1 Yolanda Gil ([email protected]) AAAI-08 Tutorial July 13, 2008 USC Information Sciences Institute Part III Computational Workflows in Wings/Pegasus AAAI-08.

1Yolanda Gil ([email protected]) AAAI-08 Tutorial July 13, 2008USC Information Sciences Institute

Part III

Computational Workflows in Wings/Pegasus

AAAI-08 Tutorial on Computational Workflows for

Large-Scale Artificial Intelligence Research


Our Approach

Express analysis as distributed workflows• Data analysis as distributed application

User-centric workflow refinement process • Start with high-level problem description, add layers of detail,

map to distributed execution environment Knowledge-rich descriptions of workflows -- OWL/RDF

• Descriptions of input data and data products (aka “metadata”)• Models of components in terms of I/O data and their function

Automation of resource allocation and optimization• Efficient scheduling algorithms for workflow graphs• Optimization techniques of broad applicability

Build on distributed computing research -- GRID• Designed, by definition, to be robust, secure, flexible


The Wings/Pegasus Workflow System[Gil et al 07; Deelman et al 03; Deelman et al 05; Kim et al 08; Gil et al forthcoming]

Grid servicescondor.uwisc.eduwww.globus.org

Pegasus:Automated workflow refinement and executionpegasus.isi.edu

WINGS:Knowledge-based workflow environmentwww.isi.edu/ikcap/wings

•Ontology-based reasoning on workflows and data (W3C’s OWL)

•Workflow library of useful analyses

•Proactive assistance +automation

•Execution-independent workflows

•Optimize for performance, cost, reliability

•Assign execution resources•Manage execution through DAGMan

•Daily operational use in many domains•Secure and controlled sharing of distributed services, computing, data

•Scalable service-oriented architecture

•Commercial quality, open sourceIBM

IBM

IBM

IBM


WorkflowSelection

WorkflowTemplate

DataSelection

WorkflowInstance

WorkflowLibraries

Data Repositories

Application Components

Ontologies:Domain terms,

Component types,Workflow Products

- Preexisting data collections- Workflow execution results

“Show meworkflows that classifydatasets”

“Run this workflowwith theweather1980 data set”

“Validate this workflowbased on the component specs”

STUDENT

SEASONED NL RESEARCHER

WorkflowCreation

ALGORITHM DEVELOPER

-Workflow templates specify complex analyses sequences- Workflow instances specify data

“Here is a newclassification algorithm,has a parameter for smoothing, is compiled for MPI”

Component Specification

Executable WorkflowPegasus

WINGS

- Specifies data requirements- Specifies execution requirements

DAGMan/Grid

(OWL)

Wings: Workflow Instance Generation and Selection


April 21, 2023

© 2005 TANGRAM

5

Globus RLSreplicamgmt

GRAMremote

submission

GridFTPdata

transfer

Condor DAGManexecution

engine

Condor-Gjob

manager

Nagiosmonitoring

probes

PegasusSite

selectionReplica

selectionWorkflow

optimization

WingsWorkflowvalidation

Data/Compselection

Metadatageneration

Workflowgeneration

NationalMiddleware

Infrastructure(NMI) software

Workflowsubmission

LEGEND:

Workflow System

All softwareis open source


Workflow Structure We take to heart the separation of “programming”

from “analysis” activities– Components are designed by programmers and can be

complex (and need testing, debugging, loops should terminate, etc)

– Workflows are composed by non-programmers and should have simple structure-- focus is on selecting application components and data

Therefore, our workflow structure is very streamlined• Only iterations handled are parallel data processing

pipelines• Only conditionals handled are data-driven component

selections• Standard workflow languages offer much more complex

constructs Workflow structure designed to:

• Be accessible to users• Facilitate automation and failure recovery


Core Workflow Concepts

C1

C2

F1

F4

F6

F2

Workflow consists of• Components: software to be executed• Links: data flow among components

Directed Acyclic Graphs (DAGs)• Facilitate automation, esp. execution

monitoring and repair Data always handled through files Special handling of some control

constructs loops (more on this later)• Choices of components• Iterations over data sets

Layered workflow refinement process• Select application components ->

select data -> select execution resources

Each layer adds more information to the same basic workflow structure

C3

F5

F3

F5


Workflow Abstraction Layers We use several layers of description of workflows


WINGS:Workflow Representation


F2-operation-SA-Median-Distance-JB F2-operation-SA-Median-VS30

Compute-F2-SA-Median-wrt-Distance-JB-given-Fault-Type-&-Basin-Depth-&-…

Compute-F2-SA-MEDIAN-wrt-VS30-given-Fault-Type-&-Basin-Depth-&-…

Hazard-Level

Hazard-Level-with-SA

Hazard-Level-with-PGA

Hazard-Level-with-PGV

Compute-Hazard-Level-given-IMR-input-parameters

. . .

. . .

Compute-Hazard-Level-with-SA-given-IMR-input-parameters

Compute-Hazard-Level-with-PGA-given-IMR-input-parameters

Compute-Hazard-Level-with-PGV-given-IMR-input-parameters

Hazard-Level-with-SA-Median

Hazard-Level-with-SA-Std-Dev

Hazard-Level-with-SA-Prob-Exc

Hazard-Level-with-Median

Hazard-Level-with-Std-Dev

Hazard-Level-with-Median

. . .

Compute-Hazard-Level-with-SA-Median-given-IMR-input-parameters

Compute-Hazard-Level-with-SA-Std-Dev-given-IMR-input-parameters

Compute-Hazard-Level-with-SA-Prob-Exc-given-IMR-input-parameters

IMR-Input-Parameter

Field-2000-Input-Parameter

Parameter

Fault-Type

Basin-Depth

Distance

. . .

