Keynote
|
Title |
|
Linux and Commodity PC Clusters: The HPCC Phase Change |
Author |
Dan Reed |
Author Inst |
NCSA, University of Illinois |
Presenter |
Daniel A. Reed |
Abstract |
A revolution is underway! Open source software and commodity
PC clusters bridge the HPC computing divide, uniting both developers of community
application codes and system software researchers. The phase change from
proprietary systems to commodity HPC clusters with extraordinarily high performance
is here -- ride the exponential!
|
Title |
Linux and Linux Clusters at IBM Clusters:
The HPCC PHase Change |
Author |
Dave Turek |
Author Inst |
IBM |
Presenter |
Dave Turek |
Abstract |
IBM has been heavily engaged in Linux activities for over
two years now. This presentation will review IBM's Linux strategy and associated
Linux activities, including recent announcements covering the creation of
an Open Source Development Laboratory in Portland as well as the investments
made in Europe and Asia for Linux porting and development centers. It will
also address our more recent activies with Linux clusters and give a perspective
on how we expect technology in this space to evolve and the solutions and
services
IBM will supply.
|
Applications Track Abstracts:
|
Applications Session I
|
Title |
Comparing Clusters
and Supercomputers for Lattice QCD |
Author |
Steven Gottlieb |
Author Inst |
Indiana University |
Presenter |
Steven Gottlieb |
Abstract |
The MILC family of codes for studying Quantum Chromodynamics
(QCD) are highly portable and have been run on supercomputers such as the
Cray T3E/D, Origin 2000, IBM SP, Intel Paragon and HP Exemplar. More recently,
they have been run on clusters such as Roadrunner, Los Lobos, the NT Supercluster
at NCSA and the Teracluster at LLNL. This talk will describe the potential
performance bottleneck and benchmarks on several of the systems mentioned
above.
Prospects for future clusters may be discussed.
|
Title |
Project Vista Azul: The Development
of a Hybrid UNIX "Hypercluster" |
Author |
Thomas More Jackman |
Author Inst |
IBM Research |
Presenter |
Thomas More Jackman |
Abstract |
Currently in progress is a collaborative research endeavor
between The University of New Mexico and IBM to construct a heterogeneous
infrastructure to do concurrent scientific and visual computing. It is called
Project Vista Azul. The project seeks to create a unified computing resource
from a hybrid of technologies which includes a cluster of IBM SP nodes running
the AIX version of UNIX and another cluster of IA32 Netfinity nodes running
Redhat Linux. This heterogeneous composite of hardware, software, and networking
has been referred to as a "hypercluster". The project seeks to investigate
the merits of leveraging the best of proprietary and commodity hardware and
software to do distributed computation and scalable visualization and to
address the issues of interoperability between the components. It is seen
as a prototype for the productive integration of the Linux operating system
into existing UNIX environments. Included in Project Vista Azul is a novel
technology, called the Scalable Graphics Engine, which is used for providing
synchronous, high bandwidth streaming of rendered pixels from nodes participating
in distributed
visualization out to an immersive system of displays.
|
Applications Session II
|
Title |
Automatically Tuned Linear Algebra Software (ATLAS) |
Author |
Clint Whaley |
Author Inst |
University of Tennesee, Knoxville |
Presenter |
Clint Whaley |
Abstract |
Geophysical models of seismic sound wave propagation, solid
state convection in the This talk will describe the ATLAS (Automatically
Tuned Linear Algebra Software) project, as well as the fundamental principles
that underly
it. ATLAS is an instantiation of a new paradigm in high performance library
production and maintenance, which we term AEOS (Automated Empirical Optimization
of Software); this style of library management has been created in order
to
allow software to keep pace with the incredible rate of hardware advancement
inherent in Moore's Law. ATLAS is the application of this new paradigm to
linear
algebra software, with the present emphasis on the Basic Linear Algebra
Subprograms (BLAS), a widely used, performance-critical, linear algebra kernel
library. Further information is available at: www.netlib.org/atlas
|
Title |
DynaProf and PAPI:
An Object Code Instrumentation System for Dynamic Profiling |
Author |
Phil Mucci |
Author Inst |
IBM ACTC/University of Tennessee, Knoxville |
Presenter |
Phil Mucci |
Abstract |
This talk will introduce PAPI and an associated tool called
DynaProf. PAPI, the Perfomance Application Programming Interface is a portable
library that gives the developer sophisticated access to the hardware performance
counters present on a variety of Microprocessors, from Pentiums to Powers.
