The Application Hosting Environment

1
The Application Hosting Environment

• Lightweight Middleware for Grid Based
  Computational Science
• Peter Coveney and Stefan Zasada Centre for
  Computational Science University College London

2
Contents

• Motivation for the AHE
• Concepts functionality
• Meeting the AHE design constraints
• Architecture of the AHE
• AHE client interaction
• Deploying the AHE
• Investigating the molecular dynamics of HIV-1
  protease using the AHE
• Future plans

3
Motivation for the AHE

• Problems with current middleware solutions
• Difficult for an end user to configure and/or
  install
• Dependant on lots of supporting software also
  being installed
• Require modified versions of common libraries
• Require non-standard ports to be opened on
  firewall
• Large footprint memory/disk space

4
The Application Hosting Environment

• Based on the idea of applications as Web Services
• Lightweight hosting environment for running
  unmodified applications on grid resources
  TeraGrid, NGS, DEISA gt potentially a uniform
  interface to everything
• Expert user installs and configures an
  application and uses the AHE to share it with
  others
• Simple clients with very limited dependencies
• Application Instance/Simulation is central
  entity represented by a stateful WS-Resource

5
Global Grid Infrastructure
UK NGS
NGS
US TeraGrid
Starlight (Chicago)
Netherlight (Amsterdam)
SDSC
NCSA
PSC
UKLight
DEISA
AHE
All sites connected by production network
Run DL_Poly, NAMD, LAMMPS, LB3D, etc. simulations
Computation
Network PoP
Visualization
6
AHE Functionality

• Launch simulations on multiple grid resources
• Single interface to monitor and manipulate all
  simulations launched on the various grid resource
• Not all resources will allow SSH access
• Can use a combination of different clients PDA,
  desktop GUI, command line

7
AHE Design Constraints

• Client does not have Globus installed locally
• Client is NAT'd and firewalled
• Client does not have to be a single machine
• Client needs to be able to upload and download
  files but doesnt have local installation of
  GridFTP
• Client doesnt maintain information on how to run
  the application
• Client doesnt care about changes to the backend
  resources

8
Meeting the Constraints

• AHE Client behind firewall gt polls server to
  update job state etc.
• Uses intermediate filestaging area gt GridFTP not
  installed
• All application specific information for running
  simulations on the grid resource is maintained on
  a central service gt user can switch clients etc.
• Location of binary on grid resource configured on
  server gt user doesnt need to know
• GridSAM provides interface to job queue

9
Architecture of the AHE
10
AHE Server Implementation

• WSRFLite
• Webdav server
• GridSAM gt Globus grid
• gt Sun Grid Engine
• gt Condor pool
• gt Unicore planned September 06
• MyProxy
• PostgrSQL database
• Apache/Tomcat container

11
Client Implementation

• GUI command line clients implemented in Java
  using Apache AXIS
• Client allows user to
• Discover Appropriate Resources
• Launch Application
• Monitor Running Jobs
• Query Registry of Running Jobs
• Stage Files to and from Resource
• Terminate Jobs
• GUI client implements application launching as a
  wizard

12
Client Extensibility

• Plugins allow application input files to be
  parsed to automatically discover the input and
  output files that need to be staged
• If no plugin is available then a default case
  will allow users to specify input and output
  files manually
• Plugins implement AHEConfParser interface and
  follow specific naming convention
• Plugin .class files dropped into plug-in
  directory and picked up by GUI/command line
  clients

13
AHE Server Deployment

• The expert user must
• Set up container to host services
• Apache/WSRFLite or modified Tomcat/WSRFLite
• Set up PostgreSQL database and WebDav server
• If not already running set up GridSAM instance
  for grid resource
• Install and configure application on grid
  resource and edit AHE configuration file to point
  to it.
• Documentation covers whole process of deploying
  AHE applications on both TeraGrid and NGS

14
AHE Client Deployment

• Deploying client is trivial for the end user
• Users machine must have Java installed
• User downloads and untars client package
• Imports X.509 certificate into Java keystore
  using provided script
• Configures client with endpoints of AHE services
  supplied by expert user
• Ready to go!

