The Pegasus Workflow Management System - Montage

The Pegasus Workflow Management System - Montage

Clouds: An Opportunity for Scientific Applications? Ewa Deelman USC Information Sciences Institute Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu Acknowledgements Yang-Suk Ki (former PostDoc, USC) Gurmeet Singh (former Ph.D. student, USC) Gideon Juve (Ph.D. student, USC) Tina Hoffa (Undergrad, Indiana University) Miron Livny (University of Wisconsin, Madison) Montage scientists: Bruce Berriman, John Good, and others Pegasus team: Gaurang Mehta, Karan Vahi, others Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu

Outline Background Science Applications Workflow Systems The opportunity of the Cloud Virtualization Availability Simulation study of an astronomy application on the Cloud Conclusions Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu Scientific Applications Complex Involve many computational steps Require many (possibly diverse resources)

Often require a custom execution environment Composed of individual application components Components written by different individuals Components require and generate large amounts of data Components written in different languages Ewa Deelman [email protected] Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu Issues Critical to Scientists Reproducibility of scientific analyses and processes is at the core of the scientific method Scientists consider the capture and generation of provenance information as a critical part of the <> generated data Sharing is an essential element

of education, and acceleration of knowledge dissemination. NSF Workshop on the Challenges of Scientific Workflows, 2006, www.isi.edu/nsf-workflows06 Y. Gil, E. Deelman et al, Examining the Challenges of Scientific Workflows. IEEE Computer, 12/2007 Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu Computational challenges faced by applications Be able to compose complex applications from smaller components Execute the computations reliably and efficiently Take advantage of any number/types of resources Cost is an issue Cluster, Shared CyberInfrastructure (EGEE, Open Science Grid, TeraGrid), Cloud Ewa Deelman, [email protected] www.isi.edu/~deelman

pegasus.isi.edu Possible solution Structure an application as a workflow Describe data and components in logical terms Provides a formal description of the application Can be mapped onto a number of execution environments Can be optimized and if faults occur the workflow management system can recover Use a workflow management system (Pegasus-WMS) to manage the application on a number of resources Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu Pegasus-Workflow Management System

Leverages abstraction for workflow description to obtain ease of use, scalability, and portability Provides a compiler to map from high-level descriptions to executable workflows Correct mapping Performance enhanced mapping Provides a runtime engine to carry out the instructions (Condor DAGMan) Scalable manner Reliable manner Can execute on a number of resources: local machine, campus cluster, Grid, Cloud Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu

Mapping Correctly Select where to run the computations Apply a scheduling algorithm for computation tasks Transform task nodes into nodes with executable descriptions Execution location Environment variables initializes Appropriate command-line parameters set Select which data to access Add stage-in nodes to move data to computations Add stage-out nodes to transfer data out of remote sites to storage Add data transfer nodes between computation nodes that execute on different resources Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu Additional Mapping Elements

Add data cleanup nodes to remove data from remote sites when no longer needed reduces workflow data footprint Cluster compute nodes in small granularity applications Add nodes that register the newly-created data products Provide provenance capture steps Information about source of data, executables invoked, environment variables, parameters, machines used, performance Scale matters--today we can handle: 1 million tasks in the workflow instance (SCEC) 10TB input data (LIGO) Ewa Deelman, [email protected] www.isi.edu/~deelman

pegasus.isi.edu Science-grade Mosaic of the Sky Point on the sky, area Image Courtesy of IPAC, Caltech Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu Generating mosaics of the sky (Bruce Berriman, Caltech) Image1 Project Background Diff Image2 Project BgModel Diff

Image3 Fitplane Background Add Fitplane Project Background Size of the mosaic is degrees square* Number of Number of Number of jobs input data Intermediate files files Total Approx. data execution time

footprint (20 procs) 1 232 53 588 1.2GB 40 mins 2 1,444 212 3,906 5.5GB 49 mins 4 4,856

747 13,061 20GB 1hr 46 mins 6 8,586 1,444 22,850 38GB 2 hrs. 14 mins 10 20,652 3,722 54,434 97GB

6 hours *The full moon is 0.5 deg. sq. when viewedwww.isi.edu/~deelman form Earth, Full Sky is ~ 400,000 deg. sq. Ewa Deelman, [email protected] pegasus.isi.edu Types of Workflow Applications Providing a service to a community (Montage project) Data and derived data products available to a broad range of users A limited number of small computational requests can be handled locally For large numbers of requests or large requests need to rely on shared cyberinfrastructure resources On-the fly workflow generation, portable workflow definition