. . .Compute-F2-SA-Median-given-Field-2000-input-parameters

Compute-F2-Hazard-Level-given-Field-2000-input-parameters

F2-Hazard-Level

. . . . . .Domain OntologyOntology of Components

IMTprobability-function

IMR

probability-function

F2-SA-Median-wrt-VS30

. . .


F1

WINGS: Representing Components

Any input or output can be defined as a file collection

• Same file type• Unspecified cardinality• Ordered

Inputs and outputs through files• Files are typed

Each input is uniquely identified by a file descriptor (~ parameterID)

Ordered lists of file descriptors for both I and O

C-one

D1

D3

D2

C-many

F1

D13

F1DC11 D12


Data Descriptions Metadata of different

kinds can be organized in ontology

Files represented as instances and classified in ontology according to their metadata

File collections also represented as instances and defined as ordered sets of file instances

A file Skolem is created for each class as a representative instance (more on this later)

Similarly, a file collection Skolem is created for each class

Application-Specific

Metadata Ontologies

ContentMetadata

FormatMetadata

Kim-Homepage

EHS-T

File Collection

Gil-Homepage

Kim-Homepage

Gil-Homepage

…

EHCS-T

IKCAP-pages


A Component in a Workflow Template

C-one

D1

D3

D2

Nodes correspond to individual application components

Links include file descriptors for origin and destination and a file Skolem

C-one

D1

D3

D2

Link

Node

C67C67

D6

D7

D6C67

D6

L1 L2

L3

L4

N1

N2

N3

FS-A FS-B

FS-C

FS-DNotation: “S” marks a Skolem


File Collections in a Workflow Template

F1

Links that include file descriptors that are collections refer to file collection Skolems

Using the same file Skolem ID or file collection Skolem ID in different links indicates identity

F1F1DC11 D12

C-many

D13

F1

C-many

F1

D13

F1DC11 D12FS-B

FS-C

L1L2

L3

N1

FCS-A


Iteration Over File Collections in a Workflow T

Iteration over sets compactly represented with single nodes that contain component collections

Will be expanded to as many jobs as files are specified for the executable workflow

Links capture formation of file collections as input

C-one

G1

Z1

D1 D2

D3

C-many

C-one

Z2

C-one

Z88

…

…

…

K1 G2 K2 G88 K88

L1 L2

L3

C-manyN2

D12

L4

FS-Y

Y1

C-one

D1

D3

D2

F1

C-many

F1

D13

F1DC11 D12F1F1F1DC11

FCS-G FCS-K

FCS-Z

C-one

NC1


Iteration With a Constant in a Workflow T

Nodes that represent component collections can take the same file from the same link when the link contains a file Skolem instead of a file collection Skolem

C-one

G1

Z1

C-many

C-one

Z2

C-one

Z88

…

…

…

K1 G2 K1 G88 K1

Y1

C-one

D1

D3

D2

F1

C-many

F1

D13

F1DC11 D12

D1 D2

D3

L1 L2

L3

C-manyN2

D12

L4

FS-YF1F1F1DC11

FCS-G

FCS-Z

C-one

NC1

FS-K1


Constraints on Workflow Templates

CybershakeTemplate

InputLink_SiteNameFile_to_BoxNameCheck

hasSiteName

InputLink_RuptureVars_to_SeisgmogramGen

hasLink

…

F-RV

C-RuptVars

CC-RuptureVariations

InputLink_SGTCollforRup_to_SeismogramGen

F-SGT

C-SGT-forRups

CC-SGTs

hasFile

hasFile

hasFile

SGTsSiteName

SiteNameFile

hasSiteName

SiteName

N_Rups

hasN_Items

hasN_Items

…

… isSameAs

Constraints on number of elements in different collections

Constraints on files/collections of different workflow components


Workflow Instances

C-one

D1

D3

D2

C67

D6

C-plenty

L1 L2

L3

N1

N2N3

FS-A FS-B

F-C

D7

C-one

D1

L5

N4

FS-ED8

D2

L6

FS-F

D3L7

FS-G

DC9

L4

File85

File28

F34254-05-06-08

FileColl54

F34256-05-06-08

F34255-05-06-08

F34257-05-06-08

Existing data

New data products

Input data selected from the file library by querying for files of the type of file Skolems

Logical names created for new data products with metadata based on file Skolems

Compact Workflow Instance = WT + bindings

Easy to understand, and easily transformed into an expanded WI and a DAX for Pegasus

Bindings

FCS-D


AUTOMATED WORKFLOW INSTANCE GENERATION

IN WINGS


Corpus

Kernel_RulesSplit

Filter_Rules

Prune_Rules

Binarize Generate_Rule_Map

Compile

XRS_Rules BRF_Rules Lexicon_Dictionary

1…n

1…n

1…n 1…n

WSJ-2001

KR-09-05

…

…

WSJ-2001KR-09-05

Workflow Instance Expressions

•Compact expression for efficient search and matching

•Expanded expression when further details are needed


Expanded Workflow Instance<rdf:RDF ..(xmlns definitions)....><wflns:WorkflowInstance rdf:ID="WFT0b"> <wflns:hasDescription rdf:datatype=MailScanner has detected a possible fraud attempt from "www.w3.org" claiming to be MailScanner has

