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
    • 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 Ipopt

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

• Namespace std
  • Functions

Classes and Structs

• Struct AmiciSimulationRunner::AmiciResultPackageSimple
  • Nested Relationships
  • Struct Documentation
    • parpe::AmiciSimulationRunner::AmiciResultPackageSimple
      • AmiciResultPackageSimple()
      • llh
      • simulationTimeSeconds
      • gradient
      • modelOutput
      • modelSigmas
      • modelStates
      • status

• Struct AmiciSimulationRunner::AmiciWorkPackageSimple
  • Nested Relationships
  • Struct Documentation
    • parpe::AmiciSimulationRunner::AmiciWorkPackageSimple
      • AmiciWorkPackageSimple()
      • optimizationParameters
      • sensitivityOrder
      • conditionIndices
      • logPrefix

• Struct JobData
  • Struct Documentation
    • parpe::JobData
      • JobData()
      • JobData()
      • jobId
      • sendBuffer
      • recvBuffer
      • jobDone
      • jobDoneChangedCondition
      • jobDoneChangedMutex
      • callbackJobFinished

• Class AmiciSimulationRunner
  • Nested Relationships
    • Nested Types
  • Class Documentation
    • parpe::AmiciSimulationRunner
      • messageHandlerFunc
      • callbackJobFinishedType
      • callbackAllFinishedType
      • AmiciSimulationRunner()
      • AmiciSimulationRunner()
      • runSharedMemory()
      • parpe::AmiciSimulationRunner::AmiciResultPackageSimple
        • AmiciResultPackageSimple()
        • llh
        • simulationTimeSeconds
        • gradient
        • modelOutput
        • modelSigmas
        • modelStates
        • status
      • parpe::AmiciSimulationRunner::AmiciWorkPackageSimple
        • AmiciWorkPackageSimple()
        • optimizationParameters
        • sensitivityOrder
        • conditionIndices
        • logPrefix

• Class AmiciSummedGradientFunction
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::AmiciSummedGradientFunction
      • WorkPackage
      • ResultPackage
      • ResultMap
      • AmiciSummedGradientFunction()
      • ~AmiciSummedGradientFunction()
      • evaluate()
      • evaluate()
      • numParameters()
      • getParameterIds()
      • getModelOutputsAndSigmas()
      • getAllMeasurements()
      • messageHandler()
      • getParameterScaling()
      • sendStates
      • AmiciSummedGradientFunction()
      • runSimulations()
      • aggregateLikelihood()
      • addSimulationGradientToObjectiveFunctionGradient()
      • setSensitivityOptions()

• Class AnalyticalParameterHdf5Reader
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::AnalyticalParameterHdf5Reader
      • AnalyticalParameterHdf5Reader()
      • AnalyticalParameterHdf5Reader()
      • AnalyticalParameterHdf5Reader()
      • getConditionsForParameter()
      • getObservablesForParameter()
      • getOptimizationParameterIndices()
      • ~AnalyticalParameterHdf5Reader()

• Class AnalyticalParameterProvider
  • Inheritance Relationships
    • Derived Types
  • Class Documentation
    • parpe::AnalyticalParameterProvider
      • ~AnalyticalParameterProvider()
      • getConditionsForParameter()
      • getObservablesForParameter()
      • getOptimizationParameterIndices()

• Class AnalyticalParameterProviderDefault
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::AnalyticalParameterProviderDefault
      • AnalyticalParameterProviderDefault()
      • getConditionsForParameter()
      • getObservablesForParameter()
      • getOptimizationParameterIndices()
      • conditionsForParameter
      • optimizationParameterIndices
      • mapping

• Class CostFunction
  • Inheritance Relationships
    • Derived Type
  • Class Documentation
    • parpe::CostFunction
      • ~CostFunction()
      • evaluate()
      • evaluate()

• Class CpuTimer
  • Class Documentation
    • parpe::CpuTimer
      • CpuTimer()
      • reset()
      • getRound()
      • getTotal()

• Class GradientFunction
  • Inheritance Relationships
    • Derived Types
  • Class Documentation
    • parpe::GradientFunction
      • evaluate()
      • evaluate()
      • numParameters()
      • getParameterIds()
      • ~GradientFunction()

• Class HDF5Exception
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::HDF5Exception
      • HDF5Exception()
      • HDF5Exception()
      • what()
      • msg
      • stackTrace

• Class HierarchicalOptimizationProblemWrapper
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::HierarchicalOptimizationProblemWrapper
      • HierarchicalOptimizationProblemWrapper()
      • HierarchicalOptimizationProblemWrapper()
      • HierarchicalOptimizationProblemWrapper()
      • HierarchicalOptimizationProblemWrapper()
      • fillInitialParameters()
      • fillParametersMin()
      • fillParametersMax()
      • fillFilteredParams()
      • getOptimizationOptions()
      • setOptimizationOptions()
      • getReporter()

• Class HierarchicalOptimizationReporter
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::HierarchicalOptimizationReporter
      • HierarchicalOptimizationReporter()
      • evaluate()
      • iterationFinished()
      • afterCostFunctionCall()
      • finished()
      • getFinalParameters()
      • evaluate()
      • hierarchical_wrapper_
      • cached_full_parameters_
      • cached_full_gradient_

• Class HierarchicalOptimizationWrapper
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::HierarchicalOptimizationWrapper
      • HierarchicalOptimizationWrapper()
      • HierarchicalOptimizationWrapper()
      • HierarchicalOptimizationWrapper()
      • evaluate()
      • evaluate()
      • getDefaultScalingFactors()
      • getDefaultOffsetParameters()
      • getDefaultSigmaParameters()
      • getUnscaledModelOutputsAndSigmas()
      • computeAnalyticalScalings()
      • applyOptimalScalings()
      • computeAnalyticalOffsets()
      • computeAnalyticalSigmas()
      • applyOptimalOffsets()
      • fillInAnalyticalSigmas()
      • evaluateWithOptimalParameters()
      • numParameters()
      • numProportionalityFactors()
      • getProportionalityFactorIndices()
      • numOffsetParameters()
      • numSigmaParameters()
      • getOffsetParameterIndices()
      • getSigmaParameterIndices()
      • getAnalyticalParameterIndices()
      • getWrappedFunction()
      • getParameterIds()
      • evaluate()

• Template Class InverseUniqueLock
  • Class Documentation
    • parpe::InverseUniqueLock
      • InverseUniqueLock()
      • InverseUniqueLock()
      • operator=()
      • InverseUniqueLock()
      • operator=()
      • ~InverseUniqueLock()

• Class LearningRateUpdater
  • Class Documentation
    • parpe::LearningRateUpdater
      • LearningRateUpdater()
      • updateLearningRate()
      • reduceLearningRate()
      • increaseLearningRate()
      • getCurrentLearningRate()
      • setReductionFactor()
      • setMaxEpochs()
      • setStartLearningRate()
      • setEndLearningRate()

• Class LinearModel
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::LinearModel
      • LinearModel()
      • evaluate()
      • evaluate()
      • evaluate()

• Class LinearModelMSE
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::LinearModelMSE
      • LinearModelMSE()
      • evaluate()
      • evaluate()
      • numParameters()
      • getParameterIds()
      • numParameters_
      • datasets
      • labels
      • lm

• Class LoadBalancerWorker
  • Class Documentation
    • parpe::LoadBalancerWorker
      • messageHandlerFunc
      • LoadBalancerWorker()
      • run()

• Class LocalOptimizationIpoptTNLP
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::LocalOptimizationIpoptTNLP
      • LocalOptimizationIpoptTNLP()
      • ~LocalOptimizationIpoptTNLP()
      • get_nlp_info()
      • get_bounds_info()
      • get_starting_point()
      • eval_f()
      • eval_grad_f()
      • eval_g()
      • eval_jac_g()
      • intermediate_callback()
      • finalize_solution()

• Class Logger
  • Class Documentation
    • parpe::Logger
      • Logger()
      • Logger()
      • getChild()
      • logmessage()
      • logmessage()
      • logmessage()
      • setPrefix()
      • getPrefix()

• Class MeanSquaredError
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::MeanSquaredError
      • evaluate()
      • evaluate()

• Template Class MinibatchOptimizationProblem
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::MinibatchOptimizationProblem
      • MinibatchOptimizationProblem()
      • MinibatchOptimizationProblem()
      • MinibatchOptimizationProblem()
      • ~MinibatchOptimizationProblem()
      • getTrainingData()
      • getGradientFunction()

