Moving changes from dev to master (Release 2026.04)

.github/workflows/build_guide.yml

@@ -0,0 +1,39 @@
+name: build_guide
+
+# Generate sphinx docs
+
+on:
+  workflow_dispatch:
+
+jobs:
+
+  build_docs_job:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write  
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2.3.4
+
+      - name: Set up Python
+        uses: actions/setup-python@v2.2.1
+        with:
+          python-version: 3.9
+
+      - name: Install dependencies
+        run: |
+          python -m pip install -U sphinx
+          python -m pip install sphinx-rtd-theme
+          python -m pip install breathe
+          python -m pip install ghp-import
+
+      - name: make the sphinx docs
+        run: |
+          make -C docs clean
+          make -C docs html
+
+      - name: Run ghp-import
+        run: |
+          ghp-import -n -p -f ~/local/doc/build/html
+
+

.github/workflows/c-cpp.yml

@@ -1,123 +1,102 @@
 name: LBPM CI
 
 on:
+  workflow_dispatch:
   push:
-    branches: [ master ]
+    branches: [master, dev]
   pull_request:
-    branches: [ master ]
+    branches: [master, dev]
 
 jobs:
   build-and-test:
-
     runs-on: ubuntu-latest
     env:
-      LBPM_ZLIB_DIR: /home/runner/extlib/zlib
-      LBPM_HDF5_DIR: /home/runner/extlib/hdf5
-      LBPM_SILO_DIR: /home/runner/extlib/silo
-      MPI_DIR: /home/runner/.openmpi
-
-    steps:      
-    - name: download dependencies
-      run: |
-        echo $LBPM_ZLIB_DIR
-        echo $LBPM_HDF5_DIR
-        echo $LBPM_SILO_DIR
-        echo $GITHUB_PATH
-        echo $GITHUB_WORKSPACE
-
-        sudo apt-get update -y
-
-        wget https://bitbucket.org/AdvancedMultiPhysics/tpl-builder/downloads/Silo-4.10.3RC.modified.tar.gz
-        wget https://www.zlib.net/fossils/zlib-1.2.11.tar.gz
-        wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.12/src/hdf5-1.8.12.tar.gz
-        #wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.10/src/hdf5-1.8.10.tar.gz 
-
-        tar -xzvf zlib-1.2.11.tar.gz
-        tar -xzvf hdf5-1.8.12.tar.gz
-        tar -xzvf Silo-4.10.3RC.modified.tar.gz
-
-
-    - name: check out commit
-      uses: actions/checkout@v2
-      with: 
-        path: LBPM
-
+      MPI_VERSION: "4.1.8"
+      ZLIB_VERSION: "1.3.2"
+      HDF5_VERSION: "1.14.6"
 
+      MPI_DIR: ${{ github.workspace }}/deps/openmpi
+      LBPM_ZLIB_DIR: ${{ github.workspace }}/deps/zlib
+      LBPM_HDF5_DIR: ${{ github.workspace }}/hdf5
 
-    - name: install-openmpi
-      run: |
-        wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.2.tar.gz
-        tar -xvf ./openmpi-3.1.2.tar.gz
-        ./openmpi-3.1.2/configure --prefix="$HOME/.openmpi"
-        make -j
-        sudo make install
-        echo "$HOME/.openmpi/bin" >> $GITHUB_PATH
-
-
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          path: LBPM
 
-    - name: install zlib dependencies
-      run: |
-        cd zlib-1.2.11
-        ./configure --prefix=$LBPM_ZLIB_DIR
-        make
-        sudo make install
-        cd ..
+      - name: Install build tools
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install -y build-essential cmake wget tar
 
+      - name: Cache compiled deps (OpenMPI, zlib, HDF5)
+        id: cache-deps
+        uses: actions/cache@v4
+        with:
+          path: |
+            deps/openmpi
+            deps/zlib
+            deps/hdf5
+          key: ${{ runner.os }}-lbpm-deps-mpi${{ env.MPI_VERSION }}-zlib${{ env.ZLIB_VERSION }}-hdf5${{ env.HDF5_VERSION }}
+          restore-keys: |
+            ${{ runner.os }}-lbpm-deps-          
 
-    - name: install hdf5 dependencies
-      run: |
-        cd hdf5-1.8.12
-        CC=/home/runner/.openmpi/bin/mpicc  CXX=/home/runner/.openmpi/bin/mpicxx  CXXFLAGS="-fPIC -O3 -std=c++14" \
-        ./configure --prefix=$LBPM_HDF5_DIR --enable-parallel --enable-shared --with-zlib=$LBPM_ZLIB_DIR
-        make
-        sudo make install
-        cd ..
+      - name: Build OpenMPI
+        if: steps.cache-deps.outputs.cache-hit != 'true'
+        run: |
+          wget -q https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-${MPI_VERSION}.tar.gz
+          tar -xzf openmpi-${MPI_VERSION}.tar.gz
+          cd openmpi-${MPI_VERSION}
+          ./configure --prefix="${MPI_DIR}"
+          make -j
+          make install
 
+      - name: Build zlib
+        if: steps.cache-deps.outputs.cache-hit != 'true'
+        run: |
+          wget -q https://zlib.net/zlib-${ZLIB_VERSION}.tar.gz
+          tar -xzf zlib-${ZLIB_VERSION}.tar.gz
+          cd zlib-${ZLIB_VERSION}
+          ./configure --prefix="${LBPM_ZLIB_DIR}"
+          make -j
+          make install
 