Statistical profiling and sampling is supported as well as traditional aggregate
counts. See http://icl.cs.utk.edu/projects/papi for
more information.
DynaProf is a tool that uses DynInst from The University of Maryland. DynInst
allows the developer to directly modify object code through a C++ interface.
DynaProf uses DynInst to insert modular instrumentation at key points in
the code. This instrumentation is in the form of loadable modules to generate
profiles based on wallclock time, hardware counters or sampling of the PC
for input to a variety of reporting tools.
|
Title |
The Interfacial Behavior
of Liquid Water |
Author |
Paul Alsing, Will Matthews, Cara Slutter, Evangelos Coutsias,
John McIver |
Author Inst |
University of New Mexico |
Presenter |
Paul Alsing |
Abstract |
The important properties of water stem from its unique structure
and the way this structure allows water to interact with electrically charged
molecules. Such properties are thought to arise from the ability of water
to form tetrahedrally coordinated hydrogen bonds. Water is unusual as both
a liquid and a solvent. The insertion of nonpolar solutes into water is strongly
unfavorable, called the ''hydrophobic effect'', while polar molecules dissolve
freely and are characterized as ''hydrophilic''. It is thought that the physics
of the hydrophilic and hydrophobic reaction is strongly affected by interfacial
curvature. This work investigates the surface arrangement and orientation
of water molecules near flat and curved hydrophobic surfaces. The effects
imposed by the hydrophobic surface on surface arrangement and orientation
of water molecules represent the balance between the tendencies of water
to maximize the number of hydrogen bonds on the one hand and maximize the
packing density of
molecules on the other.
To facilitate the investigation of water our research utilizes a 3D version
of the parallel force decomposition molecular dynamics algorithm [1,2] to
model the effects of a large number of water molecules interacting amongst
themselves and the hydrophobic surface. MD simulations involve repeated calculations
of pair-wise interactions between constituent atoms. These calculations can
be performed independent of each other and are thus ideally suited for parallelization.
We use the recently developed force decomposition algorithm wherein the pair-wise
force interactions of the form Fi,j are evenly distributed over available
processors. Here, Fi,j is the force on particle i due to particle j. In contrast
to atom decomposition and spatial decomposition techniques, this method affords
ease of load balancing and performs well for intermediate number of atoms
even for irregular geometries. The use of MPI communication splitting routines
allows independent collective communication between user defined groups of
processors. This feature is used to split the processors into row communicators
(the ith index of the force) and column communicators (the jth index of the
force). The interactions between the molecules are calculated in a separate
module and can be of van der Waals or any other user specified type. For
our model of water we use a Hartree-Fock pair potential [3] and the hydrophobic
surface is represented as a potential formed from integrating the Lennard-Jones
interaction of a single water molecule with all the molecules in the interfacial
surface [4]. In this work we investigate (1) water between two infinite slabs
in the z-direction with periodic boundary conditions in the x and y directions,
and (2) hydrophobic spheres of various radii and of uniform density imbedded
in the water.
Molecular dynamics simulations tend to produce copious amounts positional
data in exquisite detail. Visualization therefore becomes an important tool,
not only to observe results but also to monitor and analyze the real time
calculations. In this talk we will describe our work in utilizing OpenDX
[5] (IBM's Data Explorer, now open source) as a tool transfer data to and
from an executing simulation for real- time visualiztion and computational
steering. We have developed DX TCP/IP import and export modules that allow
data to be operated upon and visualized in either DX itself or a third party
visualization environment. We demonstrate the later by using these modules
to visualize our MD simulation in DX and in Flatland [6]. Flatland is an
open development shell for the creation of interactive, immersive visualizations.