Supporting community-based analysis (SCEC project) Codes are collaboratively developed Codes are strung together to model complex systems Ability to correctly connect components, scalability Processing large amounts of shared data on shared resources (LIGO project) Data captured by various instruments and cataloged in community data registries. Amounts of data necessitate reaching out beyond local clusters Automation, scalability and reliability Automating the work of one scientist (Epigenomic project, USC) Data collected in a lab needs to be analyzed in several steps Automation, efficiency, and flexibility (scripts age and are difficult to change) Need to have a record of how data was produced Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu

Outline Background Science Applications Workflow Systems The opportunity of the Cloud Virtualization Availability Simulation study of an astronomy application on the Cloud Conclusions Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu Clouds Originated in the business domain Outsourcing services to the Cloud Pay for what you use Provided by data centers that are built on compute

and storage virtualization technologies. Scientific applications often have different requirements MPI Shared file system Support for many dependent jobs Container-based Data Center Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu Available Cloud Platforms Commercial Providers Amazon EC2, Google, others

Science Clouds Nimbus (U. Chicago), Stratus (U. Florida) Experimental Roll out your own using open source cloud management software Virtual Workspaces (Argonne), Eucalyptus (UCSB), OpenNebula (C.U. Madrid) Many more to come Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu Cloud Benefits for Grid Applications Similar to the Grid Provides access to shared cyberinfrastructure Can recreate familiar grid and cluster architectures (with additional tools) Can use existing grid software and tools Resource Provisioning Resources can be leased for entire application instead of individual jobs

Enables more efficient execution of workflows Customized Execution Environments User specifies all software components including OS Administration performed by user instead of resource provider (good [user control] and bad [extra work]) Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu Amazon EC2 Virtualization Virtual Nodes You can request a certain class of machine Previous research suggests 10% performance hit Multiple virtual hosts on a single physical host You have to communicate over a wide-area network Virtual Clusters (additional software needed)

Create cluster out of virtual resources Use any resource manager (PBS, SGE, Condor) Dynamic configuration is the key issue Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu Personal Cluster Work by Yang-Suk Kee at USC System Queue Batch Resources Private Queue Resource & execution environment No Job manager Private Cluster on Demand

Can set up NFS, MPI, ssh Ewa Deelman, [email protected] www.isi.edu/~deelman Compute Clouds GT4/PBS pegasus.isi.edu EC2 Storage Options Local Storage Amazon S3 Network accessible block-based storage volumes (c.f. SAN)

Cannot be mounted on multiple workers NFS Simple put/get/delete operations Currently no interface to grid/workflow software Amazon EBS Each EC2 node has 100-300 GB of local storage Used for image too Dedicated node exports local storage, other nodes mount Parallel File Systems (Lustre, PVFS, HDFS) Combine local storage into a single, parallel file system Dynamic configuration may be difficult Ewa Deelman, [email protected] www.isi.edu/~deelman

pegasus.isi.edu Montage/IPAC Situation Provides a service to the community Delivers data to the community Delivers a service to the community (mosaics) Have their own computing infrastructure Invests ~ $75K for computing (over 3 years) Appropriates ~ $50K in human resources every year Expects to need additional resources to deliver services Wants fast responses to user requests Ewa Deelman, [email protected] www.isi.edu/~deelman

pegasus.isi.edu Cloudy Questions Applications are asking: How do I make good use of the cloud so that I use my funds wisely? What are Clouds? How do I run on them? And how do I explain Cloud computing to the purchasing people? How many resources do I allocate for my computation or my service? How do I manage data transfer in my cloud applications? How do I manage data storagewhere do I store

the input and output data? Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu Outline Background Science Applications Workflow Systems The opportunity of the Cloud Virtualization Availability Simulation study of an astronomy application on the Cloud Conclusions Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu Montage Infrastructure Ewa Deelman, [email protected]

www.isi.edu/~deelman pegasus.isi.edu Computational Model Based on Amazons fee structure $0.15 per GB-Month for storage resources $0.1 per GB for transferring data into its storage system $0.16 per GB for transferring data out of its storage system $0.1 per CPU-hour for the use of its compute resources Normalized to cost per second Does not include the cost of building and deploying an image Simulations done using a modified Gridsim Ewa Deelman, [email protected]

www.isi.edu/~deelman pegasus.isi.edu How many resources to provision? Montage 1 Degree Workflow 203 Tasks 60 cents for the 1 processor computation versus almost $4 with 128 processors, 5.5 hours versus 18 minutes Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu 4 Degree Montage 3,027 application tasks 1 processor $9, 85 hours; 128 processors, 1 hour with and $14. Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu Data Management Modes

