tions, using a finite difference time domain alg
orithm that is very compute-intensive. Parallelizing this code achieved a 30-fold speedup on the 64-processor Parsytec GC/PP machines and a 50-fold speedup on a 128-processor IBM SP2.
The benefit:
PEPSE makes it practical for the first time to simulate the effects of a lightning strike on the whole airframe of a fighter jet.
The Paramation consortium
parallelized Cambridge Animation's
Animo software
. The other participants were end-user Siriol Productions and parallel experts Perihelion Distributed Software. Animo is a 2-D animation program that Siriol used to produce a cartoon feature film (which has been sold to Disney). The program performs both automatic "in-betweening" (interpolating the sequence of transitional images between two key frames) and color rendering of frames, both of which are highly labor-intensive tasks. Parallelizing the off-line rendering functions of Animo to run on clusters of DEC Alpha, Silicon
Graphics, and Pentium workstations resulted in a fourfold speedup using five workstations.
The benefit:
Time and cost savings for commercial animation studios.
PAM-Crash
simulates car crashes by using finite element analysis. The consortium included automakers BMW, Audi, and Hyundai, with code owner ESI. The group found that parallel PAM-Crash scaled well on up to 128 processors, where it still showed a 55-fold speedup, i.e., a parallel efficiency of around 43 percent. (Parallel efficiency is a measure of how well a hardware/software combination scales. If a program runs twice as fast on two processors as on one, its parallel efficiency would be 100 percent.) A Meiko CS-2 with eight SuperSparc nodes ran PAM-Crash faster than the Cray YMP vector processor used to run the serial code.
The benefit:
Cost savings through better understanding of crash behavior.
RAPT, the RAdiotherapy Treatment Planning System,
is b
ased on a simulation library called EGS4 that's owned by EDS Systems and Management. The RAPT porting consortium included the Ospedali Galliera of Genoa and Southampton University's Parallel Applications Centre. RAPT models the radiation doses delivered during radiation therapy for tumors. It allows clinicians to develop treatment plans that are effective while minimizing consequential damage to healthy tissue.
The program builds a 3-D model of the patient's body from CT and MRI scan data and then employs Monte Carlo methods to calculate the absorbed radiation dose from any particular beam configuration. RAPT's big advantage over other prediction methods is that it doesn't assume an idealized "average" patient but works with the actual patient, so it can allow for variations in tissue density and deliver a more accurate dose prediction. The Monte Carlo algorithm, which generates millions of randomized photon trajectories, would normally need to run on a vector supercomputer, which is beyond the budget of
most medical physics departments.
The benefit:
Allows hospitals to run a full body simulation in an hour or less.
The MaxHom (Maximum Homology) consortium
involved parallel computer maker Parsytec, the pharmaceutical firm E. Merck, and the European Molecular Biology Laboratory in Heidelberg. It parallelized the search software for a protein database used in modeling 3-D receptor structures for drug design.
MaxHom
matches patterns and tries to align a target sequence of amino acids with the many thousands of sequences stored in a standard pharmaceutical database. The existing serial search software took several hours to match each protein sequence, and the goal was to reduce this sufficiently to make searches interactive.
The parallelized MaxHom code was ported to a 128-node Parsytec GC/PP, a 28-node IBM SP2, and a 64-node Silicon Graphics PowerChallenge array. In each case, the code showed a parallel efficiency of around 70 percent;
the 128-node Parsytec gave a speedup of 92 times. Merck is already using parallel MaxHom for real industrial tasks, such as finding the interaction site of the snake venom protein echistatin and its receptor on a blood protein; typical search runs took about 3 minutes.
The benefit:
Makes searches in protein databases interactive.
screen_link (18 Kbytes)
Parallel Animo renders frames faster.
screen_link (11 Kbytes)
Echistatin and a matching peptide discovered by MaxHom.
Europort Projects at a Glance
