Apple Power Mac G5 - Manual (Page 29)

Scientific and Technical Computing
Today, the typical researcher’s desktop has two or more computers: a UNIX worksta-
tion for research and analysis applications and a PC or a Macintosh for mainstream
applications such as writing, budgeting, and presentations. With the Power Mac G5,
researchers can now run both productivity applications and high-performance UNIX
applications on a single system. High-speed data analysis and visualization are within
easy reach on the 64-bit Power Mac G5. High-capacity, high-speed memory enables
scientists to manipulate large models and data sets quickly and efficiently. And the
optimized Velocity Engine and two floating-point units dramatically improve the com-
putational power of the PowerPC G5, making the Power Mac G5 ideal for users in the
life sciences, physical sciences, and technical computing disciplines.
BLAST
To demonstrate the performance advantages of the Power Mac G5 for processor-
intensive scientific analysis, Apple used Basic Local Alignment Search Tool, or BLAST.
BLAST is a popular open source biotechnology application used by life sciences
researchers to find matches in DNA and protein sequences—a highly processor-
intensive task.
BLAST searches are based on word size, or the number of nucleotide pairs specified
by the researcher to register a match. For example, a word size of 40 indicates that
two sets of genetic code have 40 nucleotides in common. Different word sizes are
used for different kinds of research, and users can adjust word size to the sensitivity
appropriate to their needs. With long-word-size (high-performance) searches, the
researcher is looking for similarities between DNA sequences that are nearly identical—
for example, comparing DNA samples from two different mice. For short-word-size
searches (fewer than 11), the researcher is comparing more distantly related sequences,
such as mouse DNA and human DNA. These searches require high resolution in order
to find the small matches between dissimilar sequences.
In common searches using a word size of more than 11, the Power Mac G5 far outperformed
the competing systems. 1
Power Mac G5 systems were tested using A/G BLAST. The Pentium 4–based Dell Dimension XPS, AMD Athlon 64 FX-51–based
Alienware Aurora, and dual Xeon-based Dell Precision 650 ran NCBI BLAST on Red Hat Linux.
DNA sequence matching
8 10 11 20 30 35 40
0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
Word length
M
illions of nucleotide
s per sec
ond
Dual 2GHz Power Mac G5
Dual 1.8GHz Power Mac G5
1.6GHz Power Mac G5
2.2GHz Alienware Aurora
3.2GHz Dell Dimension XPS
Dual 3.2GHz Dell Precision 650
29 Technology and
Performance Overview
Power Mac G5
Power Mac G5 supercomputer
at Virginia Tech
Using 1100 Power Mac G5 systems, Virginia
Tech has created the first-ever supercomputer
built with Apple’s newest and fastest desktop
computer. Called “X,” for its design goal of 10
teraflops, the cluster boasts 2200 G5 processors
and is the fastest university supercomputer and
the third most powerful supercomputer in the
world, behind Japan’s Earth Simulator and ASCI
Q, the Los Alamos National Laboratory’s dedi-
cated weapons computer. Assembled in just
two months using off-the-shelf components,
the supercomputer will be used to conduct
multidisciplinary work on such topics as nano-
electronics, aerodynamics, and the molecular
modeling of proteins. This supercomputer
cluster enables researchers to build computer
models in days rather than years, and will help
solve some of the most compute-intensive
challenges in the world.
BLAST Results