Integrated Environment for Computational Chemistry on the

APAC Grid

Dr. Vladislav VassilievDr. Vladislav Vassiliev

Supercomputer Facility, The Australian National University, Supercomputer Facility, The Australian National University,

ACT 0200, Canberra, AustraliaACT 0200, Canberra, Australia

Concept of the National Grid

Other Grids:

InstitutionalNational

International

Other Grids:

InstitutionalNational

International

Data Centres

Data Centres

Instruments

SensorNetworks

Research Teams

grid-based portalsdistributed computationfederated data access

remote controlcollaboratories

QPSF

ANU

VPAC

ac3

TPAC

CSIRO

Job Monitoring:Scope

Job Management:Globus, PBSNimrodLCG

Job Submission:Command LinePortals

Computing Systems: Peak Mid-range Special

IVEC

SAPAC

APACNational Facility

APAC National GridComputing Grid Infrastructure

QPSF(JCU)

Systems coverage•Users can access ALL systems at APAC partners•About 4600 processors and 100’s of Tbytes of disk•Around 3Pbytes of disk cached HSM systems

Integrated Environment for Computational Chemistry on the APAC

Grid

Supercomputer(s)

Client

What does it mean “Integrated Environment”?

“Integrated Environment”: Overall Architecture

JMolEditor

Shelves

Gaussian

Amber

Gamess

Gromacs

Job submissionJob MonitoringGetting results

Providers:GT2GT4SSHLocal

Tripos Mol2

PDB

Inpu

t Fil

e F

orm

ats

Inpu

t Fil

e P

repa

rati

on Gaussian

Amber

Gamess

Gromacs

Database

JMolEditor

There are two standalone programs,

JMolEditor and Shelves

“Integrated Environment”: Rich User Interface

High-performance 3D

rendering

Intuitive Intuitive interface for interface for

unexperienced unexperienced usersusers

“Integrated Environment”: Support for popular Computational Chemistry

Formats

Gaussian

GAMESS

Mopac

PBD

Tripos Mol2

Amber

Gromacs

etc.

The most popular Computational Chemistry Programs on the National Facility (1920 CPUs)

Chemistry Software Usage (%)gaussian 18.1gamess 0.01mopac 0.32amber 3.1

gromacs 1.02charmm 3.8molpro 2.1

vasp 8.5namd 4.4

nwchem 0.03siesta 1.9

Our primary targets are the most popular

programs in the Computational

Chemistry community

Of total wall time on the Altix

cluster (1920 CPUs)

“Integrated Environment”: Preparation of input files for popular programs

Simple Gaussian Input Editor

“Integrated Environment”: On-line and in-built help system and tutorials

Tracking Help

Help

“Integrated Environment”: Molecular Builder/Editor

Adding/deleting Atoms

Adding Fragments

Adding Molecules

Modifying atoms, bonds, angles, dihedral angles

Automatic filling of empty valences with hydrogens

“Integrated Environment”: Visualizing Volumetric Data (Gaussian cubes)

“Integrated Environment”: Implementing a Full Production Cycle

Structure Preparation

Input FilePreparation

Job Submission

Job Status Query

Output FilesDownload

Calculated Structure Visualization

“Integrated Environment”: Job Submission

Common options for all programs

Program specific options

Provider Specific Options

Scheduler Specific Options

All complexities of the Grid job

submission are hidden behind a

dialog

“Integrated Environment”: Job Status Monitoring

To download output files To kill selected

jobs

System requirements

• Mac OS

All is already there…

• MS Windows and Linux

1) The Java Runtime Environment (JRE) ≥ 1.5

2) Download and install Java3d (freeware optional component)

Download Site for JMolEditor

• http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.htmlOption 1: Download a program to run it on a desktop

Option 2: Run from a website using Java Web Start

• On-line Help

What will be next?

• Support for more Computational Chemistry Programs (visualization, input files preparation, analysis of final results)

• Adding new features according to the user’s requests…