_517.tar.bz2)
-    set(mkl-devel-win-64-file mkl-devel-2021.3.0-intel_524.tar.bz2)
+    set(mkl-linux-64-file mkl-2022.2.1-h6508926_16999.tar.bz2)
+    set(mkl-win-64-file mkl-2022.2.1-h4060db9_19760.tar.bz2)
+
+    set(mkl-include-linux-64-file mkl-include-2022.2.1-ha957f24_16999.tar.bz2)
+    set(mkl-include-win-64-file mkl-include-2022.2.1-h66d3029_19760.tar.bz2)
+
+    set(mkl-static-linux-64-file mkl-static-2022.2.1-h6508926_16999.tar.bz2)
+    set(mkl-static-win-64-file mkl-static-2022.2.1-h4060db9_19760.tar.bz2)
+
+    set(mkl-devel-linux-64-file mkl-devel-2022.2.1-ha957f24_16999.tar.bz2)
+    set(mkl-devel-win-64-file mkl-devel-2022.2.1-h66d3029_19760.tar.bz2)
 endif()
 
 # On Windows, `mkl-devel` contains the .lib files (needed at link time),
@@ -153,8 +121,8 @@ include(CPM)
 foreach(name IN ITEMS ${MKL_REMOTES})
     CPMAddPackage(
         NAME ${name}
-        URL https://anaconda.org/intel/${name}/${MKL_VERSION}/download/${MKL_PLATFORM}/${${name}-${MKL_PLATFORM}-file}
-        URL_MD5 ${${name}-${MKL_PLATFORM}-md5}
+        URL https://anaconda.org/conda-forge/${name}/${MKL_VERSION}/download/${MKL_PLATFORM}/${${name}-${MKL_PLATFORM}-file}
+        # URL_MD5 ${${name}-${MKL_PLATFORM}-md5}
     )
 endforeach()
 

diff --git a/codecov.yml b/codecov.yml
@@ -9,3 +9,5 @@ coverage:
         target: 75%
         threshold: 5%
         only_pulls: true
+ignore:
+  - "tests"  # ignore folders and all its contents
diff --git a/src/polysolve/linear/Solver.cpp b/src/polysolve/linear/Solver.cpp
@@ -528,11 +528,15 @@ namespace polysolve::linear
 #ifdef POLYSOLVE_WITH_PARDISO
         return "Pardiso";
 #else
+#ifdef POLYSOLVE_WITH_ACCELERATE
+        return "Eigen::AccelerateLDLT";
+#else
 #ifdef POLYSOLVE_WITH_HYPRE
         return "Hypre";
 #else
         return "Eigen::BiCGSTAB";
 #endif
+#endif
 #endif
     }
 

diff --git a/src/polysolve/linear/Solver.hpp b/src/polysolve/linear/Solver.hpp
@@ -51,22 +51,22 @@ namespace polysolve::linear
         /// Selects the correct solver based on params using the fallback or the list of solvers if necessary
         static void select_valid_solver(json &params, spdlog::logger &logger);
 
-        // Static constructor
-        //
-        // @param[in]  params   Parameter of the solver, including name and preconditioner
-        // @param[in]  logger   Logger used for error
-        // @param[in]  strict_validation    strict validation of the input paraams
-        // @param[out] a pointer to a linear solver
+        /// @brief Static constructor
+        ///
+        /// @param[in]  params   Parameter of the solver, including name and preconditioner
+        /// @param[in]  logger   Logger used for error
+        /// @param[in]  strict_validation    strict validation of the input paraams
+        /// @return a pointer to a linear solver
         //
         static std::unique_ptr<Solver> create(const json &params,
                                               spdlog::logger &logger,
                                               const bool strict_validation = true);
 
-        // Static constructor
-        //
-        // @param[in]  solver   Solver type
-        // @param[in]  precond  Preconditioner for iterative solvers
-        //
+        /// @brief Static constructor
+        ///
+        /// @param[in]  solver   Solver type
+        /// @param[in]  precond  Preconditioner for iterative solvers
+        ///
         static std::unique_ptr<Solver> create(const std::string &solver, const std::string &precond);
 
         // List available solvers
@@ -86,50 +86,45 @@ namespace polysolve::linear
         // Public interface //
         //////////////////////
 
-        // Set solver parameters
+        /// Set solver parameters
         virtual void set_parameters(const json &params) {}
 
-        // Get info on the last solve step
+        /// Get info on the last solve step
         virtual void get_info(json &params) const {};
 
-        // Analyze sparsity pattern
+        /// Analyze sparsity pattern
         virtual void analyze_pattern(const StiffnessMatrix &A, const int precond_num) {}
 
-        // Factorize system matrix
+        /// Factorize system matrix
         virtual void factorize(const StiffnessMatrix &A) {}
 