detected a possible fraud attempt from "www.w3.org" claiming to be "http://www.w3.org/2001/XMLSchema#string"> Count the number of unique words in a file </wflns:hasDescription> <wflns:hasNode rdf:resource="#N1"/> <wflns:hasNode rdf:resource="#N2"/> <wflns:hasLink rdf:resource="#L12"/> <wflns:hasLink rdf:resource="#L01"/> <wflns:hasLink rdf:resource="#L2Output"/> </wflns:WorkflowInstance> <wflns:InOutLink rdf:ID="L12"> <wflns:hasOriginFileDescription rdf:resource="http://www.isi.edu/ikcap/wings/domains/linguistics/componentLibrary.owl#remDupesOutputFile"/> <wflns:hasFile rdf:resource="http://www.isi.edu/ikcap/wings/domains/linguistics/fileLibrary.owl#F12_WFT0b_1117161532484"/> <wflns:hasDestinationFileDescription

rdf:resource="http://www.isi.edu/ikcap/wings/domains/linguistics/componentLibrary.owl#CountWordsInputFile"/> <wflns:hasDestinationNode> <wflns:Node rdf:ID="N2"> <wflns:hasComponent rdf:resource="http://www.isi.edu/ikcap/wings/domains/linguistics/componentLibrary.owl#countWordsV1"/> </wflns:Node> </wflns:hasDestinationNode> <wflns:hasOriginNode> <wflns:Node rdf:ID="N1"> <wflns:hasComponent rdf:resource="http://www.isi.edu/ikcap/wings/domains/linguistics/componentLibrary.owl#removeDuplicatesV1"/> </wflns:Node> </wflns:hasOriginNode> </wflns:InOutLink> <wflns:InputLink rdf:ID="L01"> <wflns:hasDestinationNode rdf:resource="#N1"/> <wflns:hasFile rdf:resource="http://www.isi.edu/ikcap/wings/domains/linguistics/fileLibrary.owl#test_txt_WFT0b_1117161532484"/> <wflns:hasDestinationFileDescription

rdf:resource="http://www.isi.edu/ikcap/wings/domains/linguistics/componentLibrary.owl#remDupesInputFile"/> </wflns:InputLink> <wflns:OutputLink rdf:ID="L2Output"> <wflns:hasOriginFileDescription

rdf:resource="http://www.isi.edu/ikcap/wings/domains/linguistics/componentLibrary.owl#CountWordsOutputFile"/> <wflns:hasOriginNode rdf:resource="#N2"/> <wflns:hasFile rdf:resource="http://www.isi.edu/ikcap/wings/domains/linguistics/fileLibrary.owl#F2Output_WFT0b_1117161532484"/> </wflns:OutputLink></rdf:RDF>


W Instance: “dax” for Pegasus<?xml version="1.0" encoding="UTF-8"?><adag xmlns="http://www.griphyn.org/chimera/DAX"

xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.griphyn.org/chimera/DAX http://www.griphyn.org/chimera/dax-1.8.xsd" version="1.7" count="1" index="0" name="WorkFlow0b">

 <filename file="vahi.f.a" link="input"/> <filename file="vahi.f.b1" link="inout"/> <filename file="vahi.f.b2" link="output"/> <job id="ID000001" namespace="vds" name="removeDups" version="1.0" level="3" dv-namespace="vds" dv-

name="top" dv-version="1.0"> <argument>-a top -T60 -i <filename file="vahi.f.a"/> -o <filename file="vahi.f.b1"/> </argument> <uses file="vahi.f.a" link="input" dontRegister="false" dontTransfer="false"/> <uses file="vahi.f.b1" link="output" dontRegister="true" dontTransfer="true" temporaryHint="true"/> </job> <job id="ID000002" namespace="vds" name="countWords" version="1.0" level="2" dv-namespace="vds" dv-

name="left" dv-version="1.0"> <argument>-a left -T60 -i <filename file="vahi.f.b1"/> -o <filename file="vahi.f.b2"/> -p

0.5</argument> <uses file="vahi.f.b1" link="input" dontRegister="false" dontTransfer="false" temporaryHint="true"/> <uses file="vahi.f.b2" link="output" dontRegister="true" dontTransfer="true" temporaryHint="true"/> </job> <child ref="ID000002"> <parent ref="ID000001"/> </child></adag>


AUTOMATED METADATA GENERATIONIN WINGS


Metadata Reasoning for file name generation and workflow validation

Filename Generation• Explicit representation of metadata in ontology (e.g.

source id, rupture id)• Propagate metadata attributes for all data products when

creating workflow instance• Names for intermediate files are created automatically

from the metadata Workflow Validation

• Explicit representation of metadata constraints (examples are shown below)

– Constraints on individual files and collections– Constraints on component inputs and outputs – Constraints among components in a workflow

• Check constraints while generating workflow instantiations


Propagation of metadata for filename generation: an example

SeismogramGen_Li

RVM

127_6.rvm- source_id: 127- rupture_id: 6

Rupture_variationRupture_variation

127_6.txt.variation-s0000-h0000- source_id: 127- rupture_id: 6- slip_relaization_#:0- hypo_center_#: 1




SGT



FD_SGT/PAS_1/A/SGT161- site_name: PAS- tensor_direction: 1- time_period: A- xyz_volumn_id: 161

127_6.txt.variation-s0000-h0001- source_id: 127- rupture_id: 6- slip_realization_#:0- hypo_center_#: 1

Seismogram

Seismogram_PAS_127_6.grm-site_name: PAS-source_id: 127-rupture_id: 6

… …SGT


AUTOMATIC WORKFLOW GENERATION IN WINGS


Automatic Template-Based Workflow Generation Algorithm

WR0: Workflow Template

Workflow request =

Workflow Template

+

Seed Constraints

Seed workflow from request

unified well-formed request

Find input data requirements

seeded workflows

Data source selection

binding-ready workflows

Parameter selection

bound workflows

configured workflows

Workflow instantiation

Workflow grounding

workflow instances

Workflow mapping

ground workflows

executable workflows

Workflow ranking

top-k workflows dataVariable5 data:contains data:Muti-party-communicationdataVariable0 data:creator 5048dataVariable1 data:creator 5048