-    - name: install silo dependencies
-      run: |
-        cd Silo-4.10.3RC.modified
-        CC=$MPI_DIR/bin/mpicc  CXX=$MPI_DIR/bin/mpicxx CXXFLAGS="-fPIC -O3 -std=c++14" \
-        ./configure --prefix=$LBPM_SILO_DIR -with-hdf5="$LBPM_HDF5_DIR/include,$LBPM_HDF5_DIR/lib" --enable-static
-        make 
-        sudo make install
-        cd ..
-
-
-    - name: configure cmake
-      run: |
-        mkdir build
-        cd build
-        rm -rf CMake*      
-        cmake                                           \
-        -D CMAKE_BUILD_TYPE:STRING=Release          \
-        -D CMAKE_C_COMPILER:PATH=$MPI_DIR/bin/mpicc              \
-        -D CMAKE_CXX_COMPILER:PATH=$MPI_DIR/bin/mpicxx           \
-        -D MPI_CXX_COMPILER=$MPI_DIR/bin/mpicxx            \
-        -D CMAKE_C_FLAGS="-fPIC"                    \
-        -D CMAKE_CXX_FLAGS="-fPIC"                  \
-        -D CMAKE_CXX_STD=14                         \
-        -D TEST_MAX_PROCS=1    \
-        -D USE_TIMER=0                              \
-          -D TIMER_DIRECTORY=$LBPM_TIMER_DIR     \
-        -D USE_NETCDF=0                             \
-          -D NETCDF_DIRECTORY=$LBPM_NETCDF_DIR   \
-        -D USE_SILO=0                               \
-          -D HDF5_DIRECTORY=$LBPM_HDF5_DIR         \
-          -D SILO_DIRECTORY=$LBPM_SILO_DIR         \
-        -D USE_CUDA=0                               \
-        $GITHUB_WORKSPACE/LBPM
+      - name: Build HDF5 (parallel)
+        if: steps.cache-deps.outputs.cache-hit != 'true'
+        run: |
+          wget -q https://sourceforge.net/projects/hdf5.mirror/files/hdf5_${HDF5_VERSION}/hdf5-${HDF5_VERSION}.tar.gz/download -O hdf5-${HDF5_VERSION}.tar.gz
+          tar -xzf hdf5-${HDF5_VERSION}.tar.gz
+          cd hdf5-${HDF5_VERSION}
+          CC="${MPI_DIR}/bin/mpicc" CXX="${MPI_DIR}/bin/mpicxx" CXXFLAGS="-fPIC -O3 -std=c++14" \
+            ./configure --prefix="${LBPM_HDF5_DIR}" --enable-parallel --enable-shared --with-zlib="${LBPM_ZLIB_DIR}"
+          make -j
+          make install
+
+      # Ensure the cached/restored MPI is on PATH
+      - name: Add MPI to PATH
+        run: echo "${MPI_DIR}/bin" >> $GITHUB_PATH          
 
-
+      - name: Configure CMake
+        run: |
+          cmake -S LBPM -B build \
+            -D USE_SILO=0 \
+            -D USE_TIMER=0 \
+            -D USE_CUDA=0 \
+            -D CMAKE_BUILD_TYPE=Release \
+            -D CMAKE_C_COMPILER:PATH="${MPI_DIR}/bin/mpicc" \
+            -D CMAKE_CXX_COMPILER:PATH="${MPI_DIR}/bin/mpicxx" \
+            -D MPI_CXX_COMPILER="${MPI_DIR}/bin/mpicxx" \
+            -D CMAKE_C_FLAGS="-fPIC" \
+            -D CMAKE_CXX_FLAGS="-fPIC" \
+            -D CMAKE_CXX_STD=14 \
+            -D TEST_MAX_PROCS=1 \
+            -D HDF5_DIRECTORY="${LBPM_HDF5_DIR}"
 
-    - name: build and make
-      run: |
-        cd build
-        make
-        sudo make install
-        cd ..
-
-    - name: tests
-      run: |
-        cd build
-        ctest
+      - name: build and make
+        run: |
+          cd build
+          make install
+
+      - name: tests
+        run: |
+          ctest --test-dir build --output-on-failure

IO/Mesh.cpp

@@ -598,6 +598,8 @@ std::string getString( FileFormat type )
         return "silo";
     else if ( type == FileFormat::HDF5 )
         return "hdf5";
+    else if ( type == FileFormat::VTK )
+        return "vtk";
     else
         ERROR( "Invalid type" );
     return "";

IO/Mesh.h

@@ -24,7 +24,7 @@ enum class VariableType {
 };
 enum class DataType { Double, Float, Int, Null };
 enum class MeshType { PointMesh, SurfaceMesh, VolumeMesh, Unknown };
-enum class FileFormat { OLD, NEW, NEW_SINGLE, SILO, HDF5 };
+enum class FileFormat { OLD, NEW, NEW_SINGLE, SILO, HDF5 , VTK};
 
 
 //! Convert enums to/from strings (more future-proof than static_cast<int>)

IO/Reader.cpp

@@ -5,6 +5,7 @@
 #include "IO/MeshDatabase.h"
 #include "IO/silo.h"
 #include "common/Utilities.h"
+#include "IO/silo.h"
 
 #include <ProfilerApp.h>
 #include <cstdio>