AMD’s SeaMicro Servers Accelerate Biomolecular Research

Advanced Micro Devices, Inc.
(AMD) announced that the Gene Center of
the University of Munich (Ludwig Maximilians University, or LMU) has
accelerated its research capabilities using its SeaMicro servers to gain a
computational edge for its discoveries.

SeaMicro servers aided researchers in creating the world’s first 3-D
image of the human ribosome by combining more than 800,000 images. The findings
advance the understanding of how bacteria ribosomes can be broken down without
harming human ribosomes, similar to the operation of some antibiotics. This
could lead to the discovery of new drugs that are more effective and
personalized to a person s genetic profile.

The Gene Center, a life sciences research center in Munich, Germany, conducts
research that requires intensive computational capability which up until now
has traditionally been limited to custom-built, expensive HPC
clusters. SeaMicro server with Freedom Fabric, provides 1.28Tb/s of bandwidth to scale computing performance without the
need for expensive, external IB interconnections or 10GbE networking.

"HPC is critical to the cutting-edge
research and groundbreaking discoveries of the LMU Gene Center," said
Ronald Beckmann, professor at the Gene Center at LMU. "AMD’s SeaMicro servers provide a computational edge by delivering
supercomputer-like performance in the industry s smallest form factor. The
server really is a mini-supercomputer in a box, and it is accelerating our
research and allowing us to do analysis and break new ground in the field of
structural biochemistry."

SeaMicro servers are simple to deploy due to their dense form
factor and management interface. They fit into standard server rooms,
like those used in the Gene Center, compared to HPC clusters or supercomputers
that require custom build-outs for facilities and cooling. The compact 10 rack
unit chassis (17.5", 44.5cm) creates a solution that is
essentially a mini-supercomputer in a box.

The Gene Center selected SeaMicro servers for their power efficiency,
integration and supercomputer-like performance at a fraction of the cost of
alternative solutions. A single person deployed the system, which contains 128
servers and 512 computing cores, in two days. The deployment, featured in
an AMD case study, has run flawlessly and improved the Gene Center’s other
bioinformatics services such as protein homology searches, which help to
understand unknown proteins.

"For fields such as genetic research,
computing is often a constraint due to the cost of the systems traditionally
used. We are breaking that mold to make HPC more widely available,"
said Dhiraj Mallick, corporate VP and GM, data center server solutions, AMD. "The potential benefits of the research at
the Gene Center are tremendous since they are essentially unlocking the secrets
of how life works at the molecular level."

The work at the Gene Center has the potential to make
medications safer and more effective. Some newer drugs that break down the
bacterial ribosome are only allowed for adults because they may not be safe for
children. The Gene Center’s research could help bring these medications to a
wider population. The 3-D images provide insights into how a protein is built,
which could ultimately lead to the development of new, more effective
medications.

SeaMicro SM15000 system is a high density energy-efficient
server. In 10 rack units, it links 512 compute cores, 160
gigabits of I/O networking and more than 5PB of storage with the 1.28
terabit Freedom Fabric. The SM15000 server eliminates top-of-rack switches,
terminal servers, hundreds of cables and thousands of unnecessary components
for a more efficient operational environment.

SeaMicro server product family currently supports the next generation AMD
Opteron (Piledriver) processor as well as Xeon’ E3-1260L (Sandy
Bridge), E3-1265Lv2 (Ivy Bridge) and Atom N570 processors. The SeaMicro
SM15000 also supports the Freedom Fabric Storage products, enabling a single
system to connect with more than 5PB of storage capacity in two racks. This
approach delivers the benefits of expensive and complex solutions, such as NAS
and SAN, with the simplicity and low cost of DAS.