namespace rrllvm
{
typedef std::tr1::weak_ptr<ModelResources> WeakModelPtr;
typedef std::tr1::shared_ptr<ModelResources> SharedModelPtr;
typedef std::tr1::unordered_map<std::string, WeakModelPtr> ModelPtrMap;
static Poco::Mutex cachedModelsMutex;
static ModelPtrMap cachedModels;
/**
* copy the cached model fields between a cached model, and a
* executable model.
*
* We don't want to have ExecutableModel inherit from CahcedModel
* because they do compleltly different things, and have completly
* differnt deletion semantics
*/
template <typename a_type, typename b_type>
void copyCachedModel(a_type* src, b_type* dst)
{
dst->symbols = src->symbols;
dst->context = src->context;
dst->executionEngine = src->executionEngine;
dst->errStr = src->errStr;
dst->evalInitialConditionsPtr = src->evalInitialConditionsPtr;
dst->evalReactionRatesPtr = src->evalReactionRatesPtr;
dst->getBoundarySpeciesAmountPtr = src->getBoundarySpeciesAmountPtr;
dst->getFloatingSpeciesAmountPtr = src->getFloatingSpeciesAmountPtr;
dst->getBoundarySpeciesConcentrationPtr = src->getBoundarySpeciesConcentrationPtr;
dst->getFloatingSpeciesConcentrationPtr = src->getFloatingSpeciesConcentrationPtr;
dst->getCompartmentVolumePtr = src->getCompartmentVolumePtr;
dst->getGlobalParameterPtr = src->getGlobalParameterPtr;
dst->evalRateRuleRatesPtr = src->evalRateRuleRatesPtr;
dst->getEventTriggerPtr = src->getEventTriggerPtr;
dst->getEventPriorityPtr = src->getEventPriorityPtr;
dst->getEventDelayPtr = src->getEventDelayPtr;
dst->eventTriggerPtr = src->eventTriggerPtr;
dst->eventAssignPtr = src->eventAssignPtr;
dst->evalVolatileStoichPtr = src->evalVolatileStoichPtr;
dst->evalConversionFactorPtr = src->evalConversionFactorPtr;
}
LLVMModelGenerator::LLVMModelGenerator()
{
Log(Logger::PRIO_TRACE) << __FUNC__;
}
LLVMModelGenerator::~LLVMModelGenerator()
{
Log(Logger::PRIO_TRACE) << __FUNC__;
}
bool LLVMModelGenerator::setTemporaryDirectory(const string& path)
{
return true;
}
string LLVMModelGenerator::getTemporaryDirectory()
{
return LLVMCompiler::gurgle();
}
class test
{
public:
const int* p;
};
void testt(const int** p)
{
*p = 0;
}
void testtt()
{
test *t = new test();
testt(&t->p);
}
ExecutableModel* LLVMModelGenerator::createModel(const std::string& sbml,
uint options)
{
bool computeAndAssignConsevationLaws =
options & ModelGenerator::ComputeAndAssignConsevationLaws;
bool forceReCompile = options & ModelGenerator::ForceReCompile;
string md5;
if (!forceReCompile)
{
// check for a chached copy
md5 = rr::getMD5(sbml);
ModelPtrMap::const_iterator i;
SharedModelPtr sp;
cachedModelsMutex.lock();
if ((i = cachedModels.find(md5)) != cachedModels.end())
{
sp = i->second.lock();
}
cachedModelsMutex.unlock();
// we could have recieved a bad ptr, a model could have been deleted,
// in which case, we should have a bad ptr.