WR0: Seed Constraints


Step 1: Workflow Template is Seeded



seeded workflows



Parameter selection

bound workflows



Workflow grounding

workflow instances

Workflow mapping

ground workflows


Workflow ranking

top-k workflows



Step 2: Backward Sweepunified well-formed request


seeded workflows



Parameter selection

bound workflows



Workflow grounding

workflow instances

Workflow mapping

ground workflows


Workflow ranking

top-k workflows



E-07

S-NY

Step 3: Select Data Sourcesunified well-formed request


seeded workflows



Parameter selection

bound workflows



Workflow grounding

workflow instances

Workflow mapping

ground workflows


Workflow ranking

top-k workflows



E-07

S-NY

Step 3: Select Data Sourcesunified well-formed request


seeded workflows



Parameter selection

bound workflows



Workflow grounding

workflow instances

Workflow mapping

ground workflows


Workflow ranking

top-k workflows



E-07

S-NY

Step 4: Forward Sweepunified well-formed request


seeded workflows



Parameter selection

bound workflows



Workflow grounding

workflow instances

Workflow mapping

ground workflows


Workflow ranking

top-k workflows



E-07

S-NY

Result-PartA

Result-PartB

Step 5: Workflow Instantiationunified well-formed request


seeded workflows



Parameter selection

bound workflows



Workflow grounding

workflow instances

Workflow mapping

ground workflows


Workflow ranking

top-k workflows



E-07

S-NY

Result-PartA

Result-PartB

Step 5: Workflow Instantiationunified well-formed request


seeded workflows



Parameter selection

bound workflows



Workflow grounding

workflow instances

Workflow mapping

ground workflows


Workflow ranking

top-k workflows



E-07

S-NY

Result-PartA

Result-PartB

<job id = “j42” name=“Neuman-BC”> <argument> -i E-07 17.5 -o ES-07….

parent

parentparent

parent

parent

Step 6: Workflow Grounding

Ground Workflow




seeded workflows



Parameter selection

bound workflows



Workflow grounding

workflow instances

Workflow mapping

ground workflows


Workflow ranking

top-k workflows


W1: estimated exec time 3hrs W2: estimated exec time 20hrs

W3: estimated exec time 3dW4: estimated exec time 5hrs

Step 7: Workflow RankingSeed workflow from request



seeded workflows



Parameter selection

bound workflows



Workflow grounding

workflow instances

Workflow mapping

ground workflows


Workflow ranking

top-k workflows





seeded workflows



Parameter selection

bound workflows



Workflow grounding

workflow instances

Workflow mapping

ground workflows


Workflow ranking

top-k workflows

W1: estimated exec time 3hrs W2: estimated exec time 20hrs

W3: estimated exec time 3dW4: estimated exec time 5hrs

Step 7: Workflow Ranking


Ground workflow: 15 compute nodesdevoid of resource assignment

41

85

10

9

13

12

15

9

4

837

10

13

12

15

13 data stage-in nodes

11 compute nodes (1-2&5-6 reduced based on available intermediate data)

8 inter-site data transfers

14 data stage-out nodes to long-term storage

14 data registration nodes (data cataloging)

Executable workflow: mapped to 3 sites

Step 8: Workflow MappingSeed workflow from request



seeded workflows



Parameter selection

bound workflows



Workflow grounding

workflow instances

Workflow mapping

ground workflows


Workflow ranking

top-k workflows


Why Do We Automate All This?So You Don’t Have To

Request ID

# Binding-Ready

Workflow Candidates

# Bound Workflow

Candidates

# Configured Workflow

Candidates

# Calls to c:find-DODs-given-output-requirements

# Calls to

d:find-data-

objects

# Calls to c:predict-DODs-given-input-requirements

Workflow Generation

Time

R1 6 8 8 1 6 8 5 s

R2 6 8 8 7 6 16 4 s

R3 6 24 24 7 6 48 7 s

R4 6 24 24 13 6 72 8 s

R5 18 64 48 7 18 128 22 s

R6 18 288 216 7 18 576 81 s

R7 18 16 12 7 18 32 10 s

R8 6 0 0 1 6 0 1 s




seeded workflows



Parameter selection

bound workflows



Workflow grounding

workflow instances

Workflow mapping

ground workflows


Workflow ranking

top-k workflows

Workflow candidates generated + considered(many are eliminated)

Queries aboutdata

Queries abouttools


WINGS DEMO


Editing a Seed & Template,Generating a DAX

WR0: Workflow Template

dataVariable5 data:contains data:Muti-party-communicationdataVariable0 data:creator 5048dataVariable1 data:creator 5048

WR0: Seed Constraints

Workflow seed =

Workflow Template

+

Seed Constraints




seeded workflows


candidate workflows

Parameter selection

bound workflows



Workflow grounding

workflow instances

Workflow mapping

ground workflows (DAXes)


Workflow ranking

top-k workflows


SCEC WORKFLOWS IN WINGS


InSAR Image of theHector Mine Earthquake

• A satellitegeneratedInterferometricSynthetic Radar(InSAR) image ofthe 1999 HectorMine earthquake.

• Shows thedisplacement fieldin the direction ofradar imaging

• Each fringe (e.g.,from red to red)corresponds to afew centimeters ofdisplacement.