New data objects are easily added to the environment, allowing the scientist
to locomote around the data from within a virtual vessel. This allows the
researcher to directly interact with the data, and to control any simulation
in real time that is producing the data.
References:
- S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics,
J. Comp. Phys. 117, 1
(1995); S. Plimpton and B. Hendrickson, A New Parallel Method for Molecular
Dynamics
Simulation of Macromolecular Systems, J. Comp. Chem. 17, 326 (1996).
- P.M. Alsing, E. Coutsias and J. McIver, "The Interfacial Behavior of
Liquid Water Near
Hydrophobic Surfaces: a Parallel Force Decomposition Molecular Dynamics
Code," in High
Performance Computing in Engineering VI, Eds. M. Ingber, C.A. Brebbia and
H. Power, WIT
Press, Southhampton, Boston (2000).
- F. Franks, Ed. Water: A Comprehensive Treatise, Plenum Press, N.Y., 1972-1982,
Vol 6, p317.
- C. Y. Lee, J.A. McCammon and P.J. Rossky, The Structure of Liquid Water
at an Extended
Hydrophobic Surface, J. Chem. Phys. 80, 4448 (1984).
- http://opendx.org/
- http://www.hpc.unm.edu/homunculus.
Flatland was created at the University of New Mexico's
Albuquerque High Performance Computing Center by Dr. Thomas P. Caudell,
Electrical
Engineering and Computing Engineering Department, tpc@ahpcc.unm.edu.
|
Applications Session III
|
Title |
High-Resolution
WeatherForecasting on Linux Superclusters |
Author |
Daniel B. Weber |
Author Inst |
University of Oklahoma |
Presenter |
Daniel B. Weber |
Abstract |
The history and future potential of storm-scale weather prediction
with ARPS: Are we on the verge of high-resolution continental scale weather
prediction using cluster technology?
The speaker will present a brief history regarding the development of the
Advanced Regional Prediction System (ARPS) including the forecasting joys
and failures behind the web-page glamour. The second half of the presentation
will focus on the details of running a forecast system with an emphasis on
the performance and optimization issues. Compiler developers and microprocessors
designers are encouraged to attend.
|
Title |
Binary Black
Hole Simulations on Clusters |
Author |
David Neilson |
Author Inst |
University of Texas |
Presenter |
David Neilson |
Abstract |
With the advent of gravitational wave detectors (LIGO, VIRGO,
GEO, TAMA, LISA), understanding physical systems which exhibit strong gravitational
fields is not only of mere mathematical interest, but also of fundamental
astrophysical importance. Prior knowledge of the waveforms that would be
measured by these detectors would expedite the search and characterization
of these strongly gravitating systems. This possibility opens up a new window
to the universe through which researchers will be able to obtain answers
to important questions, ranging from properties of the sources that produced
the waves to the very origin of our universe. Prime candidates for producing
detectable sources of gravitational waves of sufficent strength waves that
could be detected are binary systems containing neutron stars and/or black
holes. The dynamics of strong non-linear fields associated with these systems
can only be accurately modeled by solving Einstein equations in their full
generality. Owing to the involved nature of the equations and the generality
of the prolbem, numerical techniques must be used to obtain the solutions.
We describe our efforts aimed towards obtaining an simulation of binary black
hole
systems and our usage of RoadRunner and LosLobos for such a task.
|
Title |
EIGER on Cplant |
Author |
Joseph D. Kotulski, Roy E. Jorgenson, William A. Johnson,
and Larry Warne |
Author Inst |
Sandia National Laboratories |
Presenter |
Joseph D. Kotulski |
Abstract |
EIGER ( Electromagnetic Interactions GEneRalized) is an
electromagnetics code that solves the integral equation description of Maxwell
s
Equations. It is formulated in the frequency-domain and designed to integrate
a variety of analysis methods into a single package. The code suite consists
of a
pre-processor, computational engine, and post-processor. EIGER is written in
Fortran 90 and uses object-oriented design that results in a computational
engine that is general, flexible, and extendable. The capabilities to treat
surfaces, wires, wire-surface junctions, multi-layer media, periodic structures,
and dielectric media are present as well as the flexibility to choose different
integral equation operators. In addition coupling models have been introduced
that enable the analysis of thin-slot coupling into cavities.
