Merge pull request #11 from sergeiNikolaev/v21.06

UPDATE: plugin up to date with Sofa v21.06

.github/workflows/ubuntu.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-18.04]
-        python-version: [3.7]
+        python-version: ['3.10']
     env:
       SOFA_ROOT_DIRECTORY: /opt/sofa
       SOFA_BUILD_DIRECTORY: /opt/sofa/build_release
@@ -31,13 +31,13 @@ jobs:
 
       - name: Install requirements
         run: |
-          sudo apt install -qq libeigen3-dev libboost-all-dev libpthread-stubs0-dev libblas-dev freeglut3 freeglut3-dev libglew-dev
+          sudo apt install -qq libeigen3-dev libboost-all-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
+          git clone -b v2.8 --depth 1 https://github.com/pybind/pybind11.git /tmp/pybind11
           cd /tmp/pybind11
           cmake -DPYBIND11_TEST=OFF .
           cmake -DPYBIND11_TEST=OFF .
@@ -50,7 +50,7 @@ jobs:
 
       - name: Build SOFA
         run: |
-          git clone --branch v20.12 https://github.com/sofa-framework/sofa.git $SOFA_ROOT_DIRECTORY
+          git clone --branch v21.06 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 ..
@@ -63,7 +63,7 @@ jobs:
 
       - name: Build python3 plugin
         run: |
-          git clone --branch v20.12 https://github.com/sofa-framework/SofaPython3.git $SOFA_PYTHON3_DIRECTORY
+          git clone --branch v21.06 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 ..

CMakeLists.txt

@@ -36,7 +36,7 @@ find_package(Eigen3 3.3 REQUIRED NO_MODULE)
 
 
 include_directories(${EIGEN3_INCLUDE_DIR})
-set(LINKER_DEPENDENCIES SofaCore SofaBase SofaGeneralAnimationLoop SofaGeneralEngine SofaImplicitOdeSolver SofaGeneralLinearSolver SofaGeneralRigid SofaBoundaryCondition SofaBaseTopology SofaExporter SofaUserInteraction SofaConstraint SofaSimpleFem SofaGeneralTopology SofaTopologyMapping SofaUserInteraction SofaConstraint SofaGeneralLoader SofaMiscEngine SofaMiscFem SofaMiscForceField SofaMiscMapping SofaMiscSolver SofaMiscTopology SofaGuiCommon blas pthread Eigen3::Eigen)
+set(LINKER_DEPENDENCIES SofaCore SofaBase SofaGeneralAnimationLoop SofaGeneralEngine SofaImplicitOdeSolver SofaGeneralLinearSolver SofaGeneralRigid SofaBoundaryCondition SofaBaseTopology SofaExporter SofaUserInteraction SofaConstraint SofaSimpleFem SofaGeneralTopology SofaTopologyMapping SofaUserInteraction SofaConstraint SofaGeneralLoader SofaMiscEngine SofaMiscFem SofaMiscForceField SofaMiscMapping SofaMiscSolver SofaMiscTopology SofaGuiCommon blas Eigen3::Eigen)
 set(COMPILATION_FLAGS "-DSOFA_BUILD_OPTIMUS -Wno-unused-local-typedef -Wno-deprecated")
 
 set(STOCHASTIC_FILTERING "1" CACHE BOOL "Set to activate the compilation of the filtering module" FORCE)
@@ -168,7 +168,7 @@ add_library(${PROJECT_NAME} SHARED ${HEADER_FILES} ${SOURCE_FILES} ${README_FILE
 if(SofaPardisoSolver_FOUND)
     set(LINKER_DEPENDENCIES ${LINKER_DEPENDENCIES} SofaPardisoSolver)
 else()
-    message("SofaPardisoSolver not found, some scenes may not work")
+    message("SofaPardisoSolver not found, PardisoSolver component will not work")
 endif()
 
 target_include_directories(${PROJECT_NAME} PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}")

ReadMe.md

@@ -24,7 +24,7 @@ In order to obtain the plugin, it is necessary to perform git clone of the plugi
 Requirements
 ------------
 
-Except for SOFA, the plugin dependencies are BLAS, Eigen, pthread. It is highly recommended to use Pardiso solver with Optimus, as other solvers in SOFA are less reliable and might impact the estimation.
+Except for SOFA, the plugin dependencies are Eigen and BLAS. It is highly recommended to use Pardiso solver with Optimus, as other solvers in SOFA are less reliable and might impact the estimation.
 
