v3.4 (#203)

Author: TLCFEM

.github/ISSUE_TEMPLATE/application_execution.md

@@ -7,7 +7,7 @@ assignees: ''
 
 ---
 
-***The application officially distributed requires AVX support. Please make sure your CPU supports AVX.***
+***The application officially distributed requires AVX2 support. Please make sure your CPU supports AVX2.***
 
 ***If possible, please try to compile the application locally first to see if it executes.***
 

.github/workflows/dev-all.yml

@@ -74,7 +74,7 @@ jobs:
           fi
           go build Checker/updater.go
           mkdir build && cd build
-          cmake -DCMAKE_C_COMPILER=${{ matrix.compiler.c }} -DCMAKE_CXX_COMPILER=${{ matrix.compiler.cpp }} -DCMAKE_Fortran_COMPILER=${{ matrix.compiler.fortran }} -DCMAKE_BUILD_TYPE=${{ matrix.build }} -DTEST_COVERAGE=${{ env.COVERAGE }} -DUSE_AVX=${{ matrix.avx }} -DBUILD_MULTITHREAD=$MT -DUSE_VTK=${{ matrix.vtk }} -DVTK_DIR=/home/runner/work/suanPan/suanPan/lib/cmake/vtk-9.2/ -DUSE_MKL=${{ matrix.mkl }} -DMKLROOT=/opt/intel/oneapi/mkl/latest/ -DLINK_DYNAMIC_MKL=OFF -DUSE_INTEL_OPENMP=${{ env.IOMP }} -DCMAKE_INSTALL_PREFIX=dist ..
+          cmake -DCMAKE_C_COMPILER=${{ matrix.compiler.c }} -DCMAKE_CXX_COMPILER=${{ matrix.compiler.cpp }} -DCMAKE_Fortran_COMPILER=${{ matrix.compiler.fortran }} -DCMAKE_BUILD_TYPE=${{ matrix.build }} -DTEST_COVERAGE=${{ env.COVERAGE }} -DUSE_AVX2=${{ matrix.avx }} -DBUILD_MULTITHREAD=$MT -DUSE_VTK=${{ matrix.vtk }} -DVTK_DIR=/home/runner/work/suanPan/suanPan/lib/cmake/vtk-9.2/ -DUSE_MKL=${{ matrix.mkl }} -DMKLROOT=/opt/intel/oneapi/mkl/latest/ -DLINK_DYNAMIC_MKL=OFF -DUSE_INTEL_OPENMP=${{ env.IOMP }} -DCMAKE_INSTALL_PREFIX=dist ..
           make install -j"$(nproc)" && make package
       - name: Pack
         run: |
@@ -124,12 +124,14 @@ jobs:
           for SRC in `find . | egrep '\.o'`; do gcov -n $SRC > /dev/null; done
       - name: Report
         if: env.COVERAGE == 'ON'
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
-          gcov: true
+          plugin: gcov
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
   macos-dev:
     if: ${{ !contains(github.event.head_commit.message, '[skip]') }}
-    runs-on: macos-11
+    runs-on: macos-13
     timeout-minutes: 100
     strategy:
       matrix:
@@ -142,10 +144,6 @@ jobs:
     steps:
       - name: Clone
         uses: actions/checkout@v4
-      - name: Golang
-        uses: actions/setup-go@v5
-        with:
-          cache: false
       - name: VTK
         if: matrix.vtk == 'ON'
         run: |
@@ -154,17 +152,18 @@ jobs:
           brew install glfw glew
       - name: Compile
         run: |
+          brew install go libomp
           go build Checker/updater.go
           mkdir build && cd build
+          export CXXFLAGS="-Wl,-ld_classic"
+          export FC=gfortran-11
           if [ "${{ matrix.compiler }}" == "clang" ]; then
             export CC=$(brew --prefix llvm@15)/bin/clang
             export CXX=$(brew --prefix llvm@15)/bin/clang++
-            export FC=gfortran-11
             cmake -DCMAKE_C_STANDARD_INCLUDE_DIRECTORIES=$(brew --prefix libomp)/include -DCMAKE_CXX_STANDARD_INCLUDE_DIRECTORIES=$(brew --prefix libomp)/include -DCMAKE_Fortran_STANDARD_INCLUDE_DIRECTORIES=$(brew --prefix libomp)/include -DCMAKE_BUILD_TYPE=${{ matrix.build }} -DUSE_VTK=${{ matrix.vtk }} -DVTK_DIR=/Users/runner/work/suanPan/suanPan/lib/cmake/vtk-9.2/ -DCMAKE_INSTALL_PREFIX=dist ..
           else
             export CC=gcc-11
             export CXX=g++-11
-            export FC=gfortran-11
             cmake -DCMAKE_BUILD_TYPE=${{ matrix.build }} -DUSE_VTK=${{ matrix.vtk }} -DVTK_DIR=/Users/runner/work/suanPan/suanPan/lib/cmake/vtk-9.2/ -DCMAKE_INSTALL_PREFIX=dist ..
           fi
           make install -j4
@@ -219,7 +218,7 @@ jobs:
         run: |
           go build Checker/updater.go
           mkdir build && cd build
-          cmake -G "${{ matrix.compiler }}" -DCMAKE_BUILD_TYPE=${{ matrix.build }} -DUSE_AVX=${{ matrix.avx }} -DUSE_VTK=${{ matrix.vtk }} -DVTK_DIR=D:/a/suanPan/suanPan/lib/cmake/vtk-9.2/ -DCMAKE_INSTALL_PREFIX=dist ..
+          cmake -G "${{ matrix.compiler }}" -DCMAKE_BUILD_TYPE=${{ matrix.build }} -DUSE_AVX2=${{ matrix.avx }} -DUSE_VTK=${{ matrix.vtk }} -DVTK_DIR=D:/a/suanPan/suanPan/lib/cmake/vtk-9.2/ -DCMAKE_INSTALL_PREFIX=dist ..
           cmake --build . --target install --config ${{ matrix.build }} -j 4
       - name: Pack
         shell: bash

