v3.1 (#152)

TLCFEM · Sep 1, 2023 · 934f7d6 · 934f7d6
1 parent 3a3cea4
commit 934f7d6
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Showing 337 changed files with 94,552 additions and 15,011 deletions.
diff --git a/.ci-ignore b/.ci-ignore
@@ -6,3 +6,4 @@ Toolbox/metis-src
 Toolbox/mumps-src
 Toolbox/superlu-src
 Toolbox/superlumt-src
+Toolbox/lis-src
diff --git a/.github/.codecov.yml b/.github/.codecov.yml
@@ -19,9 +19,11 @@ ignore:
   - "Toolbox/arpack-src"
   - "Toolbox/feast-src"
   - "Toolbox/lapack-ext"
+  - "Toolbox/lis-src"
   - "Toolbox/metis-src"
   - "Toolbox/mumps-src"
   - "Toolbox/superlu-src"
   - "Toolbox/superlumt-src"
   - "Toolbox/argument.cpp"
   - "Toolbox/command.cpp"
+  - "Toolbox/tester.pardiso.cpp"
diff --git a/.github/workflows/dev-mkl-vtk.yml b/.github/workflows/dev-mkl-vtk.yml
@@ -33,8 +33,8 @@ jobs:
           ./suanPan-linux-mkl-vtk/bin/suanPan -v
       - uses: actions/upload-artifact@v3
         with:
-          name: suanPan-3.0.0-1.x86_64.deb
-          path: suanPan-3.0.0-1.x86_64.deb
+          name: suanPan-3.1.0-1.x86_64.deb
+          path: suanPan-3.1.0-1.x86_64.deb
   fedora-mkl-vtk-dev:
     runs-on: ubuntu-22.04
     timeout-minutes: 60
@@ -68,10 +68,10 @@ jobs:
           make package -j"$(nproc)"
       - name: Test
         run: |
-          dnf install ./suanPan-3.0.0-1.x86_64.rpm -y
+          dnf install ./suanPan-3.1.0-1.x86_64.rpm -y
           suanPan -v
       - name: Upload
         uses: actions/upload-artifact@v3
         with:
-          name: suanPan-3.0.0-1.x86_64.rpm
-          path: suanPan-3.0.0-1.x86_64.rpm
+          name: suanPan-3.1.0-1.x86_64.rpm
+          path: suanPan-3.1.0-1.x86_64.rpm
diff --git a/.github/workflows/dev-vtk.yml b/.github/workflows/dev-vtk.yml
@@ -30,8 +30,8 @@ jobs:
           ./suanPan-linux-openblas-vtk/bin/suanPan -v
       - uses: actions/upload-artifact@v3
         with:
-          name: suanPan-3.0.0-1.x86_64.deb
-          path: suanPan-3.0.0-1.x86_64.deb
+          name: suanPan-3.1.0-1.x86_64.deb
+          path: suanPan-3.1.0-1.x86_64.deb
   macos-openblas-vtk-dev:
     runs-on: macos-11
     timeout-minutes: 100
@@ -48,7 +48,7 @@ jobs:
         run: |
           export CC=$(brew --prefix llvm@15)/bin/clang && export CXX=$(brew --prefix llvm@15)/bin/clang++ && export FC=gfortran-11
           go build Checker/updater.go
-          brew install glfw glew libomp
+          brew install glfw glew
           cmake -DCMAKE_C_STANDARD_INCLUDE_DIRECTORIES=$(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=Debug -DBUILD_MULTITHREAD=ON -DUSE_HDF5=ON -DUSE_EXTERNAL_VTK=ON -DVTK_DIR=./lib/cmake/vtk-9.2/ -DCMAKE_INSTALL_PREFIX=suanPan-macos-openblas-vtk .
           make install -j4
       - name: Test

diff --git a/.github/workflows/dev.yml b/.github/workflows/dev.yml
@@ -39,7 +39,6 @@ jobs:
         run: |
           export CC=gcc-11 && export CXX=g++-11 && export FC=gfortran-11
           go build Checker/updater.go
-          brew install libomp
           cmake -DCMAKE_BUILD_TYPE=Debug -DUSE_HDF5=ON .
           make -j4
           export DYLD_LIBRARY_PATH=Libs/mac/

