C.W. Smith, S. Tran, O. Sahni, and M.S. Shephard, Rensselaer Polytechnic Institute

Raminder SinghIndiana Universityramifnu@iu.edu

Enabling HPC Simulation Workflows

for Complex Industrial Flow

Parallel Data & Services

Domain Topology

Mesh Topology/Shape

Dynamic Load Balancing

Simulation Fields

Physics and Model Parameters Input Domain Definition with Attributes

PHASTA

Parasolidor

GeomSim

MeshSim and MeshSim Adapt

Paraview

SolutionTransfer

Hessian-based error indicator

NS, FELevel set

Solution transfer constraints

mesh with fields

mesh with fields

calculated fields

mesh size field

meshes and fields

meshing

operation geometricinterrogation

Attributed topology

non-manifoldmodel construction

geometry updates

mesh size field

mesh

Partition Control

Complex Flow Simulations

Project challenges

High barrier to run HPC workflows

– Requires knowledge of file system

– scheduler

– scripting

– runtime environment

– compilers … - for each HPC system

Other Challenges

– Must have very high degree of automation –human in the loop kills scalability and performance

– Need easy access to parallel computers

User specifies

• problem definition

• simulation parameters

• required compute resources

through experiment creation web page

• Workflow steps are executed on

HPC system

• user is emailed

• output is prepared for download

option to delete or archive

• Scales to multiple users and systems

Science gateway for PHASTA lowers the barrier

• Used PHP Gateway framework with Airavata to develop gateway and enable PHASTA application

• Setup a community account to support the community

• Defining resources to run the application

– TACC Stampede

– CCI IBM Blue Gene.

• Define the PHASTA application.

PHASTA Solution

What is PGA?

• PGA is the sample gateway implemented to demonstrate Airavata middleware features.

• You can download and use it as it is or modify it according to your requirements.

• There is an Ansible script available and dockerimage worked on by a GSOC Student.

• PGA is developed using PHP.

• Visit PGA at;

– https://testdrive.airavata.org/

2

Landing page

User login and creation

Resource definition

Application definition

Create Experiment

Monitor Experiment

Experiment Statistics

Other Examples using PGA

Gateway Features for Default User

• In the gateway default user can;

– Create and Launch Experiments.

– Monitor Experiments.

– Create Projects (Experiment grouping).

– Clone, Cancel and Edit Experiment.

– Report Issues & Provide Feedback.

6

Apache Airavata

• Address user requests

• Allow staging data from user desktop to resource and vice-versa

• Tail on remote application logs

• User key generation and CCI user accounts

Future work

Industry Challenge Talk Wednesday @ 4

Workflow Diagram for SEQC Transcriptome Assembly and Evaluation

Yes

Pre-processing,Input:SequencingReadsFASTQFiles• AdapterTrimming(cutadaptso ware)• PolyA/TTrimming,andRemovingmtRNA,rRNA(customscript)• ErrorCorrec onforRAN-Seqreads(SEECER)

Sta s calcomparisonofallthe~60assemblies(Sta s calTes ngforpopula onofAssemblies)• NovelScore:EfficientlyCoveredBasesforAllGenes(EC-BAG)Score(CustomScript)• Sta s calTes ng,e.g.ANOVA

PassedQC?(customscriptneededtochecktheaboveQCcriteria,e.g.:

If(CEGMA_CEGs>235)thenCEGMA_flag=Passed)

TranscriptomeAssemblies,Input:TrimmedSequencingReadsFASTQFiles• AssemblingSamplesAandBforsixcenters,usingdifferentreplicate-combina ons(Trinityso ware)• ~60TranscriptomeAssemblies

GenomeCoverage–SNPDetec onforFASTQTrimmedInputReads• MappingInputReadstotheReferenceGenome(TopHatso ware)• SNPdetec on(GATKso ware):OutputCalledSNP_Reads• GenomeCoverage,usingMappedReads(featureCounts–RBioconductorPackage)

QualityControl(QC),Input:AssembledCon gsFiles(FASTAFormat)• DETONATE(DETONATEso ware,usinghumanreferencegenome)• CEGMA(CEGMAso ware)• Assembliessta s caloutputs(providedbyTrinityforeachassembly)• Mappingreadsbacktothecon gs(TopHatso ware)

Discardthe

Assembly

No

GenomeCoverage–SNPDetec onforFASTAAssembledCon gs• Mappingassembledcon gstotheReferenceGenome(GMAPso ware)• SNPdetec on(GATKso ware):OutputCalledSNP_Con gs• GenomeCoverage,usingMappedCon gs(featureCounts–RBioconductorPackage)

SNPCompariosn• ComparingDetectedSNP_Con gswithdbSNP(CustomScriptandSnpSi )• ComparingDetectedSNP_ReadswithdbSNP(CustomScriptandSnpSi )

Thanks!!!Questions?

ramifnu@iu.edu

sgg@iu.edu

https://iu.box.com/xsede15