-        // Analyze sparsity pattern of a dense matrix
+        /// Analyze sparsity pattern of a dense matrix
         virtual void analyze_pattern_dense(const Eigen::MatrixXd &A, const int precond_num) {}
 
-        // Factorize system matrix of a dense matrix
+        /// Factorize system matrix of a dense matrix
         virtual void factorize_dense(const Eigen::MatrixXd &A) {}
 
-        // If solver uses dense matrices
+        /// If solver uses dense matrices
         virtual bool is_dense() const { return false; }
 
-        // Set block size for multigrid solvers
+        /// Set block size for multigrid solvers
         virtual void set_block_size(int block_size) {}
 
-        // If the problem is nullspace for multigrid solvers
+        /// If the problem is nullspace for multigrid solvers
         virtual void set_is_nullspace(const VectorXd &x) {}
 
-        //
-        // @brief         { Solve the linear system Ax = b }
-        //
-        // @param[in]     b     { Right-hand side. }
-        // @param[in,out] x     { Unknown to compute. When using an iterative
-        //                      solver, the input unknown vector is used as an
-        //                      initial guess, and must thus be properly allocated
-        //                      and initialized. }
-        //
+        ///
+        /// @brief         { Solve the linear system Ax = b }
+        ///
+        /// @param[in]     b     { Right-hand side. }
+        /// @param[in,out] x     { Unknown to compute. When using an iterative
+        ///                      solver, the input unknown vector is used as an
+        ///                      initial guess, and must thus be properly allocated
+        ///                      and initialized. }
+        ///
         virtual void solve(const Ref<const VectorXd> b, Ref<VectorXd> x) = 0;
 
-    public:
-        ///////////
-        // Debug //
-        ///////////
-
-        // Name of the solver type (for debugging purposes)
+        /// @brief Name of the solver type (for debugging purposes)
         virtual std::string name() const { return ""; }
     };
 

diff --git a/src/polysolve/nonlinear/Problem.hpp b/src/polysolve/nonlinear/Problem.hpp
@@ -10,6 +10,7 @@
 
 namespace polysolve::nonlinear
 {
+    /// @brief Class defining optimization problem to be solved. To be defined by user code
     class Problem
     {
     public:

diff --git a/src/polysolve/nonlinear/Solver.hpp b/src/polysolve/nonlinear/Solver.hpp
@@ -41,7 +41,7 @@ namespace polysolve::nonlinear
             spdlog::logger &logger,
             const bool strict_validation = true);
 
-        // List available solvers
+        /// @brief List available solvers
         static std::vector<std::string> available_solvers();
 
     public:
@@ -82,10 +82,17 @@ namespace polysolve::nonlinear
         /// @brief If true the solver will not throw an error if the maximum number of iterations is reached
         bool allow_out_of_iterations = false;
 
+
         /// @brief Get the line search object
         const std::shared_ptr<line_search::LineSearch> &line_search() const { return m_line_search; };
 
     protected:
+        /// @brief Compute direction in which the argument should be updated 
+        /// @param objFunc Problem to be minimized
+        /// @param x Current input (n x 1)
+        /// @param grad Gradient at current step (n x 1)
+        /// @param[out] direction Current update direction (n x 1)
+        /// @return True if update direction was found, False otherwises
         virtual bool compute_update_direction(
             Problem &objFunc,
             const TVector &x,
@@ -116,6 +123,10 @@ namespace polysolve::nonlinear
 
         FiniteDiffStrategy gradient_fd_strategy = FiniteDiffStrategy::NONE;
         double gradient_fd_eps = 1e-7;
+        /// @brief Check gradient versus finite difference results
+        /// @param objFunc Problem defining relevant objective function
+        /// @param x Current input (n x 1)
+        /// @param grad Current gradient (n x 1)
         virtual void verify_gradient(Problem &objFunc, const TVector &x, const TVector &grad) final;
 
     private:
@@ -128,8 +139,9 @@ namespace polysolve::nonlinear
         // ====================================================================
         //                           Solver state
         // ====================================================================
-
-        // Reset the solver at the start of a minimization
+
+        /// @brief Reset the solver at the start of a minimization
+        /// @param ndof number of degrees of freedom
         void reset(const int ndof);
 
         std::string descent_strategy_name() const { return m_strategies[m_descent_strategy]->name(); };
@@ -143,8 +155,14 @@ namespace polysolve::nonlinear
         //                            Solver info
         // ====================================================================
 
+        /// @brief Update solver info JSON object
+        /// @param energy 
         void update_solver_info(const double energy);
+
+        /// @brief Reset timing members to 0
         void reset_times();
+
+        /// @brief Log time taken in different phases of the solve
         void log_times() const;
 
         json solver_info;
-Original file line number
+Diff line change
@@ Expand Up / @@ -10,6 +10,7 @@ @@
     namespace polysolve::nonlinear
     {
+        /// @brief Class defining optimization problem to be solved. To be defined by user code
         class Problem
         {
         public:
@@ Expand Down @@