Changing number of Worknodes

CompuCell3D allows multi-core executions of simulations. We use checker-board algorithm to deal with the CPM part of the simulation. This algorithm restricts minimum partition size. As a rule of thumb, if you have cells that are large or are fragmented and spread out throughout the lattice, you should not use multiple cores. If your cells are relatively small using multiple cores can give you substantial boost in terms of simulation run times. But what does a small cell mean? If we are on a 100 x 100 lattice and cells have approx. 5-7 pixels in “diameter” then if we use 4 cores then each core will be responsible for 50 x 50 piece of the lattice. This is much bigger than our cell. However as we increase number of cores it may happen that lattice area processed by a single core is comparable in size to a single cell. This is a recipe for disaster. In such a case two (or more) CPUs may modify attributes of the same cell at the same time. This is known as race condition and CC3D does not provide any protection against such situation. The reason CC3D leaves it up to the user to ensure that race conditions do not occur is performance – protecting against race conditions would lead to slower code putting in question the whole effort to parallelize CC3D.

PDE solvers used in CC3D don’t exhibit any side effects associated with increasing number of cores. As a matter of fact parallelizing PDE solvers provides the biggest boost to the simulation. We estimate that with 3-4 diffusing fields in the simulation, CC3D spends 80-90% of its runtime solving PDEs.

An example, DynamicNumberOfProcessors in Demos/SimulationSettings demonstrates how to change number of CPUs used by the simulation:

from cc3d.core.PySteppables import *

class DynamicNumberOfProcessorsSteppable(SteppableBasePy):

    def __init__(self, frequency=1):
        SteppableBasePy.__init__(self, frequency)

    def step(self, mcs):
        if mcs == 10:
            self.resize_and_shift_lattice(new_size=(400, 400, 1), shift_vec=(100, 100, 0))

        if mcs == 100:

At MCS = 10 we resize the lattice and shift its content and at MCS = 100 we change number of CPU’s to 8. Actually what we do here is we chane number of computational threads to 8 and it is up to operating system to assign those threads to different processors. When we have 8 processors usually operating system will try to use all 8 CPU’s In case our CPU count is lower some CPU’s will execute more than one computational CC3D thread and this will give lower performance compared to the case when each CPU handles one CC3D thread.

As usual Twedit++ offers help in pasting template code ,simply go to CC3D Python->Simulation menu and choose appropriate option.