My certificate is still valid.
I’ve downloaded the latest openmole version and now the error is about the workflow, there’s a problem with “–”?
org.openmole.core.console.ScalaREPL$CompilationError: (line 60) overloaded method value -- with alternatives:
(parameters: org.openmole.core.workflow.transition.TransitionParameter*)org.openmole.core.workflow.puzzle.Puzzle <and>
(head: org.openmole.core.workflow.puzzle.Puzzle,tail: org.openmole.core.workflow.puzzle.Puzzle*)org.openmole.core.workflow.puzzle.Puzzle <and>
(to: org.openmole.core.workflow.puzzle.Puzzle,condition: org.openmole.core.expansion.Condition,filter: org.openmole.core.workflow.transition.BlockList)org.openmole.core.workflow.puzzle.Puzzle
cannot be applied to (org.openmole.core.workflow.puzzle.OutputEnvironmentPuzzleContainer)
EmptyTask() -- (profilesPi: _*)
^
Error in imports header:
(line -128) overloaded method value -- with alternatives:
(parameters: org.openmole.core.workflow.transition.TransitionParameter*)org.openmole.core.workflow.puzzle.Puzzle <and>
(head: org.openmole.core.workflow.puzzle.Puzzle,tail: org.openmole.core.workflow.puzzle.Puzzle*)org.openmole.core.workflow.puzzle.Puzzle <and>
(to: org.openmole.core.workflow.puzzle.Puzzle,condition: org.openmole.core.expansion.Condition,filter: org.openmole.core.workflow.transition.BlockList)org.openmole.core.workflow.puzzle.Puzzle
cannot be applied to (org.openmole.core.workflow.puzzle.OutputEnvironmentPuzzleContainer)
EmptyTask() -- (profilesPi: _*)
^
Compiling code:
class _833bca1d34d1a7a3175d137396b4813d25fc9433Class {
lazy val _imports = new {
lazy val _parent_ = new {
lazy val _parent_ = new {
lazy val envDef = _603d6824d64b8730186b4f46e3dee6ba9a5791fa
}
}
lazy val RModel = _8e136744fccfa68444ae43a0cc8be9e9510dd951
lazy val Objectif_Loglik = _ee6e2edf0e008d6974d0f7b8f3c5cd45a00b6f44
}
import _imports._
private lazy val workDirectory = File(new java.net.URI("file:/home/helene_arduin/.openmole/bfitou/webui/projects/estimation/tous_scenarios/").getPath)
import _parent_._parent_.envDef._
import RModel._
import Objectif_Loglik._
def profile(variable: Val[Double], nbPoints: Int, file: File) = {
val profileGen =
GenomeProfile(
x = variable,
nX = nbPoints,
genome = Seq(
beta in (0.3, 0.7),
xi in (-50.0, 150.0),
p0 in (3.0, 4.0),
pi in (-50.0, 450.0)
),
objective = loglik
)
val evolution = SteadyStateEvolution(
algorithm = profileGen,
evaluation = rTask(file) -- objective,
termination = 5 minutes
//termination = 10000
)
val island = IslandEvolution(
evolution,
parallelism = 50,
termination = 10000
)
val savePopulationHook = SavePopulationHook(
island,
//evolution,
//workDirectory / "cosSeason" / s"${file.getName.dropRight(6)}" / s"${variable.name}"
workDirectory / "noSeason" / s"${file.getName.dropRight(6)}" / s"${variable.name}"
)
(island on egi hook savePopulationHook)
//(evolution on local4 hook savePopulationHook)
}
val profilesXi =
for {
//f <- (workDirectory / "cosSeason" / "data").listFiles
f <- (workDirectory / "noSeason" / "data").listFiles
v <- List(xi)
} yield profile(v, 400, f)
val profilesPi =
for {
//f <- (workDirectory / "cosSeason" / "data").listFiles
f <- (workDirectory / "noSeason" / "data").listFiles
v <- List(pi)
} yield profile(v, 1000, f)
EmptyTask() -- (profilesPi: _*)
// DirectSampling(
// sampling = scenario in List("baseline1.RData",
// "acquisition2.RData", "acquisition4.RData", "acquisition10.RData", "acquisition50.RData",
// "transmission2.RData", "transmission4.RData", "transmission7.RData", "transmission10.RData", "transmission17.RData",
// "pathogenicity5.RData", "pathogenicity10.RData", "pathogenicity22.RData", "pathogenicity32.RData", "pathogenicity50.RData"),
