OGF28, Munich [email protected]
description
Transcript of OGF28, Munich [email protected]
Web: www.omii.ac.uk Email: [email protected]
Running applications on interoperable Grid infrastructures,
focusing on OMII-UK supported software or
HPC-BP Interoperability TutorialOGF28, Munich
Steve Crouch, David Wallom, Matteo Turilli, Morris Riedel, Shahbaz Memon, Balazs Konya, Gabor Roczei, Peter
Stefan, Andrew Grimshaw, Mark Morgan , Katzushige Saga, Justin Bradley, Richard Boardman
Web: www.omii.ac.uk Email: [email protected]
Objectives
• To give participants practical experience of:o Using individual middleware clients to submit jobs
to HPC-BP compliant serviceso Using the HPC-BP interop demo framework, used
for previous HPC-BP demos, to submit jobs to HPC-BP compliant services
• To give participants opportunity (and starting point) to learn about:
o Basic techniques and approaches for interoperability – what do I need, and how can I do this?
o Some of the limitations of standards support across middlewares – what can’t I do?
Web: www.omii.ac.uk Email: [email protected]
Tutorial Approach
• ‘Presentation-lite’
• Learn at your own pace via online web tutorial…• …or follow my lead
• Pragmatic
• Generous in terms of time
• Tutorial remains available after OGF28
• Ask for help!
Web: www.omii.ac.uk Email: [email protected]
Schedule
• Session 1: Using individual clients to invoke HPC-BP services
o Overview of the demo + demo, Introduction to GridSAMo Download, Install and Configure GridSAM o Submit a Trivial Compute-only JSDL Job to HPC-BP
Compliant Services o Download, Build and Configure the BES++ Client o Running the BES++ Client Against HPC-BP Compliant
Services • Session 2: Using HPC-BP demo framework to
invoke multiple HPC-BP services simultaneouslyo Download, Install and Configure the Demo Framework o Running the Demo Against Multiple HPC-BP Compliant
Services o The Demo in Detail: Adding Another Endpoint to the
Demo
Web: www.omii.ac.uk Email: [email protected]
The Interoperability Demonstrator
Web: www.omii.ac.uk Email: [email protected]
Background
• Motivation:o Researchers are often reaching the limits of locally
available resources to conduct researcho They are beginning to realise the potential of using
much larger-scale resourceso Compute resources are becoming more numerous and
available across Europe
• However, using different Grid middleware deployments is traditionally difficult
o Middleware clients for different deployments not compatible
o Require different security policies/configuration for each
Web: www.omii.ac.uk Email: [email protected]
Background
• Possible solutions:o Maintain infrastructure that enables use of different clients for
each middleware – interoperation• Not scalable - user learning curve, operation and maintenance
o Each middleware supports a common service interface, enabled through adoption of accepted open standards – interoperability
• Need only learn, use and maintain single client infrastructure
• Still leaves security!
• What can be practically achieved, in terms of interoperability, with middlewares that adopt OGF compute-related standards?
o What is possible?o Limitations?
