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London e-Science Centre
GridSAMGridSAMA Standards Based Approach to Job Submission
A. Stephen MCGough
Imperial College London
A Standards Based Approach to Job Submission
A. Stephen MCGough
Imperial College London
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London e-Science Centre
Common Grid SystemsCommon Grid Systems
There are many Grid Systems. Though they are not compatible.
Globus Condor gLite Grid Engine LSF PBS LoadLeveler Unicore …
• Different job description languages• Different submission interfaces
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London e-Science Centre
If all DRM systems supported the same interface…
If all DRM systems supported the same interface…
If we had: One interface definition for job submission One job description language
Then life would be easier! We’re getting there
JSDL is a proposed standard job submission description language
OGSA-BES is a proposed standard basic execution service interface
One day hopefully everyone will support this Till then…
If we had: One interface definition for job submission One job description language
Then life would be easier! We’re getting there
JSDL is a proposed standard job submission description language
OGSA-BES is a proposed standard basic execution service interface
One day hopefully everyone will support this Till then…
London e-Science Centre
GridSAM Job Submission and Monitoring Web Service
GridSAM Job Submission and Monitoring Web Service
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London e-Science Centre
GridSAM OverviewGrid Job Submission and Monitoring Service
GridSAM OverviewGrid Job Submission and Monitoring Service
What is GridSAM? A Job Submission and Monitoring Web Service Funded by the Open Middleware Infrastructure
Institute (OMII) managed programme V2.0.0 Available as part of the OMII 2.x release Open source (BSD) One of the first system to support the GGF Job
Submission Description Language (JSDL)
What is GridSAM? A Job Submission and Monitoring Web Service Funded by the Open Middleware Infrastructure
Institute (OMII) managed programme V2.0.0 Available as part of the OMII 2.x release Open source (BSD) One of the first system to support the GGF Job
Submission Description Language (JSDL)
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London e-Science Centre
What’s not?What’s not?
GridSAM is not a scheduling service
That’s the role of the underlying launching mechanism
That’s the role of a super-scheduler that brokers jobs to a set of GridSAM services
a provisioning service GridSAM runs what’s been told to run GridSAM does not resolve software
dependencies and resource requirements
GridSAM is not a scheduling service
That’s the role of the underlying launching mechanism
That’s the role of a super-scheduler that brokers jobs to a set of GridSAM services
a provisioning service GridSAM runs what’s been told to run GridSAM does not resolve software
dependencies and resource requirements
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London e-Science Centre
GridSAM OverviewGrid Job Submission and Monitoring Service
GridSAM OverviewGrid Job Submission and Monitoring Service
What is GridSAM to the resource owners? A Web Service to expose heterogeneous
execution resources uniformly Single machine through Forking or SSH Condor Pool Grid Engine 6 through DRMAA Globus 2.4.3 exposed resources OR use our plug-in API to implement …
What is GridSAM to the resource owners? A Web Service to expose heterogeneous
execution resources uniformly Single machine through Forking or SSH Condor Pool Grid Engine 6 through DRMAA Globus 2.4.3 exposed resources OR use our plug-in API to implement …
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London e-Science Centre
GridSAM OverviewGrid Job Submission and Monitoring Service
GridSAM OverviewGrid Job Submission and Monitoring Service
What is GridSAM to end-users? A set of end-user tools and client-side APIs to
interact with a GridSAM web service Submit and Start Jobs Monitor Jobs Terminate Jobs File transfer Client-side submission scripting Client-side Java API
What is GridSAM to end-users? A set of end-user tools and client-side APIs to
interact with a GridSAM web service Submit and Start Jobs Monitor Jobs Terminate Jobs File transfer Client-side submission scripting Client-side Java API
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London e-Science Centre
Integration with OMII Distribution
Integration with OMII Distribution
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London e-Science Centre
GridSAM ImplementationGridSAM Implementation
Virtual File System API (Apache VFS) FTP / GSIFTP / HTTP / WEBDAV / SFTP
POSIX Shell API Fork / SSH
Event dispatches (OpenSymphony Quartz) Job Persistence (Hibernate - JDBC databases) Runtime Monitoring and Control (Java Management Extension)
Virtual File System API (Apache VFS) FTP / GSIFTP / HTTP / WEBDAV / SFTP
POSIX Shell API Fork / SSH
Event dispatches (OpenSymphony Quartz) Job Persistence (Hibernate - JDBC databases) Runtime Monitoring and Control (Java Management Extension)
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London e-Science Centre
Example Pipeline: Condor
GridSAM ArchitectureGridSAM Architecture
A staged event-driven architecture* Submission pipeline is constructed as a network
of stages connected by event queues Each stage perform specific action upon incoming
events
A staged event-driven architecture* Submission pipeline is constructed as a network
of stages connected by event queues Each stage perform specific action upon incoming
events *M. Welsh and D. Culler and E. Brewer. Seda: An architecture for well-connected scalable internet
services. In Eighteenth Symposium on Operating Systems Principles (SOSP-18), October 2001.
