Free memory when running multiple simulations from same python script

[etagliabue]

Hi everyone,

I am trying to run a set of sequential simulations from the same python3 script. The basic structure of my main .py file looks like:

import Sofa, Sofa.Core
# do something at the beginning

# initialize first simulation
root = Sofa.Core.Node("root")
root.addObject( myFirstSofaCoreController )
Sofa.Simulation.init(root)

# run 10 simulation steps
for i in range(10):
    Sofa.Simulation.animate(root, root.dt.value)

# Here I need to clear all simulation-related stuff

# initialize second simulation
root = Sofa.Core.Node("root")
root.addObject( mySecondSofaCoreController )
Sofa.Simulation.init(root)

# run 10 simulation steps
for i in range(10):
    Sofa.Simulation.animate(root, root.dt.value)

# other simulations...

# do other stuff

Basically, I just need to run 10 steps for each simulation. Once those steps are done, I do not need any simulation-related variable anymore. Thus, I would like to delete all the simulation-related stuff after those 10 simulation steps, and free the memory. This does not happen at the moment, because cleanup is never called. I tried both to delete root and to call Sofa.Simulation.unload(root), but none of them does what I need.

Is there a way to force the cleanup and free all the simulation-related memory in python? I would like to avoid running each simulation within a different runsofa/python process in order to ensure that.

I am using SOFA 21.12 with python3.8 on Ubuntu 20.04.
Thanks in advance for any suggestion!

[hugtalbot]

Oh oh oh @etagliabue :) good to have you back here!

For such a question @damienmarchal would be the man.

[damienmarchal]

Hello, Sorry for the late reply.

Normally it should work and do cleaning as long as there is no reference pointing to the objects.
But the dual implmentation of reference counting in both Sofa and Python is rather complex so I need more time to check what is actually happening.

In any case, thank @etagliabue for providing an example.

[hugtalbot]

did you have time to investigate this @damienmarchal ?

[etagliabue]

I have investigated this a little bit further and I have found out that I needed to import SofaRuntime at the beginning of my script (even though not explicitly using SofaRuntime in my code) to remove a series of cleanup warnings that I was getting when the simulation finished. However, at a first sight, it seems that the memory leak problem persists. I will try to replicate the issue with an example and share it with you.

[hugtalbot]

up @damienmarchal

[ScheiklP]

Hi!
I encountered a similar problem, but were not able to resolve it.
I adapted the SofaPython3 pygame_example.py to include some resets and more objects in the scene:

import Sofa
import Sofa.SofaGL
import SofaRuntime
import Sofa.Simulation as sim
import os
sofa_directory = os.environ['SOFA_ROOT']
import pygame
from OpenGL.GL import *
from OpenGL.GLU import *

display_size = (800, 600)


def init_display(node):
    pygame.display.init()
    pygame.display.set_mode(display_size, pygame.DOUBLEBUF | pygame.OPENGL)

    glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT)
    glEnable(GL_LIGHTING)
    glEnable(GL_DEPTH_TEST)
    Sofa.SofaGL.glewInit()
    Sofa.Simulation.initVisual(node)
    Sofa.Simulation.initTextures(node)
    glMatrixMode(GL_PROJECTION)
    glLoadIdentity()
    gluPerspective(45, (display_size[0] / display_size[1]), 0.1, 50.0)

    glMatrixMode(GL_MODELVIEW)
    glLoadIdentity()

def simple_render(rootNode):
    """
     Get the OpenGL Context to render an image (snapshot) of the simulation state
     """
    glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT)
    glEnable(GL_LIGHTING)
    glEnable(GL_DEPTH_TEST)
    glMatrixMode(GL_PROJECTION)
    glLoadIdentity()
    gluPerspective(45, (display_size[0] / display_size[1]), 0.1, 50.0)
    glMatrixMode(GL_MODELVIEW)
    glLoadIdentity()

    cameraMVM = rootNode.camera.getOpenGLModelViewMatrix()
    glMultMatrixd(cameraMVM)
    Sofa.SofaGL.draw(rootNode)

    pygame.display.get_surface().fill((0,0,0))
    pygame.display.flip()


