Merge pull request #2 from sergeiNikolaev/plugin_keep_up_to_date_sofa…

…_python3_v20.12

Plugin keep up to date sofa python3 v20.12

CMakeLists.txt

@@ -13,15 +13,30 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
 find_package(SofaFramework REQUIRED)
 find_package(SofaSimulation REQUIRED)
 find_package(SofaBase REQUIRED)
-find_package(SofaGeneral REQUIRED)
-find_package(SofaMisc REQUIRED)
+find_package(SofaGeneralAnimationLoop REQUIRED)
+find_package(SofaGeneralEngine REQUIRED)
+find_package(SofaImplicitOdeSolver REQUIRED)
+find_package(SofaGeneralLinearSolver REQUIRED)
+find_package(SofaGeneralRigid REQUIRED)
+find_package(SofaSimpleFem REQUIRED)
+find_package(SofaGeneralTopology REQUIRED)
+find_package(SofaTopologyMapping REQUIRED)
+find_package(SofaUserInteraction REQUIRED)
+find_package(SofaConstraint REQUIRED)
+find_package(SofaGeneralLoader REQUIRED)
+find_package(SofaMiscEngine REQUIRED)
+find_package(SofaMiscForceField REQUIRED)
+find_package(SofaMiscMapping REQUIRED)
+find_package(SofaMiscSolver REQUIRED)
+find_package(SofaMiscTopology REQUIRED)
+find_package(SofaMiscFem REQUIRED)
 find_package(SofaExporter REQUIRED)
 find_package(SofaGui REQUIRED)
 find_package(Eigen3 3.3 REQUIRED NO_MODULE)
 
 
 include_directories(${EIGEN3_INCLUDE_DIR})
-set(LINKER_DEPENDENCIES SofaCore SofaBase SofaGeneral SofaBoundaryCondition SofaBaseTopology SofaExporter SofaSimulationTree SofaUserInteraction SofaConstraint SofaMisc 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 pthread 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)

benchmarks/assimBC_liver_geomagic_cutting_yaml/liver_geomagic_cutting_scene_SDA_bench.py

@@ -21,7 +21,7 @@ def createScene(rootNode):
     rootNode.createObject('RequiredPlugin', name='SimpleFem', pluginName='SofaSimpleFem')
     rootNode.createObject('RequiredPlugin', name='GraphComponent', pluginName='SofaGraphComponent')
     rootNode.createObject('RequiredPlugin', name='Python', pluginName='SofaPython')
-    rootNode.createObject('RequiredPlugin', pluginName='Optimus')
+    rootNode.createObject('RequiredPlugin', name='Optimus', pluginName='Optimus')
 
     try:
         sys.argv[0]

benchmarks/assimBC_liver_geomagic_cutting_yaml/verify.sh

@@ -1,9 +1,11 @@
 #!/bin/bash
 
-if [ $# == "1" ]; then
-        SOFA_EXEC="$1 -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaPython.so -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaExporter.so"
+if [ $# == "2" ]; then
+        SOFA_EXEC="$1 -l $2/libSofaPython.so -l $2/libSofaExporter.so"
+elif [ $# == "1" ]; then
+        SOFA_EXEC="$1 -l libSofaPython.so -l libSofaExporter.so"
 else
-        SOFA_EXEC="runSofa -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaPython.so -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaExporter.so"
+        SOFA_EXEC="runSofa -l libSofaPython.so -l libSofaExporter.so"
 fi
 echo "Using SOFA executable: " $SOFA_EXEC
 

benchmarks/assimBC_liver_polynomial_springs_point_cloud_yaml/verify.sh

@@ -1,9 +1,11 @@
 #!/bin/bash
 
-if [ $# == "1" ]; then
-        SOFA_EXEC="$1 -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaPython.so -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaExporter.so"
+if [ $# == "2" ]; then
+        SOFA_EXEC="$1 -l $2/libSofaPython.so -l $2/libSofaExporter.so"
+elif [ $# == "1" ]; then
+        SOFA_EXEC="$1 -l libSofaPython.so -l libSofaExporter.so"
 else
-        SOFA_EXEC="runSofa -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaPython.so -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaExporter.so"
+        SOFA_EXEC="runSofa -l libSofaPython.so -l libSofaExporter.so"
 fi
 echo "Using SOFA executable: " $SOFA_EXEC
 

