Speaker
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
At the moment PFGR is used by skilled people of the biophysics
community and it under
testing and improvement in order to make it a final tool for a
larger (and less
skilled) biophysics community.
It has to be noted that the computational characteristics of the
BEM algorithm fits
almost perfectly on the EGEE infrastructures and the computing
power available would
allow, along with the EGEE grid computational resources, to fold
the structure of
complex systems (like small DNA chains, by example).
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.
PFGR is a combination of a pre-existent folding program with an
added layer that
allows it to exchange data on the grid transparently and without
MPI (thus enabling
multi CE execution and dynamic recruitment of resources).
The system is completed with an easy to use (though still in
development) user
interface which guides the user through most of the workflow.
The key functionality used by PFGR is outbound connectivity on
the WNs (to enable
comunication) and the data access (that actually uses the very
low level GSI
protocol, but can be easily reverted to use the SRM protocol).
PFGR features:
* Put Biased Meta dynamic folding on the grid.
* Dynamic recruitment of resources.
* Simulations can use multiple CE at a time.
* Easy to use user interface.
* Real time logging of the simulation.
The PFGR protein folding algorithm is based on the Gromacs
software (with substantial
modifications made by Alessandro Laio et al.) and the
communication layer is built in
python 2.5
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).
PFGR is a grid-enabled system that aims to harness the power of
the EGEE
infrastructure to run simulations based on the "biased exchange
metadynamic (BEM)
algorithm" which is routenely used in the biosimulation community
to investigate
protein folding mechanisms.
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 main issue affecting the developement of PFGR has been the
the old version of the
software installed on the various WNs.
The Scientific Linux distribution presently installed on WNs is
quite old missing
important software (compilers and basic developement tools) and
with out-of-date
packages (like for istance python). This combination makes the
development and the
optimization for heterogeneuos resources complex and time consuming.