def createScene(root):
    # Register all the common component in the factory.
    SofaRuntime.PluginRepository.addFirstPath(os.path.join(sofa_directory, 'bin'))
    root.addObject("RequiredPlugin", name="SofaOpenglVisual")  # visual stuff
    root.addObject("RequiredPlugin", name="SofaLoader")  # geometry loaders
    root.addObject("RequiredPlugin", name="SofaSimpleFem")  # diffusion fem
    root.addObject("RequiredPlugin", name="SofaBoundaryCondition")  # constraints
    root.addObject("RequiredPlugin", name="SofaEngine")  # Box Roi
    root.addObject("RequiredPlugin", name="SofaImplicitOdeSolver")  # implicit solver
    root.addObject("RequiredPlugin", name="SofaMiscForceField")  # meshmatrix
    root.addObject("RequiredPlugin", name="SofaGeneralEngine")  # TextureInterpolation
    root.addObject("RequiredPlugin", name="CImgPlugin")  # for loading a bmp image for texture
    root.addObject("RequiredPlugin", name="SofaBaseLinearSolver")
    root.addObject("RequiredPlugin", name="SofaGeneralVisual")
    root.addObject("RequiredPlugin", name="SofaTopologyMapping")
    root.addObject("RequiredPlugin", name="SofaGeneralTopology")
    root.addObject("RequiredPlugin", name="SofaGeneralLoader")

    ### these are just some things that stay still and move around
    # so you know the animation is actually happening
    root.gravity = [0, -1., 0]
    root.addObject("VisualStyle", displayFlags="showAll")

    root.addObject("EulerImplicitSolver")
    root.addObject("CGLinearSolver", iterations="200",
                   tolerance="1e-09", threshold="1e-09")

    for i in range(20):
        liver = root.addChild(f"liver_{i}")
        liver.addObject("MeshGmshLoader", name="meshLoaderCoarse",
                       filename="mesh/liver.msh", translation=[i*10, 0, 0])

        liver.addObject("TetrahedronSetTopologyContainer",
                        name="topo", src="@./meshLoaderCoarse")
        liver.addObject("TetrahedronSetGeometryAlgorithms",
                        template="Vec3d", name="GeomAlgo")
        liver.addObject("MechanicalObject",
                        template="Vec3d",
                        name="MechanicalModel", showObject="1", showObjectScale="3")

        liver.addObject("TetrahedronFEMForceField", name="fem", youngModulus="1000",
                        poissonRatio="0.4", method="large")

        liver.addObject("MeshMatrixMass", massDensity="1")
        liver.addObject("FixedConstraint", indices="2 3 50")
        visual = liver.addChild("visual")
        visual.addObject('MeshObjLoader', name="meshLoader_0", filename="mesh/liver-smooth.obj", handleSeams="1")
        visual.addObject('OglModel', name="VisualModel", src="@meshLoader_0", color='red', translation=[i*10, 0, 0])
        visual.addObject('BarycentricMapping', input="@..", output="@VisualModel", name="visual mapping")

    # place light and a camera
    root.addObject("LightManager")
    root.addObject("DirectionalLight", direction=[0,1,0])
    root.addObject("InteractiveCamera", name="camera", position=[0,15, 0],
                            lookAt=[0,0,0], distance=37,
                            fieldOfView=45, zNear=0.63, zFar=55.69)


if __name__ == '__main__':
    root = Sofa.Core.Node("myroot")
    createScene(root)
    Sofa.Simulation.init(root)
    init_display(root)
    counter = 0
    resets = 0
    try:
        while True:
            if counter == 1000:
                Sofa.Simulation.reset(root)
                counter = 0
                resets += 1
                print(f"{resets}/100")
            if resets == 100:
                break
            Sofa.Simulation.animate(root, root.getDt())
            Sofa.Simulation.updateVisual(root)
            simple_render(root)
            counter += 1
    except KeyboardInterrupt:
        pass

And let it run for a while. This is the memory usage after 20 or so resets:

When removing the Sofa.Simulation.reset(root) the profile looks like this:

With a reset after every 20 steps:

So pretty similar, right?
@damienmarchal @hugtalbot @etagliabue

Cheers,
Paul

[ScheiklP]

sofa-framework/SofaPython3#292

[hugtalbot]

sofa-framework/SofaPython3#293

[hugtalbot]

Fixed in sofa-framework/SofaPython3#301