benchmarks/assimBC_synthBrick/verify.sh

@@ -1,9 +1,11 @@
 #!/bin/bash
 
-if [ $# == "1" ]; then
-        SOFA_EXEC="$1 -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaPython.so -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaExporter.so"
+if [ $# == "2" ]; then
+        SOFA_EXEC="$1 -l $2/libSofaPython.so -l $2/libSofaExporter.so"
+elif [ $# == "1" ]; then
+        SOFA_EXEC="$1 -l libSofaPython.so -l libSofaExporter.so"
 else
-        SOFA_EXEC="runSofa -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaPython.so -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaExporter.so"
+        SOFA_EXEC="runSofa -l libSofaPython.so -l libSofaExporter.so"
 fi
 echo "Using SOFA executable: " $SOFA_EXEC
 

benchmarks/assimStiffness_cylinder_UKFSimCorr_yaml/verify.sh

@@ -1,9 +1,11 @@
 #!/bin/bash
 
-if [ $# == "1" ]; then
-        SOFA_EXEC="$1 -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaPython.so -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaExporter.so"
+if [ $# == "2" ]; then
+        SOFA_EXEC="$1 -l $2/libSofaPython.so -l $2/libSofaExporter.so"
+elif [ $# == "1" ]; then
+        SOFA_EXEC="$1 -l libSofaPython.so -l libSofaExporter.so"
 else
-        SOFA_EXEC="runSofa -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaPython.so -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaExporter.so"
+        SOFA_EXEC="runSofa -l libSofaPython.so -l libSofaExporter.so"
 fi
 echo "Using SOFA executable: " $SOFA_EXEC
 

benchmarks/assimStiffness_cylinder_geomagic_yaml/verify.sh

@@ -1,9 +1,11 @@
 #!/bin/bash
 
-if [ $# == "1" ]; then
-        SOFA_EXEC="$1 -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaPython.so -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaExporter.so"
+if [ $# == "2" ]; then
+        SOFA_EXEC="$1 -l $2/libSofaPython.so -l $2/libSofaExporter.so"
+elif [ $# == "1" ]; then
+        SOFA_EXEC="$1 -l libSofaPython.so -l libSofaExporter.so"
 else
-        SOFA_EXEC="runSofa -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaPython.so -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaExporter.so"
+        SOFA_EXEC="runSofa -l libSofaPython.so -l libSofaExporter.so"
 fi
 echo "Using SOFA executable: " $SOFA_EXEC
 

benchmarks/assimStiffness_cylinder_python3_yaml/verify.sh

@@ -1,9 +1,11 @@
 #!/bin/bash
 
-if [ $# == "1" ]; then
-        SOFA_EXEC="$1 -l /home/sergei/Optimus_test/plugin.SofaPython3/build_release/lib/libSofaPython3.so"
+if [ $# == "2" ]; then
+        SOFA_EXEC="$1 -l $2/libSofaPython3.so"
+elif [ $# == "1" ]; then
+        SOFA_EXEC="$1 -l libSofaPython3.so"
 else
-        SOFA_EXEC="runSofa -l /home/sergei/Optimus_test/plugin.SofaPython3/build_release/lib/libSofaPython3.so"
+        SOFA_EXEC="runSofa -l libSofaPython3.so"
 fi
 echo "Using SOFA executable: " $SOFA_EXEC
 

benchmarks/assimStiffness_cylinder_yaml/verify.sh

@@ -1,9 +1,11 @@
 #!/bin/bash
 
-if [ $# == "1" ]; then
-        SOFA_EXEC="$1 -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaPython.so -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaExporter.so"
+if [ $# == "2" ]; then
+        SOFA_EXEC="$1 -l $2/libSofaPython.so -l $2/libSofaExporter.so"
+elif [ $# == "1" ]; then
+        SOFA_EXEC="$1 -l libSofaPython.so -l libSofaExporter.so"
 else
-        SOFA_EXEC="runSofa -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaPython.so -l /home/sergei/Optimus_test/sofa/build_release/lib/libSofaExporter.so"
+        SOFA_EXEC="runSofa -l libSofaPython.so -l libSofaExporter.so"
 fi
 echo "Using SOFA executable: " $SOFA_EXEC
 