SeismicHazardModel

Seismicity Seismicity PaleoseismologyPaleoseismology Local site effectsLocal site effects Geologic structureGeologic structure

FaultsFaults

StressStresstransfertransfer

CrustalCrustalmotionmotion

CrustalCrustaldeformationdeformation

Seismic velocitySeismic velocitystructurestructure

RuptureRupturedynamicsdynamics

Seismic Hazard Analysis in Southern California Earthquake Center (SCEC) [Slide from T. Jordan]


Intensional descriptions of data sets

Intensional descriptions of parallel computations

Querying results of other data creation subworkflows

Rich metadata descriptions for all data products

Reusable High-Level Workflow Templates


Workflows for Seismic Hazard Analysis [Gil et al 06; Kim et al 06; Gil et al 07]

Input data: a site and an earthquake forecast model

• thousands of possible fault ruptures and rupture variations, each a file, unevenly distributed

• ~110,000 rupture variations to be simulated for a given site

High-level template combines 11 application codes

8048 application nodes in the workflow instance generated by Wings

24,135 nodes in the executable workflow generated by Pegasus, including:

• data stage-in jobs, data stage-out jobs, data registration jobs

Executed in USC HPCC cluster, 1820 nodes w/ dual processors) but only < 144 available

• Including MPI jobs, each runs on hundreds of processors for 25-33 hours

• Runtime was 1.9 CPU years Provenance records kept throughout the

generation and execution process for 100,000 workflow data products


DAX automatically generated from WINGS

14,639 jobs for 4,626 ruptures with 106,124 rupture variations for USC site


Summary:Creating Workflows with WINGS

Separates analysis spec from data• Workflow template as reusable well-defined acceptable analysis process• Workflow instance binds template to data for particular analyses

Ensures that the data complies with the component specifications and their constraints within the workflow

Represents data collections (nominal or otherwise) within the workflow specification

Automatically generates descriptions and metadata to new data products to be created by the workflow execution

Compact workflow instance is user-friendly and reusable • Separates data provenance (workflow instance) and pedigree (workflow

template) Expands workflow instance into DAX for Pegasus, which creates

the executable workflow


Key Benefits

Efficient and correct creation of new workflows• By retrieving a template and filling in the data

Framework ensures adherence to methodology• Represents as templates widely-accepted analysis

methodologies• Supports repeatability of experiments/analyses• Enables controlled variations

Ensures better quality of data analysis results• Attaches provenance and pedigree information


Ongoing and Future Work

Interactive assistance in creating valid workflow templates• Based on CAT (Composition Analysis Tool) [Kim et al 05]

More sophisticated models of components Automatic completion of workflow’s data conversion

and formatting steps through AI planning techniques Tracking new versions of components, invalidate

data and workflows from old versions Workflow template libraries

• Indexing, retrieval Managing collections of workflows as part of an

overall analysis activity• Eg: parameter sweeping, variants of analysis


BACKUP SLIDES


…

Extension 1: Handle Collections of Collections

SGTSGT127_6.txt.variation-s0000-h0000127_6.txt.variation-s0000-h0000127_6.txt.variation-s0000-h0001127_6.txt.variation-s0001-h0000127_6.txt.variation-s0001-h0001 …20_0.txt.variation-s0000-h0000 …150_11.txt.variation-s0000-h0000…

SGTSGT127_6SGT20_0.txt.variation-s0000-h0000

SGT150_11.txt.variation-s0000-h0000

…

For rupture 127_6 (source ID 127, rupture ID 6), there are 8 variationsFor rupture 20_0(source ID 20, rupture ID 0), there are 1352 variationsA set of ruptures, each with a set of variationsEach variation in a separate file


Extending Wings to Handle Collections of Collections

File Collection

File

Variation FileCollection

has-type

Variation File

Collection ofCollections

has-type

has-type

Ruptures-PAS

…

SGTSGT127_6.txt.variation-s0000-h0000



…

127_6.txt.variation-s000-h000

Vars_127_6 Vars_127_7




… …

127_6.txt.variation-s0000-h0000127_6.txt.variation-s0000-h0001127_6.txt.variation-s0001-h0000127_6.txt.variation-s0001-h0001 …20_0.txt.variation-s0000-h0000 …150_11.txt.variation-s0000-h0000…


Wings Coll/Coll

150_11127_7

L1

F1F1F1RupVar

L2

F1F1F1SGT

SeismogramGen_Li

NC1

L3

seism

seism

L4SA

FCS-S

FCS-SA

PeakValCalc_Okaya

NC2

FCS-Var

CCS-Rup


SeisGen_Li

PeakValCalc

Seismograms_PAS_127_6.grm

PeakVals_allPAS_127_6.bsa

SGT161 SGTSGT127_7.txt.variation-s000-h000

SeisGen_Li

PeakValCalc




SeisGen_Li

PeakValCalc



SGT161

FCS-SGTColCCS-SGT

RV_127_6150_11127_7S_127_6


Constraints (in OWL ontology)

Constraints on Files • metadata attributes: data types and default valuese.g. simulation_out_timesamples of SeisParamValsFile should be an integer and the default value is 1801• File name format with respect to metadata attributese.g. rupture variation file: e.g. 127_6.txt.variation-s0002-h0000

Format: <source_id>_<rupture_id>.txt.variation-s[4 digit slip_realization#]-h000[4 digit hypo center #]

Constraints on collections and collection of collection• Type of each element• Relations between metadata of a collection and metadata of individual itemse.g. Each rupture variation has the same source/rupture ids as the rupture

variation collection Component level constraints on metadata attributes of input/output files

or collections• Deriving metadata of output files from metadata of input filese.g. The output of PeakValCalc_Okaya (SA output file) should have the same site

name as the seismogram file Template level constraints on metadata attributes of files or collections

• Input/output files of different components can have the same metadatae.g. The RVM collection input for SeismogramGen_Li should have the same site

name as the CollOfCollection rupture variations input• Checking number of items in collectionse.g. number of RVM files and the number of rupture var collections should be equal


