# Restarting Simulations¶

Very often when you run CC3D simulations you would like to save the state of the simulation and later restart it from the place where you interrupted it. For example let’s say that you are running vascularized tumor simulation on a 500x500x500 lattice. After the simulated tumor reaches certain size or mass you may want to simulate various treatment strategies. Instead of running full simulations from the beginning and turning on treatment at specific MCS you may run a simulation up to the point when tumor reaches required mass and then start new set of simulations. This would save you a lot of computational time. Another advantage of the ability to restart simulations at arbitrary time point is when you run your job on a cluster or cloud and there is a risk that your simulation may get interrupted. In this case you could periodically save state of the simulation and then restart it from the latest snapshot. CompuCell3D makes all such tasks very easy as you will shortly see. First let’s learn how to set up a simulation that can save itself and later restart:

Open Twedit++ and open the simulation you’d like to serialize and the restart. For example let’s choose SBMLSolverOscillatorDemo.cc3d:

Here we right-click on project tab (SBMLSolverOscillatorDemo.cc3d) and choose Add Serializer… . In the pop-up window we change snapshot Output Frequency to 100 , click Allow Serialization and click OK:

At this point our simulation is set up to take complete snapshots every 100 MCS.

Important: If you want to keep every single snapshot you need to click Allow multiple restart snapshots otherwise only the most recent snapshot will be kept on the hard drive

Before we proceed we need to save the simulation by right clicking on project tab (SBMLSolverOscillatorDemo.cc3d) and choosing Save CC3D Project:

Notice how Serializer was added at the bottom of our CC3D project. If you right-click on it you can make changes to serialization configurations. Just remember to Save CC3D Project when you are done.

If we run our project in Player it will run as usual except that every 100 MCS it will save complete restart snapshot of itself to the hard drive. If you wonder where the snapshots will go open op CC3D Player settings and look at the Output Tab (as you can tell all the output will go to /Users/m/CC3DWorkspace):

Here is the screenshot of the simulation that we ran up to 300 MCS:

Let’s take a look at the content of Simulation output directory (/Users/m/CC3DWorkspace):

As you can see, CC3D saved time-stamped simulation output directory /Users/m/CC3DWorkspace/SBMLSolverOscilatorDemo_cc3d_07_04_2016_13_09_19/ and inside it you can find restart_00300 folder that contains all the information needed to restart the simulation at t = 300 MCS. To restart the simulation we need to do one important step - open in Twedit++ saved simulation (SBMLSovlerOscillatorDemo.cc3d) from restart folder /Users/m/CC3DWorkspace/SBMLSolverOscilatorDemo_cc3d_07_04_2016_13_09_19/restart_00300 , disable serialization and enable restart:

Important: At this step we are modifying simulation from the restart folder NOT the original simulation that we started with and NOT the simulation stored in the top-level output folder - /Users/m/CC3DWorkspace/SBMLSolverOscilatorDemo_cc3d_07_04_2016_13_09_19/

Here we go:

Notice, at the top of the Twedit++ window, that we are working with the saved snapshot of the simulation stored in the restart_00300 sub-folder. We will edit Serializer settings of the .cc3d project stored in this sub-folder to allow restart and disable serialization. As before after we make changes we need to remember to save our project:

If you are curious what happened here when we change serialization settings you may open .cc3d project before and after you make changes and you will see that with serialization enabled our .cc3d project looks as follows:

<Simulation version="3.5.1">
<XMLScript Type="XMLScript">Simulation/SBMLSolverOscilatorDemo.xml</XMLScript>
<PythonScript Type="PythonScript">Simulation/SBMLSolverOscilatorDemo.py</PythonScript>
<Resource Type="Python">Simulation/SBMLSolverOscilatorDemoSteppables.py</Resource>
<Resource Type="SBML">Simulation/oscli.sbml</Resource>
<SerializeSimulation AllowMultipleRestartDirectories="False" FileFormat="text" OutputFrequency="100"/>
</Simulation>


but after the change the last line will get replaced to allow restart:

<Simulation version="3.5.1">
<XMLScript Type="XMLScript">Simulation/SBMLSolverOscilatorDemo.xml</XMLScript>
<PythonScript Type="PythonScript">Simulation/SBMLSolverOscilatorDemo.py</PythonScript>
<Resource Type="Python">Simulation/SBMLSolverOscilatorDemoSteppables.py</Resource>
<Resource Type="SBML">Simulation/oscli.sbml</Resource>
<RestartSimulation RestartDirectory="restart"/>
</Simulation>


If you do not like clicking you can easily ope up your favorite editor and modify content of the .cc3d project file to allow saving of restart snapshots and to allow restarting from the snapshots.

Let’s see what happens if we run our project form the snapshot saved snapshot. In Player we navigate to /Users/m/CC3DWorkspace/SBMLSolverOscilatorDemo_cc3d_07_04_2016_13_09_19/restart_00300 and open SBMLSolverOscillatorDemo.cc3d:

We got an error which is quite easy to explain. During the restart start functions of steppables are run. Because in our original simulation we create plots inside start function, clearly the plots are not created during the restart and since step function refers to plot window object the error arises. Take a look at our original code and see if you can follow what I explained here:

class SBMLSolverOscilatorDemoSteppable(SteppableBasePy):
def __init__(self, _simulator, _frequency=10):
SteppableBasePy.__init__(self, _simulator, _frequency)

def start(self):
_xAxisTitle='MonteCarlo Step (MCS)', _yAxisTitle='Variables')

# iterating over all cells in simulation
for cell in self.cellList:
# you can access/manipulate cell properties here
cell.targetVolume = 25
cell.lambdaVolume = 2.0

...

def step(self, mcs):
...

self.pW.showAllPlots()
self.timestepSBML()


A simple fix (not necessarily optimal one) would be to introduce a new function initialize_plots that first checks if self.pW plot window object is None and if so it creates a plot otherwise it exits. Of course for this to work self.pW will need to be declared in the steppable constructor __init__ (constructors of steppables are called during restart initialization)

Here is the code – changes are highlighted using bold code:

class SBMLSolverOscilatorDemoSteppable(SteppableBasePy):

def __init__(self,_simulator,_frequency=10):
SteppableBasePy.__init__(self,_simulator,_frequency)
self.pW = None

def initialize_plots(self):
if self.pW:
return

_xAxisTitle='MonteCarlo Step (MCS)',_yAxisTitle='Variables')

def start(self):
self.initialize_plots()

# iterating over all cells in simulation
for cell in self.cellList:
# you can access/manipulate cell properties here
cell.targetVolume=25
cell.lambdaVolume=2.0

...

def step(self,mcs):

self.initialize_plots()

...

self.pW.showAllPlots()
self.timestepSBML()


To wrap up, setting up simulation restart is quite easy in CC3D. Making sure that simulation restarts properly may require you to slightly modify your code to account for the fact that start functions of steppables are not called during restart.

After we make all those changes in our simulation code and rerun it we will get the following:

Notice that the cell layout is identical to the one we got at t = 300 MCS and that out plot restarts at t = 300 MCS. If we let simulation run for a few more MCS you will see that the S1 concentration will start falling as it would if we had continued our original run: