parPE C++ API

parPE C++ library functions

Class Hierarchy

• • Namespace parpe
    • Struct JobData
    • Class AmiciSimulationRunner
      • Struct AmiciSimulationRunner::AmiciResultPackageSimple
      • Struct AmiciSimulationRunner::AmiciWorkPackageSimple
    • Class AmiciSummedGradientFunction
    • Class AnalyticalParameterHdf5Reader
    • Class AnalyticalParameterProvider
    • Class AnalyticalParameterProviderDefault
    • Class CostFunction
    • Class CpuTimer
    • Class GradientFunction
    • Class HDF5Exception
    • Class HierarchicalOptimizationProblemWrapper
    • Class HierarchicalOptimizationReporter
    • Class HierarchicalOptimizationWrapper
    • Template Class InverseUniqueLock
    • Class LearningRateUpdater
    • Class LinearModel
    • Class LinearModelMSE
    • Class LoadBalancerWorker
    • Class LocalOptimizationIpoptTNLP
    • Class Logger
    • Class MeanSquaredError
    • Template Class MinibatchOptimizationProblem
    • Template Class MinibatchOptimizer
    • Template Class Model
    • Class MultiConditionDataProvider
    • Class MultiConditionDataProviderDefault
    • Class MultiConditionDataProviderHDF5
    • Class MultiConditionProblem
    • Class MultiConditionProblemMultiStartOptimizationProblem
    • Class MultiStartOptimization
    • Class MultiStartOptimizationProblem
    • Class OptimizationApplication
    • Class OptimizationOptions
    • Class OptimizationProblem
    • Class OptimizationProblemImpl
    • Class OptimizationReporter
    • Class OptimizationResultWriter
    • Class Optimizer
    • Class OptimizerCeres
    • Class OptimizerDlibLineSearch
    • Class OptimizerFides
    • Class OptimizerFsqp
    • Class OptimizerIpOpt
    • Class OptimizerToms611TrustRegionSumsl
    • Class ParameterUpdater
    • Class ParameterUpdaterAdam
    • Class ParameterUpdaterAdamClassic
    • Class ParameterUpdaterMomentum
    • Class ParameterUpdaterRmsProp
    • Class ParameterUpdaterVanilla
    • Class ParPEException
    • Class SimulationResultWriter
    • Class StandaloneSimulator
    • Template Class SummedGradientFunction
    • Template Class SummedGradientFunctionGradientFunctionAdapter
    • Class WallTimer
    • Enum ErrorModel
    • Enum FunctionEvaluationStatus
    • Enum interceptType
    • Enum learningRateInterp
    • Enum loglevel_tag
    • Enum minibatchExitStatus
    • Enum optimizerName

File Hierarchy

• • Directory include
    • Directory parpeamici
      • File amiciMisc.h
      • File amiciSimulationRunner.h
      • File hierarchicalOptimization.h
      • File hierarchicalOptimizationAnalyticalParameterProvider.h
      • File multiConditionDataProvider.h
      • File multiConditionProblem.h
      • File optimizationApplication.h
      • File simulationResultWriter.h
      • File standaloneSimulator.h
    • Directory parpecommon
      • File costFunction.h
      • File functions.h
      • File hdf5Misc.h
      • File logging.h
      • File misc.h
      • File model.h
      • File parpeException.h
    • Directory parpeloadbalancer
      • File loadBalancerMaster.h
      • File loadBalancerWorker.h
    • Directory parpeoptimization
      • File localOptimizationCeres.h
      • File localOptimizationDlib.h
      • File localOptimizationFides.h
      • File localOptimizationFsqp.h
      • File localOptimizationIpopt.h
      • File localOptimizationIpoptTNLP.h
      • File localOptimizationToms611.h
      • File minibatchOptimization.h
      • File multiStartOptimization.h
      • File optimizationOptions.h
      • File optimizationProblem.h
      • File optimizationResultWriter.h
      • File optimizer.h

Full API

Namespaces

• Namespace boost
  • Namespaces

• Namespace boost::serialization
  • Functions

• Namespace parpe
  • Classes
  • Enums
  • Functions
  • Typedefs
  • Variables

• Namespace std
  • Functions

Classes and Structs

• Struct AmiciSimulationRunner::AmiciResultPackageSimple
  • Nested Relationships
  • Struct Documentation

• Struct AmiciSimulationRunner::AmiciWorkPackageSimple
  • Nested Relationships
  • Struct Documentation