benchmarks/crontask/plugin_list.conf.default

@@ -1,46 +1,47 @@
 
-SofaSimpleFem 20.06.99
-SofaRigid 20.06.99
-SofaDeformable 20.06.99
-SofaObjectInteraction 20.06.99
-SofaMeshCollision 20.06.99
-SofaEngine 20.06.99
-SofaExplicitOdeSolver 20.06.99
-SofaImplicitOdeSolver 20.06.99
-SofaLoader 20.06.99
-SofaGeneralVisual 20.06.99
-SofaGraphComponent 20.06.99
-SofaGeneralMeshCollision 20.06.99
-SofaBoundaryCondition 20.06.99
-SofaGeneralAnimationLoop 20.06.99
-SofaGeneralDeformable 20.06.99
-SofaGeneralEngine 20.06.99
-SofaGeneralExplicitOdeSolver 20.06.99
-SofaGeneralImplicitOdeSolver 20.06.99
-SofaGeneralLinearSolver 20.06.99
-SofaGeneralRigid 20.06.99
-SofaGeneralObjectInteraction 20.06.99
-SofaGeneralSimpleFem 20.06.99
-SofaGeneralTopology 20.06.99
-SofaTopologyMapping 20.06.99
-SofaUserInteraction 20.06.99
-SofaConstraint 20.06.99
-SofaGeneralLoader 20.06.99
-SofaSparseSolver 20.06.99
-SofaPreconditioner 20.06.99
-SofaHaptics 20.06.99
-SofaValidation 20.06.99
-SofaDenseSolver 20.06.99
-SofaNonUniformFem 20.06.99
-SofaOpenglVisual 20.06.99
-SofaMiscTopology 20.06.99
-SofaMiscExtra 20.06.99
-SofaMiscForceField 20.06.99
-SofaMiscEngine 20.06.99
-SofaMiscSolver 20.06.99
-SofaMiscFem 20.06.99
-SofaMiscMapping 20.06.99
+SofaSimpleFem 20.12.00
+SofaRigid 20.12.00
+SofaDeformable 20.12.00
+SofaObjectInteraction 20.12.00
+SofaMeshCollision 20.12.00
+SofaEngine 20.12.00
+SofaExplicitOdeSolver 20.12.00
+SofaImplicitOdeSolver 20.12.00
+SofaLoader 20.12.00
+SofaGeneralVisual 20.12.00
+SofaGraphComponent 20.12.00
+SofaGeneralMeshCollision 20.12.00
+SofaBoundaryCondition 20.12.00
+SofaGeneralAnimationLoop 20.12.00
+SofaGeneralDeformable 20.12.00
+SofaGeneralEngine 20.12.00
+SofaGeneralExplicitOdeSolver 20.12.00
+SofaGeneralImplicitOdeSolver 20.12.00
+SofaGeneralLinearSolver 20.12.00
+SofaGeneralRigid 20.12.00
+SofaGeneralObjectInteraction 20.12.00
+SofaGeneralSimpleFem 20.12.00
+SofaGeneralTopology 20.12.00
+SofaTopologyMapping 20.12.00
+SofaUserInteraction 20.12.00
+SofaConstraint 20.12.00
+SofaGeneralLoader 20.12.00
+SofaSparseSolver 20.12.00
+SofaPreconditioner 20.12.00
+SofaHaptics 20.12.00
+SofaValidation 20.12.00
+SofaDenseSolver 20.12.00
+SofaNonUniformFem 20.12.00
+SofaOpenglVisual 20.12.00
+SofaMiscTopology 20.12.00
+SofaMiscExtra 20.12.00
+SofaMiscForceField 20.12.00
+SofaMiscEngine 20.12.00
+SofaMiscSolver 20.12.00
+SofaMiscFem 20.12.00
+SofaMiscMapping 20.12.00
 CImgPlugin 0.1
 SofaMiscCollision 1.0
 DiffusionSolver 0.1
 image 0.1
+CGALPlugin 0.1