Constraints on Files

RuptureVarFile

Int

Metadata:4DigitInt

hasSourceID

hasRuptureID

hasSlipRealization

hasHypoCenter

FileNameFormathasNameFormat

List of Metadata or StringConstant

File

SkolemInstances

RupVar-SK

xsd:inthasDefaultVal

hasMetadata

Metadata

SourceID1

RuptureID1

SlipRealz1

HypoCent1

RupVar_FileNameFormat1

hasDefaultValue

_

.txt.variation

0

Constraints on default values

Constraints on file names…

hasSourceID

hasRuptureID

usedAs

Domain independent definitions

SCEC dependentdefinitions

: classes

: instances

: roles


Constraints on Collections

RuptureVariations

CollOf Collection

CollectionhasType:hasCollectionType

FilehasType:hasFileType

RuptureVarsForForRupture

RuptureVarFile

RupVar-SK

C-RuptVars-SK

CC-RuptureVariations-SK

hasCollectionType

hasSiteName

Metadata:String

hasFileType

hasSourceID

hasRuptureIDMetadata:Int

hasSourceID

hasRuptureID

SkolemInstances

hasSiteName SiteName1

hasSiteName

SourceID1hasSourceID

hasSourceID

RuptureID1

Constraints on collection element types

metadata constraints on collections & their elements

…


Constraints on Components

SeismogramGen

ComponentType

hasInputs FileOrCollection

hasOutputs

SeismogramGen_LiSkolemInstances

hasInputs

SeismogramGenLi_Inputs

SeismogramGenLi_Outputs

hasOutputs

RVM1

Seismogram1

S-RV1

S-RuptVarsForRup1

hasSourceID

RVM_SourceID1

RVM_RuptureID1hasRuptureID

hasSiteName

SGTsSiteName1

metadata constraints on input and output files

Constraints on the types of input and output file and collections

…

SGT1

C-SGT1

…


Workflow Templates: a set of nodes and links

TemplatehasNode Node

hasLink Link(Input, Output, InOut, LinkMaping)

CybershakeTemplate1

Node_SeismogramGen_Collection

ComponentType orComponentCollection

hasComponent

hasFile File orCollection

hasNode

hasDestinationNode, hasOriginNode, hasDestinationFileDesc, hasOriginFileDesc, …

hasComponent

ComponentCollection_SeismogramGen

hasComponentType


hasLink

hasDestinationNode…

hasFile

F-RV1

C-RuptVars1

CC-RuptureVariations1

SeismogramGen_Li

S-RV1

S-RuptVarsForRup1hasDestinationFileDesc

InputOutLink_Seismogram_from_SeismGen_to_PeakValCalc

SkolemInstances


Constraints on Templates

CybershakeTemplate1

InputLink_SiteNameFile_to_BoxNameCheck

hasSiteName


hasLink

…

F-RV1

C-RuptVars1

CC-RuptureVariations1

InputLink_SGTCollforRup_to_SeismogramGen

F-SGT1

C-SGT-forRups1

CC-SGTs1

hasFile

hasFile

hasFile

SGTsSiteName1

SiteNameFile1

hasSiteName

SiteName1

N_Rups

hasN_Items

hasN_Items

…

… isSameAs

SkolemInstances

Constraints on number of elements in different collections

metadata constraints on files/collections of different components


Example OWL definitions

Filename format for rupture variation files

Definitions for metadatapropagation (SynthSGT)

Constraints on files/collections of different components


Extension 3: Creating many workflow instantiations


SeisGen_Li

PeakValCalc



SGT161SGTSGT127_7.txt.variation-s000-h000

SeisGen_Li

PeakValCalc




SeisGen_Li

PeakValCalc



SGT161

4262 independent instances for each rupture, >100,000 variations for a site

Memory Bottleneck: handling many files in the file library e.g. rupture variations

. . .

BNC

GenMD

BNC BNC

GenMD GenMD


Creating many workflow instantiations (on-going work)

Independent instances are generated separately• Instantiations for different ruptures are generated

separately On-demand creation of files and collections in the

file library• If files or collections are not used in metadata reasoning,

we don’t need to create file library objects for them (e.g. rupture variations) and only an ID is generated for them

Currently Wings needs 5-6 hrs to generate DAXes for 4626 ruptures with 106,124 variations


Extension 4: Interleaving execution with workflow generation

Extensions in the WF template representations• System links: a link from a component that generates

results needed in template instantiation E.g. BoxNameCheck generates a file that contains SGT file

names Template navigation algorithm: while navigating

links, identify partial workflows that can be executed based on system links & steps that are already executed

Wings and Pegasus interaction• On-going work: Client/server style interaction

e.g. use secure shell


Partial DAX generation: Workflow Navigation Algorithm

System link

Template navigation

Used for Partial DAX generation


Summary: Current System

MCS

On

tolo

gy

AP

I

file

&

mat

adat

a A

PI

OWL ontologiesWings File Ont

Wings Component Ont

Domain component Ont

Template Library

CC-Rup-Vars

C-Rup-Vars-for-Rup

File Library

Domain File Ont

…

Metadata constraints

Metadata reasoner

F-RV1F-RV1-current wf instance-logical files used-bindings -new file objects and metadata created

Jena

TemplateInstantiator

Pegasus

CAT TemplateValidator

TemplateSelection

DAXgenerator

User

WINGS


Ongoing Work

Approaches for handling many thousands of files• Use of MCS for storing logical file names and metadata• Use of more efficient OWL reasoners

(e.g. Sesame can handle 100 million triples) Client/server style interactions with Pegasus