.github/workflows/master-all.yml

@@ -41,7 +41,7 @@ jobs:
         run: |
           go build Checker/updater.go
           mkdir build && cd build
-          cmake -DCMAKE_BUILD_TYPE=Release -DUSE_AVX=${{ matrix.avx }} -DBUILD_MULTITHREAD=ON -DUSE_VTK=${{ matrix.vtk }} -DVTK_DIR=/home/runner/work/suanPan/suanPan/lib/cmake/vtk-9.2/ -DUSE_MKL=${{ matrix.mkl }} -DMKLROOT=/opt/intel/oneapi/mkl/latest/ -DLINK_DYNAMIC_MKL=OFF -DUSE_INTEL_OPENMP=OFF -DCMAKE_INSTALL_PREFIX=dist ..
+          cmake -DCMAKE_BUILD_TYPE=Release -DUSE_AVX2=${{ matrix.avx }} -DBUILD_MULTITHREAD=ON -DUSE_VTK=${{ matrix.vtk }} -DVTK_DIR=/home/runner/work/suanPan/suanPan/lib/cmake/vtk-9.2/ -DUSE_MKL=${{ matrix.mkl }} -DMKLROOT=/opt/intel/oneapi/mkl/latest/ -DLINK_DYNAMIC_MKL=OFF -DUSE_INTEL_OPENMP=OFF -DCMAKE_INSTALL_PREFIX=dist ..
           make install -j"$(nproc)" && make package
       - name: Pack
         run: |
@@ -76,18 +76,14 @@ jobs:
           prerelease: true
           overwrite: true
   macos-master:
-    runs-on: macos-11
+    runs-on: macos-13
     timeout-minutes: 100
     strategy:
       matrix:
         vtk: [ ON, OFF ]
     steps:
       - name: Clone
         uses: actions/checkout@v4
-      - name: Golang
-        uses: actions/setup-go@v5
-        with:
-          cache: false
       - name: Prepare
         run: |
           echo "SP_TIME=daily-$(date +''%y%m%d'')" >> $GITHUB_ENV
@@ -99,11 +95,13 @@ jobs:
           brew install glfw glew
       - name: Compile
         run: |
+          brew install go libomp
           go build Checker/updater.go
           mkdir build && cd build
           export CC=$(brew --prefix llvm@15)/bin/clang
           export CXX=$(brew --prefix llvm@15)/bin/clang++
           export FC=gfortran-11
+          export CXXFLAGS="-Wl,-ld_classic"
           cmake -DCMAKE_C_STANDARD_INCLUDE_DIRECTORIES=$(brew --prefix libomp)/include -DCMAKE_CXX_STANDARD_INCLUDE_DIRECTORIES=$(brew --prefix libomp)/include -DCMAKE_Fortran_STANDARD_INCLUDE_DIRECTORIES=$(brew --prefix libomp)/include -DCMAKE_BUILD_TYPE=Release -DUSE_VTK=${{ matrix.vtk }} -DBUILD_MULTITHREAD=ON -DVTK_DIR=/Users/runner/work/suanPan/suanPan/lib/cmake/vtk-9.2/ -DCMAKE_INSTALL_PREFIX=dist ..
           make install -j4
       - name: Pack
@@ -156,7 +154,7 @@ jobs:
         run: |
           go build Checker/updater.go
           mkdir build && cd build
-          cmake -DCMAKE_BUILD_TYPE=Release -DUSE_AVX=${{ matrix.avx }} -DBUILD_MULTITHREAD=ON -DUSE_VTK=${{ matrix.vtk }} -DVTK_DIR=D:/a/suanPan/suanPan/lib/cmake/vtk-9.2/ -DCMAKE_INSTALL_PREFIX=dist ..
+          cmake -DCMAKE_BUILD_TYPE=Release -DUSE_AVX2=${{ matrix.avx }} -DBUILD_MULTITHREAD=ON -DUSE_VTK=${{ matrix.vtk }} -DVTK_DIR=D:/a/suanPan/suanPan/lib/cmake/vtk-9.2/ -DCMAKE_INSTALL_PREFIX=dist ..
           cmake --build . --target install --config Release -j 4
       - name: Pack
         shell: bash