• Demonstrate through proof-of-concept, client-side, application-focused demo
Web: www.omii.ac.uk Email: [email protected]
History
• Initiated by UK National Grid Service, OMII-UK and FZJ
• Initially shown at OGF27, Banff, Canada, Oct 09
• SuperComputing, Nov 09
• ETSI Plugtests, FZJ, UK AHM, Dec 09
• GIN-CG, OGF28, Mar 10• Demonstrators: David
Wallom, Peter Stefan, Morris/Shahbaz Memon, Steve Crouch
Video available at http://www.omii.ac.uk/wiki/Videos
Web: www.omii.ac.uk Email: [email protected]
Compute Related Standards - OGF
Job ManagementOGSA-BES(GFD 108)
Job ManagementOGSA-BES(GFD 108)
HPC Domain Specific ProfileHPC Basic Profile
(GFD 114)
HPC Domain Specific ProfileHPC Basic Profile
(GFD 114)
ArchitectureOGSA EMS Scenarios
(GFD 106)
Use CasesGrid Scheduling Use Cases
(GFD 64)
EducationISV Primer (GFD 141)
AgreementWS-Agreement
(GFD 107)
Programming InterfaceDRMAA
(GFD 22/133)
Programming InterfaceSAGA
(GFD 90)
AccountingUsage Record
(GFD 98)
InformationGLUE Schema 2.0
(GFD. 147)
Job Definition
File TransferHPC File Staging
(GFD 135)
File TransferHPC File Staging
(GFD 135)
Job DescriptionJSDL
(GFD 56/136)
Job DescriptionJSDL
(GFD 56/136)
Application DescriptionHPC Application
(GFD 111)
Application DescriptionHPC Application
(GFD 111)
Application DescriptionSPMD Application
(GFD 115)
Job ParameterizationParameter Sweep
(GFD. 149)
Extend
Uses
Produces
Describes
Supports
Profiles
Web: www.omii.ac.uk Email: [email protected]
Standards/Data Protocols/Security Supported
• Standards:o HPC Basic Profile v1.0
• OGSA BES (Basic Execution Service) v1.0• JSDL (Job Submission Description Language) v1.0• HPC Profile Application Extension v1.0
o HPC File Staging Profile – UNICORE, GridSAM• Data protocols:
o UNICORE, ARC, BES++ – ftpo GridSAM – GridFTP
• Security:o Direct middleware -> certificate CA trust (just
import CAs)
Web: www.omii.ac.uk Email: [email protected]
Participation
• Currently:o DEISA/FZJ – UNICORE, SuSE, AMD 64-bit, 1 coreo NorduGrid/NIIF – ARC NOX Release, Debian Linux, i686, 16
coreo UK NGS/OMII-UK – GridSAM, Scientific Linux 4.7, AMD 64-bit,
256 coreo NAREGI-NII/Platform Computing – BES++, 2 nodes
• Coming soon:o University of Virginia Campus Grid – GENESIS2, Ubuntu
Linux, i686, 8 coreo POZNAN Supercomputing Centre – SMOA Computing
• Platform Computing BES++ Client used as interop client
Web: www.omii.ac.uk Email: [email protected]
Example Application: Plasma Charge Minimization
• Provided by David Wallom, NGS
• Undergraduate project• Total system energy
minimization of point charges around the surface of a sphere
• Three different applications o Pre processing – generate input
fileso Main processing – parallel
distributed processingo Post-processing – choose optimal
solution
Web: www.omii.ac.uk Email: [email protected]
System Requirements
• System requirements (for building and running):
o Linux - see the Linux client pre-requisites in OMII-UK Development Kit supported platforms
o Sun Java JDK 1.6 or aboveo C compiler - gcc and related development
libraries o Lexical analyser - flex – Fast Lexical Analysero Parser generator - bison
• Soon to appear on OGF Forge – hopefully by end of week
Web: www.omii.ac.uk Email: [email protected]
JSDL Template<?xml version="1.0" ?><JobDefinition xmlns="http://schemas.ggf.org/jsdl/2005/11/jsdl"> <JobDescription> <Application> <HPCProfileApplication xmlns="http://schemas.ggf.org/jsdl/2006/07/jsdl-hpcpa"> <Executable>@MINEM_INSTALL_LOCATION@/update_file</Executable> <Argument>input.txt</Argument> <Argument>output.txt</Argument> <Output>stdout.txt</Output> <Error>stderr.txt</Error> @OPTIONAL_WORKING_DIR_ELEMENT@ </HPCProfileApplication> @OPTIONAL_JOBRESOURCE_CREDENTIAL@ </Application>
<DataStaging> <FileName>input.txt</FileName> <CreationFlag>overwrite</CreationFlag> <Source> <URI>@INPUT_FILE_URI@</URI> </Source> @OPTIONAL_HPCFSP_CREDENTIAL@ </DataStaging> <DataStaging> <FileName>output.txt</FileName> <CreationFlag>overwrite</CreationFlag> <Target> <URI>@OUTPUT_FILE_URI@</URI> </Target> @OPTIONAL_HPCFSP_CREDENTIAL@ </DataStaging>
