9. Optimizing Your Simulation

The simplistic simulations covered in these tutorials should not be overly taxing on a relatively recent desktop machine. However, you may likely want to develop simulations which have many more molecules possibly on large dense mesh objects. There are a couple of strategies you can use to speed up your simulations (and/or to save disk space). The following topics will address some of these issues:

9.1. Increase Time Step

One of the easiest things you can do to speed up your simulations is to increase your time step. Generally, you’ll want to increase it as much as possible while keeping the reaction probabilities below one. If any of the reaction probabilities exceed one, you’ll see the following message:


If you do, you should take a closer look at the logs. You can enable logs by checking the Save Text Logs under the Output/Control Options panel:


When you re-run the simulation, you’ll need to switch to the Scripting layout:


Notice that it refers to the specific reaction or reactions at fault.

For this particular model, we can decrease the time step by an order of magnitude (from 1e-6 to 1e-7) to prevent the missed reactions:


Here’s the new log:


There’s still a warning about the lifetime being short relative to the time step, but we are no longer missing any reactions. The simulation now has a time step that is about as large as it can reasonably be.

9.2. Adding Partitions

Partitions are a simple but highly effective method of speeding up MCell simulations. When MCell checks to see if a reaction occurs, partitions lower the number of potential partners it must check against. However, care must be taken not to use so many partitions that your computer begins to run out of memory (ultimately slowing the simulation down).

Download and open the partitions.blend file. You will see a tilted Cube object. If you look through the CellBlender settings, you will notice that we are releasing two species of molecules (vol1 and vol2) inside of the Cube, and there are two sets of reactions:

vol1 + vol2 -> vol1 + vol3
vol1 + vol3 -> vol2 + vol3

Expand the Define and Visualize Partitions panel. Select Include Partitions. Click Show Boundaries, and you will see a wireframe of a cube that goes from -1.0 to 1.0 along each axis. These represent the boundaries of the partitions. Now, hit Automatically Generate Boundaries and you should see the partition boundaries grow to encompass the entire Cube object. Change each Step value to 0.15.


So what is happening here exactly? We are creating arrays of planes along each axis specified. The intersection of these planes creates subvolumes. Specifically, it takes two XY, two XZ, and two YZ planes to create a single subvolume. The length of these subvolumes should generally not be smaller than the mean diffusion distance of the fastest molecules in your simulation.

Now, expand the Run Simulation panel and hit the Run Simulation button. A green check mark will appear when the simulations have completed. Look at the console (or log files if enabled in /home/user/mcell_tutorial/partitions/partitions_files/). Notice the section near the end, which should say something like this:

Total wall clock time = 2 seconds
Done running.

Now, disable the partitions and run it again. Check the newly created log file and you will likely see the total simulation time increase (i.e. a decrease in iterations/second) like this:

Total wall clock time = 22 seconds
Done running.

Your results will likely vary, as the speed improvement will depend on the machine running the simulation. You may want to experiment with changing the Step value. For example try decreasing it to 0.10. If the wall clock time increases (i.e. the simulation is running slower), try making the Step value larger than the original value (e.g. set the Step value to 0.20). It may take a few tries to find an optimal value.

9.3. Target Only

If you have a reaction between two molecules in which there are many of one species and very few of another, you might want to consider using the Target Only option when defining the species with the high concentration. Normally, a diffusing molecule will check to see if there are any potential molecules to react with. However, a molecule that is marked as Target Only can only be the target of a reaction, and will not search for partners to react with.

Download and open the target_only.blend file. If you look through the CellBlender settings, you will see that we are using the Target Only option in the molecule definition of vol2:


Additionaly, you will notice that we are releasing two species (vol1 and vol2) inside of the Cube and that there is one reaction:

vol1 + vol2 -> vol1 + vol3

This means that vol1 reacts with vol2 to create vol3 and recreate vol1. Without the Target Only command, every vol2 molecule would have to check to see if there were vol1 molecules to react with and vice versa. With this command, only vol1 must search for reaction partners. Given that there are 100 vol1 and 50000 vol2, this second method is much more efficient.

Now, expand the Run Simulation panel and hit the Run Simulation button. A green check mark will appear when the simulations have completed. Try running it again without Target Only selected for vol2 and check the log files for the two runs.

9.4. Only Export What You Need

Visualization data can be great if you are making a figure to accompany a paper, or you are trying to troubleshoot a problem in your simulation, but there’s probably no need to export every molecule at every iteration. You could either disable viz data entirely when you don’t need it or only export the molecules you need. Also, you can choose to export viz data for a subset of your entire simulation (e.g. imagine your simulation runs for 10000 iterations, but you only need every tenth iteration from 9000 to 10000). Both of these solutions can speed up your simulation and save you disk space.