• Template Class MinibatchOptimizer
  • Class Documentation
    • parpe::MinibatchOptimizer
      • optimize()
      • evaluate()
      • finish()
      • rescueInterceptor()
      • handleStep()
      • performLineSearch()
      • parameterUpdater
      • interceptor
      • lineSearchSteps
      • batchSize
      • maxEpochs
      • gradientNormThreshold
      • learningRate
      • learningRateUpdater

• Template Class Model
  • Class Documentation
    • parpe::Model
      • ~Model()
      • evaluate()
      • evaluate()

• Class MultiConditionDataProvider
  • Inheritance Relationships
    • Derived Types
  • Class Documentation
    • parpe::MultiConditionDataProvider
      • ~MultiConditionDataProvider()
      • getNumberOfSimulationConditions()
      • getSimulationToOptimizationParameterMapping()
      • mapSimulationToOptimizationGradientAddMultiply()
      • mapAndSetOptimizationToSimulationVariables()
      • getParameterScaleOpt()
      • getParameterScaleOpt()
      • getParameterScaleSim()
      • getParameterScaleSim()
      • updateSimulationParametersAndScale()
      • getExperimentalDataForCondition()
      • getAllMeasurements()
      • getAllSigmas()
      • getNumOptimizationParameters()
      • getProblemParameterIds()
      • getModel()
      • getSolver()

• Class MultiConditionDataProviderDefault
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::MultiConditionDataProviderDefault
      • MultiConditionDataProviderDefault()
      • ~MultiConditionDataProviderDefault()
      • getNumberOfSimulationConditions()
      • getSimulationToOptimizationParameterMapping()
      • mapSimulationToOptimizationGradientAddMultiply()
      • mapAndSetOptimizationToSimulationVariables()
      • getParameterScaleOpt()
      • getParameterScaleOpt()
      • getParameterScaleSim()
      • getParameterScaleSim()
      • updateSimulationParametersAndScale()
      • getExperimentalDataForCondition()
      • getAllMeasurements()
      • getAllSigmas()
      • getNumOptimizationParameters()
      • getModel()
      • getSolver()
      • getProblemParameterIds()
      • edata_

• Class MultiConditionDataProviderHDF5
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::MultiConditionDataProviderHDF5
      • MultiConditionDataProviderHDF5()
      • MultiConditionDataProviderHDF5()
      • MultiConditionDataProviderHDF5()
      • MultiConditionDataProviderHDF5()
      • ~MultiConditionDataProviderHDF5()
      • getNumberOfSimulationConditions()
      • getSimulationToOptimizationParameterMapping()
      • mapSimulationToOptimizationGradientAddMultiply()
      • mapAndSetOptimizationToSimulationVariables()
      • getParameterScaleOpt()
      • getParameterScaleOpt()
      • getParameterScaleSim()
      • getParameterScaleSim()
      • checkDataIntegrity()
      • readFixedSimulationParameters()
      • getExperimentalDataForCondition()
      • getSensitivityParameterList()
      • getAllMeasurements()
      • getAllSigmas()
      • getSigmaForSimulationIndex()
      • getMeasurementForSimulationIndex()
      • getOptimizationParametersLowerBounds()
      • getOptimizationParametersUpperBounds()
      • getNumOptimizationParameters()
      • getModel()
      • getSolver()
      • updateSimulationParametersAndScale()
      • copyInputData()
      • getSimAndPreeqConditions()
      • getReinitializationIndices()
      • getHdf5File()
      • setModel()
      • getProblemParameterIds()
      • updateFixedSimulationParameters()

• Class MultiConditionProblem
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::MultiConditionProblem
      • MultiConditionProblem()
      • MultiConditionProblem()
      • MultiConditionProblem()
      • ~MultiConditionProblem()
      • earlyStopping()
      • getDataProvider()
      • getResultWriter()
      • setInitialParameters()
      • setParametersMin()
      • setParametersMax()
      • fillParametersMin()
      • fillParametersMax()
      • fillInitialParameters()
      • getReporter()
      • getTrainingData()

• Class MultiConditionProblemMultiStartOptimizationProblem
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::MultiConditionProblemMultiStartOptimizationProblem
      • MultiConditionProblemMultiStartOptimizationProblem()
      • getNumberOfStarts()
      • restartOnFailure()
      • getLocalProblem()

• Class MultiStartOptimization
  • Class Documentation
    • parpe::MultiStartOptimization
      • MultiStartOptimization()
      • ~MultiStartOptimization()
      • run()
      • runMultiThreaded()
      • runSingleThreaded()
      • setRunParallel()

• Class MultiStartOptimizationProblem
  • Inheritance Relationships
    • Derived Type
  • Class Documentation
    • parpe::MultiStartOptimizationProblem
      • getNumberOfStarts()
      • restartOnFailure()
      • getLocalProblem()
      • ~MultiStartOptimizationProblem()

• Class OptimizationApplication
  • Class Documentation
    • parpe::OptimizationApplication
      • OptimizationApplication()
      • ~OptimizationApplication()
      • initProblem()
      • run()
      • runMaster()
      • runSingleProcess()
      • OperationType
        • parameterEstimation
        • gradientCheck
      • finalizeTiming()
      • processResultFilenameCommandLineArgument()
      • isMaster()
      • isWorker()
      • parseCliOptionsPreMpiInit()
      • parseCliOptionsPostMpiInit()
      • printUsage()
      • logParPEVersion()
      • shortOptions
      • longOptions
      • dataFileName
      • resultFileName
      • first_start_idx
      • multiStartOptimizationProblem
      • problem
      • h5File
      • operationType
      • loadBalancer
      • withMPI
      • initMPI()

• Class OptimizationOptions
  • Class Documentation
    • parpe::OptimizationOptions
      • OptimizationOptions()
      • createOptimizer()
      • toString()
      • getIntOption()
      • getDoubleOption()
      • getStringOption()
      • setOption()
      • setOption()
      • setOption()
      • for_each()
      • optimizer
      • logFile
      • printToStdout
      • maxOptimizerIterations
      • numStarts
      • retryOptimization
      • hierarchicalOptimization
      • multistartsInParallel
      • fromHDF5()
      • fromHDF5()
      • getStartingPoint()

• Class OptimizationProblem
  • Inheritance Relationships
    • Derived Types
  • Class Documentation
    • parpe::OptimizationProblem
      • OptimizationProblem()
      • OptimizationProblem()
      • OptimizationProblem()
      • ~OptimizationProblem()
      • fillInitialParameters()
      • fillParametersMin()
      • fillParametersMax()
      • getOptimizationOptions()
      • setOptimizationOptions()
      • getReporter()
      • cost_fun_
      • logger_

• Class OptimizationProblemImpl
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::OptimizationProblemImpl
      • fillParametersMin()
      • fillParametersMax()
      • setParametersMin()
      • setParametersMax()
      • setInitialParameters()
      • fillInitialParameters()
      • OptimizationProblem()
      • OptimizationProblem()
      • OptimizationProblem()

• Class OptimizationReporter
  • Inheritance Relationships
    • Base Type
    • Derived Type
  • Class Documentation
    • parpe::OptimizationReporter
      • OptimizationReporter()
      • OptimizationReporter()
      • evaluate()
      • numParameters()
      • starting()
      • iterationFinished()
      • beforeCostFunctionCall()
      • afterCostFunctionCall()
      • finished()
      • getFinalCost()
      • getFinalParameters()
      • setGradientFunction()
      • getParameterIds()
      • result_writer_
      • cpu_time_total_sec_
      • cpu_time_iteration_sec_
      • logger_
      • printObjectiveFunctionFailureMessage()
      • wall_timer_
      • num_function_calls_
      • num_iterations_
      • num_parameters_
      • started_
      • grad_fun_
      • have_cached_cost_
      • have_cached_gradient_
      • cached_gradient_
      • cached_cost_
      • cached_status_
      • final_cost_
      • cached_parameters_
      • default_logger_prefix_

• Class OptimizationResultWriter
  • Class Documentation
    • parpe::OptimizationResultWriter
      • OptimizationResultWriter()
      • OptimizationResultWriter()
      • operator=()
      • OptimizationResultWriter()
      • ~OptimizationResultWriter()
      • logObjectiveFunctionEvaluation()
      • logOptimizerIteration()
      • setLoggingEachIteration()
      • setLoggingEachFunctionEvaluation()
      • starting()
      • saveOptimizerResults()
      • getH5File()
      • getRootPath()
      • setRootPath()
      • logParametersEachFunctionEvaluation
      • logGradientEachFunctionEvaluation
      • logGradientEachIteration
      • flushResultWriter()

• Class Optimizer
  • Inheritance Relationships
    • Derived Types
  • Class Documentation
    • parpe::Optimizer
      • optimize()
      • ~Optimizer()

• Class OptimizerCeres
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::OptimizerCeres
      • OptimizerCeres()
      • optimize()

• Class OptimizerDlibLineSearch
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::OptimizerDlibLineSearch
      • OptimizerDlibLineSearch()
      • optimize()

• Class OptimizerFides
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::OptimizerFides
      • OptimizerFides()
      • optimize()

• Class OptimizerFsqp
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::OptimizerFsqp
      • OptimizerFsqp()
      • optimize()

• Class OptimizerIpOpt
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::OptimizerIpOpt
      • OptimizerIpOpt()
      • optimize()

• Class OptimizerToms611TrustRegionSumsl
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::OptimizerToms611TrustRegionSumsl
      • OptimizerToms611TrustRegionSumsl()
      • optimize()

• Class ParameterUpdater
  • Inheritance Relationships
    • Derived Types
  • Class Documentation
    • parpe::ParameterUpdater
      • updateParameters()
      • undoLastStep()
      • clearCache()
      • initialize()
      • ~ParameterUpdater()

• Class ParameterUpdaterAdam
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::ParameterUpdaterAdam
      • ParameterUpdaterAdam()
      • updateParameters()
      • undoLastStep()
      • clearCache()
      • initialize()

• Class ParameterUpdaterAdamClassic
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::ParameterUpdaterAdamClassic
      • ParameterUpdaterAdamClassic()
      • updateParameters()
      • undoLastStep()
      • clearCache()
      • initialize()

• Class ParameterUpdaterMomentum
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::ParameterUpdaterMomentum
      • ParameterUpdaterMomentum()
      • updateParameters()
      • undoLastStep()
      • clearCache()
      • initialize()

• Class ParameterUpdaterRmsProp
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::ParameterUpdaterRmsProp
      • ParameterUpdaterRmsProp()
      • updateParameters()
      • undoLastStep()
      • clearCache()
      • initialize()

• Class ParameterUpdaterVanilla
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::ParameterUpdaterVanilla
      • ParameterUpdaterVanilla()
      • updateParameters()
      • undoLastStep()
      • clearCache()
      • initialize()

• Class ParPEException
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • parpe::ParPEException
      • ParPEException()
      • ParPEException()
      • ~ParPEException()
      • what()

• Class SimulationResultWriter
  • Class Documentation
    • parpe::SimulationResultWriter
      • SimulationResultWriter()
      • SimulationResultWriter()
      • SimulationResultWriter()
      • SimulationResultWriter()
      • ~SimulationResultWriter()
      • createDatasets()
      • createDatasets()
      • saveSimulationResults()
      • saveTimepoints()
      • saveMeasurements()
      • saveModelOutputs()
      • saveStates()
      • saveParameters()
      • saveLikelihood()
      • reopenFile()
      • saveX
      • saveLlh
      • saveYSim
      • saveYMes
      • save_parameters_
      • yMesPath
      • ySimPath
      • xPath
      • llhPath
      • timePath
      • parametersPath

• Class StandaloneSimulator
  • Class Documentation
    • parpe::StandaloneSimulator
      • StandaloneSimulator()
      • run()
      • messageHandler()

• Template Class SummedGradientFunction
  • Inheritance Relationships
    • Derived Type
  • Class Documentation
    • parpe::SummedGradientFunction
      • evaluate()
      • evaluate()
      • numParameters()
      • getParameterIds()
      • ~SummedGradientFunction()

• Template Class SummedGradientFunctionGradientFunctionAdapter
  • Inheritance Relationships
    • Base Types
  • Class Documentation
    • parpe::SummedGradientFunctionGradientFunctionAdapter
      • SummedGradientFunctionGradientFunctionAdapter()
      • evaluate()
      • evaluate()
      • evaluate()
      • numParameters()
      • getParameterIds()
      • getWrappedFunction()

• Class WallTimer
  • Class Documentation
    • parpe::WallTimer
      • WallTimer()
      • reset()
      • getRound()
      • getTotal()

Enums

• Enum ErrorModel
  • Enum Documentation
    • ErrorModel
      • normal

• Enum FunctionEvaluationStatus
  • Enum Documentation
    • FunctionEvaluationStatus
      • functionEvaluationSuccess
      • functionEvaluationFailure

