Normally, when simulating or analyzing a model in SimBiology®, the model is expressed in MATLAB® code. You can accelerate the simulation by converting the model to compiled C code, which executes faster. Because this compilation step has a small time overhead, acceleration is not recommended for individual simulations of small models. However, for large models, or for repeated simulations during analysis, acceleration can provide a significant speed increase that outweighs the small time overhead.
The functionality to accelerate simulations performs optimally under the following conditions:
Running repeated simulations with different initial conditions
Running very long simulations (for example, simulations that take longer than a minute to run)
To prepare your models for accelerated simulations, install and set up a compiler:
Install a C compiler (if one is not already installed on your system). For a current list of supported compilers, see Supported and Compatible Compilers.
Ensure that any user-defined functions in your model can be used for code generation from MATLAB, so they can convert to compiled C. For more information, see Language, Function, and Object support for C and C++ code generation (MATLAB Coder) or contact MathWorks Technical Support.
Note
On 32-bit Windows® platforms, the LCC compiler is automatically installed. However, for better performance of the acceleration functionality, you may want to install a supported compiler other than LCC, and it will be selected automatically.
On 64-bit Windows platforms, if you have not installed another compiler, SimBiology uses the LCC64 compiler for model accelerations. If you have installed another supported compiler, it will be selected automatically.
Microsoft® Visual Studio® 2010 run-time libraries must be available on any computer running accelerated models generated using Microsoft Windows SDK.
If you plan to redistribute your accelerated models to other MATLAB users, be sure they have the same run-time libraries.
Use sbioaccelerate if you are
accelerating a SimBiology model. For a SimFunction object and an exported
model (SimBiology.export.Model), use the
corresponding accelerate method.
Follow the two-step process for acceleration.
Run sbioaccelerate to prepare your model for
accelerated simulations. Use the same input arguments that you plan to
use with sbiosimulate in the
next step. For example:
sbioaccelerate(model,configset,doses);
For a very large model, this step may take a minute or longer to complete.
Run sbiosimulate with the
same input arguments that you used with
sbioaccelerate. For example:
simdata= sbiosimulate(model,configset,doses);
If you pass in an array of doses to sbioaccelerate, you
can simulate the model using any subset of these doses and do not need to run
acceleration again.
For illustrated examples, see the following.
A SimFunction object is automatically accelerated at the
first function execution. Hence it is not necessary to accelerate the model
before you create the object. However, manually accelerate using the accelerate method of the object
if you want it accelerated in your deployment applications.
For exported model, see accelerate.
If you make any modifications to the model, such as changes to reactions or adding events, you need to rerun the acceleration, before running simulations.
However, there are exceptions. You do not need to accelerate again if you are making the changes to:
Any variants
InitialAmount property
of species
Capacity property of
compartments
Value property of
parameters
StopTime property of
configset
OutputTimes property of
SolverOptions
Active, Amount, and Rate properties of
ScheduleDose and
RepeatDose
Time property of
ScheduleDose
Interval, RepeatCount, and
StartTime properties of
RepeatDose
Notes, Tag, and UserData properties of
any applicable objects
You can enable the model acceleration in the SimBiology Model Analyzer app by checking the Prepare the model for accelerated simulation box in the Model step of the program.
If you have custom functions, use persistent variables only for those (constant) variables that you do not want to recalculate or reload every function call. The reason is that during the acceleration process, SimBiology converts the model and custom functions to compiled C code. If you try to use a persistent variable to share data across generated (or compiled) C functions, you may have different results. For instance, if you use a persistent variable to count how many times a function is called, each compiled function will have a separate count. Those persistent variables in the corresponding compiled functions will be different from the one used in the MATLAB function that you defined.
If you specify custom functions in SimBiology expressions, you might see the following warning if your code is not compatible with code generation from MATLAB:
The SimBiology Expression and any user-defined functions
could not be accelerated. Please check that these expressions
and any user-defined functions are supported for code generation
as described in the Code Generation from MATLAB documentation.where Expression is any of the following:
Reaction rate/rule expression
Initial assignment rule expression
Repeated assignment rule expression
Event trigger expression
Event function expression
For more information, see Language, Function, and Object support for C and C++ code generation (MATLAB Coder) or contact MathWorks Technical Support.
accelerate | accelerate | sbioaccelerate | SimBiology.export.Model | SimFunction object