Ra a 0 0 Remote I/O b Wb b 1 c 2 Regular Rb 1 Wc Good for non-shared file systems Rb

Rc 2 Cleanup Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu How to manage data? 1 Degree Montage Ewa Deelman, [email protected] 4 Degree Montage www.isi.edu/~deelman pegasus.isi.edu How do data cost affect total cost?

Data stored outside the cloud Computations run at full parallelism Paying only for what you use Assume you have enough requests to make use of all provisioned resources Cost in $ Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu Where to keep the data? Storing all of 2 Mass data

12 TB of data $1,800 per month on the Cloud Calculating a 1 degree mosaic and delivering it to the user $2.22 (with data outside the cloud) Same mosaic but data inside the cloud: $2.12 To overcome the storage costs, users would need to request at least $1,800/($2.22-$2.12) = 18,000 mosaics per month Does not include the initial cost of transferring the data to the cloud, which would be an additional $1,200 Is $1,800 per month reasonable? ~$65K over 3 years (does not include data access costs from outside the cloud) Cost of 12TB to be hosted at Caltech $15K over 3 years for hardware Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu The cost of doing science Computing a mosaic of the entire sky (3,900 4-degree-square mosaics)

3,900 x $8.88 = $34,632 How long it makes sense to store a mosaic? Storage vs computation costs Cost of generation Mosaic size Length of time to save 1 degree^2 $0.56 173MB 21.52 months 2 degree^2 $2.03 558MB 24.25 months

4 degree^2 $8.40 2.3GB 25.12 months Remember virtual data from GriPhyN? Now we can quantify things a bit better. Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu Optimizations during Mapping in Grid and Clouds Data reuse in case intermediate data products are available Performance and reliability advantagesworkflow-level checkpointing On the cloudit means that the data is stored in the cloud or can be readily staged in, but could be faster/cheaper to recompute Data cleanup nodes can reduce workflow data footprint

by ~50% for Montage, applications such as LIGO need restructuring On the clouddata cleanup can reduce the footprint but increase computational costs Node clustering for fine-grained computations Can obtain significant performance benefits for some applications (in Montage ~80%, SCEC ~50% ) Potentially very good for clouds because of wide area delays Workflow partitioning to adapt to changes in the environment Map and execute small portions of the workflow at a time Provides scalability Not so important in cloud environments Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu Conclusions Part 1 We started asking the question of how can a scientific workflow best make use of clouds Assumed a simple cost model based on the Amazon fee structure Conducted simulations Need to find balance between cost and performance Computational cost outweighs storage costs

Did not explore issues of data security and privacy, reliability, availability, ease of use, etc Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu Will scientific applications move into clouds? There is interest in the technology from applications They often dont understand what are the implications Need tools to manage the cloud Build and deploy images Request the right number of resources Manage costs for individual computations Manage project costs Projects need to perform cost/benefit analysis

Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu Issues Critical to Scientists Reproducibility yesmaybe--through virtual images, if we package the entire environment, the application and the VMs behave Provenance still need tools to capture what happened Sharing can be easier to share entire images and data Data could be part of the image Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu Relevant Links

Amazon Cloud: http://aws.amazon.com/ec2/ Pegasus-WMS: pegasus.isi.edu DAGMan: www.cs.wisc.edu/condor/dagman Gil, Y., E. Deelman, et al. Examining the Challenges of Scientific Workflows. IEEE Computer, 2007. Workflows for e-Science, Taylor, I.J.; Deelman, E.; Gannon, D.B.; Shields, M. (Eds.), Dec. 2006 LIGO: www.ligo.caltech.edu/ SCEC: www.scec.org Montage: montage.ipac.caltech.edu/ Condor: www.cs.wisc.edu/condor/ Ewa Deelman, [email protected] www.isi.edu/~deelman pegasus.isi.edu

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