• Enum interceptType
  • Enum Documentation
    • interceptType
      • none
      • reduceStep
      • reduceStepAndRestart

• Enum learningRateInterp
  • Enum Documentation
    • learningRateInterp
      • linear
      • inverseLinear
      • logarithmic

• Enum loglevel
  • Enum Documentation
    • loglevel
      • critical
      • error
      • warning
      • info
      • debug

• Enum minibatchExitStatus
  • Enum Documentation
    • minibatchExitStatus
      • gradientNormConvergence
      • maxEpochsExceeded
      • invalidNumber

• Enum optimizerName
  • Enum Documentation
    • optimizerName
      • OPTIMIZER_IPOPT
      • OPTIMIZER_CERES
      • OPTIMIZER_DLIB
      • OPTIMIZER_TOMS611
      • OPTIMIZER_FSQP
      • OPTIMIZER_FIDES
      • OPTIMIZER_MINIBATCH_1

Functions

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

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

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

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

• Function parpe::almostEqual
  • Function Documentation
    • almostEqual()

• Function parpe::applyChainRule
  • Function Documentation
    • applyChainRule()

• Function parpe::applyOptimalOffset
  • Function Documentation
    • applyOptimalOffset()

• Function parpe::applyOptimalScaling
  • Function Documentation
    • applyOptimalScaling()

• Function parpe::checkGradientForAnalyticalParameters
  • Function Documentation
    • checkGradientForAnalyticalParameters()

• Template Function parpe::clipToBounds
  • Function Documentation
    • clipToBounds()

• Function parpe::computeAnalyticalOffsets
  • Function Documentation
    • computeAnalyticalOffsets()

• Function parpe::computeAnalyticalScalings
  • Function Documentation
    • computeAnalyticalScalings()

• Function parpe::computeAnalyticalSigmas
  • Function Documentation
    • computeAnalyticalSigmas()

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

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

• Function parpe::fillArrayRandomDoubleIndividualInterval
  • Function Documentation
    • fillArrayRandomDoubleIndividualInterval()

• Function parpe::fillArrayRandomDoubleSameInterval
  • Function Documentation
    • fillArrayRandomDoubleSameInterval()

• Function parpe::fillFilteredParams
  • Function Documentation
    • fillFilteredParams()

• Function parpe::finalizeMpiIfNeeded
  • Function Documentation
    • finalizeMpiIfNeeded()

• Function parpe::getBacktrace
  • Function Documentation
    • getBacktrace()

• Template Function parpe::getBatches
  • Function Documentation
    • getBatches()

• Function parpe::getDefaultOffsetParameter
  • Function Documentation
    • getDefaultOffsetParameter()

• Function parpe::getDefaultScalingFactor
  • Function Documentation
    • getDefaultScalingFactor()

• Function parpe::getFinalParameters
  • Function Documentation
    • getFinalParameters()

• Function parpe::getFunctionEvaluationWithMinimalCost
  • Function Documentation
    • getFunctionEvaluationWithMinimalCost()

• Function parpe::getLocalOptimum
  • Function Documentation
    • getLocalOptimum()

• Template Function parpe::getMinibatchOptimizer
  • Function Documentation
    • getMinibatchOptimizer()

• Function parpe::getModelOutputsAndSigmas
  • Function Documentation
    • getModelOutputsAndSigmas()

• Function parpe::getMpiActive
  • Function Documentation
    • getMpiActive()

• Function parpe::getMpiCommSize
  • Function Documentation
    • getMpiCommSize()

• Function parpe::getMpiRank
  • Function Documentation
    • getMpiRank()

• Function parpe::getNumStarts
  • Function Documentation
    • getNumStarts()

• Function parpe::getOuterParameters
  • Function Documentation
    • getOuterParameters()

• Function parpe::getParameterTrajectory
  • Function Documentation
    • getParameterTrajectory()

• Function parpe::getVectorDifference
  • Function Documentation
    • getVectorDifference()

• Function parpe::getVectorNorm
  • Function Documentation
    • getVectorNorm()

• Function parpe::hdf5AttributeExists
  • Function Documentation
    • hdf5AttributeExists()

• Function parpe::hdf5CreateExtendableDouble2DArray
  • Function Documentation
    • hdf5CreateExtendableDouble2DArray()