 
 In-tree build

benchmarks/assimBC_synthBrick/assimBC_synthBrick_GenObs.py

@@ -15,6 +15,7 @@ def createScene(rootNode):
     rootNode.addObject('RequiredPlugin', name='Deformable', pluginName='SofaDeformable')
     rootNode.addObject('RequiredPlugin', name='MeshCollision', pluginName='SofaMeshCollision')
     rootNode.addObject('RequiredPlugin', name='Loader', pluginName='SofaLoader')
+    rootNode.addObject('RequiredPlugin', name='Exporter', pluginName='SofaExporter')
     rootNode.addObject('RequiredPlugin', name='Visual', pluginName='SofaOpenglVisual')
     # rootNode.addObject('RequiredPlugin', name='Python3', pluginName='SofaPython3')
     rootNode.addObject('RequiredPlugin', name='Optimus', pluginName='Optimus')

benchmarks/assimStiffness_cylinder_geomagic_yaml/cyl3PartsGeomagic_GenObs_bench.py

@@ -17,7 +17,7 @@ def createScene(rootNode):
     rootNode.addObject('RequiredPlugin', name='GeneralImplicitOdeSolver', pluginName='SofaGeneralImplicitOdeSolver')
     rootNode.addObject('RequiredPlugin', name='SparseSolver', pluginName='SofaSparseSolver')
     rootNode.addObject('RequiredPlugin', name='BoundaryCondition', pluginName='SofaBoundaryCondition')
-    rootNode.addObject('RequiredPlugin', name='Loader', pluginName='SofaLoader')
+    rootNode.addObject('RequiredPlugin', name='DataLoader', pluginName='SofaLoader')
     rootNode.addObject('RequiredPlugin', name='MiscForceField', pluginName='SofaMiscForceField')
     rootNode.addObject('RequiredPlugin', name='Rigid', pluginName='SofaRigid')
     rootNode.addObject('RequiredPlugin', name='SimpleFem', pluginName='SofaSimpleFem')

benchmarks/assimStiffness_cylinder_python3_yaml/cyl3PartsConstForce_GenObs_bench.py

@@ -12,7 +12,16 @@
 
 
 def createScene(rootNode):
-    rootNode.addObject('RequiredPlugin', name='SofaGeneralEngine')
+    rootNode.addObject('RequiredPlugin', name='GeneralEngine', pluginName='SofaGeneralEngine')
+    rootNode.addObject('RequiredPlugin', name='Engine', pluginName='SofaEngine')
+    rootNode.addObject('RequiredPlugin', name='BoundaryCondition', pluginName='SofaBoundaryCondition')
+    rootNode.addObject('RequiredPlugin', name='ImplicitOdeSolver', pluginName='SofaImplicitOdeSolver')
+    rootNode.addObject('RequiredPlugin', name='SparseSolver', pluginName='SofaSparseSolver')
+    rootNode.addObject('RequiredPlugin', name='MiscForceField', pluginName='SofaMiscForceField')
+    rootNode.addObject('RequiredPlugin', name='SimpleFem', pluginName='SofaSimpleFem')
+    rootNode.addObject('RequiredPlugin', name='Deformable', pluginName='SofaDeformable')
+    rootNode.addObject('RequiredPlugin', name='Loader', pluginName='SofaLoader')
+    rootNode.addObject('RequiredPlugin', name='Visual', pluginName='SofaOpenglVisual')
     rootNode.addObject('RequiredPlugin', name='Optimus', pluginName='Optimus')
     # rootNode.addObject('RequiredPlugin', name='Python3', pluginName='SofaPython3')
 

benchmarks/assimStiffness_cylinder_python3_yaml/cyl3PartsConstForce_SDA_bench.py

@@ -13,7 +13,15 @@
 
 
 def createScene(rootNode):
-    rootNode.addObject('RequiredPlugin', name='SofaGeneralEngine')
+    rootNode.addObject('RequiredPlugin', name='GeneralEngine', pluginName='SofaGeneralEngine')
+    rootNode.addObject('RequiredPlugin', name='Engine', pluginName='SofaEngine')
+    rootNode.addObject('RequiredPlugin', name='BoundaryCondition', pluginName='SofaBoundaryCondition')
+    rootNode.addObject('RequiredPlugin', name='ImplicitOdeSolver', pluginName='SofaImplicitOdeSolver')
+    rootNode.addObject('RequiredPlugin', name='SparseSolver', pluginName='SofaSparseSolver')
+    rootNode.addObject('RequiredPlugin', name='MiscForceField', pluginName='SofaMiscForceField')
+    rootNode.addObject('RequiredPlugin', name='SimpleFem', pluginName='SofaSimpleFem')
+    rootNode.addObject('RequiredPlugin', name='Deformable', pluginName='SofaDeformable')
+    rootNode.addObject('RequiredPlugin', name='Loader', pluginName='SofaLoader')
     rootNode.addObject('RequiredPlugin', name='Optimus', pluginName='Optimus')
     # rootNode.addObject('RequiredPlugin', name='Python3', pluginName='SofaPython3')
 

