Contents:
NBodyLab has been demonstrated and presented at three
Astronomical Data Analysis Software and Systems (ADASS) conferences:
The
GRAPE family of special purpose computers has two branches, GRAPE's
designed
for astrophysics, and MD-GRAPE's, whose force-functions have been
extended for molecular dynamics (MD) and biological applications.
See the GRAPE
History page for more
information.
Development began when Vicki Johnson, an entrepreneur and software systems engineer, was given a small contract in 2002 by Pomona College to get a MD-GRAPE2 card working to enable students studying cosmology to run stellar dynamics simulations. This was a challenge. The MD-GRAPE2 hardware and software developers work in Japan; little documentation was available; no numerical integration program was available to access the MD-GRAPE libraries for the force calculations, and the astronomy professor was unfamiliar with the MD-GRAPE2 and software options for n-body simulations. Furthermore, most of the students didn't know Unix or X-windows, or even how to program. Theft was a risk if the expensive MD-GRAPE2 server was physically accessible to students. The best solution seemed to be to develop server-side integrators to access the MD-GRAPE hardware, incorporate existing routines for analysis and visualization from an existing Nbody toolboxes like NEMO, and front the package with a web interface. Time and budget were quite limited. With luck, perseverance, and assistance especially from Dr. Peter Tueben and Dr. Bruce Elmegreen, Vicki engineered a successful system. Dr. Tueben suggested the name "NBodyLab." The MD-GRAPE2 NBodyLab system has been used by students for course assignments - in a cosmology course 1, 2, 3, a senior project, an AAS poster, and a master's thesis. The Pomona College NBodyLab MD-GRAPE2 system is usually accessible; Pomona College lacks funds to maintain it.
After
concluding the contract with Pomona College in 2002, Vicki
explored R&D and business prospects. She visited Japan
and met many (MD)GRAPE researchers, all experienced PhD's.
She met Prof. Jun Makino at Tokyo University, designer of the GRAPE, and and during a visit to RIKEN scientists she installed her software
on their demonstration MD-GRAPE2 machine. She was shown
the large
supercomputers with arrays of GRAPE (left photo below) and MD-GRAPE2 boards (right photo below)
that have won the prestigious Gordon Bell Prizes:
 Useful letters of recommendation were provided to Vicki: 1, 2, 3, 4, 5 . In 2003 Vicki led the writing of a multi-million dollar proposal to the NSF for a GRAPE-based Nbody simulation facility, by an international interdisciplinary team. The proposal was not funded; one reviewer wrote that the hardware was not specified (!). It was an interesting process developing a large academic proposal. On the business side,
Vicki has discussed commercial applications of MD-GRAPE systems with
senior managers at
several leading US research laboratories specializing in hardware
development and biotechnology. Concerns were expressed about the
business viability of
incorporating research-grade technology
developed by the Japanese in commercial US products;
uncertain
service and support costs for research-grade technology (the MD-GRAPE2
was sensitive to
voltage fluctuations, since resolved); limitations of the
MD-GRAPE algorithms for efficient MD (e.g., neighbor list handling);
difficulties quantifying the performance
benefits of the MD-GRAPE hardware acceleration for
applications such as drug design; the high level of expertise
required to
adapt the MD-GRAPE2 into commercial packages used for biotech research;
and
the general conviction that general-purpose desktop and cluster
computing performance will continue to rapidly
improve and displace special-purpose hardware. Vicki believes researchers and software developers will
benefit from learning about current GRAPE technologies because Japan
continues to
fund GRAPE development at a high level, for more general
applications
and for biocomputing
applications such as protein
modeling with the MD-GRAPE family. Vicki continues to discuss GRAPE applications with academic, business and government sectors. For the Nbodylab.org website, she has enjoyed improving the numerical integration algorithms and visualization options to demonstrate the new GRAPE-6a.
To sign up for news, get help or request permission for longer simulations,
write to nbodylab@interconnect.com. |
The
first version
of Nbodylab.org was implemented using an MD-GRAPE2 board
(generously loaned to Vicki Johnson by RIKEN/
In
2004,
Alper Ates completed his
master's thesis using NbodyLab. Mr.
Ates shared his love of astronomy
in many discussions, some held in a local observatory on beautiful
nights. A 2004 