• Struct JobData
  • Struct Documentation

• Class AmiciSimulationRunner
  • Nested Relationships
    • Nested Types
  • Class Documentation

• Class AmiciSummedGradientFunction
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class AnalyticalParameterHdf5Reader
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class AnalyticalParameterProvider
  • Inheritance Relationships
    • Derived Types
  • Class Documentation

• Class AnalyticalParameterProviderDefault
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class CostFunction
  • Inheritance Relationships
    • Derived Type
  • Class Documentation

• Class CpuTimer
  • Class Documentation

• Class GradientFunction
  • Inheritance Relationships
    • Derived Types
  • Class Documentation

• Class HDF5Exception
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class HierarchicalOptimizationProblemWrapper
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class HierarchicalOptimizationReporter
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class HierarchicalOptimizationWrapper
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Template Class InverseUniqueLock
  • Class Documentation

• Class LearningRateUpdater
  • Class Documentation

• Class LinearModel
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class LinearModelMSE
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class LoadBalancerWorker
  • Class Documentation

• Class LocalOptimizationIpoptTNLP
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class Logger
  • Class Documentation

• Class MeanSquaredError
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Template Class MinibatchOptimizationProblem
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Template Class MinibatchOptimizer
  • Class Documentation

• Template Class Model
  • Class Documentation

• Class MultiConditionDataProvider
  • Inheritance Relationships
    • Derived Types
  • Class Documentation

• Class MultiConditionDataProviderDefault
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class MultiConditionDataProviderHDF5
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class MultiConditionProblem
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class MultiConditionProblemMultiStartOptimizationProblem
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class MultiStartOptimization
  • Class Documentation

• Class MultiStartOptimizationProblem
  • Inheritance Relationships
    • Derived Type
  • Class Documentation

• Class OptimizationApplication
  • Class Documentation

• Class OptimizationOptions
  • Class Documentation

• Class OptimizationProblem
  • Inheritance Relationships
    • Derived Types
  • Class Documentation

• Class OptimizationProblemImpl
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class OptimizationReporter
  • Inheritance Relationships
    • Base Type
    • Derived Type
  • Class Documentation

• Class OptimizationResultWriter
  • Class Documentation

• Class Optimizer
  • Inheritance Relationships
    • Derived Types
  • Class Documentation

• Class OptimizerCeres
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class OptimizerDlibLineSearch
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class OptimizerFides
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class OptimizerFsqp
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class OptimizerIpOpt
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class OptimizerToms611TrustRegionSumsl
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class ParameterUpdater
  • Inheritance Relationships
    • Derived Types
  • Class Documentation

• Class ParameterUpdaterAdam
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class ParameterUpdaterAdamClassic
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class ParameterUpdaterMomentum
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class ParameterUpdaterRmsProp
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class ParameterUpdaterVanilla
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class ParPEException
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class SimulationResultWriter
  • Class Documentation

• Class StandaloneSimulator
  • Class Documentation

• Template Class SummedGradientFunction
  • Inheritance Relationships
    • Derived Type
  • Class Documentation

• Template Class SummedGradientFunctionGradientFunctionAdapter
  • Inheritance Relationships
    • Base Types
  • Class Documentation

• Class WallTimer
  • Class Documentation

Enums

• Enum ErrorModel
  • Enum Documentation

• Enum FunctionEvaluationStatus
  • Enum Documentation

• Enum interceptType
  • Enum Documentation

• Enum learningRateInterp
  • Enum Documentation

• Enum loglevel_tag
  • Enum Documentation

• Enum minibatchExitStatus
  • Enum Documentation

• Enum optimizerName
  • Enum Documentation

Functions

• Template Function boost::serialization::serialize(Archive&, parpe::AmiciSimulationRunner::AmiciWorkPackageSimple&, const unsigned)
  • Function Documentation

• Template Function boost::serialization::serialize(Archive&, parpe::AmiciSimulationRunner::AmiciResultPackageSimple&, const unsigned)
  • Function Documentation

• Template Function operator<<(std::ostream&, std::vector<T> const&)
  • Function Documentation

• Template Function operator<<(std::ostream&, gsl::span<T> const&)
  • Function Documentation

• Function parpe::almostEqual
  • Function Documentation

• Function parpe::applyChainRule
  • Function Documentation

• Function parpe::applyOptimalOffset
  • Function Documentation

• Function parpe::applyOptimalScaling
  • Function Documentation

• Function parpe::checkGradientForAnalyticalParameters
  • Function Documentation

• Template Function parpe::clipToBounds
  • Function Documentation

• Function parpe::computeAnalyticalOffsets
  • Function Documentation

• Function parpe::computeAnalyticalScalings
  • Function Documentation

• Function parpe::computeAnalyticalSigmas
  • Function Documentation

• Function parpe::computeNegLogLikelihood(std::vector<std::vector<double>> const&, std::vector<std::vector<double>> const&, const std::vector<std::vector<double>>&)
  • Function Documentation

• Function parpe::computeNegLogLikelihood(std::vector<double> const&, std::vector<double> const&, const std::vector<double>&)
  • Function Documentation

• Function parpe::error
  • Function Documentation

• Function parpe::fillArrayRandomDoubleIndividualInterval
  • Function Documentation

• Function parpe::fillArrayRandomDoubleSameInterval
  • Function Documentation

• Function parpe::fillFilteredParams
  • Function Documentation

• Function parpe::finalizeMpiIfNeeded
  • Function Documentation

• Function parpe::getBacktrace
  • Function Documentation

• Template Function parpe::getBatches
  • Function Documentation

• Function parpe::getDefaultOffsetParameter
  • Function Documentation

• Function parpe::getDefaultScalingFactor
  • Function Documentation

• Function parpe::getFinalParameters
  • Function Documentation

• Function parpe::getFunctionEvaluationWithMinimalCost
  • Function Documentation

• Function parpe::getLocalOptimum
  • Function Documentation

• Function parpe::getLocalOptimumThreadWrapper
  • Function Documentation

• Template Function parpe::getMinibatchOptimizer
  • Function Documentation

• Function parpe::getModelOutputsAndSigmas
  • Function Documentation

• Function parpe::getMpiActive
  • Function Documentation

• Function parpe::getMpiCommSize
  • Function Documentation

• Function parpe::getMpiRank
  • Function Documentation

• Function parpe::getNumStarts
  • Function Documentation

• Function parpe::getOuterParameters
  • Function Documentation

• Function parpe::getParameterTrajectory
  • Function Documentation

• Function parpe::getScalarProduct
  • Function Documentation

• Function parpe::getVectorDifference
  • Function Documentation

• Function parpe::getVectorNorm
  • Function Documentation

• Function parpe::hdf5AttributeExists
  • Function Documentation

• Function parpe::hdf5CreateExtendableDouble2DArray
  • Function Documentation

• Function parpe::hdf5CreateExtendableDouble3DArray
  • Function Documentation

• Function parpe::hdf5CreateExtendableInt2DArray
  • Function Documentation

• Function parpe::hdf5CreateExtendableString1DArray
  • Function Documentation

• Function parpe::hdf5CreateFile
  • Function Documentation

• Function parpe::hdf5CreateGroup
  • Function Documentation

• Function parpe::hdf5CreateOrExtendAndWriteToDouble2DArray
  • Function Documentation

• Function parpe::hdf5CreateOrExtendAndWriteToDouble3DArray
  • Function Documentation

• Function parpe::hdf5CreateOrExtendAndWriteToInt2DArray
  • Function Documentation

• Function parpe::hdf5CreateOrExtendAndWriteToString1DArray
  • Function Documentation

• Function parpe::hdf5EnsureGroupExists
  • Function Documentation

• Function parpe::hdf5ErrorStackWalker_cb
  • Function Documentation

• Function parpe::hdf5Extend2ndDimensionAndWriteToDouble2DArray
  • Function Documentation

• Function parpe::hdf5Extend2ndDimensionAndWriteToInt2DArray
  • Function Documentation

• Function parpe::hdf5Extend3rdDimensionAndWriteToDouble3DArray
  • Function Documentation

• Function parpe::hdf5ExtendAndWriteToString1DArray
  • Function Documentation

• Function parpe::hdf5Get3DDoubleHyperslab
  • Function Documentation

• Function parpe::hdf5GetDatasetDimensions
  • Function Documentation

• Function parpe::hdf5GroupExists
  • Function Documentation

• Function parpe::hdf5MutexGetLock
  • Function Documentation

• Function parpe::hdf5OpenForAppending
  • Function Documentation

• Function parpe::hdf5OpenForReading
  • Function Documentation

• Function parpe::hdf5Read1DIntegerHyperslab
  • Function Documentation

• Function parpe::hdf5Read1dStringDataset
  • Function Documentation

• Function parpe::hdf5Read2DDoubleHyperslab
  • Function Documentation

• Function parpe::hdf5Read2DIntegerHyperslab
  • Function Documentation

• Function parpe::hdf5Read3DDoubleHyperslab
  • Function Documentation

• Function parpe::hdf5Write1dStringDataset
  • Function Documentation

• Function parpe::hdf5WriteStringAttribute
  • Function Documentation

• Function parpe::initHDF5Mutex
  • Function Documentation

• Function parpe::ipOptGetLock
  • Function Documentation

• Function parpe::ipOptReleaseLock
  • Function Documentation

• Function parpe::logmessage(loglevel, std::string const&)
  • Function Documentation