Mappings in a Workflow Template

Link mappings specify the order of inputs to a node that accepts a collection

F1

C-plenty

F1

D8

F1DC9

C-one

G1

Z1

C-plenty

C-one

Z2

C-one

Z88

…

…

…

K1 G2 K2 G88 K88

Y1

C-spl

H1

C-one

D1

D3

D2

C-spl

D17

D18 C-plentyN3

L4

FS-Y

C-splN2

M5

D18

#1

#2

F1F1F1DC9

D1 D2

D3

L1 L2

L3

F1F1F1DC11

FCS-G FCS-K

FCS-Z

C-one

NC1

FCS-T


…

Nested File Collections

SGTSGT127_6.txt.variation-s0000-h0000127_6.txt.variation-s0000-h0000127_6.txt.variation-s0000-h0001127_6.txt.variation-s0001-h0000127_6.txt.variation-s0001-h0001 …20_0.txt.variation-s0000-h0000 …150_11.txt.variation-s0000-h0000…



…

For rupture 127_6 (source ID 127, rupture ID 6), there are 8 variationsFor rupture 20_0(source ID 20, rupture ID 0), there are 1352 variationsA set of ruptures, each with a set of variationsEach variation in a separate file



File Collection

File

Variation FileCollection

has-type

Variation File

Collection ofCollections

has-type

has-type

Ruptures-PAS

…




…


Vars_127_6 Vars_127_7




… …

127_6.txt.variation-s0000-h0000127_6.txt.variation-s0000-h0001127_6.txt.variation-s0001-h0000127_6.txt.variation-s0001-h0001 …20_0.txt.variation-s0000-h0000 …150_11.txt.variation-s0000-h0000…



150_11127_7

L1

F1F1F1RupVar

L2

F1F1F1SGT

SeismogramGen_Li

NC1

L3

seism

seism

L4SA

FCS-S

FCS-SA

PeakValCalc_Okaya

NC2

FCS-Var

CCS-Rup


SeisGen_Li

PeakValCalc




SeisGen_Li

PeakValCalc




SeisGen_Li

PeakValCalc



SGT161

FCS-SGTColCCS-SGT

RV_127_6150_11127_7S_127_6


Example OWL definitions

Filename format for rupture variation files

Definitions for metadatapropagation (SynthSGT)

Constraints on files/collections of different components


Component Ontology in OWL <owl:Class rdf:ID="ComponentType"/> <owl:FunctionalProperty rdf:ID="hasInputs"><rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/> <rdfs:domain rdf:resource="#ComponentType"/><rdfs:range rdf:resource="#FileAndPrefixList"/> </owl:FunctionalProperty><owl:ObjectProperty rdf:ID="hasOutputs"> <rdf:type

rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/> <rdfs:domain rdf:resource="#ComponentType"/> <rdfs:range rdf:resource="#FileAndPrefixList"/> </owl:ObjectProperty><owl:FunctionalProperty rdf:ID=”hasFile"> <rdfs:range> <owl:Class> <owl:unionOf rdf:parseType="Collection"> <rdf:Description

rdf:about="http://www.isi.edu/ikcap/wings/fileOntology.owl#File"/> <rdf:Description

rdf:about="http://www.isi.edu/ikcap/wings/fileOntology.owl#FileCollection"/>

</owl:unionOf> </owl:Class> </rdfs:range> <rdfs:domain rdf:resource="#FileAndPrefix"/> <rdf:type

rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/> </owl:FunctionalProperty><owl:DatatypeProperty rdf:ID="hasPrefix"> <rdfs:domain rdf:resource="#FileAndPrefix"/> <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/> <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/> </owl:DatatypeProperty>

<owl:FunctionalProperty rdf:ID="hasVersion">

<rdfs:domain rdf:resource="#ComponentType"/> <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/> <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/> </owl:FunctionalProperty> <owl:FunctionalProperty rdf:ID="hasExecutionRequirements"> <rdfs:domain rdf:resource="#ComponentType"/> <rdfs:range rdf:resource="http://www.isi.edu/ikcap/wings/executionRequirements.owl#ExecutionRequirements"/> <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/> </owl:FunctionalProperty><owl:DatatypeProperty rdf:ID="hasExecutablePath">

<rdfs:domain rdf:resource="#ComponentType"/> <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/> <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/> </owl:DatatypeProperty><owl:FunctionalProperty rdf:ID="hasNamespace"> <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/> <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/> <rdfs:domain rdf:resource="#ComponentType"/> </owl:FunctionalProperty><owl:FunctionalProperty rdf:ID="hasTranslationArgument"> <rdfs:domain rdf:resource="#ComponentType"/> <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/> <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/> </owl:FunctionalProperty>

<owl:Class rdf:ID="ComponentCollection"/> <owl:ObjectProperty rdf:ID="hasComponentType"> <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/> <rdfs:range rdf:resource="#ComponentType"/> <rdfs:domain rdf:resource="#ComponentCollection"/> </owl:ObjectProperty>


A Component Description from the Library <owl:Class rdf:ID="RemoveCommonWords"> <rdfs:subClassOf

rdf:resource="http://www.isi.edu/ikcap/wings/componentOntology.owl#ComponentType"/>

</owl:Class> <RemoveCommonWords rdf:ID="removeCommonWordsV1"> <clns:hasInputs> <clns:FileAndPrefixList rdf:ID="componentLibrary_RDFResource_5"> <rdf:rest rdf:resource="#componentLibrary_RDFResource_6"/> <rdf:first rdf:resource="#removeCommonWordsInput1"/> </clns:FileAndPrefixList> </clns:hasInputs> <clns:hasExecutionRequirements

rdf:resource="#countWordsExecutionReq"/> <clns:hasNamespace

rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >vds</clns:hasNamespace> <clns:hasOutputs> <clns:FileAndPrefixList rdf:ID="componentLibrary_RDFResource_7"> <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-

ns#nil"/> <rdf:first rdf:resource="#removeCommonWordsOutput"/> </clns:FileAndPrefixList> </clns:hasOutputs> <clns:hasVersion

rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >1</clns:hasVersion> <clns:hasExecutablePath

rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >/nfs/isd/varunr/wings/removeCommonWords</clns:hasExecutablePath> </RemoveCommonWords>