.github/workflows/stale.yml

@@ -0,0 +1,18 @@
+name: Stale
+on:
+  schedule:
+    - cron: '30 1 * * *'
+jobs:
+  stale:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/stale@v9
+        with:
+          stale-issue-message: 'This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 5 days.'
+          stale-pr-message: 'This PR is stale because it has been open 60 days with no activity. Remove stale label or comment or this will be closed in 10 days.'
+          close-issue-message: 'This issue was closed because it has been stalled for 5 days with no activity.'
+          close-pr-message: 'This PR was closed because it has been stalled for 10 days with no activity.'
+          days-before-issue-stale: 30
+          days-before-pr-stale: 60
+          days-before-issue-close: 5
+          days-before-pr-close: 10

CHANGELOG.md

@@ -4,9 +4,17 @@
 
 1. The `MKL` includes outdated `FEAST`, the external names in `FEAST` library are modified to avoid linking error.
 2. The `SPIKE` solver may occasionally freeze, to circumvent, try to avoid mixing compilers from different vendors.
-3. The `MUMPS` solver throws segfaults with large matrices.
+3. The `MUMPS` solver throws segfaults with large matrices, appears to be quite slow.
 4. The `FGMRES` solver requires refinements.
 
+## version 3.4
+
+1. update `Armadillo` to version `12.8.2` [#193](https://github.com/TLCFEM/suanPan/pull/193)
+2. plane strain Duncan-Selig soil model [#195](https://github.com/TLCFEM/suanPan/pull/195)
+3. update `Catch2` to version `3.5.4`
+4. update `TBB` to version `2021.12.0` [#199](https://github.com/TLCFEM/suanPan/pull/199)
+5. update `MUMPS` to version `5.7.1` [#202](https://github.com/TLCFEM/suanPan/pull/202)
+
 ## version 3.3
 
 1. (breaking) revise syntax for `ConcreteTsai`, `Concrete21` and `Concrete22` using a more consistent definition

CITATION.cff

@@ -28,5 +28,5 @@ keywords:
   - IGA
   - Solid Mechanics
 license: GPL-3.0
-version: '3.2'
-date-released: '2024-01-24'
+version: '3.4'
+date-released: '2024-05-11'

