Merge pull request #10 from sergeiNikolaev/main

Base automatic script for benchmark tests and documentation.

.github/workflows/ubuntu.yml

@@ -0,0 +1,101 @@
+name: Benchmark_tests_Ubuntu
+
+on:
+  schedule:
+    - cron:  '00 2 * * *'
+
+  workflow_dispatch:
+
+jobs:
+  build_and_test:
+    name: Building on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-18.04]
+        python-version: [3.7]
+    env:
+      SOFA_ROOT_DIRECTORY: /opt/sofa
+      SOFA_BUILD_DIRECTORY: /opt/sofa/build_release
+      SOFA_PYTHON3_DIRECTORY: /opt/SofaPython3
+      SOFA_PYTHON3_BUILD_DIRECTORY: /opt/SofaPython3/build_release
+
+    steps:
+      - name: Checkout source code
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install requirements
+        run: |
+          sudo apt install -qq libeigen3-dev libboost-all-dev libpthread-stubs0-dev libblas-dev freeglut3 freeglut3-dev libglew-dev
+          python3 -m pip install --upgrade pip
+          python3 -m pip install numpy pyyaml
+
+      - name: Build pybind11
+        run: |
+          git clone -b v2.4 --depth 1 https://github.com/pybind/pybind11.git /tmp/pybind11
+          cd /tmp/pybind11
+          cmake -DPYBIND11_TEST=OFF .
+          cmake -DPYBIND11_TEST=OFF .
+          make
+
+      - name: Install pybind11
+        run: |
+          cd /tmp/pybind11
+          sudo make install
+
+      - name: Build SOFA
+        run: |
+          git clone --branch v20.12 https://github.com/sofa-framework/sofa.git $SOFA_ROOT_DIRECTORY
+          mkdir $SOFA_BUILD_DIRECTORY
+          cd $SOFA_BUILD_DIRECTORY
+          cmake -DSOFAGUI_QGLVIEWER=OFF -DSOFAGUI_QT=OFF -DSOFAGUI_QTVIEWER=OFF ..
+          make -j 8
+
+      - name: Install SOFA
+        run: |
+          cd $SOFA_BUILD_DIRECTORY
+          sudo make install
+
+      - name: Build python3 plugin
+        run: |
+          git clone --branch v20.12 https://github.com/sofa-framework/SofaPython3.git $SOFA_PYTHON3_DIRECTORY
+          mkdir $SOFA_PYTHON3_BUILD_DIRECTORY
+          cd $SOFA_PYTHON3_BUILD_DIRECTORY
+          cmake -DCMAKE_PREFIX_PATH=$SOFA_BUILD_DIRECTORY/install ..
+          make -j 8
+
+      - name: Install python3 plugin
+        run: |
+          cd $SOFA_PYTHON3_BUILD_DIRECTORY
+          sudo make install
+      
+      - name: Build Optimus
+        run: |
+          mkdir $GITHUB_WORKSPACE/build_release
+          cd $GITHUB_WORKSPACE/build_release
+          cmake -DCMAKE_PREFIX_PATH=$SOFA_BUILD_DIRECTORY/install ..
+          make -j 8
+        
+      - name: Install Optimus
+        run: |
+          cd $GITHUB_WORKSPACE/build_release
+          sudo make install
+
+      - name: Optimus tests
+        run: |
+          export LD_LIBRARY_PATH=$GITHUB_WORKSPACE/build_release
+          export SOFA_PLUGIN_PATH=$GITHUB_WORKSPACE/build_release
+          FOLDER_LIST=`find $GITHUB_WORKSPACE/benchmarks -maxdepth 1`
+          for FOLDER in $FOLDER_LIST; do
+              if [ -f $FOLDER/verify.sh ]; then
+                  cd $FOLDER
+                  echo "Perform test: $FOLDER"
+                  $FOLDER/verify.sh $SOFA_BUILD_DIRECTORY/bin/runSofa $SOFA_PYTHON3_BUILD_DIRECTORY/lib
+              fi
+          done
+          echo "All tests have been executed"

ReadMe.md

@@ -153,7 +153,7 @@ Compilation of these components must be activated by CMake macro STOCHASTIC_FILT
 -   Main methods are initializeStep(), computePrediction() and computeCorrection(), all called by the FilteringAnimationLoop.
 