// evaluation = EmptyTask() -- (profile(xi, scenario), profile(pi, scenario))
// )
}
lazy val _833bca1d34d1a7a3175d137396b4813d25fc9433 = new _833bca1d34d1a7a3175d137396b4813d25fc9433Class
class _603d6824d64b8730186b4f46e3dee6ba9a5791faClass {
lazy val _imports = new {
}
import _imports._
private lazy val workDirectory = File(new java.net.URI("file:/home/helene_arduin/.openmole/bfitou/webui/projects/").getPath)
val local4 = LocalEnvironment(4)
val local6 = LocalEnvironment(6)
val local8 = LocalEnvironment(8)
val tars = SLURMEnvironment(
"harduin",
"tars.pasteur.fr",
workDirectory = "/local/scratch/",
qos = "fast"
)
val egi = EGIEnvironment("vo.complex-systems.eu")
}
lazy val _603d6824d64b8730186b4f46e3dee6ba9a5791fa = new _603d6824d64b8730186b4f46e3dee6ba9a5791faClass
class _8e136744fccfa68444ae43a0cc8be9e9510dd951Class {
lazy val _imports = new {
}
import _imports._
private lazy val workDirectory = File(new java.net.URI("file:/home/helene_arduin/.openmole/bfitou/webui/projects/estimation/tous_scenarios/").getPath)
// Variables
val beta = Val[Double]
val xi = Val[Double]
val p0 = Val[Double]
val pi = Val[Double]
// Données
val dossier = Val[String]
// Outputs
// val simu = Val[File]
val param = Val[File]
// R task
def rTask(file: File) = CARETask(
workDirectory / "profilsLulla.tgz.bin",
"R -f mainLulla.R --slave --args ${beta} ${xi} ${p0} ${pi} ${dossier} /tmp/${dossier}/data/file.RData") set (
(inputs, outputs) += (beta, xi, p0, pi, dossier),
resources += (file, "/tmp/${dossier}/data/file.RData"),
// Si un fichier est créé dans le script R
// il faut le mettre dans les outputFiles
// avec le même nom que dans R
// outputFiles += ("simu.csv", simu),
outputFiles += ("param.txt", param),
// Default values
beta := 0.45,
xi := 79.067060,
p0 := 3.5,
pi := 92.0,
//dossier := "cosSeason"
dossier := "noSeason"
)
EmptyTask()
// Récupérer le fichier de simulation
// val getSimu = CopyFileHook(
// simu,
// workDirectory / "${dossier}" / "simu_${beta}.csv"
// )
// Récupérer les valeurs de paramètres et de loglik
// val catSimuFile = AppendToFileHook(
// // Fichier dans lequel copier
// workDirectory / "${dossier}" / "simuFile.txt",
// // Contenu à copier
// "${param.content}"
// )
// rTask hook (getSimu, catSimuFile)
}
lazy val _8e136744fccfa68444ae43a0cc8be9e9510dd951 = new _8e136744fccfa68444ae43a0cc8be9e9510dd951Class
class _ee6e2edf0e008d6974d0f7b8f3c5cd45a00b6f44Class {
lazy val _imports = new {
lazy val RModel = _8e136744fccfa68444ae43a0cc8be9e9510dd951
}
import _imports._
private lazy val workDirectory = File(new java.net.URI("file:/home/helene_arduin/.openmole/bfitou/webui/projects/estimation/tous_scenarios/").getPath)
import RModel._
val loglik = Val[Double]
val objective =
ScalaTask("val loglik = if (param.content.isEmpty) 1000000000 else -param.content.toDouble") set (
inputs += (param),
outputs += (loglik)
)
objective
}
lazy val _ee6e2edf0e008d6974d0f7b8f3c5cd45a00b6f44 = new _ee6e2edf0e008d6974d0f7b8f3c5cd45a00b6f44Class
def runOMSScript(): org.openmole.core.workflow.puzzle.Puzzle = {
import _833bca1d34d1a7a3175d137396b4813d25fc9433._imports._
import _parent_._parent_.envDef._
import RModel._
import Objectif_Loglik._
def profile(variable: Val[Double], nbPoints: Int, file: File) = {
val profileGen =
GenomeProfile(
x = variable,
nX = nbPoints,
genome = Seq(
beta in (0.3, 0.7),
xi in (-50.0, 150.0),
p0 in (3.0, 4.0),
pi in (-50.0, 450.0)
),
objective = loglik
)
val evolution = SteadyStateEvolution(
algorithm = profileGen,
evaluation = rTask(file) -- objective,
termination = 5 minutes
//termination = 10000
)
val island = IslandEvolution(
evolution,
parallelism = 50,
termination = 10000
)
val savePopulationHook = SavePopulationHook(