benchmarks/assimStiffness_cylinder_yaml/AppliedForces_SDA_bench.py

@@ -17,6 +17,7 @@ def createScene(rootNode):
     rootNode.addObject('RequiredPlugin', name='BoundaryCondition', pluginName='SofaBoundaryCondition')
     rootNode.addObject('RequiredPlugin', name='SLoader', pluginName='SofaLoader')
     rootNode.addObject('RequiredPlugin', name='SimpleFem', pluginName='SofaSimpleFem')
+    rootNode.addObject('RequiredPlugin', name='Exporter', pluginName='SofaExporter')
     rootNode.addObject('RequiredPlugin', name='GraphComponent', pluginName='SofaGraphComponent')
     # rootNode.addObject('RequiredPlugin', name='Python3', pluginName='SofaPython3')
     rootNode.addObject('RequiredPlugin', name='Optimus', pluginName='Optimus')

benchmarks/crontask/runOptimusTests.sh

@@ -22,7 +22,8 @@ SOFA_PYTHON3_BUILD_DIRECTORY=$SOFA_PYTHON3_DIRECTORY/build_release
 ### export pardiso license
 export PARDISO_LIC_PATH=$HOME_DIRECTORY/External_libraries/Pardiso
 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME_DIRECTORY/External_libraries/Pardiso
-export PYTHONPATH=$SOFA_PYTHON3_BUILD_DIRECTORY/lib/site-packages
+export SOFA_ROOT=$BUILD_DIRECTORY/install
+export PYTHONPATH=$SOFA_PYTHON3_BUILD_DIRECTORY/lib/python3/site-packages
 export SOFA_PLUGIN_PATH=$OPTIMUS_BUILD_DIRECTORY
 
 
@@ -66,15 +67,10 @@ fi
 echo "Recompile sofa sources"
 cd $BUILD_DIRECTORY
 /usr/bin/make clean
-/usr/local/bin/cmake -DSOFA_BUILD_TESTS=ON -DSOFAGUI_BUILD_TESTS=ON -DSOFA_EXTERNAL_DIRECTORIES=/home/sergei/Optimus_test/sofaconfig/sergei .. 2>&1 >> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
+/usr/local/bin/cmake .. 2>&1 >> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
 /usr/bin/make -B -j 8 2>&1 >> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
 /usr/bin/make install 2>&1 >> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
 
-### remove SofaPython plugin with python2 from the plugins default list (use local version of list)
-cp $OPTIMUS_DIRECTORY/benchmarks/crontask/plugin_list.conf.default $BUILD_DIRECTORY/lib/plugin_list.conf.default
-cp $OPTIMUS_DIRECTORY/benchmarks/crontask/plugin_list.conf.default $BUILD_DIRECTORY/install/lib/plugin_list.conf.default
-
-
 echo "Recompile python3 plugin"
 if ! [ -d "$SOFA_PYTHON3_BUILD_DIRECTORY" ]; then
     mkdir $SOFA_PYTHON3_BUILD_DIRECTORY
@@ -106,7 +102,7 @@ do
     cd $FOLDER
     if [ -f $FOLDER/verify.sh ]; then
         echo "Perform test: $FOLDER"
-        $FOLDER/verify.sh $BUILD_DIRECTORY/bin/runSofa $SOFA_PYTHON3_BUILD_DIRECTORY/lib >> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
+        $FOLDER/verify.sh $BUILD_DIRECTORY/install/bin/runSofa $SOFA_PYTHON3_BUILD_DIRECTORY/lib >> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
     fi
 done
 echo "All tests have been executed"

benchmarks/crontask/runOptimusTests_without_compiling.sh

@@ -22,7 +22,8 @@ SOFA_PYTHON3_BUILD_DIRECTORY=$SOFA_PYTHON3_DIRECTORY/build_release
 ### export pardiso license
 export PARDISO_LIC_PATH=$HOME_DIRECTORY/External_libraries/Pardiso
 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME_DIRECTORY/External_libraries/Pardiso
-export PYTHONPATH=$SOFA_PYTHON3_BUILD_DIRECTORY/lib/site-packages
+export SOFA_ROOT=$BUILD_DIRECTORY/install
+export PYTHONPATH=$SOFA_PYTHON3_BUILD_DIRECTORY/lib/python3/site-packages
 export SOFA_PLUGIN_PATH=$OPTIMUS_BUILD_DIRECTORY
 