benchmarks/crontask/runOptimusTests.sh

@@ -14,14 +14,16 @@ SOFA_DIRECTORY=$GENERAL_DIRECTORY/sofa
 BUILD_DIRECTORY=$GENERAL_DIRECTORY/sofa/build_release
 SOFACONFIG_DIRECTORY=$GENERAL_DIRECTORY/sofaconfig
 OPTIMUS_DIRECTORY=$GENERAL_DIRECTORY/Optimus
-PLUGIN_PYTHON3_DIRECTORY=$GENERAL_DIRECTORY/plugin.SofaPython3
-PLUGIN_PYTHON3_BUILD_DIRECTORY=$PLUGIN_PYTHON3_DIRECTORY/build_release
+OPTIMUS_BUILD_DIRECTORY=$OPTIMUS_DIRECTORY/build_release
+SOFA_PYTHON3_DIRECTORY=$GENERAL_DIRECTORY/SofaPython3
+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:$HOME_DIRECTORY/External_libraries/Pardiso
-export PYTHONPATH=$PLUGIN_PYTHON3_BUILD_DIRECTORY/lib/site-packages
+export PYTHONPATH=$SOFA_PYTHON3_BUILD_DIRECTORY/lib/site-packages
+export SOFA_PLUGIN_PATH=$OPTIMUS_BUILD_DIRECTORY
 
 
 ### checkout source code
@@ -39,6 +41,16 @@ if ! [ -d "$BUILD_DIRECTORY" ]; then
     mkdir $BUILD_DIRECTORY
 fi
 
+### checkout Python3
+if [ -d "$SOFA_PYTHON3_DIRECTORY" ]; then
+    echo "Update Python3 repository"
+    cd $SOFA_PYTHON3_DIRECTORY
+    /usr/bin/git pull --progress https://github.com/sofa-framework/SofaPython3.git 2>> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
+else
+    /usr/bin/git clone --progress https://github.com/sofa-framework/SofaPython3.git $SOFA_PYTHON3_DIRECTORY 2>> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
+    echo "Clone data from Python3 repository"
+fi
+
 ### checkout Optimus
 if [ -d "$OPTIMUS_DIRECTORY" ]; then
     echo "Update Optimus repository"
@@ -49,16 +61,6 @@ else
     echo "Clone data from Optimus repository"
 fi
 
-### checkout Python3
-if [ -d "$PLUGIN_PYTHON3_DIRECTORY" ]; then
-    echo "Update Optimus repository"
-    cd $PLUGIN_PYTHON3_DIRECTORY
-    /usr/bin/git pull --progress https://github.com/sofa-framework/plugin.SofaPython3.git 2>> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
-else
-    /usr/bin/git clone --progress https://github.com/sofa-framework/plugin.SofaPython3.git $PLUGIN_PYTHON3_DIRECTORY 2>> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
-    echo "Clone data from Optimus repository"
-fi
-
 
 ### configure and make the system
 echo "Recompile sofa sources"
@@ -68,15 +70,26 @@ cd $BUILD_DIRECTORY
 /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 from the plugins default list (use local version of list)
+### 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 "$PLUGIN_PYTHON3_BUILD_DIRECTORY" ]; then
-    mkdir $PLUGIN_PYTHON3_BUILD_DIRECTORY
+if ! [ -d "$SOFA_PYTHON3_BUILD_DIRECTORY" ]; then
+    mkdir $SOFA_PYTHON3_BUILD_DIRECTORY
+fi
+cd $SOFA_PYTHON3_BUILD_DIRECTORY
+/usr/bin/make clean
+/usr/local/bin/cmake -DSP3_BUILD_TEST=OFF -DCMAKE_PREFIX_PATH=$BUILD_DIRECTORY/install .. 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 >> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
+
+echo "Recompile Optimus plugin"
+if ! [ -d "$OPTIMUS_BUILD_DIRECTORY" ]; then
+    mkdir $OPTIMUS_BUILD_DIRECTORY
 fi
-cd $PLUGIN_PYTHON3_BUILD_DIRECTORY
+cd $OPTIMUS_BUILD_DIRECTORY
 /usr/bin/make clean
 /usr/local/bin/cmake -DCMAKE_PREFIX_PATH=$BUILD_DIRECTORY/install .. 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
@@ -93,7 +106,11 @@ do
     cd $FOLDER
     if [ -f $FOLDER/verify.sh ]; then
         echo "Perform test: $FOLDER"
-        $FOLDER/verify.sh $BUILD_DIRECTORY/bin/runSofa >> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
+        if [[ "$FOLDER" == *"python3"* ]]; then
+            $FOLDER/verify.sh $BUILD_DIRECTORY/bin/runSofa $SOFA_PYTHON3_BUILD_DIRECTORY/lib >> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
+        else
+            $FOLDER/verify.sh $BUILD_DIRECTORY/bin/runSofa $BUILD_DIRECTORY/lib >> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
+        fi
     fi
 done
 echo "All tests have been executed"

