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Z Joint Cell Competence Center

OGLE observatory in Las Campas (Chile)
OGLE observatory in Las Campas (Chile)

Astronomical Period Searching on Cell BE, OGLE-III Project (G32-3)

Description: Period searching is widely used in astronomy for analyzing observatory data.Computer programs used for these tasks can be opitmized to work on novel computer architectures, such as Cell Broadband Engine. We have implemented and optimized an astronomical period searching application Fnpeaks on the Cell BE architecture. Fnpeaks application is used in the Optical Gravitational Lensing Experiment (phase III). The scientific results obtained with the use of Cell-accelerated computer program are already available in three astrophysical publications. The original code was ported using the Cell SDK and its SPE library in a relatively short time. We achieved an overall speedup of 9.68 over current workstations.In the course of our work we encountered many important aspects of Cell programming and learned how to identify codes whose performance could benefit from this architecture.

Publications, presentations:

Authors: Maciej Cytowski (ICM, University of Warsaw), Maciej Remiszewski (IBM), Igor Soszyński (Astronomical Observatory, University of Warsaw)

Contact: Maciej Cytowski (ICM, University of Warsaw)

Interactive Ray Tracer (iRT)

Description: Rendering of a 3D scene is a highly complex task. Modern 3D graphics processors deal with this problem by rasterization process accompanied by, so called, shaders. But rasterization, being a highly local algorithm, is just a simple approximation of the desired effects. To obtain more realistic images the rendering process must be calulated on a basis of more real and global algorithm. Ray tracing and ambient occlusion are the algorithms which simulate basic physical behaviour of light in a 3D scene in a global approach. Unfortunately from the computational point of view those algorithms are extremely complex. But on the other hand they are easily parallelizable and can utilize the large computing powers of Cell Processors and Cell Blade clusters. Interactive Ray Tracer is the software, made by IBM, which gives a user the opportunity to render, even a highly complex, 3D scenes in real-time using ray tracing and ambient occlusion algorithms, and to manipulate the world interactively, including objects and lights on-the-fly modifications.

The goal of this project at ICM is to take advantage of the high efficiency and quality of the rendering process of iRT and utilize it for the visualization of higly complex models, especially in the fields of bio-sciences including medical imaging.

Contact: Bartosz Borucki

Links: iRT homepage

RedMD (Reduced Molecular Dynamics) on Cell

Description: RedMD is a an open source software to perform molecular dynamics simulations for coarse-grained models of proteins, nucleic acids and their complexes. Simulations can be carried out in the microcanonical ensemble, with Berendsen and Langevin thermostats, as well as with Brownian dynamics. Our goal is to replace OpenMP parallelization with SPE accelerated threads using libspe2 library.

Authors: Arkadiusz Niegowski (ICM, University of Warsaw)

Contact: Arkadiusz Niegowski (ICM, University of Warsaw)

Links: RedMD Homepage

Simulation of influenza pandemic. Polish area.
Simulation of influenza pandemic. Polish area.

Exploring epidemic spread scenarios on Cell BE (RIVERS Project).

Description: A simulation platform was used to create a virtual society of Poland, with a particular emphasis on the contact patterns arising from a daily commuting to schools or workplaces. In order to reproduce the contacts' map, we are using a geo-referenced Agent Based Model. This platform serve as a base for large scale epidemiological and transportation simulation studies. Recently we reported the putative scenarios of disease spread in Poland. The application scope of the platform extends beyond the simulations of epidemic or transportation and pertains to any situation where there are no easily available means, other than computer simulations, to conduct large scale investigations of complex population dynamics. The simulation platform was ported and optimized on CellBE architecture.

