Using an actor framework for scientific computing

opportunities and challenges

author: Krzysztof Borowski

supervisor: Ph. D. Bartosz Baliś

@liosedhel

Workflow

  • Directed Graph
  • Many inputs/Many outputs
  • Nodes - activities
  • Edges - dependencies (control flow)
  • Each node activity == fun(Data): Result

Scientific workflow

  • Data elements can be big
  • Activities can be long-running and resource intensive
  • Often invoke legacy code (e.g. Fortran, C) or external services

Scientific workflow - requirements

  • Parallelization and distribution of computations
  • Persistence and recovery
  • Fault tolerance

Actor Model

  • State isolation
  • Async communication
  • Behavior changing
  • Spawning new actors

But why exactly the actor model?

But why exactly the actor model?

Similarities. Why not to give it a shot?

Actor Model difficulties

Aspect Flow activity Actors
Input data Many typed input channels One input mailbox
Output data Many typed output channels Lack of output channels
Flow patterns Complicated patterns Simple async messages in "fire and forget" manner

Akka-streams to the rescue!

  • Build with actor model
  • Support for complicated flows (beautiful graph oriented API)
  • Concurrent data processing

But...

Scientific workflows Akka streams
bounded input data set unbounded data stream
big data elements small data elements
focused on scaling focused on back-pressure (reactive streams implementation)
important recovery mechanism important high message throughput 

Current workflow engines

  • Kepler, Teverna, Pegasus
  • Focused on graphical interface for non programmers, or has complicated API
  • Complex 
  • At the end of the day you always must write external program

Scaflow - New Hope

  • Simple workflow engine for scientific computations
  • For programmers
  • Build with modern technologies in less then 1.5k lines of code (Scala, Akka, Cassandra)

Components

Source

Data processing

Data filtering

Data grouping

Components

Broadcast data

Merge data

Components

Synchronize data

Data sink

Scaflow API

StandardWorkflow.source(List(1, 2, 3, 4, 5, 6))
      .map(a => a * a)
      .group(3)
      .map(_.sum)
      .sink(println).run

Concurrent computations in actor model

Push model

Pull model

Scalability in actor model

Workflow persistent state

  • Event sourcing 
  • Persistent actors
  override def receiveRecover: Receive = receiveRecoverWithAck {
    case n: NextVal[A] =>
      if (filter(n.data)) deliver(destination, n)
  }

  override def receiveCommand: Receive = receiveCommandWithAck {
    case n: NextVal[A] =>
      persistAsync(n) { e =>
        if (filter(e.data)) deliver(destination, n)
      }
  }

/* ... */
PersistentWorkflow.source("source", List(1, 2, 3, 4, 5, 6))
      .map("square", a => a * a)
      .group("group", 3)
      .map("sum", _.sum)
      .sink(println).run

Fault tolerance

 val HTTPSupervisorStrategy = OneForOneStrategy(10, 5.seconds) {
    case e: TimeoutException => Restart //retry
    case _ => Stop //drop the message
  }

 PersistentWorkflow.connector[String]("pngConnector")
      .map("getPng", getPathwayMapPng, Some(HTTPSupervisorStrategy))
      .sink("sinkPng", id => println(s"PNG map downloaded for $id"))

Real world example

Real world example cont.

val HTTPSupervisorStrategy = OneForOneStrategy(10, 10.seconds) {
      case e: TimeoutException => Restart // try to perform operation again
      case _ => Stop // drop the message
}

val savePathwayPngFlow = PersistentWorkflow.connector[String]("pngConnector")
      .map("getPng", getPathwayMapPng, Some(HTTPSupervisorStrategy), workersNumber = 8)
      .sink("sinkPng", id => println(s"PNG map downloaded for $id"))

val savePathwayTextFlow = PersistentWorkflow.connector[String]("textConnector")
      .map("getTxt", getPathwayDetails, Some(HTTPSupervisorStrategy), workersNumber = 8)
      .sink("sinkTxt", id => println(s"TXT details downloaded for pathway $id"))

PersistentWorkflow
  .source("source", List("hsa"))
  .map("getSetOfPathways", getSetOfPathways, Some(HTTPSupervisorStrategy))
  .split[String]("split")
  .broadcast("broadcast", savePathwayPngFlow, savePathwayTextFlow)
  .run

Real world example - scaling

val remoteWorkersHostLocations = 
    Seq(AddressFromURIString("akka.tcp://workersActorSystem@localhost:5150"),
        AddressFromURIString("akka.tcp://workersActorSystem@localhost:5151"))

val HTTPSupervisorStrategy = OneForOneStrategy(10, 10.seconds) {
      case e: TimeoutException => Restart // try to perform operation again
      case _ => Stop // drop the message
}

val savePathwayPngFlow = PersistentWorkflow.connector[String]("pngConnector")
      .map("getPng", getPathwayMapPng, Some(HTTPSupervisorStrategy), 
            workersNumber = 8, remoteAddresses = remoteWorkersHostLocations)
      .sink("sinkPng", id => println(s"PNG map downloaded for $id"))

val savePathwayTextFlow = PersistentWorkflow.connector[String]("textConnector")
      .map("getTxt", getPathwayDetails, Some(HTTPSupervisorStrategy), workersNumber = 8)
      .sink("sinkTxt", id => println(s"TXT details downloaded for pathway $id"))

PersistentWorkflow
  .source("source", List("hsa"))
  .map("getSetOfPathways", getSetOfPathways, Some(HTTPSupervisorStrategy))
  .split[String]("split")
  .broadcast("broadcast", savePathwayPngFlow, savePathwayTextFlow)
  .run

Event sourcing - performance

Future development

  • Graph API
  • Extensive usage of Akka clusters
  • Workflow monitoring

https://github.com/liosedhel/scaflow

Special thanks go to 

Ph.D. Bartosz Baliś

from AGH Universisty

for the idea, work supervision, advices and all other help during the research and Scaflow development

https://github.com/liosedhel/scaflow

Bibliography

  • Akka - http://akka.io/
  • Cassandra - http://cassandra.apache.org/
  • Pegasus - pegasus.isi.edu
  • Taverna - http://www.taverna.org.uk/
  • Kepler - https://kepler-project.org/
  • akka-streams - http://doc.akka.io/docs/akka-stream-and-http-experimental/2.0.3/scala.html

Scaflow-LambdaDays2016

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Scaflow-LambdaDays2016

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