Biomedical Engineering Reference
In-Depth Information
The rest of this chapter is organized as follows. The next section describes
TaskSpaces, our prototype software framework for grid computing, which is based
on tuple space concepts and implemented in Java. Section 26.3 describes a loosely
coupled parallel bioinformatics application that we investigated on a computational
grid, namely, the problem of finding correctly folded RNA motifs in sequence space.
Section 26.4 describes our experience with operating the software framework on a
computational grid comprised of local workstations and parallel clusters at super-
computer centers. Brief results for the RNA motif problem are presented in Section
26.5. The chapter concludes with a section on future work and a summary.
26.2 THE TASKSPACES FRAMEWORK
TaskSpaces is a prototype lightweight grid computing framework for scientific com-
puting characterized by two major design choices: decentralization, provided by an
underlying tuple space concept, and object-orientation and platform-independence,
provided by implementation in Java. The TaskSpaces framework has been described
in detail in Ref. [1]; in this section, we summarize its main properties.
Tuple spaces were pioneered in the late 1970s and were first realized in the Linda
system and language [2]. In a tuple space distributed computing environment, pro-
cesses communicate solely by adding tuples to and taking them from a tuple space, a
formof independent associativememory.A tuple is a sequence of fields, each of which
has a type and contains a value. Figure 26.2 shows conceptually how distributed com-
putation works in a tuple space environment. An application program places subtasks
resulting from the partitioning of a large computational problem into a tuple space
(which in the bag-of-tasks paradigm is called a “task bag” [3]), in which each subtask
is represented as a tuple. “Worker processes” take the task objects from the task bag,
execute the tasks, and place the result in a “result bag” as another tuple. The tuple space
Worker
Worker
...
Task bag
Result bag
Task
Task
Result
Result
Task
Result
...
...
Task
Application
Worker
Figure 26.2
The tuple space paradigm for distributed computing.
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