 
-`EnTKFilter`
+`ETKFilter`
 
 -   Ensemble Transform Kalman filter. Its description is given in Axel Hutt (2020) "Divergence of the ensemble transform kalman filter by nonlocal observations". Instead of sigma points the transformation are performed with Ensemble members.
 

benchmarks/assimBC_liver_geomagic_cutting_yaml/liver_geomagic_cutting_scene_config_bench.yml

@@ -9,7 +9,7 @@ general_parameters:
     density: 200 # total_mass: 0.2
     delta_time: 0.01
     solver_kind: "Euler"   # options are "Euler", "Newton", and "Symplectic"
-    linear_solver_kind: "Pardiso"   # options are "CG", "Pardiso", and "LDL"
+    linear_solver_kind: "LDL"   # options are "CG", "Pardiso", and "LDL"
     rayleigh_mass: 0.1
     rayleigh_stiffness: 0.1
     boundary_conditions_list:

benchmarks/assimBC_liver_polynomial_springs_point_cloud_yaml/liver_nonlinear_BC_point_cloud_scene_config_bench.yml

@@ -12,7 +12,7 @@ general_parameters:
         &time
         0.001
     solver_kind: "Euler"   # options are "Euler", "Newton", and "Symplectic"
-    linear_solver_kind: "Pardiso"   # options are "CG", "Pardiso", and "LDL"
+    linear_solver_kind: "LDL"   # options are "CG", "Pardiso", and "LDL"
     rayleigh_mass: 0.1
     rayleigh_stiffness: 0.1
 

benchmarks/assimStiffness_cylinder_UKFSimCorr_yaml/cylConstForce_scene_config_bench.yml

@@ -9,7 +9,7 @@ general_parameters:
     density: 200 # total_mass: 0.2
     delta_time: 0.01
     solver_kind: "Euler"   # options are "Euler", "Newton", and "Symplectic"
-    linear_solver_kind: "Pardiso"   # options are "CG", "Pardiso", and "LDL"
+    linear_solver_kind: "LDL"   # options are "CG", "Pardiso", and "LDL"
     rayleigh_mass: 20.1
     rayleigh_stiffness: 0.1
     boundary_conditions_list:

benchmarks/assimStiffness_cylinder_geomagic_yaml/cyl3PartsRestShape_scene_config_bench.yml

@@ -10,7 +10,7 @@ general_parameters:
     delta_time: 0.01
     solver_kind: "Symplectic"   # options are "Euler", "Newton", and "Symplectic"
     da_solver_kind: "Euler"   # options are "Euler", "Newton", and "Symplectic"
-    linear_solver_kind: "Pardiso"   # options are "CG", "Pardiso", and "LDL"
+    linear_solver_kind: "LDL"   # options are "CG", "Pardiso", and "LDL"
     rayleigh_mass: 0.1
     rayleigh_stiffness: 0.1
     boundary_conditions_list:

benchmarks/assimStiffness_cylinder_python3_yaml/cyl3PartsConstForce_scene_config_bench.yml

@@ -9,7 +9,7 @@ general_parameters:
     density: 200 # total_mass: 0.2
     delta_time: 0.01
     solver_kind: "Euler"   # options are "Euler", "Newton", and "Symplectic"
-    linear_solver_kind: "Pardiso"   # options are "CG", "Pardiso", and "LDL"
+    linear_solver_kind: "LDL"   # options are "CG", "Pardiso", and "LDL"
     rayleigh_mass: 0.12
     rayleigh_stiffness: 0.1
     boundary_conditions_list:

benchmarks/assimStiffness_cylinder_yaml/cyl10_appliedGravity_bench.yml

@@ -11,7 +11,7 @@ model:
 
     int:   # temporal integrator properties
         type: 'Euler'
-        linear_type: "Pardiso"   # options are "CG", "Pardiso", and "LDL"
+        linear_type: "LDL"   # options are "CG", "Pardiso", and "LDL"
         rmass: 0.1
         rstiff: 3
         maxit: 1

doc/OptimusDoc/ConceptsBehindOptimus.tex → doc/OptimusTEX/ConceptsBehindOptimus.tex

@@ -196,7 +196,7 @@ \section{Components}
 \item Main methods are initializeStep(), computePrediction() and computeCorrection(), all called by the \al.
 \end{itemize}
 \medskip
-{\large \entkf}
+{\large \etkf}
 \begin{itemize}
 \item Ensemble Transform Kalman filter described in~\cite{HuttDivergenceOfTheEnsembleTransformKalmanFilter2020}. Instead of sigma points the transformation are performed with Ensemble members.
 \item Main methods are initializeStep(), computePrediction() and computeCorrection(), all called by the \al.

doc/OptimusDoc/macros.tex → doc/OptimusTEX/macros.tex

@@ -32,6 +32,6 @@
 \newcommand{\ukf}{\texttt{UKFilter}}
 \newcommand{\roukf}{\texttt{ROUKFilter}}
 \newcommand{\ukfsc}{\texttt{UKFilterSimCorr}}
-\newcommand{\entkf}{\texttt{EnTKFilter}}
+\newcommand{\etkf}{\texttt{ETKFilter}}
 \newcommand{\opr}{\texttt{OptimParams}}
 \newcommand{\mobs}{\texttt{MappedStateObservationManager}}