benchmarks/crontask/runOptimusTests_without_compiling.sh

@@ -15,11 +15,15 @@ BUILD_DIRECTORY=$GENERAL_DIRECTORY/sofa/build_release
 SOFACONFIG_DIRECTORY=$GENERAL_DIRECTORY/sofaconfig
 PARDISO_SOLVER_DIRECTORY=$GENERAL_DIRECTORY/SofaPardisoSolver
 OPTIMUS_DIRECTORY=$GENERAL_DIRECTORY/Optimus
+OPTIMUS_BUILD_DIRECTORY=$GENERAL_DIRECTORY/Optimus/build_release
+SOFA_PYTHON3_DIRECTORY=$GENERAL_DIRECTORY/SofaPython3
+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:$HOME_DIRECTORY/External_libraries/Pardiso
-export PYTHONPATH=$PLUGIN_PYTHON3_BUILD_DIRECTORY/lib/site-packages
+export PYTHONPATH=$SOFA_PYTHON3_BUILD_DIRECTORY/lib/site-packages
+export SOFA_PLUGIN_PATH=$OPTIMUS_BUILD_DIRECTORY
 
 
 ### verify benchmark tests
@@ -31,7 +35,11 @@ do
     cd $FOLDER
     if [ -f $FOLDER/verify.sh ]; then
         echo "Perform test: $FOLDER"
-        $FOLDER/verify.sh $BUILD_DIRECTORY/bin/runSofa >> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
+        if [[ "$FOLDER" == *"python3"* ]]; then
+            $FOLDER/verify.sh $BUILD_DIRECTORY/bin/runSofa $SOFA_PYTHON3_BUILD_DIRECTORY/lib >> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
+        else
+            $FOLDER/verify.sh $BUILD_DIRECTORY/bin/runSofa $BUILD_DIRECTORY/lib >> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
+        fi
     fi
 done
 echo "All tests have been executed"

examples/MultipleParameterIdentification/identify10YoungMods_GenObs.py

@@ -12,10 +12,17 @@
 
 
 def createScene(rootNode):
-    rootNode.createObject('RequiredPlugin', name='Optimus', pluginName='Optimus')
-    rootNode.createObject('RequiredPlugin', name='Python', pluginName='SofaPython')
+    rootNode.createObject('RequiredPlugin', name='Engine', pluginName='SofaEngine')
+    rootNode.createObject('RequiredPlugin', name='GeneralEngine', pluginName='SofaGeneralEngine')
+    rootNode.createObject('RequiredPlugin', name='ImplicitOdeSolver', pluginName='SofaImplicitOdeSolver')
+    rootNode.createObject('RequiredPlugin', name='BoundaryCondition', pluginName='SofaBoundaryCondition')
+    rootNode.createObject('RequiredPlugin', name='Loader', pluginName='SofaLoader')
+    rootNode.createObject('RequiredPlugin', name='MiscForceField', pluginName='SofaMiscForceField')
+    rootNode.createObject('RequiredPlugin', name='SimpleFem', pluginName='SofaSimpleFem')
     rootNode.createObject('RequiredPlugin', name='Exporter', pluginName='SofaExporter')
     rootNode.createObject('RequiredPlugin', name='Visual', pluginName='SofaOpenglVisual')
+    rootNode.createObject('RequiredPlugin', name='Python', pluginName='SofaPython')
+    rootNode.createObject('RequiredPlugin', name='Optimus', pluginName='Optimus')
 
     try:
         sys.argv[0]
@@ -131,7 +138,6 @@ def createGraph(self, rootNode):
         simuNode.createObject('MechanicalObject', src='@loader', name='Volume')
         simuNode.createObject('TetrahedronSetTopologyContainer', name="Container", src="@loader", tags=" ")
         simuNode.createObject('TetrahedronSetTopologyModifier', name="Modifier")
-        simuNode.createObject('TetrahedronSetTopologyAlgorithms', name="TopoAlgo")
         simuNode.createObject('TetrahedronSetGeometryAlgorithms', name="GeomAlgo")
 
         if 'total_mass' in self.opt['model'].keys():