island,
//evolution,
//workDirectory / "cosSeason" / s"${file.getName.dropRight(6)}" / s"${variable.name}"
workDirectory / "noSeason" / s"${file.getName.dropRight(6)}" / s"${variable.name}"
)
(island on egi hook savePopulationHook)
//(evolution on local4 hook savePopulationHook)
}
val profilesXi =
for {
//f <- (workDirectory / "cosSeason" / "data").listFiles
f <- (workDirectory / "noSeason" / "data").listFiles
v <- List(xi)
} yield profile(v, 400, f)
val profilesPi =
for {
//f <- (workDirectory / "cosSeason" / "data").listFiles
f <- (workDirectory / "noSeason" / "data").listFiles
v <- List(pi)
} yield profile(v, 1000, f)
EmptyTask() -- (profilesPi: _*)
// DirectSampling(
// sampling = scenario in List("baseline1.RData",
// "acquisition2.RData", "acquisition4.RData", "acquisition10.RData", "acquisition50.RData",
// "transmission2.RData", "transmission4.RData", "transmission7.RData", "transmission10.RData", "transmission17.RData",
// "pathogenicity5.RData", "pathogenicity10.RData", "pathogenicity22.RData", "pathogenicity32.RData", "pathogenicity50.RData"),
// evaluation = EmptyTask() -- (profile(xi, scenario), profile(pi, scenario))
// )
}
runOMSScript()
at org.openmole.core.console.ScalaREPL$CompilationError.copy(ScalaREPL.scala:54)
at org.openmole.core.console.ScalaREPL$CompilationError$$anon$3$$anonfun$modifyF$1.apply(ScalaREPL.scala:54)
at org.openmole.core.console.ScalaREPL$CompilationError$$anon$3$$anonfun$modifyF$1.apply(ScalaREPL.scala:54)
at scalaz.Monad$$anonfun$map$1$$anonfun$apply$2.apply(Monad.scala:14)
at scalaz.IdInstances$$anon$1.point(Id.scala:20)
at scalaz.Monad$$anonfun$map$1.apply(Monad.scala:14)
at scalaz.IdInstances$$anon$1.bind(Id.scala:22)
at scalaz.Monad$class.map(Monad.scala:14)
at scalaz.IdInstances$$anon$1.map(Id.scala:19)
at org.openmole.core.console.ScalaREPL$CompilationError$$anon$3.modifyF(ScalaREPL.scala:54)
at org.openmole.core.console.ScalaREPL$CompilationError$$anon$3.modifyF(ScalaREPL.scala:54)
at monocle.PLens$$anon$5.modifyF(Lens.scala:190)
at monocle.PTraversal$$anon$2.modifyF(Traversal.scala:113)
at monocle.PTraversal$$anon$2.modifyF(Traversal.scala:113)
at monocle.PTraversal$$anon$2.modifyF(Traversal.scala:113)
at monocle.PTraversal$$anon$2.modifyF(Traversal.scala:113)
at monocle.PTraversal.monocle$PTraversal$$$anonfun$8(Traversal.scala:69)
at scala.Function1$$anonfun$andThen$1.apply(Function1.scala:52)
at org.openmole.core.project.Project.compile$1(Project.scala:155)
at org.openmole.core.project.Project.compile(Project.scala:161)
at org.openmole.gui.server.core.ApiImpl.runScript(ApiImpl.scala:316)
at org.openmole.gui.server.core.GUIServlet$$anonfun$2$$anonfun$applyOrElse$24.apply$mcV$sp(GUIServlet.scala:332)
at org.openmole.gui.server.core.GUIServlet$$anonfun$2$$anonfun$applyOrElse$24.apply(GUIServlet.scala:332)
at org.openmole.gui.server.core.GUIServlet$$anonfun$2$$anonfun$applyOrElse$24.apply(GUIServlet.scala:332)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.liftedTree1$1(Future.scala:24)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.run(Future.scala:24)
at scala.concurrent.impl.ExecutionContextImpl$AdaptedForkJoinTask.exec(ExecutionContextImpl.scala:121)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
Caused by: javax.script.ScriptException: compile-time error
at scala.tools.nsc.interpreter.IMain.compiled(IMain.scala:602)
at scala.tools.nsc.interpreter.IMain.eval(IMain.scala:1074)
at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
at scala.tools.nsc.interpreter.IMain.compile(IMain.scala:1068)
at org.openmole.core.console.ScalaREPL.compile(ScalaREPL.scala:194)
at org.openmole.core.project.Project.compile$1(Project.scala:132)
... 12 more