<DataStaging> <FileName>stdout.txt</FileName> <CreationFlag>overwrite</CreationFlag> <Target> <URI>@STDOUT_FILE_URI@</URI> </Target> @OPTIONAL_HPCFSP_CREDENTIAL@ </DataStaging> <DataStaging> <FileName>stderr.txt</FileName> <CreationFlag>overwrite</CreationFlag> <Target> <URI>@STDERR_FILE_URI@</URI> </Target> @OPTIONAL_HPCFSP_CREDENTIAL@ </DataStaging> </JobDescription>
</JobDefinition>
Web: www.omii.ac.uk Email: [email protected]
Endpoint Configuration
# UNICORE interop config fileendpoint_file=unicore.xmlapplication_type=HPCProfileApp
licationapplication_type_namespace=ht
tp://schemas.ggf.org/jsdl/2006/07/jsdl-hpcpa
working_dir=data_mode=ftpdata_input_base=ftp://
zam1161v01.zam.kfa-juelich.de:8004/ogf27/unicore
data_output_base=ftp://zam1161v01.zam.kfa-juelich.de:8004/ogf27/unicore
minem_install=/tmp/minemmyproxy=no
hpcfsp=yeshpcfsp_username=interopdatahpcfsp_password=89zukunft()
auth_utoken=yesauth_x509=yesauth_x509_credential=auth/
client.pemauth_x509_keypass=not_usedauth_x509_cert_dir=auth/
certificatesauth_utoken_username=ogfauth_utoken_password=ogf
Web: www.omii.ac.uk Email: [email protected]
How it Fits Together…
BES++Client
UNICORE
GridSAM
ARC
FTP
GridFTP
FTPClient Job Service
Data Service
Minem
Application
minem-interop.pl
MyProxy
Minem
Minem
Minem
Security Service
1. Create Minem input files
1. Create Minem input files
12. Generate JSDLs from
template2. Generate JSDLs from
template 2
7. Select best result7. Select best result
7
8. Generate/upload image to web server8. Generate/upload image to web server
8
5. Monitor jobs until completion
5. Monitor jobs until completion
5 BES++
FTP
4. Submit JSDLs across middlewares
4. Submit JSDLs across middlewares
4
6. Download output files6. Download output files
6
3. Upload input files3. Upload input files
3
Minem
Web: www.omii.ac.uk Email: [email protected]
The Demo…
Web: www.omii.ac.uk Email: [email protected]
Future Work• Standards integration:
o Integrate GENESIS II and SMOA Computingo Replacement of BES++ Client with SAGA
• SAGA BES adapter currently in development!• Schedule across BES/non-BES endpoints (e.g. Globus)
o GLUE2 (e.g. using OMII-UK Grimoires software)• Service discovery (static)• Dynamic allocation (dynamic)
o Integrate CREAM-BES?• Security: ‘Static’ trust set up of security, proper VO set
up?• Middleware client ‘audit’ of interoperability?
o Leads to ability to configure and use different middleware HPC-BP clients…
• Use of HARC for advance reservation• Clean up the code, upload to OGF Forge within GIN-CG• Participation very much an open process – if you wish to
donate an HPC-BP compliant endpoint, please let me know!
Web: www.omii.ac.uk Email: [email protected]
Verifi
ed/In
crea
sing
Inte
roper
abili
ty
Future Direction
• Interface:o Workflow engine
integration• To replace/provide
alternative to the Perl script
• Taverna2 good candidate
o Application abstraction
• Use of endpoints:o Utilise production-
level deploymentso Utilise production-
level security
Abstraction level
Uti
lise
pro
du
cti
on
-le
vel
de
plo
ym
en
ts
Now
Future
Web: www.omii.ac.uk Email: [email protected]
Dissemination
• Thanks to the OMII-UK publicity machine:o HPCWire: http://www.hpcwire.com/offthewire/European-
Grid-Interoperability-Goes-Global-79343767.html o SuperComputing Online:
http://www.supercomputingonline.com/latest/european-interoperability-goes-global
o EGEE: http://www.eu-egee.com/index.php?id=193&tx_ttnews[tt_news]=125&tx_ttnews[backPid]=65&cHash=90bb3f97cc
o http://www.d4science.eu/aggregator/sources/2?page=1 o http://www.it-tude.com/grid_interoperability_eu.html o http://www.beliefproject.org/zero-in/zero-in-fourth-issue-
emagazine/news o + numerous OMII-UK website articles & UK NGS articles
• Just type ‘European Interoperability Goes Global’ into Google…
Web: www.omii.ac.uk Email: [email protected]
GridSAM
OMII-UKLondon e-Science Centre, Imperial College, LondonInstitute of Computing
Technology, Chinese Academy of Sciences (Beijing)
Web: www.omii.ac.uk Email: [email protected]
GridSAM Overview
• What is GridSAM to the resource owners?o A web service to uniformly expose a computational
resource• Condor (via local or SSH submission)• Portable Batch Scheduler (PBS) (via local or SSH submission)• Globus• Sun GridEngine• Platform Load Sharing Facility (LSF)• Single machine through Fork or SSH
o Acts as a client to these resources• What is GridSAM to end-users?