• Function parpe::hdf5CreateExtendableDouble3DArray
  • Function Documentation
    • hdf5CreateExtendableDouble3DArray()

• Function parpe::hdf5CreateExtendableInt2DArray
  • Function Documentation
    • hdf5CreateExtendableInt2DArray()

• Function parpe::hdf5CreateExtendableString1DArray
  • Function Documentation
    • hdf5CreateExtendableString1DArray()

• Function parpe::hdf5CreateFile
  • Function Documentation
    • hdf5CreateFile()

• Function parpe::hdf5CreateGroup
  • Function Documentation
    • hdf5CreateGroup()

• Function parpe::hdf5CreateOrExtendAndWriteToDouble2DArray
  • Function Documentation
    • hdf5CreateOrExtendAndWriteToDouble2DArray()

• Function parpe::hdf5CreateOrExtendAndWriteToDouble3DArray
  • Function Documentation
    • hdf5CreateOrExtendAndWriteToDouble3DArray()

• Function parpe::hdf5CreateOrExtendAndWriteToInt2DArray
  • Function Documentation
    • hdf5CreateOrExtendAndWriteToInt2DArray()

• Function parpe::hdf5CreateOrExtendAndWriteToString1DArray
  • Function Documentation
    • hdf5CreateOrExtendAndWriteToString1DArray()

• Function parpe::hdf5EnsureGroupExists
  • Function Documentation
    • hdf5EnsureGroupExists()

• Function parpe::hdf5ErrorStackWalker_cb
  • Function Documentation
    • hdf5ErrorStackWalker_cb()

• Function parpe::hdf5Extend2ndDimensionAndWriteToDouble2DArray
  • Function Documentation
    • hdf5Extend2ndDimensionAndWriteToDouble2DArray()

• Function parpe::hdf5Extend2ndDimensionAndWriteToInt2DArray
  • Function Documentation
    • hdf5Extend2ndDimensionAndWriteToInt2DArray()

• Function parpe::hdf5Extend3rdDimensionAndWriteToDouble3DArray
  • Function Documentation
    • hdf5Extend3rdDimensionAndWriteToDouble3DArray()

• Function parpe::hdf5ExtendAndWriteToString1DArray
  • Function Documentation
    • hdf5ExtendAndWriteToString1DArray()

• Function parpe::hdf5Get3DDoubleHyperslab
  • Function Documentation
    • hdf5Get3DDoubleHyperslab()

• Function parpe::hdf5GetDatasetDimensions
  • Function Documentation
    • hdf5GetDatasetDimensions()

• Function parpe::hdf5GroupExists
  • Function Documentation
    • hdf5GroupExists()

• Function parpe::hdf5MutexGetLock
  • Function Documentation
    • hdf5MutexGetLock()

• Function parpe::hdf5OpenForAppending
  • Function Documentation
    • hdf5OpenForAppending()

• Function parpe::hdf5OpenForReading
  • Function Documentation
    • hdf5OpenForReading()

• Function parpe::hdf5Read1DIntegerHyperslab
  • Function Documentation
    • hdf5Read1DIntegerHyperslab()

• Function parpe::hdf5Read1dStringDataset
  • Function Documentation
    • hdf5Read1dStringDataset()

• Function parpe::hdf5Read2DDoubleHyperslab
  • Function Documentation
    • hdf5Read2DDoubleHyperslab()

• Function parpe::hdf5Read2DIntegerHyperslab
  • Function Documentation
    • hdf5Read2DIntegerHyperslab()

• Function parpe::hdf5Read3DDoubleHyperslab
  • Function Documentation
    • hdf5Read3DDoubleHyperslab()

• Function parpe::hdf5Write1dStringDataset
  • Function Documentation
    • hdf5Write1dStringDataset()

• Function parpe::hdf5WriteStringAttribute
  • Function Documentation
    • hdf5WriteStringAttribute()

• Function parpe::initHDF5Mutex
  • Function Documentation
    • initHDF5Mutex()

• Function parpe::ipOptGetLock
  • Function Documentation
    • ipOptGetLock()

• Function parpe::ipOptReleaseLock
  • Function Documentation
    • ipOptReleaseLock()

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

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

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

• Function parpe::logProcessStats
  • Function Documentation
    • logProcessStats()