The solution process consists of generating a matrix equation using the
Method of Moments. This complex-dense matrix is solved using LU factorization
configured and optimized for parallel platforms.
The solution to some representative problems that expose the code capabilities
will be presented as well as performance on the Cplant parallel platform.
.
|
Clusters Abstracts:
|
Clusters I
|
Title |
Scalable
Cluster Interconnect: Overview and Technology |
Author |
Charles L. Seitz |
Author Inst |
Myricom, Inc. |
Presenter |
Charles L. Seitz |
Abstract |
Physics and technology govern the speed of "tightly coupled" computing
devices. Within a given technology, the smaller the device, the faster and
more efficiently can it function. In the interests of performance, efficiency,
and reliability, large computing systems must necessarily be composed of
parts that can operate relatively independently (concurrently), and can tolerate
some latency in the communication between these parts. Computing clusters
apply this "principle of locality" at the scale of parts that are programmable
computers, referred to as hosts or nodes, tied together with a message-passing
network. Clusters are scalable in two senses. They are arbitrarily scalable
in the number of host computers, and are thus open-ended in aggregate peak
performance. One does not need to reduce the clock rate of the host computers
as the diameter of a cluster grows. However, the utilization or efficiency
of the hosts may be limited by the way in which a computation is distributed
amongst processes -- the same principle coming into play at the higher level
of processes as parts. Clusters also scale well with technology. Inasmuch
as the cluster architecture and distributed programming respect the principle
of locality, clusters will directly and easily exploit future advances in
circuit technology.
|
Title |
The Linux/IA64 Project |
Author |
Khalid Aziz |
Author Inst |
Hewlett Packard Co. |
Presenter |
Khalid Aziz |
Abstract |
IA-64 is the next generation high performance 64-bit architecture
designed jointly by HP and Intel. This talk will focus on HP Labs' effort
on porting Linux to IA-64 architecture. We will take a look at the IA-64
architecture highlights and the Linux/ia64 project. We will delve into IA-64
Linux kernel design and take a look at the tools used during the porting
process.
|
Clusters II
|
Title |
Cplant Architecture |
Author |
Rolf Riesen |
Author Inst |
Sandia National Laboratories |
Presenter |
Rolf Riesen |
Abstract |
The Computational Plant (Cplant(tm)) project at Sandia National
Laboratories started out as a small research project with a 96-node cluster.
Over the last three years new hardware has been added and we are about to
deploy a ~1600-node Linux cluster later this Fall. In this talk I will describe
the hardware architecture we have developed and the design decisions we have
made to scale a cluster to this size. The talk will go into details on how
the hardware and system software is organized so it can be managed as a single
machine even
though it consists of thousands of off-the-shelf components.
|
Title |
Clusters for a Multi-User, Production-Computing
Environment |
Author |
Robert Eades |
Author Inst |
Pacific Northwest National Laboratory |
Presenter |
Robert Eades |
Abstract |
The Pacific Northwest National Laboratory is active in developing
and porting so ftware to increase the production quality computing capabilities
for clusters in a multi-user environment. The primary PNNL Linux cluster
system, a 194-processo r system, is located in the Molecular Science Computing
Facility. Cluster softwa re development activities encompass
- system infrastructure software (scheduling, resource allocation management,
etc.),
- parallel programming tools and libraries (Global Arrays),
- parallel scientific applications software (NWChem, NWGrid/NWPhys, etc.),
and
- problem solving environments (Ecce).
An overview of these activities will be presented, along with performance
results.
|
Clusters III
|
Title |
The Flatland Visualization
Environment |
Author |
Thomas P. Caudell |
Author Inst |
University of New Mexico |
Presenter |
Thomas P. Caudell |
Abstract |
Flatland is a visualization/virtual reality application development
tool developed at the University of New Mexico. It allows software authors
to construct and users to interact with arbitrarily complex graphical and
aural representations of scientific data sets and complex software systems.