15
HIV-1 Protease

• Enzyme of HIV responsible for protein maturation
• Target for Anti-retroviral Inhibitors
• Example of Structure Assisted Drug Design
• 8 FDA inhibitors of HIV-1 protease

So whats the problem ?

• Emergence of drug resistant mutations in protease
• Render drug ineffective
• Drug Resistant mutants have emerged for all FDA
  inhibitors

16
Molecular Dynamics Simulations of HIV-1 Protease

• AIMS
• Study the differential interactions between
  wild-type and mutant proteases with an inhibitor
• Gain insight at molecular level into dynamical
  cause of drug resistance
• Determine conformational differences of the drug
  in the active site
• Calculate drug binding affinities

Mutant 1 G48V (Glycine to Valine)
Inhibitor Saquinavir
Mutant 2 L90M (Leucine to Methionine)
17
Computational Techniques

• Ensemble MD is suited for HPC GRID
• Simulate each system many times from same
  starting position
• Each run has randomized atomic energies fitting a
  certain temperature
• Allows conformational sampling

End Conformations
Start Conformation
Series of Runs
Launch simultaneous runs (60 sims, each 1.5 ns)
C1
C2
Cx
C3
Equilibration Protocols
C4
eq1 eq2 eq3 eq4 eq5 eq6 eq7 eq8
S.K. Sadiq, S. Wan and P.V. Coveney, (submitted
2006)
18
Thermodynamic integration is ideally suited for
a HPC Grid
V
Combine and calculate integral
Starting conformation
Check for convergence
?V/??
?0.1
time
?0.2
?0.3

Seed successive simulations (10 sims, each 2ns)
?
?0.9
P.W. Fowler, S. Jha and P.V. Coveney, Phil.
Trans. R. Soc. A., 363,1999-2015 (2005)
19
HPC Requirements

• Simultaneous use of multiple and heterogeneous
  supercomputing resources
• Improved policies
• resource co-allocation
• capability computing vs task farming

EMD and TI are techniques that can really take
advantage of a HPC GRID
20
Constructing workflows with the AHE

• By calling command line clients from Perl script
  complex workflows can be achieved
• Easily create chained or ensemble simulations
• E.g. HIV equilibration protocol implemented by
• ahe-prepare ? prepare a new simulation for the
  first step
• ahe-start ? start the step
• ahe-monitor ? poll until step complete
• ahe-getoutput ? download output files
• repeat for next step

21
Future Plans

• Integrate into OMII stack (www.omii.ac.uk) - SC06
• Integrate with RealityGrid steering web service
• Coupled models host applications which are made
  up of other application components
• Orchestrate complex workflows (using BPEL?)
• Clients to run on a PDA
• Interface client with HARC resource co-scheduler
• Develop GridSAM UNICORE plug-in

22
Summary

• The AHE provides a lightweight, easily deployable
  environment for running unmodified scientific
  applications on the grid
• The AHE server is designed to be deployed by an
  expert user who uses it to share applications
  installed on grid resources
• The client is easily installed by any end user,
  requiring no intervention by system/network
  administrators
• By calling the command line clients from scripts,
  complex scientific workflows can be implemented

23
Acknowledgements

• UCL Matt Harvey, Laurent Pedesseau, Radhika
  Saksena, James Suter, Phil Fowler, Kashif Sadiq,
  Mary-Ann Thyveetil, Giovanni Giupponni, Simon
  Clifford
• Manchester Mark McKeown, Stephen Pickles, Rob
  Haines, Andy Porter
• EPSRC
• OMII

24
Further Information

• AHE Demo, Thursday 10-11am Room 206
• RealityGrid web site
• http//www.realitygrid.org/AHE
• NeSCForge
• http//forge.nesc.ac.uk/projects/ahe/
• Mailing list
• http//www.mailinglists.ucl.ac.uk/mailman/listinfo
  /ahe-discuss
• OMII
• http//www.omii.ac.uk