# 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. The only thing you need to do is to click Enable output of restart snapshots

Alternatively if you run simulation using command line script runScript you need to pass the following argument to your command line:

--restart-snapshot-frequency=<restart snapshot output frequency>


CompuCell3D will write simulation snapshots to the restart folder. You can navigate to the output folder and load such simulation as if it were a regular one

Warning

When you run simulation from restart snapshot start functions of steppables are not called. Therefore you need to take steps to ensure that any type of initialization that might still be required gets executed in the step function. Let’s study example below:

Supose that 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, frequency=10):
SteppableBasePy.__init__(self, frequency)
self.pW = None

def start(self):
self.pW = self.add_new_plot_window(title='S1 concentration', x_axis_title='MonteCarlo Step (MCS)',
y_axis_title='Variables')

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

def step(self, mcs):
...

self.timestep_sbml()


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, frequency=10):
SteppableBasePy.__init__(self, frequency)
self.pW = None

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

self.pW = self.add_new_plot_window(title='S1 concentration', x_axis_title='MonteCarlo Step (MCS)',
y_axis_title='Variables')

def start(self):
self.initialize_plots()

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

...

def step(self, mcs):
...
self.initialize_plots()
self.timestep_sbml()


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.