Cluster Computing through an Application-oriented Computational Chemistry Grid Kent Milfeld and Chona Guiang, Sudhakar Pamidighantam, Jim Giuliani Supported by the NSF NMI Program under Award # 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 Environment the GridChem Client Compute Intensive 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 Atoms, 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 TACC CCT NCSA CCSOSC

Resources Over 400 processors and 3,525,000 CPU hours available annually System (Site)Procs AvailTotal CPU Hours/Year HP Intel Cluster (OSC)12100,000 Intel Cluster (OSC)36315,000 Intel Cluster (UKy)96840,000 HP Integrity Superdome33290,000 Intel Cluster (NCSA)64560,000 SGI Origin2000 (NCSA)1281,000,000 Intel Cluster (LSU)32280,000 IBM Power4 (TACC)16140,000

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 ClientGC Middleware ServerHPC Resources Authentication Kerberos MyProxy SSH modules Resource specs.  into Local Batch Specs  Batch Script  Queue Submission Application Execution + Output & File Transfers inputs, resource specs. & temp. cert. transfer Kerb. & MyProxy Servers Input Preparation Molecular Editor Application Options Site Info (stat./dyn.) J2EE MySQL Site Monitors Site Preference Job Submission Resource Management File Management Remote Storage Molecular Editor + 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 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 HTTP HTML,PHP,… Service Login DB Batch cron Filter

Job-Status-Monitor = JSM

Consulting Database Report Problem User Interface Consultant Interface Notification Further Interaction Consultant Monitor Page Front-line triage Ticket Transfer & Response Page Ticket Owner & CCs Problem Form Personalized Monitor Page Notification Notifications

User Submission

Consultant View Consultant’s View

Post Processing 2d 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