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London e-Science Centre
Deployment Scenario: ForkingDeployment Scenario: Forking
HTTP + WS-Sec./ HTTPS + WS-Sec. /
HTTPS mutual.
Local FS
Local FS
GSIFTPGSIFTPFTPFTP WEBDAVWEBDAV HTTPHTTP…
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London e-Science Centre
Deployment Scenario: Secure Shell (SSH)
Deployment Scenario: Secure Shell (SSH)
HTTP + WS-Sec./ HTTPS + WS-Sec. /
HTTPS mutual.
GSIFTPGSIFTPFTPFTP WEBDAVWEBDAV HTTPHTTP…
SFTP - FS
SFTP - FS
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London e-Science Centre
Deployment Scenario: Condor Pool
Deployment Scenario: Condor Pool
Condor command-line
wrapper
HTTP + WS-Sec./ HTTPS + WS-Sec. / HTTPS mutual.
GSIFTPGSIFTPFTPFTP WEBDAVWEBDAV HTTPHTTP…
NetworkFS
NetworkFS
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London e-Science Centre
Deployment Scenario: Globus 2.4.3
Deployment Scenario: Globus 2.4.3
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London e-Science Centre
Deployment Scenario: Grid Engine 6
Deployment Scenario: Grid Engine 6
GSIFTPGSIFTPFTPFTP WEBDAVWEBDAV HTTPHTTP…
NetworkFS
NetworkFS
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London e-Science Centre
Latest FeaturesLatest Features
Available in v2.0.0 (released 1/7/06) MPI Application through GT2 plugin
Simple non-standard JSDL extension <mpi:MPIApplication/> that extends <posix:POSIXApplication/> with a <mpi:ProcessorCount/> element
Authorisation based on JSDL structure Allow / deny submission based on a set of XPath rules and the
identities of the submitter (e.g. distinguished name).
Prototype Basic Execution Service (ogsa-bes) interface Demonstrated in the mini face-to-face in London last December Shown interoperability with the Uni. Of Virginia BES (.NET
based) implementation.
Available in v2.0.0 (released 1/7/06) MPI Application through GT2 plugin
Simple non-standard JSDL extension <mpi:MPIApplication/> that extends <posix:POSIXApplication/> with a <mpi:ProcessorCount/> element
Authorisation based on JSDL structure Allow / deny submission based on a set of XPath rules and the
identities of the submitter (e.g. distinguished name).
Prototype Basic Execution Service (ogsa-bes) interface Demonstrated in the mini face-to-face in London last December Shown interoperability with the Uni. Of Virginia BES (.NET
based) implementation.
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London e-Science Centre
Upcoming FeaturesUpcoming Features
New DRMConnectors PBS, EGEE, LSF, CCS
GridBS Using the Condor matchmaker with
GridSAM With Oxford University
Basic Execution Service Continue tracking the changes in the ogsa-
bes specification Support dual submission WS-interfaces
New DRMConnectors PBS, EGEE, LSF, CCS
GridBS Using the Condor matchmaker with
GridSAM With Oxford University
Basic Execution Service Continue tracking the changes in the ogsa-
bes specification Support dual submission WS-interfaces
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London e-Science Centre
GridSAM deploymentGridSAM deployment
UK NGS Supported by the Belfast e-Science Centre
UCL Newcastle Reading University Imperial College London … JSDL Portlet from DL
UK NGS Supported by the Belfast e-Science Centre
UCL Newcastle Reading University Imperial College London … JSDL Portlet from DL
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London e-Science Centre
GridSAM and AHEGridSAM and AHE
The Application Hosting Environment (AHE) uses GridSAM for deploying their application wrappers to resources on the Grid.
