Speaker
Report on the experience (or the proposed activity). It would be very important to mention key services which are essential for the success of your activity on the EGEE infrastructure.
We have deployed a WSRF-based Grid metascheduler (GMarte) that
enables biomedical
experts to access a computational infrastructure, composed of
different clusters of
PCs within our research group. This provides transparent access
to computing power
for users. However, the multi-user support of the metascheduler
combined with large
cardiac studies can often overload these computing resources.
Therefore, we plan to provide a computational gateway to LCG-2,
so that those
simulations that can not be executed in our Grid are
automatically delegated to a
Resource Broker for its execution on a production Grid. This
would require
coordinated data staging to Storage Elements, using the
functionality provided by a
File Catalog to manage different replicas of simulation data. The
usage of MyProxy is
ideal to automatically renew the proxy for long simulations.
Also, the Logging &
Bookkepping service is fundamental to integrate the lifecycle of
tasks within our
metascheduler.
With a forward look to future evolution, discuss the issues you have encountered (or that you expect) in using the EGEE infrastructure. Wherever possible, point out the experience limitations (both in terms of existing services or missing functionality)
The application is MPI-based, thus requiring parallel executions
on LCG-2 resources.
In addition, it uses MPI-2 I/O techniques for parallel I/O, what
demands a shared
file system among all the worker nodes. On the other hand, the
application is complex
enough to try an in-place compilation before execution. Thus, we
are producing
statically-linked self-contained executable files which we expect
to be able to run.
We would be interested in using Java APIs to interact with LCG-2
services.
Describe the added value of the Grid for the scientific/technical activity you (plan to) do on the Grid. This should include the scale of the activity and of the potential user community and the relevance for other scientific or business applications
The electrical activity enables to analyse the influence of
certain drugs to heart
diseases as well as the influence of different cellular
parameters to the electrical
activity. Moreover, cardiac case studies are inherently composed
of lots of
independent multi-parametric jobs, and the Grid is the
appropriate infrastructure to
accelerate their execution.
On average, we have estimated a requirement of 96 CPUs per day
producing a total
amount of data in the order of 120 GBytes. This would include
research lines that
investigate the genesis of reentrant activity under acutely
ischemic (phase Ia)
conditions, and the effects of antiarrhythmic drugs such as
lidocaine or pinacidil.
Potential user community is composed by cardiac
electrophysiologists interested in
using detailed cellular models to study effects on electrical
activity. In addition,
this activity fits within the goals of the Virtual Physiological
Human by providing
an effective simulation tool for action potential propagation.
Describe the scientific/technical community and the scientific/technical activity using (planning to use) the EGEE infrastructure. A high-level description is needed (neither a detailed specialist report nor a list of references).
The understanding of cardiac electrical behaviour is essential to
comprehend the
genesis of cardiac arrhythmias and to develop new therapeutic
methods based on the
use of antiarrhythmic drugs. Computer simulations are an
essential tool, as the
mathematical models that predict ionic currents and propagating
wavefronts have
reached a high level of electrophysiological detail. However,
these simulations are
both computationally and memory intensive, producing a large
amount of simulation data.
