Cluster Computingthrough an

Application-orientedComputational Chemistry Grid

Kent Milfeld and Chona Guiang, Sudhakar Pamidighantam, Jim Giuliani

Supported by the NSF NMI Program under Award #04-

38312http://www.GridChem.org

April 24, 2005

Outline

• Computational Chemistry Grid Overview

• HPC Application Computing through a Client Interface

• Architecture for the GridChem Client

• Supporting the Virtual Organization

The Big Picture

Computation Chemistry Grid (CCG)“GridChem”

• A collection of “grid-enabled” resources to routinely run chemical physics applications

• Integrates a desktop environment into an infrastructure for a specific community of users– comp. chemists with large/small scale needs– experimental chemists who occasionally need

simulation capabilities to verify experimental results

• Establishes a distributed infrastructure for open scientific research– a virtual organization

The Components

• Applications

• Resources

• Desktop Environmentthe GridChem Client

Compute Intensive 0.1-100 hrs runs

High Speed Infrastructure Not Needed

4 – 16 CPUS/job

Batch Support

Secure Access (grid-enabled)

Multi-platform support (XP, OS X, Linux)

Responsive

Client Interface to the Grid

Cluster Systems

Ψ=ΗΨ EAtoms, Small Molecules, Clusters

Electronic Structure

Applications• GridChem supports some apps already

– Gaussian 98/03, GAMESS, MolPro

• Schedule of integration of additional software– NWChem– ACES-2– Crystal– Q-Chem– NBO– Wein2K– MCCCS Towhee

• homegrown computational chemistry codes developed at LSU

Computational Chemistry Resource Providers

TACCCCT

NCSA

CCS OSC

Resources

Over 400 processors and 3,525,000 CPU hours available annually

System (Site) Procs Avail Total CPU Hours/Year

HP Intel Cluster (OSC) 12 100,000

Intel Cluster (OSC) 36 315,000

Intel Cluster (UKy) 96 840,000

HP Integrity Superdome 33 290,000

Intel Cluster (NCSA) 64 560,000

SGI Origin2000 (NCSA) 128 1,000,000

Intel Cluster (LSU) 32 280,000

IBM Power4 (TACC) 16 140,000

Desktop

Use your workstation!

Data Storage

Graphics

Computing Resource

596 MB for Internet Files

Intel: GMA 900 Graphics,…Mac: ATI Radeon 9200 with 32MB DDR

Gigaflop Processors

GigaBytes for Storage

Desktop -- GridChem• Java Based Client

– “Same” Look and Feel on “every” machine.– Consistent Environment

• No Globus Installation

• Designed for “Application Services” through a Server; but

• Can be used as Stand-Alone Client for job submission

3-tier Architecture

GridChem Client GC Middleware Server HPC Resources

Authentication

KerberosMyProxySSHmodules

Resource specs. into Local Batch SpecsBatch Script Queue Submission

Application Execution +Output & File Transfers

inputs, resource specs. & temp. cert. transfer

Kerb. & MyProxyServers

Input PreparationMolecular Editor

Application OptionsSite Info (stat./dyn.)

J2EE

MySQL

Site Monitors

Site PreferenceJob Submission Resource

Management

File Management

RemoteStorage

MolecularEditor +Visualization

User See Two-Tier Architecture

Infrastructure (now)• Server, GridChem Client*

– MyProxy (X-500 Certs), Kerberos (Security)– CGI Scripts GSI

( for Data Movement & Job Launch)

• Job Monitoring– Perl filters, MySQL

• Support– PCS, Portable Consulting Service

• EOT– OSU

*

Infrastructure (future)• Server

– Condor + ? (Job Launch)– GSI ( Data Transfer, uberftp)– Information Repository (IGRID, GPIR,…?)

• Support– GridPort 3.0 Monitoring,

Consulting (PCS), Accounting…

Infrastructure (future)• GridClient

– 3-rd party file transfers (Trebuchet)– More intelligence in input construction– Increase Application Space– Web Start– Indirect DB access for preferences– Advanced visualization support (Molden,…)

• Resource Sites– Condor– Globus Utils

GridChem Client

GridChem Client

GridChem Nanocad Molecular Editor

Lexical Analysis And Parsing

• Follows the progress of the calculation while it is still running or has completed.

• Plots the energy, gradient, etc versus iteration number.

Monitoring

User

Storage

HTTPHTML,PHP,…

Service

Login

DB

Batchcron

Filter

Job-Status-Monitor = JSM

Consulting

Database

Report Problem

User Interface

Consultant Interface

Email Notification

Further Interaction

ConsultantMonitorPage

Front-line triage

TicketTransfer &ResponsePage

Ticket Owner& CCs

Problem Form

PersonalizedMonitorPage

Email Notification

Notifications

User Submission

Consultant ViewConsultant’s View

Post Processing2d and 3d Orbital isosurfaces

Using NCSAChem/Slice/Molden/Cartona/Free Software

Molecule Viewers

Electron Structure: Orbitals or electron densities,…

5-dehydro-m-xylylene triradical

Transcription Regulator(molecular modeling)

Summary

• GridChem Client

• Resources

• Community

“Better Living Through Chemistry”

References

• www.gridchem.org

• www.grids-center.org

• www.gridlab.org/