3. Getting Started¶
ExTASY 0.2 uses the Ensemble Toolkit API for composing the application. In this section we will run you through the basics building blocks of the API. We will introduce the SimulationAnalysisLoop pattern and then work through simple examples using the same pattern in the next section. Once you are comfortable with these examples, we will then move to two molecular dynamics applications created using this API.
3.1. SimulationAnalysisLoop (SAL): The Pattern¶
The SAL pattern supports multiple iterations of two chained bag of tasks (BoT). The first bag consists of ‘n’ instances of simulations followed by the second bag which consists of ‘m’ instances of analysis. These analysis instances work on the output of the simulation instances and hence they are chained. There can be multiple iterations of these two BoTs. Depending on the application, it is possible to have the simulation instances of iteration ‘i+1’ work on the output of the analysis instances of iteration ‘i’. There also exist two steps - pre_loop and post_loop to perform any pre- or post- processing. A graphical representation of the pattern is given below:
There are also a set of data references that can be used to reference the data in a particular step or instance.
$PRE_LOOP- References the pre_loop step
$PREV_SIMULATION- References the previous simulation step with the same instance number.
$PREV_SIMULATION_INSTANCE_Y- References instance Y of the previous simulation step.
$SIMULATION_ITERATION_X_INSTANCE_Y- References instance Y of the simulation step of iteration number X.
$PREV_ANALYSIS- References the previous analysis step with the same instance number.
$PREV_ANALYSIS_INSTANCE_Y- References instance Y of the previous analysis step.
$ANALYSIS_ITERATION_X_INSTANCE_Y- References instance Y of the analysis step of iteration number X.
3.2. Components of the API¶
There are three components that the user interacts with in order to implement the application:
- Resource Handle: The resource handle can be see as a container that acquires the resources on the remote machine and provides application level control of these resources.
- Execution Pattern: A pattern can be seen as a parameterized template for an execution trajectory that implements a specific algorithm. A pattern provides placeholder methods for the individual steps or stages of an execution trajectory. These placeholders are populated with Kernels that get executed when it’s the step’s turn to be executed. In ExTASY, we will be using the SAL pattern.
- Application Kernel: A kernel is an object that abstracts a computational task in EnsembleMD. It represents an instantiation of a specific science tool along with its resource specific environment.