• Function parpe::messageHandler
  • Function Documentation
    • messageHandler()

• Function parpe::operator==
  • Function Documentation
    • operator==()

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

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

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

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

• Function parpe::optimizerFactory
  • Function Documentation
    • optimizerFactory()

• Function parpe::printAvailableOptimizers
  • Function Documentation
    • printAvailableOptimizers()

• Function parpe::printBacktrace
  • Function Documentation
    • printBacktrace()

• Function parpe::printDebugInfoAndWait
  • Function Documentation
    • printDebugInfoAndWait()

• Function parpe::printfToString
  • Function Documentation
    • printfToString()

• Function parpe::printMPIInfo
  • Function Documentation
    • printMPIInfo()

• Function parpe::randDouble
  • Function Documentation
    • randDouble()

• Template Function parpe::removeInnerParameters
  • Function Documentation
    • removeInnerParameters()

• Function parpe::run_amici_simulation
  • Function Documentation
    • run_amici_simulation()

• Function parpe::runAlongTrajectory
  • Function Documentation
    • runAlongTrajectory()

• Function parpe::runAndLogSimulation
  • Function Documentation
    • runAndLogSimulation()

• Function parpe::runFinalParameters
  • Function Documentation
    • runFinalParameters()

• Function parpe::runMinibatchOptimization
  • Function Documentation
    • runMinibatchOptimization()

• Function parpe::runSimulator
  • Function Documentation
    • runSimulator()

• Function parpe::saveSimulation
  • Function Documentation
    • saveSimulation()

• Function parpe::saveTotalCpuTime
  • Function Documentation
    • saveTotalCpuTime()

• Function parpe::setIpOptOption
  • Function Documentation
    • setIpOptOption()

• Function parpe::setMinibatchOption
  • Function Documentation
    • setMinibatchOption()

• Function parpe::spliceParameters
  • Function Documentation
    • spliceParameters()

• Function parpe::strFormatCurrentLocaltime
  • Function Documentation
    • strFormatCurrentLocaltime()

• Function parpe::swap
  • Function Documentation
    • swap()

• Template Function parpe::withinBounds
  • Function Documentation
    • withinBounds()

• Template Function std::make_unique
  • Function Documentation
    • make_unique()

Variables

• Variable MPI_TAG_EXIT_SIGNAL
  • Variable Documentation
    • MPI_TAG_EXIT_SIGNAL

• Variable parpe::ANSI_COLOR_BLUE
  • Variable Documentation
    • ANSI_COLOR_BLUE

• Variable parpe::ANSI_COLOR_CYAN
  • Variable Documentation
    • ANSI_COLOR_CYAN

• Variable parpe::ANSI_COLOR_GREEN
  • Variable Documentation
    • ANSI_COLOR_GREEN

• Variable parpe::ANSI_COLOR_MAGENTA
  • Variable Documentation
    • ANSI_COLOR_MAGENTA

• Variable parpe::ANSI_COLOR_RED
  • Variable Documentation
    • ANSI_COLOR_RED

• Variable parpe::ANSI_COLOR_RESET
  • Variable Documentation
    • ANSI_COLOR_RESET

• Variable parpe::ANSI_COLOR_YELLOW
  • Variable Documentation
    • ANSI_COLOR_YELLOW

• Variable parpe::minimumLogLevel
  • Variable Documentation
    • minimumLogLevel

• Variable parpe::mutexIpOpt
  • Variable Documentation
    • mutexIpOpt

Defines

• Define H5_RESTORE_ERROR_HANDLER
  • Define Documentation
    • H5_RESTORE_ERROR_HANDLER

• Define H5_SAVE_ERROR_HANDLER
  • Define Documentation
    • H5_SAVE_ERROR_HANDLER

• Define HAVE_CSTDDEF
  • Define Documentation
    • HAVE_CSTDDEF

• Define RELEASE_ASSERT
  • Define Documentation
    • RELEASE_ASSERT

Typedefs

• Typedef parpe::LoadBalancerMaster
  • Typedef Documentation
    • LoadBalancerMaster

• Typedef parpe::LoadBalancerWorker
  • Typedef Documentation
    • LoadBalancerWorker

• Typedef parpe::mutexHdfType
  • Typedef Documentation
    • mutexHdfType

• Typedef parpe::mutexIpOptType
  • Typedef Documentation
    • mutexIpOptType