Flatland is written in C/C++ and uses the standard OpenGL graphics language
extensions to produce the 3D graphics. In addition, Flatland uses the standard
GLUT library for window, mouse, and keyboard management, and therefor supports
any type of display technology. Flatland is multithreaded and uses dynamically
linked libraries (DLL) to load applications that construct or modify its
virtual environment (VE). In addition, Flatland is currently being parallelized
to run on Linux clusters, and to interact with the NSF Access Grid. This
talk will give an overview of the features Flatland , give examples of applications
that use
Flatland, and discuss current research issues.
|
Title |
PowerPC Linux |
Author |
Gregory P. Rodgers |
Author Inst |
IBM |
Presenter |
Gregory P. Rodgers |
Abstract |
Of the many architectures that Linux runs on, PowerPC is
the most scaleable platform. Linux on PowerPC spans from embedded processors
through high end 64-bit SMP supercomputers. The variety of features supported
by PowerPC Linux is evident in the many Linux configuration options found
in the arch/ppc branch of the Linux source tree. This talk will sort through
the key features of PowerPC Linux. These features include support for POWER3
and POWER4 that will be
available with Linux 2.4.
|
Building a Computational Grid
|
Title |
Clustering Ohio: From the TeraFlop
to the Desktop |
Author |
Al Stutz |
Author Inst |
Ohio Supercomputer Center |
Presenter |
Al Stutz |
Abstract |
OSC has been active in cluster computing since 1994, building
a total four clusters so far with the largest system (132 processors) being
shown on the exhibit floor of Supercomputing 1999 in Portland, Oregon. OSC
develops hardware acquisition plans in concert with the Ohio user community's
needs. OSC and the Ohio user community have recently set a more aggressive
direction in cluster computing. A new program has been created to encourage
faculty throughout the state to build a local clusters in their labs to compliment
the central cluster at OSC. This concept centers around a state wide software
licensing program and a hardware grant program.
OSC will present several user success stories, including experiences and
performance metrics.
.
|
Networking
|
Title |
Portals 3.0: A High-Performance,
Message-Passing Layer Supporting Application-Bypass |
Author |
Arthur B. (Barney) Maccabe |
Author Inst |
University of New Mexico |
Presenter |
Arthur B. (Barney) Maccabe |
Abstract |
OS-Bypass involves putting the policies of the host operating
system on the network interface card (NIC) so that communication need not
incur the costs associated with interrupting the host processor. Application-Bypass
takes OS-Bypass to the next step, putting the policies of the application
on the NIC. This talk will review the common themes that have evolved in
high-performance networking over the past several years, including zero-copy
message passing and OS-bypass. We will then present examples motivating Application-Bypass
and describe the Portals 3.0 interface that has been designed explicitly
to support Application-Bypass.
|
Title |
MPICH on Clusters: Future
Directions |
Author |
Rajeev Thakur |
Author Inst |
Argonne National Laboratory |
Presenter |
Rajeev Thakur |
Abstract |
We are redesigning and reimplementing MPICH from scratch
to support newer networking technologies such as Myrinet and VIA, multithreading,
MPI-2 functionality, and also for better performance and scalability of existing
communication methods such as TCP and shared memory. Key to the new design
is a new internal abstract-device interface for MPICH called ADI-3. This
talk will describe the design of the new version of MPICH and provide an
update on the
implementation status.
|
Title |
M-VIA and MVICH:
Status and Future Plans
|
Author |
Michael L. Welcome |
Author Inst |
NERSC Future Technologies Group |
Presenter |
Michael L. Welcome |
Abstract |
The Virtual Interface Architecture (VIA) is an industry standard
that enables high-performance communication on a cluster. It provides user-level
zero-copy data transfers, enabling low latency and high bandwidth communication.
M-VIA is a modular implementation of VIA for Linux that provides high performance
and ease of portability to new network interfaces. MVICH is an MPICH-based
implementation of MPI using VIA at the transport layer. This talk will discuss
the current status of both software projects and indicate future
directions.
Both M-VIA and MVICH are available under a BSD-style license. For more information
and instruction on how to download the current versions, please see:
http://www.nersc.gov/research/FTG/via
http://www.nersc.gov/research/FTG/mvich
|