Publications, presentations:

  • F. Rakowski, M. Gruziel, M. Krych, J.P. Radomski Large Scale Social Mobility Model - an Individual-Based Countrywide Simulation Study for Poland, JASSS, submitted
  • F.Rakowski, M.Gruziel, Ł.Bieniasz-Krzywiec, J.P.Radomski Influenza epidemic simulation spread for Poland - a very large scale, individual agent-based model study Physica A, submitted

Authors: Franciszek Rakowski, Magdalena Gruziel, Łukasz Bieniasz-Krzywiec, Jan Radomski

Contact: Franciszek Rakowski

Links: Rivers Project

Applicability Assessment of the Cell Broadband Engine Architecture to Solving Optimization and Optimal Control Problems

Description: The purpose of this thesis is to evaluate the potential of the Cell Broadband Engine Architecture to solving optimization and optimal control problems. The applicability study was performed by implementing several optimization methods on the Cell processor. Different programming approaches were applied ranging from developing new code to porting and tuning existing reference implementations. An extensive number of performance tests have been conducted on a number of systems in order to measure improvements over general purpose processors. Throughout the process, several limitations of the currently available software tools have been detected and have been passed on to IBM developers. The resulting assessment provides recommendations on programming strategies to employ when developing optimization and optimal control codes on the Cell BE processor.

Authors: Maciej Remiszewski (Warsaw University of Technology), Andrzej Karbowski (thesis adviser, Warsaw University of Technology)

Contact: Maciej Remiszewski

The Virgo antenna, built in Cascina (Italy)
The Virgo antenna, built in Cascina (Italy)

Gravitational waves detection on Cell BE, Virgo Project (G32-1)

Description: The code used for analysis of signals from Virgo interferometer was ported to Cell architecture. The code uses FFTW library which implements Fast Fourier Transform algorithm. FFTW was already ported to Cell by IBM Austin Research and achieves very good performance when compared to standard computer architectures (Read more..). Our implementation is already almost 5 times faster than the one used previously in the project. The optimization process is still in progress..

Publications, presentations:

Authors: Maciej Cytowski (ICM, University of Warsaw), Maciej Piętka (University of Białystok)

Contact: Maciej Cytowski,

Links: Virgo Project, FFTW on Cell

3D protein structure (GNU FDL)
3D protein structure (GNU FDL)

3Dpair - bioinformatics on Cell BE

Description: 3Dpair is a software to detect similar regions between two three-dimensional protein sequences in order to examine their functional, structural or evolutionary correspondence. Program performs sequence alignment computations which are based on customized versions of Smith-Waterman algorithm. It seems that this software is a good candidate to achieve significant speedup on Cell BE architecture. Our goal is to port original sequential code using SPE library and making the most of SIMD mechanism and SPU-BLAS routines.

Authors: Leszek Rychlewski, Dariusz Plewczyński, Łukasz Bieniasz-Krzywiec

Contact: Łukasz Bieniasz-Krzywiec

Siesta on Cell (PRACE project)

Description: Siesta is an ab initio molecular dynamics simulations code for molecules and solids. It is also one of the application considered as a benchmark code in the PRACE project. The aim of our work is to benchmark single processor as well as parallel performance of the Siesta code on Cell clusters. The code itself has been already ported and profiled on Cell with the use of XLF compiler and PAT tools like Oprofile and Visual Performance Analyzer. Currently we are working on porting specific subroutines to SPUs.

Publications, presentations:

Authors: Maciej Cytowski (ICM, University of Warsaw), Maciej Szpindler (ICM, University of Warsaw)

Contact: Maciej Cytowski (ICM, University of Warsaw)

Links: Siesta code, PRACE project

Ulam spiral: prime numbers arranged in a form of a spiral of size 150 x 150.
Ulam spiral: prime numbers arranged in a form of a spiral of size 150 x 150.

A search for unique primitive roots modulo a prime number (G33-18)

Description: So far there are known only two examples of prime numbers p for which the least primitive root modulo p is different from the least primitive root modulo p^2. The present research in this matter has been carried out up to p < 1,26 * 10^12. The aim of our project is an exhaustive search for such primes in the interval p < 10^14. In our research we take advantage of the multi-precision integer arithmetic library libmpm contained in the Cell SDK. On the basis of it we have developed some effective number-theoretic software, such as the deterministic variant of the Miller-Rabin primality test and a very fast implementation of R. Brent's version of Rho factorization algorithm (with the use of Montgomery modular arithmetic). Since particular algebraic parameters can be calculated for each prime separately, the project allows rather coarse-grain parallelism with an easy load-balance between SPU-s and minimal communication overheads.

Authors: Andrzej Paszkiewicz (Warsaw University of Technology), Piotr Bartosik

Contact: Andrzej Paszkiewicz, Piotr Bartosik

Links: "A new prime p for which the least primitive root mod p and the least primitive root mod p2 are not equal."