 
@@ -35,7 +36,7 @@ do
     cd $FOLDER
     if [ -f $FOLDER/verify.sh ]; then
         echo "Perform test: $FOLDER"
-        $FOLDER/verify.sh $BUILD_DIRECTORY/bin/runSofa $SOFA_PYTHON3_BUILD_DIRECTORY/lib >> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
+        $FOLDER/verify.sh $BUILD_DIRECTORY/install/bin/runSofa $SOFA_PYTHON3_BUILD_DIRECTORY/lib >> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
     fi
 done
 echo "All tests have been executed"

src/genericComponents/AddNoiseEngine.cpp

@@ -27,6 +27,7 @@
 //#include <sofa/helper/accessor.h>
 
 
+
 namespace sofa
 {
 
@@ -36,8 +37,6 @@ namespace component
 namespace engine
 {
 
-using namespace defaulttype;
-
 
 
 SOFA_DECL_CLASS(AddNoiseEngine)
@@ -50,6 +49,7 @@ int AddNoiseEngineClass = core::RegisterObject("AddNoiseEngine")
 template class AddNoiseEngine<defaulttype::Vec3Types>;
 
 
+
 } // namespace engine
 
 } // namespace component

src/genericComponents/AddNoiseEngine.h

@@ -30,12 +30,12 @@
 #include <sofa/simulation/AnimateEndEvent.h>
 #include <sofa/simulation/AnimateBeginEvent.h>
 
-#include <sofa/defaulttype/Mat.h>
-#include <sofa/defaulttype/Vec.h>
+#include <sofa/type/Mat.h>
+#include <sofa/type/Vec.h>
 
 #include <sofa/core/topology/Topology.h>
 #include <sofa/helper/AdvancedTimer.h>
-#include <sofa/helper/gl/template.h>
+#include <sofa/gl/template.h>
 
 #include <random>
 #include <chrono>
@@ -64,7 +64,7 @@ class AddNoiseEngine : public sofa::core::DataEngine
     typedef typename DataTypes::Coord Coord;
     typedef typename DataTypes::Deriv Deriv;
     typedef typename DataTypes::Real Real;
-    typedef typename sofa::defaulttype::Vec3d Vector3;
+    typedef typename sofa::type::Vec3d Vector3;
     typedef sofa::core::topology::Topology::Edge Edge;
 
     AddNoiseEngine();

src/genericComponents/CorrectionForceField.cpp

@@ -21,9 +21,11 @@
 ******************************************************************************/
 
 #include "genericComponents/CorrectionForceField.inl"
-#include <sofa/core/visual/DrawTool.h>
+#include <sofa/helper/visual/DrawTool.h>
 #include <sofa/core/ObjectFactory.h>
 
+
+
 namespace sofa
 {
 
@@ -36,13 +38,13 @@ namespace forcefield
 
 SOFA_DECL_CLASS(CorrectionForceField)
 
-
 int CorrectionForceFieldClass = core::RegisterObject("Simple elastic springs applied to given degrees of freedom between their current and rest shape position")
     .add< CorrectionForceField<defaulttype::Rigid3Types> >()
     .add< CorrectionForceField<defaulttype::Vec3Types> >()
     ;
 
 
+
 } // namespace forcefield
 
 } // namespace component

src/genericComponents/CorrectionForceField.h

@@ -65,24 +65,27 @@ class CorrectionForceField : public core::behavior::ForceField<DataTypes>
     typedef typename DataTypes::CPos CPos;
     typedef typename DataTypes::Deriv Deriv;
     typedef typename DataTypes::Real Real;
-    typedef helper::vector< unsigned int > VecIndex;
-    typedef helper::vector< Real >	 VecReal;
+    typedef type::vector< unsigned int > VecIndex;
+    typedef type::vector< Real > VecReal;
     typedef sofa::component::topology::PointSubsetData< VecIndex > SetIndex;
 
     typedef core::objectmodel::Data<VecCoord> DataVecCoord;
     typedef core::objectmodel::Data<VecDeriv> DataVecDeriv;
 
 
     Data< Deriv > d_force;
-    SetIndex                   d_indices;
-    Data< VecDeriv >           d_forces;
-    Data<helper::vector<double>> d_Optimforces;
-    Data<double>         d_delta;
-    Data<double>         d_paramF;
+    SetIndex d_indices;
+    Data< VecDeriv > d_forces;
+    Data< type::vector<double> > d_Optimforces;
+    Data< double > d_delta;
+    Data< double > d_paramF;
 
+    type::vector<bool> m_active;
+
+
+protected:
+    CorrectionForceField();
 
-    protected:
-        CorrectionForceField();
 public:
     /// BaseObject initialization method.
     void bwdInit() override;
@@ -101,15 +104,10 @@ class CorrectionForceField : public core::behavior::ForceField<DataTypes>
         return 0.0;
     }
 
-
     virtual void draw(const core::visual::VisualParams* /* vparams */) override;
-     void plusF();
-     void minusF();
+    void plusF();
+    void minusF();
     void handleEvent(sofa::core::objectmodel::Event *event) override;
-
-    helper::vector<bool> m_active;
-
-
 };