diff --git a/.github/workflows/master-mkl-vtk.yml b/.github/workflows/master-mkl-vtk.yml
@@ -24,7 +24,7 @@ jobs:
         run: |
           go build Checker/updater.go
           sudo apt-get update && sudo apt-get install mesa-common-dev mesa-utils freeglut3-dev libglvnd-dev intel-oneapi-mkl-devel dpkg-dev
-          cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_MULTITHREAD=ON -DUSE_HDF5=ON -DUSE_EXTERNAL_VTK=ON -DVTK_DIR=./lib/cmake/vtk-9.2/ -DUSE_MKL=ON -DMKLROOT=/opt/intel/oneapi/mkl/latest/ -DUSE_INTEL_OPENMP=OFF -DLINK_DYNAMIC_MKL=OFF -DCMAKE_INSTALL_PREFIX=suanPan-linux-mkl-vtk .
+          cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_MULTITHREAD=ON -DUSE_HDF5=ON -DUSE_MIMALLOC=ON -DUSE_EXTERNAL_VTK=ON -DVTK_DIR=./lib/cmake/vtk-9.2/ -DUSE_MKL=ON -DMKLROOT=/opt/intel/oneapi/mkl/latest/ -DUSE_INTEL_OPENMP=OFF -DLINK_DYNAMIC_MKL=OFF -DCMAKE_INSTALL_PREFIX=suanPan-linux-mkl-vtk .
           make install -j"$(nproc)"
           make package
       - name: Pack
@@ -33,7 +33,7 @@ jobs:
           tar czf suanPan-linux-mkl-vtk.tar.gz suanPan-linux-mkl-vtk
       - name: Test
         run: |
-          sudo apt-get install ./suanPan-3.0.0-1.x86_64.deb -y
+          sudo apt-get install ./suanPan-3.1.0-1.x86_64.deb -y
           suanPan -v
           export LD_LIBRARY_PATH=/home/runner/work/suanPan/suanPan/suanPan-linux-mkl-vtk/lib
           cd suanPan-linux-mkl-vtk/bin
@@ -51,8 +51,8 @@ jobs:
         uses: svenstaro/upload-release-action@v2
         with:
           repo_token: ${{ secrets.GITHUB_TOKEN }}
-          file: suanPan-3.0.0-1.x86_64.deb
-          asset_name: suanPan-3.0.0-1.x86_64.deb
+          file: suanPan-3.1.0-1.x86_64.deb
+          asset_name: suanPan-3.1.0-1.x86_64.deb
           tag: ${{ env.SP_TIME }}
           prerelease: true
           overwrite: true
@@ -75,7 +75,7 @@ jobs:
         run: |
           go build Checker/updater.go
           sudo apt-get update && sudo apt-get install mesa-common-dev mesa-utils freeglut3-dev libglvnd-dev intel-oneapi-mkl-devel dpkg-dev
-          cmake -DCMAKE_BUILD_TYPE=Release -DUSE_AVX=OFF -DBUILD_MULTITHREAD=ON -DUSE_HDF5=ON -DUSE_EXTERNAL_VTK=ON -DVTK_DIR=./lib/cmake/vtk-9.2/ -DUSE_MKL=ON -DMKLROOT=/opt/intel/oneapi/mkl/latest/ -DUSE_INTEL_OPENMP=OFF -DLINK_DYNAMIC_MKL=OFF -DCMAKE_INSTALL_PREFIX=suanPan-linux-mkl-vtk-no-avx .
+          cmake -DCMAKE_BUILD_TYPE=Release -DUSE_AVX=OFF -DBUILD_MULTITHREAD=ON -DUSE_HDF5=ON -DUSE_MIMALLOC=ON -DUSE_EXTERNAL_VTK=ON -DVTK_DIR=./lib/cmake/vtk-9.2/ -DUSE_MKL=ON -DMKLROOT=/opt/intel/oneapi/mkl/latest/ -DUSE_INTEL_OPENMP=OFF -DLINK_DYNAMIC_MKL=OFF -DCMAKE_INSTALL_PREFIX=suanPan-linux-mkl-vtk-no-avx .
           make install -j"$(nproc)"
           make package
       - name: Pack
@@ -124,14 +124,14 @@ jobs:
           make package -j"$(nproc)"
       - name: Test
         run: |
-          dnf install ./suanPan-3.0.0-1.x86_64.rpm -y
+          dnf install ./suanPan-3.1.0-1.x86_64.rpm -y
           suanPan -v
       - name: RPM
         uses: svenstaro/upload-release-action@v2
         with:
           repo_token: ${{ secrets.GITHUB_TOKEN }}
-          file: suanPan-3.0.0-1.x86_64.rpm
-          asset_name: suanPan-3.0.0-1.x86_64.rpm
+          file: suanPan-3.1.0-1.x86_64.rpm
+          asset_name: suanPan-3.1.0-1.x86_64.rpm
           tag: ${{ env.SP_TIME }}
           prerelease: true
           overwrite: true
diff --git a/.github/workflows/master-mkl.yml b/.github/workflows/master-mkl.yml
@@ -22,7 +22,7 @@ jobs:
         run: |
           go build Checker/updater.go
           sudo apt-get update && sudo apt-get install intel-oneapi-mkl-devel
-          cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_MULTITHREAD=ON -DUSE_HDF5=ON -DUSE_MKL=ON -DMKLROOT=/opt/intel/oneapi/mkl/latest/ -DUSE_INTEL_OPENMP=OFF -DLINK_DYNAMIC_MKL=OFF -DCMAKE_INSTALL_PREFIX=suanPan-linux-mkl .
+          cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_MULTITHREAD=ON -DUSE_HDF5=ON -DUSE_MIMALLOC=ON -DUSE_MKL=ON -DMKLROOT=/opt/intel/oneapi/mkl/latest/ -DUSE_INTEL_OPENMP=OFF -DLINK_DYNAMIC_MKL=OFF -DCMAKE_INSTALL_PREFIX=suanPan-linux-mkl .
           make install -j"$(nproc)"
       - name: Pack
         run: |

