KeLP Applications and Transitions
A number of applications use the KeLP library, or the underlying techniques.
- Cell microphysiology. The MCell-K simulator enables large
scale simulations of cell physiology at unprecedented scales and is a
parallel variant of the successful MCell simulator. This is
joint work with Terry
Sejnowksi and Tom
Bartol, Jr. who are with the Computational Neurobiology Laboratory
at The Salk Institute. Further information is available on the MCell-K website.
- Scalable free space Poisson solver. We have developed a
fast 3-D Poisson solver based on a method of local corrections
algorithm, called SCALLOP. This solver currently scales to 1000 IBM SP
processors, and our ultimate target is to run on 4096 processors this
year. This is joint work with Phil Colella in the Applied Numerical
Algorithms Group at Lawrence Berkeley National Laboratory, and is part
of an NPACI Alpha project involving an Immersed
Boundary Method for modeling biological systems (with Kathy Yelick
at the University of California, Berkeley). Further information is
available on the SCALLOP
- Structured adaptive mesh refinement. KeLP defines what an
API should look like for handling communication in a way that
encapsulates the details of low level message passing, e.g. MPI. As a
proof of this concept the techniques embodied in KeLP have been
transitioned into CHOMBO, and library for
structured adaptive mesh refinement developed in the Applied Numerical
Algorithms Group at Lawrence Berkeley National Laboratory. This is
joint work with Phil Colella and Brian van Straalen, and is supported
- Parallel reservoir simulation. Mary Wheeler and
co-workers at the University of Texas at Austin are using
KeLP to implement UTPROJ3D, a single phase flow code for porous
media. UTPROJ3D employs mortar spaces to provide clean numerical
coupling between blocks, which generally are not aligned along the
Manhattan directions. The problem is complicated by the fact that when
we include chemical transport, different numerical computations may be
carried out on different blocks which complicates load balancing. KeLP
facilitates the development and enhancement of this application by
managing the complexity of the underlying irregular representation.
For more information, see the url http://king.ticam.utexas.edu/NPACI/IPARS_KELP_DAGH.
This project is supported by NPACI
as an Alpha project.
- Turbulence simulation. KDISTUF employs Direct
Numerical Simulation to model turbulence and is based on a 10,000 line
legacy fortran code called DISTUF. We are using KDISTUF modernized a
10,000 to simultaneously explore: new algorithms for handling
chemical reaction, high performance animation, and
algorithmic formulation for realizing communication overlap. This is
joint work with M.S. student Bill Kerney, and Dr. Keiko Nomura of the
UCSD MAE Dept. along with Ph.D. students Tamara Grimmet and Peter
Diamessis. For an interesting visualization carried out by
Nicole Borde see the URL http://vis.sdsc.edu/research/smallturublence.html.
This effort is supported by the National Science Foundation.
- Out-of-core KeLP library. KelpIO is a high-level C++ I/O library
for application I/O,checkpointing, snapshoting, and out-of-core execution
for programs written in the KeLP programming system. It was written by
Bradley Broom and Robert Fowler with the Telescoping Compiler project headed
by Ken Kennedy. This library allows users of KeLP to easily
write and optimize I/O using the same high-level, abstract paradigm they
use with KeLP. Moreover, it allows users to quickly convert in-core applications
developed with KeLP into out-of-core applications, using a KelpIO out-of-core
derivative of KeLP's XArrayX construct. For more information
see the URL http://www.cs.rice.edu/~dsystem/kelpio/
- Real space adaptive code for local spin density
computations arising in first principles simulation of real
materials. At 30,000 lines, this is the longest KeLP application we
know of. The code was written by Scott Kohn with the Center for
Applied Scientific Computing at Lawrence Livermore National
Laboratory, and is part of a collaboration involving John Weare
(Chemistry, UCSD), Beth Ong (CASC, LLNL), and Ryoichi Kawai (Physics,
U. Alabama, Birmingham). For more information see the URL http://www.cse.ucsd.edu/groups/hpcl/scg/Research/first.html.
This project was supported by the National Science Foundation.
Maintained by Jacob Sorensen. Last