rr::LoadSBMLOptions Class Reference

Options for loading SBML into RoadRunner. More...

#include <rrRoadRunnerOptions.h>

Inheritance diagram for rr::LoadSBMLOptions:

Public Types
enum	LLVM_BACKEND_VALUES { MCJIT = (0x1 << 14) , LLJIT = (0x1 << 15) }
enum	LLJIT_OPTIMIZATION_LEVELS { NONE = (0x1 << 16) , LESS = (0x1 << 17) , DEFAULT = (0x1 << 18) , AGGRESSIVE = (0x1 << 19) }
enum	ModelGeneratorOpt {   CONSERVED_MOIETIES = (0x1 << 0) , RECOMPILE = (0x1 << 1) , READ_ONLY = (0x1 << 2) , MUTABLE_INITIAL_CONDITIONS = (0x1 << 3) ,   OPTIMIZE_GVN = (0x1 << 4) , OPTIMIZE_CFG_SIMPLIFICATION = (0x1 << 5) , OPTIMIZE_INSTRUCTION_COMBINING = (0x1 << 6) , OPTIMIZE_DEAD_INST_ELIMINATION = (0x1 << 7) ,   OPTIMIZE_DEAD_CODE_ELIMINATION = (0x1 << 8) , OPTIMIZE_INSTRUCTION_SIMPLIFIER = (0x1 << 9) , OPTIMIZE , USE_MCJIT = (0x1 << 10) ,   LLVM_SYMBOL_CACHE = (0x1 << 11) , TURN_ON_VALIDATION = (0x1 << 12) }
enum	LoadOpt { NO_DEFAULT_SELECTIONS = (0x1 << 0) , NO_DEFAULT_STEADY_STATE_SELECTIONS = (0x1 << 1) }
Public Types inherited from rr::BasicDictionary
using	item = std::pair< std::string, Setting >

Public Member Functions
	LoadSBMLOptions ()
	initializes the struct with the default options.
	LoadSBMLOptions (const Dictionary *dict)
	creates an object from an existing dictionary.
void	setItem (const std::string &key, const rr::Setting &value) override
	sets an item in the internal unordered std::map.
Setting	getItem (const std::string &key) const override
	gets an item from the internal unordered std::map.
bool	hasKey (const std::string &key) const override
	is there a key matching this name. More...
size_t	deleteItem (const std::string &key) override
	remove a value
std::vector< std::string >	getKeys () const override
	list of keys in this object.
bool	getConservedMoietyConversion () const
void	setConservedMoietyConversion (bool val)
void	setValidation (bool val)
void	setLLVMBackend (LoadSBMLOptions::LLVM_BACKEND_VALUES val)
void	setLLJitOptimizationLevel (LLJIT_OPTIMIZATION_LEVELS levels)
Public Member Functions inherited from rr::BasicDictionary
	BasicDictionary (std::initializer_list< item > initializerList)
	~BasicDictionary () override=default
	Pure virtual interface, you should never have to delete an instance of this type directly.
Public Member Functions inherited from rr::Dictionary
virtual	~Dictionary ()
	Pure virtual interface, you should never have to delete an instance of this type directly.

Static Public Member Functions
static std::vector< LLVM_BACKEND_VALUES >	getAllLLVMBackendValues ()
static std::vector< LLJIT_OPTIMIZATION_LEVELS >	getAllLLJitOptimizationValues ()

Public Attributes
std::uint16_t	version
	the version this struct
std::uint16_t	size
	sizeof this struct
std::uint32_t	modelGeneratorOpt
std::uint32_t	loadFlags

Additional Inherited Members
Protected Types inherited from rr::BasicDictionary
typedef std::unordered_map< std::string, Setting >	VariantMap
Protected Attributes inherited from rr::BasicDictionary
VariantMap	items

Detailed Description

Options for loading SBML into RoadRunner.

Future version may add additional fields to the end of this struct, this way we can maintain binary compatibility with older RoadRunner versions.

Member Enumeration Documentation

LoadOpt

enum rr::LoadSBMLOptions::LoadOpt

Enumerator
NO_DEFAULT_SELECTIONS	Do not create a default selection list when the model is loaded.
NO_DEFAULT_STEADY_STATE_SELECTIONS	Do not create a default steady state selection list when the model is loaded.

ModelGeneratorOpt

enum rr::LoadSBMLOptions::ModelGeneratorOpt

Enumerator
CONSERVED_MOIETIES	perform conservation analysis. This causes a re-ordering of the species, so results generated with this flag enabled can not be compared index wise to results generated otherwise. currently only implemented with the C code generating model
RECOMPILE	Should the model be recompiled? The LLVM ModelGenerator maintins a hash table of currently running models. If this flag is NOT set, then the generator will look to see if there is already a running instance of the given model and use the generated code from that one. If only a single instance of a model is run, there is no need to cache the models, and this can safetly be enabled, realizing some performance gains.
READ_ONLY	If this is set, then a read-only model is generated. A read-only model can be simulated, but no code is generated to set model values, i.e. parameters, amounts, values, etc... It takes a finite amount of time to generate the model value setting functions, and if they are not needed, one may see some performance gains, especially in very large models.
MUTABLE_INITIAL_CONDITIONS	Generate accessor functions to allow changing of initial conditions.
OPTIMIZE_GVN	GVN - This pass performs global value numbering and redundant load elimination cotemporaneously.
OPTIMIZE_CFG_SIMPLIFICATION	CFGSimplification - Merge basic blocks, eliminate unreachable blocks, simplify terminator instructions, etc...
OPTIMIZE_INSTRUCTION_COMBINING	InstructionCombining - Combine instructions to form fewer, simple instructions. This pass does not modify the CFG, and has a tendency to make instructions dead, so a subsequent DCE pass is useful.
OPTIMIZE_DEAD_INST_ELIMINATION	DeadInstElimination - This pass quickly removes trivially dead instructions without modifying the CFG of the function. It is a BasicBlockPass, so it runs efficiently when queued next to other BasicBlockPass's.
OPTIMIZE_DEAD_CODE_ELIMINATION	DeadCodeElimination - This pass is more powerful than DeadInstElimination, because it is worklist driven that can potentially revisit instructions when their other instructions become dead, to eliminate chains of dead computations.
OPTIMIZE_INSTRUCTION_SIMPLIFIER	InstructionSimplifier - Remove redundant instructions.
OPTIMIZE	all optimizations, use to check if bit mask has any optimizations.
USE_MCJIT	Use the LLVM MCJIT JIT engine. Defaults to false. The MCJIT is the new LLVM JIT engine, it is not as well tested as the original JIT engine. Does NOT work on LLVM 3.1
TURN_ON_VALIDATION	Turn on SBML validation.

Member Function Documentation

hasKey()

bool rr::LoadSBMLOptions::hasKey ( const std::string &  key ) const

overridevirtual

is there a key matching this name.

Returns

true if this key exists, false otherwise.

Reimplemented from rr::BasicDictionary.

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The documentation for this class was generated from the following files:

• rrRoadRunnerOptions.h
• rrRoadRunnerOptions.cpp