diff --git a/.github/workflows/master-vtk.yml b/.github/workflows/master-vtk.yml
@@ -22,7 +22,7 @@ jobs:
         run: |
           go build Checker/updater.go
           sudo apt-get update && sudo apt-get install mesa-common-dev mesa-utils freeglut3-dev libglvnd-dev
-          cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_MULTITHREAD=ON -DUSE_HDF5=ON -DUSE_EXTERNAL_VTK=ON -DVTK_DIR=./lib/cmake/vtk-9.2/ -DCMAKE_INSTALL_PREFIX=suanPan-linux-openblas-vtk .
+          cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_MULTITHREAD=ON -DUSE_HDF5=ON -DUSE_MIMALLOC=ON -DUSE_EXTERNAL_VTK=ON -DVTK_DIR=./lib/cmake/vtk-9.2/ -DCMAKE_INSTALL_PREFIX=suanPan-linux-openblas-vtk .
           make install -j"$(nproc)"
       - name: Pack
         run: |
@@ -56,7 +56,7 @@ jobs:
         run: |
           export CC=$(brew --prefix llvm@15)/bin/clang && export CXX=$(brew --prefix llvm@15)/bin/clang++ && export FC=gfortran-11
           go build Checker/updater.go
-          brew install glfw glew libomp
+          brew install glfw glew
           cmake -DCMAKE_C_STANDARD_INCLUDE_DIRECTORIES=$(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 -DBUILD_MULTITHREAD=ON -DUSE_HDF5=ON -DUSE_EXTERNAL_VTK=ON -DVTK_DIR=./lib/cmake/vtk-9.2/ -DCMAKE_INSTALL_PREFIX=suanPan-macos-openblas-vtk .
           make install -j4
       - name: Pack
@@ -92,7 +92,7 @@ jobs:
         run: |
           export CC=$(brew --prefix llvm@15)/bin/clang && export CXX=$(brew --prefix llvm@15)/bin/clang++ && export FC=gfortran-11
           go build Checker/updater.go
-          brew install glfw glew libomp
+          brew install glfw glew
           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_AVX=OFF -DBUILD_MULTITHREAD=ON -DUSE_HDF5=ON -DUSE_EXTERNAL_VTK=ON -DVTK_DIR=./lib/cmake/vtk-9.2/ -DCMAKE_INSTALL_PREFIX=suanPan-macos-openblas-vtk-no-avx .
           make install -j4
       - name: Pack

diff --git a/.github/workflows/master.yml b/.github/workflows/master.yml
@@ -17,7 +17,7 @@ jobs:
         run: |
           go build Checker/updater.go
           echo "SP_TIME=daily-$(date +''%Y%m%d%H'')" >> $GITHUB_ENV
-          cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_MULTITHREAD=ON -DUSE_HDF5=ON -DCMAKE_INSTALL_PREFIX=suanPan-linux-openblas .
+          cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_MULTITHREAD=ON -DUSE_HDF5=ON -DUSE_MIMALLOC=ON -DCMAKE_INSTALL_PREFIX=suanPan-linux-openblas .
           make install -j"$(nproc)"
       - name: Pack
         run: |

diff --git a/.gitignore b/.gitignore
@@ -41,6 +41,9 @@ $RECYCLE.BIN/
 /MSVC/suanPan/suanPan/x64/*
 /MSVC/suanPan/superlu/x64/*
 /MSVC/suanPan/superlumt/x64/*
+/MSVC/suanPan/solver.pardiso/x64/*
+/MSVC/suanPan/tester.pardiso/x64/*
+/MSVC/suanPan/lis/x64/*
 venv
 .cache
 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,12 @@
 2. The `SPIKE` solver may occasionally hang, to circumvent, try to avoid mixing compilers from different vendors.
 3. The `MUMPS` solver throws segfaults with large matrices.
 
+## version 3.1
+
+1. iterative solvers by the Lis library [#145](https://github.com/TLCFEM/suanPan/pull/145)
+2. update `Armadillo` to version `12.6.3` [#149](https://github.com/TLCFEM/suanPan/pull/149)
+3. add `TimberPD` 3D material for timber [#151](https://github.com/TLCFEM/suanPan/pull/151)
+
 ## version 3.0
 
 1. add experimental `MAGMA` based GPU sparse solver [#123](https://github.com/TLCFEM/suanPan/pull/123)
@@ -30,7 +36,7 @@
 
 ## version 2.8
 
-1. better on screen display with the fmt library [#99](https://github.com/TLCFEM/suanPan/pull/99)
+1. better on screen display with the `fmt` library [#99](https://github.com/TLCFEM/suanPan/pull/99)
 2. add command `overview`
 3. update `OpenBLAS` to version `0.3.21`
 4. add Euler buckling load check for `T2D2` [#104](https://github.com/TLCFEM/suanPan/pull/104)