CMakeLists.txt

@@ -413,7 +413,7 @@ if (CMAKE_SYSTEM_NAME MATCHES "Linux")
         set(CPACK_PACKAGE_ICON ${ROOT}/Resource/suanPan-ua.svg)
         set(CPACK_PACKAGE_RELEASE 1)
         set(CPACK_PACKAGE_VENDOR "tlcfem")
-        set(CPACK_PACKAGE_VERSION "3.3.0")
+        set(CPACK_PACKAGE_VERSION "3.4.0")
         set(CPACK_PACKAGE_DESCRIPTION "An Open Source, Parallel and Heterogeneous Finite Element Analysis Framework")
         set(CPACK_PACKAGE_HOMEPAGE_URL "https://github.com/TLCFEM/suanPan")
 

Checker/updater.go

@@ -93,8 +93,8 @@ func downloadLatestVersion(versionString string) error {
 	fmt.Printf("      If performance degradation is spotted on your platform, consider switch to `openblas` version.\n")
 	fmt.Printf("  `vtk` uses VTK for visualisation.\n")
 	fmt.Printf("      Visualisation may be useful when it comes to post-processing, but it requires OpenGL support. Please make sure the corresponding packages are installed.\n")
-	fmt.Printf("  `no-avx` disables AVX.\n")
-	fmt.Printf("      For CPUs that do not support AVX, please use this version.\n")
+	fmt.Printf("  `no-avx` disables AVX2.\n")
+	fmt.Printf("      For CPUs that do not support AVX2, please use this version.\n")
 	fmt.Printf("\nDownload the new version:\n")
 
 	var package_array []string

Domain/Factory.hpp

@@ -92,6 +92,8 @@ template<sp_d T> class Factory final {
     SolverType solver = SolverType::LAPACK;
     SolverSetting<T> setting{};
 
+    SolverType sub_solver = SolverType::LAPACK;
+
     T error = T(0); // error produced by certain solvers
 
     Col<T> ninja; // the result from A*X=B
@@ -204,7 +206,10 @@ template<sp_d T> class Factory final {
     [[nodiscard]] bool is_nonviscous() const;
 
     void set_solver_type(SolverType);
-    [[nodiscard]] SolverType get_solver_type() const;
+    [[nodiscard]] bool contain_solver_type(SolverType) const;
+
+    void set_sub_solver_type(SolverType);
+    [[nodiscard]] bool contain_sub_solver_type(SolverType) const;
 
     void set_solver_setting(const SolverSetting<double>&);
     [[nodiscard]] const SolverSetting<double>& get_solver_setting() const;
@@ -726,7 +731,11 @@ template<sp_d T> bool Factory<T>::is_nonviscous() const { return nonviscous; }
 
 template<sp_d T> void Factory<T>::set_solver_type(const SolverType E) { solver = E; }
 
-template<sp_d T> SolverType Factory<T>::get_solver_type() const { return solver; }
+template<sp_d T> void Factory<T>::set_sub_solver_type(const SolverType E) { sub_solver = E; }
+
+template<sp_d T> bool Factory<T>::contain_solver_type(const SolverType ST) const { return ST == solver; }
+
+template<sp_d T> bool Factory<T>::contain_sub_solver_type(const SolverType ST) const { return ST == sub_solver; }
 
 template<sp_d T> void Factory<T>::set_solver_setting(const SolverSetting<double>& SS) { setting = SS; }
 
