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and workflow for a gridified analysis in greater
detail. The input data consists of three files: a host
tree file, a parasite tree file, and a host-parasite
association list. In the reminder of this article, the
following terminology is used:
The overall workflow is depicted in Figure
2. The most important Grid-enhancement is the
interface to the Grid (represented by the Perl
program AxParafit.pl in Figure 2). Once the input
files are validated, CopyCat uses AxParafit.pl to
determine a specific set of tasks (to be registered
with a Task Server as indicated in Figure 3) and
Grid jobs which are then submitted to Grid com-
puting resources using the gLite middleware. Each
individual Grid job then requests tasks from the
Task Server, processes them, and stores the result
on a Grid Storage Element.
AxParafit.pl will constantly monitor the over-
all Grid job status and presents intermediate results
in a CopyCat control window. Once all results are
obtained and merged, CopyCat indicates where
the final result can be obtained. Further details
about AxParafit.pl, AxWorker.pl etc. will be
given in the other section.
Individual test ( job ) : an individual test is
the minimal “work unit” or processing en-
tity that has to be conducted by AxParafit
to calculate a single host-parasite associa-
tion. In the context of AxParafit this is also
referred to as job . In total, nz individual
tests have to be computed to achieve the
final result.
Task: a task consists of a fraction (subset)
of the nz individual tests that have to be
conducted by AxParafit.
Grid job: a Grid job is an executable that
is scheduled by the Grid middleware to
be executed on a Worker Node of a Grid
computing resource (also referred to as
Computing Element). In our model, a
single Grid job can execute one or several
such tasks.
Implementation Details
In the following section we describe the neces-
sary modifications and adaptations of the existing
Figure 3. Interaction of AxParafit.pl with the gLite Grid middleware, a Task Server and a Storage Ele-
ment. Each submitted Grid job will execute on a Grid Worker Node
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