• Function parpe::logmessage(loglevel, const char *, …)
  • Function Documentation

• Function parpe::logmessage(loglevel, const char *, va_list)
  • Function Documentation

• Function parpe::logProcessStats
  • Function Documentation

• Function parpe::messageHandler
  • Function Documentation

• Function parpe::operator==
  • Function Documentation

• Function parpe::optimizationProblemGradientCheck(OptimizationProblem *, int, double)
  • Function Documentation

• Function parpe::optimizationProblemGradientCheck(OptimizationProblem *, gsl::span<const int>, double)
  • Function Documentation

• Function parpe::optimizationProblemGradientCheckMultiEps(OptimizationProblem *, int)
  • Function Documentation

• Function parpe::optimizationProblemGradientCheckMultiEps(OptimizationProblem *, gsl::span<const int>, gsl::span<double>)
  • Function Documentation

• Function parpe::optimizerFactory
  • Function Documentation

• Function parpe::printAvailableOptimizers
  • Function Documentation

• Function parpe::printBacktrace
  • Function Documentation

• Function parpe::printDebugInfoAndWait
  • Function Documentation

• Function parpe::printfToString
  • Function Documentation

• Function parpe::printMPIInfo
  • Function Documentation

• Function parpe::randDouble
  • Function Documentation

• Template Function parpe::removeInnerParameters
  • Function Documentation

• Function parpe::runAlongTrajectory
  • Function Documentation

• Function parpe::runAndLogSimulation
  • Function Documentation

• Function parpe::runFinalParameters
  • Function Documentation

• Function parpe::runInParallelAndWaitForFinish
  • Function Documentation

• Function parpe::runMinibatchOptimization
  • Function Documentation

• Function parpe::runSimulator
  • Function Documentation

• Function parpe::saveSimulation
  • Function Documentation

• Function parpe::saveTotalCpuTime
  • Function Documentation

• Function parpe::setIpOptOption
  • Function Documentation

• Function parpe::setMinibatchOption
  • Function Documentation

• Function parpe::spliceParameters
  • Function Documentation

• Function parpe::strFormatCurrentLocaltime
  • Function Documentation

• Function parpe::swap
  • Function Documentation

• Function parpe::warning
  • Function Documentation

• Template Function parpe::withinBounds
  • Function Documentation

• Template Function std::make_unique
  • Function Documentation

Variables

• Variable MPI_TAG_EXIT_SIGNAL
  • Variable Documentation

• Variable parpe::ANSI_COLOR_BLUE
  • Variable Documentation

• Variable parpe::ANSI_COLOR_CYAN
  • Variable Documentation

• Variable parpe::ANSI_COLOR_GREEN
  • Variable Documentation

• Variable parpe::ANSI_COLOR_MAGENTA
  • Variable Documentation

• Variable parpe::ANSI_COLOR_RED
  • Variable Documentation

• Variable parpe::ANSI_COLOR_RESET
  • Variable Documentation

• Variable parpe::ANSI_COLOR_YELLOW
  • Variable Documentation

• Variable parpe::minimumLogLevel
  • Variable Documentation

• Variable parpe::mutexIpOpt
  • Variable Documentation

Defines

• Define H5_RESTORE_ERROR_HANDLER
  • Define Documentation

• Define H5_SAVE_ERROR_HANDLER
  • Define Documentation

• Define HAVE_CSTDDEF
  • Define Documentation

• Define RELEASE_ASSERT
  • Define Documentation

Typedefs

• Typedef parpe::LoadBalancerMaster
  • Typedef Documentation

• Typedef parpe::LoadBalancerWorker
  • Typedef Documentation

• Typedef parpe::loglevel
  • Typedef Documentation

• Typedef parpe::mutexHdfType
  • Typedef Documentation

• Typedef parpe::mutexIpOptType
  • Typedef Documentation