@@ -1475,34 +1484,37 @@ template<sp_d T> unique_ptr<MetaMat<T>> Factory<T>::get_basic_container() {
     switch(storage_type) {
     case StorageScheme::FULL:
 #ifdef SUANPAN_CUDA
-        if(SolverType::CUDA == solver) return std::make_unique<FullMatCUDA<T>>(n_size, n_size);
+        if(contain_solver_type(SolverType::CUDA)) return std::make_unique<FullMatCUDA<T>>(n_size, n_size);
 #endif
         return std::make_unique<FullMat<T>>(n_size, n_size);
     case StorageScheme::BAND:
-        if(SolverType::SPIKE == solver) return std::make_unique<BandMatSpike<T>>(n_size, n_lobw, n_upbw);
+        if(contain_solver_type(SolverType::SPIKE)) return std::make_unique<BandMatSpike<T>>(n_size, n_lobw, n_upbw);
+#ifdef SUANPAN_MAGMA
+        if(contain_solver_type(SolverType::MAGMA)) return std::make_unique<BandMatMAGMA<T>>(n_size, n_lobw, n_upbw);
+#endif
         return std::make_unique<BandMat<T>>(n_size, n_lobw, n_upbw);
     case StorageScheme::BANDSYMM:
         return std::make_unique<BandSymmMat<T>>(n_size, n_lobw);
     case StorageScheme::SYMMPACK:
         return std::make_unique<SymmPackMat<T>>(n_size);
     case StorageScheme::SPARSE:
-        if(SolverType::MUMPS == solver) return std::make_unique<SparseMatMUMPS<T>>(n_size, n_size, n_elem);
-        if(SolverType::LIS == solver) return std::make_unique<SparseMatLis<T>>(n_size, n_size, n_elem);
-        if(SolverType::SUPERLU == solver) return std::make_unique<SparseMatSuperLU<T>>(n_size, n_size, n_elem);
+        if(contain_solver_type(SolverType::MUMPS)) return std::make_unique<SparseMatMUMPS<T>>(n_size, n_size, n_elem);
+        if(contain_solver_type(SolverType::LIS)) return std::make_unique<SparseMatLis<T>>(n_size, n_size, n_elem);
+        if(contain_solver_type(SolverType::SUPERLU)) return std::make_unique<SparseMatSuperLU<T>>(n_size, n_size, n_elem);
 #ifdef SUANPAN_MKL
-        if(SolverType::PARDISO == solver) return std::make_unique<SparseMatPARDISO<T>>(n_size, n_size, n_elem);
-        if(SolverType::FGMRES == solver) return std::make_unique<SparseMatFGMRES<T>>(n_size, n_size, n_elem);
+        if(contain_solver_type(SolverType::PARDISO)) return std::make_unique<SparseMatPARDISO<T>>(n_size, n_size, n_elem);
+        if(contain_solver_type(SolverType::FGMRES)) return std::make_unique<SparseMatFGMRES<T>>(n_size, n_size, n_elem);
 #endif
 #ifdef SUANPAN_CUDA
-        if(SolverType::CUDA == solver) return std::make_unique<SparseMatCUDA<T>>(n_size, n_size, n_elem);
+        if(contain_solver_type(SolverType::CUDA)) return std::make_unique<SparseMatCUDA<T>>(n_size, n_size, n_elem);
 #ifdef SUANPAN_MAGMA
-        if(SolverType::MAGMA == solver) return std::make_unique<SparseMatMAGMA<T>>(n_size, n_size, magma_setting);
+        if(contain_solver_type(SolverType::MAGMA)) return std::make_unique<SparseMatMAGMA<T>>(n_size, n_size, magma_setting);
 #endif
 #endif
         return std::make_unique<SparseMatSuperLU<T>>(n_size, n_size, n_elem);
     case StorageScheme::SPARSESYMM:
 #ifdef SUANPAN_MKL
-        if(SolverType::FGMRES == solver) return std::make_unique<SparseSymmMatFGMRES<T>>(n_size, n_size, n_elem);
+        if(contain_solver_type(SolverType::FGMRES)) return std::make_unique<SparseSymmMatFGMRES<T>>(n_size, n_size, n_elem);
 #endif
         return std::make_unique<SparseSymmMatMUMPS<T>>(n_size, n_size, n_elem);
     default:

Domain/MetaMat/BandMat.hpp

@@ -38,11 +38,12 @@ template<sp_d T> class BandMat : public DenseMat<T> {
     static T bin;
 
     const uword s_band;
-    const uword m_rows; // memory block layout
 
     int solve_trs(Mat<T>&, Mat<T>&&);
 
 protected:
+    const uword m_rows; // memory block layout
+
     const uword l_band;
     const uword u_band;