national center for supercomputing applications gridchem: integrated cyber infrastructure for...

National Center for Supercomputing Applications

GridChem: Integrated Cyber Infrastructure for Computational

Chemistryhttp://www.gridchem.org

Sudhakar [email protected]

10 Oct 2005

http://www.gridchem.org/


Acknowledgements


Motivation

Software - Mature and easy to use to address chemists

questions of interest

Community of Users - Need and capable of using the software Some are non traditional computational

chemistsResources - Various in capacity and capability


Background

Qauntum Chemistry Remote Job Monitor

( Quantum Chemistry Workbench)

1998, NCSA

Chemviz

1999-2001, NSF


Technologies

Web Based Client Server Models

Visual Interfaces

Distributed computing


GridChem

NCSA Alliance was commissioned 1998

Diverse HPC systems deployed

both at NCSA and Alliance Partner Sites

Batch schedulers different at sites

Policies favored different classes and modes of

use at different sites/HPC systems


Grid and Gridlock

Alliance lead to Physical Grid

Grid lead to TeraGrid

Homogenous Grid was planned but it was difficult to keep it homogenous

Things got more complicated and we have heterogeneous grid now!


Extended TeraGrid Facility

www.teragrid.org


Initial Grid Status

Grid Hardware

Middleware

ScientificApplications


Current Grid Status

Grid Hardware

Middleware

Scientific Applications

Interfaces


User Community

Chemistry and Computational Biology

User BaseSep 03 – Oct 04

NRAC AAB Small Allocations

-------------------------------------------------------------

#PIs 26 23 64

#SUs 5,953,100 1,374,100 640,000


User Issues• New systems meant learning new commands• Porting Codes• Learning new job submissions and

monitoring protocols• New proposals for time• Computational modeling became more

popular and users increased • Batch queues are longer / waiting increased• Find resources where to compute - probably

multiple distributed sites• Multiple proposals/allocations/logins• Authentication and Data Security • Data management


Computational Chemistry Grid

Integrated Cyber Infrastructure for Computational Chemistry

Integrates Applications, Middleware, HPC

resources, Scheduling and Data

management

Allocations, User Services and Training


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)IA32 Linux Cluster

12864

1,000,000560,000

Intel Cluster (LSU)Intel Cluster (LSU)

321024

280,0001,000,000

IBM Power4 (TACC) 16 140,000


Other Resources

Extant HPC resources at variousSupercomputer CentersNCSA Tungsten and Copper

Optionally TeraGrid/local/personal resources

These may require existing allocations/Authorization


Applications

• GridChem supports some apps already– Gaussian 98/03, GAMESS, Molpro, NWChem

• Schedule of integration of additional software– ACES-2– Crystal– Q-Chem– Wein2K– MCCCS Towhee – More …..


Details

• Three tiered architecture– GridChem client– middleware server– computational

resources


Grid Middleware Proxy Server

GridChem System

user user useruser user

PPortal Clientortal Client

Grid ServicesGrid Services

GridGrid

applicationapplicationapplicationapplication

Mass Storage

http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0438312


GridChem Client• Graphical user

interface (GUI)• Java desktop

application• Pre and Post

Processing

– helps scientists generate input

– submit and monitor quantum chemistry jobs remotely

– visualize output data

• Leverages internal development projects


GridChem Client Architecture• Composed of several

modules– authentication– job-editor

• molecule builder• visual molecular editor• molecular fragment

database• crystal structure database

– job submission– job manager

• job status info• output monitoring and

retrieval


Allocation

• GridChem is in friendly user mode• GridChem allocations are ready!

Visit https://www.gridchem.org/allocations/policy.htm

Simple one page submission

Password is user generated ( with strong suggestions of the type)

Registration of External allocations possible“Add Users” Facility Available for PI’s

https://www.gridchem.org/allocations/policy.htm


GridChem Client Launch


GridChem AuthenticationRequires a GridChem Login


GridChem Allocation Information


User Preferences


Creating Jobs


GridChem Job Editor


GridChem Job EditorGamess Template


GridChem Job EditorNWChem Template


GridChem Nanocad Molecular Editor


Molecular Editor Based Input


GridChem Job SubmissionJob Object

.

http://www.ncsa.uiuc.edu/UserInfo/Grid/Security/


Submit Jobs


GridChem Job Management


Job Status Information


Monitor Output


Post-ProcessingLexical 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.

• Displays the current (optimized) structure in the Molecular Editor


Post ProcessingResults


Allocations

Existing allocations at various extant

resources are supported

Community allocation to reduce proposal

writing/review “headaches” for already

“funded” research.


User/Community Support• Support provided by distributed set of staff involved in the

project - Chemists, Programmers, Systems Engineers

• Problems tracking through single mechanism - PCS Ticketing System

https://www.gridchem.org/consult/

• Online documentation to be provided on the CCG website - FAQs, Benchmarking Informations, Tips/Tricks etc..

https://www.gridchem.org/consult/


Training and Outreach Integration

• Develop modules on a set of topics– interface fundamentals (e.g., inputs, choice lists, controls, etc.)

authentication/authorization molecular builderjob manager resource managementpost-processing visualizationintegration of additional applications

• Provide as workshops and seminars– 5th Annual Computational Chemistry Conference at the UIUC, April

17-19, 2005 • Annual updates

– track advancements and additional technologies developed and integrate them into CCG


Work In Progress

New Resource Integration Easily manageable Resource Description

Facility to add or remove resources and validation Software Provide Pre and Post Processing for additional

Application SoftwareAutomated Distributed computingMetascheduling across Grid


Applications

• Gamess

• NWChem

• MolPro

Pre and Post Processing Support


Post Processing

Some example Visuals Arginine Gamess/6-31G*Total electronic density 2D - Slices


Molecular Orbitals 2D


3D VRML Views


Questions

We would like to be responsive to community requests

Source is OPEN. Contributions welcome!https://www.gridchem.org/software/software.htm

national center for supercomputing applications gridchem: integrated cyber infrastructure for...

Documents

computational chemistryhttp

teragridhomogenous grid

heterogeneous grid

monitor quantum chemistry

data managementallocations

different classes

user issuesnew systems

user services