o A means to access computational resources in an open standards-based uniform way
o A set of end-user command-line tools and client-side APIs to interact with GridSAM Web Services
• Submit and monitor compute jobs• Cross-protocol file transfer (gsiftp, ftp, sftp, WebDav, http, https,
soon SRB, iRODS) via Commons-VFS (http://sourceforge.net/projects/commonsvfsgrid)
Web: www.omii.ac.uk Email: [email protected]
Supported OGF Standards
• OGSA Basic Execution Service (BES) v1.0
• JSDL v1.0• HPC Basic Profile v1.0• HPC Profile Application Extension v1.0• HPC File Staging Profile v1.0• HPC Common Case Profile: Activity
Credential v0.1• JSDL SPMD Application Extension v1.0
Web: www.omii.ac.uk Email: [email protected]
GridSAM – Publications & Enabled Activities
+ in 2009/2010 – ICHEC Bioinformatics Portal, eSysBio, NAREGI/RENKEI
Web: www.omii.ac.uk Email: [email protected]
For Resource Owners…
ComputationalResourceManager
ComputationalResourceManager
DRMDRM
…
One of:PBS (Torque/OpenPBS/PBSPro)LSF, Condor, Sun GridEngine, Globus, Fork
GridSAMService
GridSAMService
X509certificate
Linux Many flavours:RHEL 3,4,5, Fedora 7,8, Scientific Linux 4Java: JDK 1.5.0+
Linux + JavaLinux + Java
Tomcat/AxisTomcat/Axis
Tomcat: 5.0.23, 5.0.28, 5.5.23Axis: v1.2.1
Persistence provided by one of:Hypersonic, PostgreSQL, or existing MySQL
Web: www.omii.ac.uk Email: [email protected]
For End-Users…
GridSAMService
GridSAMService
JSDL
HTTPS/HTTP
WS-Security:X509User/Password
Service InterfaceService Interface
Any/all of:GridSAM native interface, OGSA-BES v1.0, HPC Basic Profile v1.0
…
MyProxy (for Globus/GridFTP)
MyProxy (for Globus/GridFTP)
Globus-
styl
e
Proxy
Certif
icat
e
+ MyProxycredentials
Windows/Linux + Java
Windows/Linux + Java
GridSAM ClientGridSAM Client
Many flavours:RHEL 3,4,5, Fedora 7,8, Debian, Ubuntu, Scientific Linux 4, Windows XP, Windows VistaJava: JDK 1.5.0+
AxisAxisX509certificate
Generic BES/HPC Basic ProfileClient
Generic BES/HPC Basic ProfileClient
OSGA-BESOSGA-BESHPC Basic Profile
HPC Basic Profile
Web: www.omii.ac.uk Email: [email protected]
Open Community Development
• GridSAM is Open Source, Open Community Development
• GridSAM SourceForge project:
o 99.03% activity, 1 release/month
o SVN source code repositoryo Developer & discuss
mailing lists
http://sourceforge.net/projects/gridsam/
Web: www.omii.ac.uk Email: [email protected]
GridSAM e.g. with Condor
• A staged event-driven architectureo Submission pipeline is constructed as a network of
stages connected by event queueso Each stage performs a specific action upon incoming
events
Example Pipeline: Condor
Web: www.omii.ac.uk Email: [email protected]
Planned Future Developments
• For end-users:o Full support for JSDL Resource selection
across PBS, Globus, Condor & Fork DRMso JSDL Parameter Sweep Extensiono Support for SRB and iRODS
• For resource owners:o LCAS/LCMAPS supporto Packaging option as a standalone, manually
configurable web archive (WAR) file
• Direct PBS deployment throughout NGS sites
Web: www.omii.ac.uk Email: [email protected]
The tutorial begins… all you need is to go to:
http://www.omii.ac.uk/wiki/HPCBPTutorial