<clns:FileAndPrefix rdf:ID="removeCommonWordsOutput"> <clns:hasFile rdf:resource="#removeCommonWordsOutputFile"/> <clns:hasPrefix

rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >-o</clns:hasPrefix> </clns:FileAndPrefix> <lingflns:EnglishFile rdf:ID="removeCommonWordsOutputFile"/>

<clns:FileAndPrefixList rdf:ID="componentLibrary_Individual_34"> <rdf:rest> <clns:FileAndPrefixList rdf:ID="componentLibrary_Individual_37"> <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-

syntax-ns#nil"/> <rdf:first> <clns:FileAndPrefix rdf:ID="removeCommonWordsInput2"> <clns:hasFile> <lingflns:EnglishFile rdf:ID="removeCommonWordsInputFile"/> </clns:hasFile> </clns:FileAndPrefix> </rdf:first> </clns:FileAndPrefixList> </rdf:rest> <rdf:first> <clns:FileAndPrefix rdf:ID="removeCommonWordsInput1"> <clns:hasPrefix

rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >-i</clns:hasPrefix> <clns:hasFile> <lingflns:EnglishFile rdf:ID="CommonWordsFile"/> </clns:hasFile> </clns:FileAndPrefix> </rdf:first> </clns:FileAndPrefixList>

<clns:FileAndPrefixList rdf:ID="componentLibrary_Individual_40"> <rdf:first rdf:resource="#removeCommonWordsOutput"/> <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-

ns#nil"/> </clns:FileAndPrefixList>

<clns:FileAndPrefixList rdf:ID="componentLibrary_RDFResource_6"> <rdf:first rdf:resource="#removeCommonWordsInput2"/> <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-

ns#nil"/> </clns:FileAndPrefixList>


Formats for Filenames (examples)

SGT file: e.g. FD_SGT/USC_1/A/SGT161 Format: FD_SGT/<site_id>_[1-2]/[A-L]/SGT[3-digit-alphanumeric] - site_name: e.g. USC - tensor direction[1-2]: 1 (EW) 2(NS) - time_period [A-L]: A (0-15 seconds) B(15-30 seconds), etc. - 3-digit-alphanumeric :xyz volumn id rupture variation file: e.g. 127_6.txt.variation-s0002-h0000

Format: <source_id>_<rupture_id>.txt.variation-s[4 digit slip_realization#]-h000[4 digit hypo center #] - source_id: e.g. 127

- rupture_id: e.g. 6 - 4 digit slip_realization# : 2

- 4 digit hypo center #: 0 SA output file: e.g. PeakVals_allLADT_127_6.bsa

Format: PeakVals_all<site_id>_<source_id>_<rupture_id>.bsa seismogram file : e.g. Seismogram_LADT_127_6.grm

Format: Seismogram_<Site>_<source_id>_<rupture_id>.grm SRL file: e.g. USC-sorted_by_rupture_variations.srl

Format: <site_id>-sorted_by_rupture_variations.srl additional metadata:


All Data Products Have Rich Metadata <flns:File

rdf:about="http://www.isi.edu/ikcap/wings/domains/NLP/fileLibrary.owl#kernelRules_RulePruningWorkflow1_1118895460046">

<flns:usedAs rdf:resource="http://www.isi.edu/ikcap/wings/domains/NLP/componentLibrary.owl#KernelRulesFile"/>

<wflns:createdBy rdf:resource="http://www.isi.edu/ikcap/wings/domains/NLP/workflows/RulePruningInstance1.owl#"/>

<wflns:usedBy rdf:resource="http://www.isi.edu/ikcap/wings/domains/NLP/workflows/RulePruningInstance2.owl#"/>

</flns:File>

<nlpflns:TextFile rdf:about="http://www.isi.edu/ikcap/wings/domains/NLP/fileLibrary.owl#TextFileCollection_RulePruningWorkflow1_1118895460046_item_1"/>

<flns:FileCollection rdf:about="http://www.isi.edu/ikcap/wings/domains/NLP/fileLibrary.owl#RulePruningWorkflow1_1119042891296_FilteredRulesCollection">

<flns:usedAs rdf:resource="http://www.isi.edu/ikcap/wings/domains/NLP/componentLibrary.owl#FilterRulesOutputFile"/>

<flns:usedAs rdf:resource="http://www.isi.edu/ikcap/wings/domains/NLP/componentLibrary.owl#PruneRulesInputFile"/>

<wflns:createdBy rdf:resource="http://www.isi.edu/ikcap/wings/domains/NLP/workflows/RulePruningInstance2.owl#"/>

<flns:hasFiles rdf:parseType="Collection">

<flns:File rdf:about="http://www.isi.edu/ikcap/wings/domains/NLP/fileLibrary.owl#RulePruningWorkflow1_1119042891296_FilteredRulesCollection_item_0"/>

<flns:File rdf:about="http://www.isi.edu/ikcap/wings/domains/NLP/fileLibrary.owl#RulePruningWorkflow1_1119042891296_FilteredRulesCollection_item_1"/>

</flns:hasFiles>

</flns:FileCollection>

1 Yolanda Gil ([email protected]) AAAI-08 Tutorial July 13, 2008 USC Information Sciences Institute Part III Computational Workflows in Wings/Pegasus AAAI-08.

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