As part of the SPICE (Simulated Pore Interactive Computing Environment) demonstrator for SuperComputing’05 GridSAM (along with the AHE) was used to deploy exeutables on resources both part of the UK National Grid Service and the US TeraGrid. This helped towards SPICE winning the HPC Analytics
Challenge for demonstrating the use of innovative techniques in rigorous data analysis and high-end visualisation to solve a complex, real-world problem.
The Application Hosting Environment (AHE) uses GridSAM for deploying their application wrappers to resources on the Grid.
As part of the SPICE (Simulated Pore Interactive Computing Environment) demonstrator for SuperComputing’05 GridSAM (along with the AHE) was used to deploy exeutables on resources both part of the UK National Grid Service and the US TeraGrid. This helped towards SPICE winning the HPC Analytics
Challenge for demonstrating the use of innovative techniques in rigorous data analysis and high-end visualisation to solve a complex, real-world problem.
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London e-Science Centre
GridSAM and e-proteinGridSAM and e-protein
e-protein is performing protein annotation Using GridSAM for executing
bioinformatics jobs on the Grid
e-protein is performing protein annotation Using GridSAM for executing
bioinformatics jobs on the Grid
Web Interface
DRM
Job
Scheduler
Java ControlProgram
WorkflowPipeline
Job
3D-GENOMICS
Web Portal
DRM
Job
ControlProgram
Workflow
GridSAMGridSAM
Job
Job Descriptiondocument
Job Identifier
Sequence files
SSH tunn
el
Dasty Viewer
Level 1
Level 2
Level 3
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London e-Science Centre
GridSAM and MicroArrayGridSAM and MicroArray
Simple, robust access to up-to-date resources for microarray data storage and analysis
Distributed availability of the portal, allowing access to large compute power facilities required for microarray analysis and storage
Simple, robust access to up-to-date resources for microarray data storage and analysis
Distributed availability of the portal, allowing access to large compute power facilities required for microarray analysis and storage
Grid Compute clusterEMAAS Server
Scatter Plots
Simple Affy
PLM plots
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London e-Science Centre
GridSAM and eMineralsGridSAM and eMinerals
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London e-Science Centre
GridSAM at UCLGridSAM at UCL
GridSAMGridSAM
SGESGE ForkFork CondorCondor
ClientClient
Middle-tier
JSDLJSDLSOAP
• Integrating GridSAM with BPEL• Providing Condor WS DRMConnector
CondorCondor
Submissionmachine(s)
Schedd
SOAPClassAdClassAd
Condor-WSCondor-WS
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London e-Science Centre
GridSAM and NeuroGridGridSAM and NeuroGrid
The aim of the NeuroGrid consortium is to enhance collaboration between clinical, imaging and e-scientists to create a Grid-based network of neuroimaging centres and a neuroimaging tool-kit. Sharing data, experience and expertise will facilitate the archiving, curation, retrieval and analysis of imaging data from multiple sites and enable large-scale clinical studies.
The aim of the NeuroGrid consortium is to enhance collaboration between clinical, imaging and e-scientists to create a Grid-based network of neuroimaging centres and a neuroimaging tool-kit. Sharing data, experience and expertise will facilitate the archiving, curation, retrieval and analysis of imaging data from multiple sites and enable large-scale clinical studies.
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London e-Science Centre
GridSAM and HPCP InteropGridSAM and HPCP Interop
GridSAM was one of over 10 OGSA-BES (HPCP profile) services demonstrating interop Managed to interop with all but one other
system Profile was restrictive
Simple Security No data staging
Taking part in the SC07 interop
GridSAM was one of over 10 OGSA-BES (HPCP profile) services demonstrating interop Managed to interop with all but one other
system Profile was restrictive
Simple Security No data staging
Taking part in the SC07 interop
London e-Science Centre
Questions?Questions?Official Download
http://www.omii.ac.ukProject Information and Documentation
http://gridsam.sourceforge.net
Official Downloadhttp://www.omii.ac.uk
Project Information and Documentationhttp://gridsam.sourceforge.net