if (sp)
{
Log(Logger::PRIO_DEBUG) << "found a cached model for " << md5;
return new LLVMExecutableModel(sp);
}
else
{
Log(Logger::PRIO_TRACE) << "no cached model found for " << md5
<< ", creating new one";
}
}
SharedModelPtr rc(new ModelResources());
ModelGeneratorContext context(sbml, computeAndAssignConsevationLaws);
rc->evalInitialConditionsPtr =
EvalInitialConditionsCodeGen(context).createFunction();
rc->evalReactionRatesPtr =
EvalReactionRatesCodeGen(context).createFunction();
rc->getBoundarySpeciesAmountPtr =
GetBoundarySpeciesAmountCodeGen(context).createFunction();
rc->getFloatingSpeciesAmountPtr =
GetFloatingSpeciesAmountCodeGen(context).createFunction();
rc->getBoundarySpeciesConcentrationPtr =
GetBoundarySpeciesConcentrationCodeGen(context).createFunction();
rc->getFloatingSpeciesConcentrationPtr =
GetFloatingSpeciesConcentrationCodeGen(context).createFunction();
rc->getCompartmentVolumePtr =
GetCompartmentVolumeCodeGen(context).createFunction();
rc->getGlobalParameterPtr =
GetGlobalParameterCodeGen(context).createFunction();
rc->evalRateRuleRatesPtr =
EvalRateRuleRatesCodeGen(context).createFunction();
rc->getEventTriggerPtr =
GetEventTriggerCodeGen(context).createFunction();
rc->getEventPriorityPtr =
GetEventPriorityCodeGen(context).createFunction();
rc->getEventDelayPtr =
GetEventDelayCodeGen(context).createFunction();
rc->eventTriggerPtr =
EventTriggerCodeGen(context).createFunction();
rc->eventAssignPtr =
EventAssignCodeGen(context).createFunction();
rc->evalVolatileStoichPtr =
EvalVolatileStoichCodeGen(context).createFunction();
rc->evalConversionFactorPtr =
EvalConversionFactorCodeGen(context).createFunction();
if (options & ModelGenerator::ReadOnlyModel)
{
rc->setBoundarySpeciesAmountPtr = 0;
rc->setBoundarySpeciesConcentrationPtr = 0;
rc->setFloatingSpeciesConcentrationPtr = 0;
rc->setCompartmentVolumePtr = 0;
rc->setFloatingSpeciesAmountPtr = 0;
rc->setGlobalParameterPtr = 0;
}
else
{
rc->setBoundarySpeciesAmountPtr = SetBoundarySpeciesAmountCodeGen(
context).createFunction();
rc->setBoundarySpeciesConcentrationPtr =
SetBoundarySpeciesConcentrationCodeGen(context).createFunction();
rc->setFloatingSpeciesConcentrationPtr =
SetFloatingSpeciesConcentrationCodeGen(context).createFunction();
rc->setCompartmentVolumePtr =
SetCompartmentVolumeCodeGen(context).createFunction();
rc->setFloatingSpeciesAmountPtr = SetFloatingSpeciesAmountCodeGen(
context).createFunction();
rc->setGlobalParameterPtr =
SetGlobalParameterCodeGen(context).createFunction();
}
// if anything up to this point throws an exception, thats OK, because
// we have not allocated any memory yet that is not taken care of by
// something else.
// Now that everything that could have thrown would have thrown, we
// can now create the model and set its fields.
// * MOVE * the bits over from the context to the exe model.
context.stealThePeach(&rc->symbols, &rc->context,
&rc->executionEngine, &rc->errStr);
if (!forceReCompile)
{
// check for a chached copy, another thread could have
// created one while we were making ours...
ModelPtrMap::const_iterator i;
SharedModelPtr sp;
cachedModelsMutex.lock();
// whilst we have it locked, clear any expired ptrs
for (ModelPtrMap::const_iterator j = cachedModels.begin();
j != cachedModels.end();)
{
if (j->second.expired())
{
Log(Logger::PRIO_INFORMATION) <<
"removing expired model resource for hash " << md5;
j = cachedModels.erase(j);
}
else
{
++j;
}
}
if ((i = cachedModels.find(md5)) == cachedModels.end())
{
Log(Logger::PRIO_INFORMATION) << "could not find existing cached resource "
"resources, for hash " << md5 <<
", inserting new resources into cache";
cachedModels[md5] = rc;
}
cachedModelsMutex.unlock();
}
return new LLVMExecutableModel(rc);
}
Compiler* LLVMModelGenerator::getCompiler()
{
return &compiler;
}
bool LLVMModelGenerator::setCompiler(const string& compiler)
{
return true;
}
/************ LLVM Utility Functions, TODO: Move To Separate File ************/
/**
* C++ 11 style to_string for LLVM types
*/
std::string to_string(const llvm::Value *value)
{
std::string str;
llvm::raw_string_ostream stream(str);
value->print(stream);
return str;
}
} /* namespace rr */
ExecutableModel* LLVMModelGenerator::createModel(const std::string& sbml,
uint options)
{
bool forceReCompile = options & LoadSBMLOptions::RECOMPILE;
string md5;
if (!forceReCompile)
{
// check for a chached copy
md5 = rr::getMD5(sbml);
if (options & LoadSBMLOptions::CONSERVED_MOIETIES)
{
md5 += "_conserved";
}
ModelPtrMap::const_iterator i;
SharedModelPtr sp;
cachedModelsMutex.lock();
if ((i = cachedModels.find(md5)) != cachedModels.end())
{
sp = i->second.lock();
}
cachedModelsMutex.unlock();
// we could have recieved a bad ptr, a model could have been deleted,
// in which case, we should have a bad ptr.
if (sp)
{
Log(Logger::LOG_DEBUG) << "found a cached model for " << md5;
return new LLVMExecutableModel(sp, createModelData(*sp->symbols, sp->random));
}
else
{
Log(Logger::LOG_TRACE) << "no cached model found for " << md5
<< ", creating new one";
}
}
SharedModelPtr rc(new ModelResources());
ModelGeneratorContext context(sbml, options);
rc->evalInitialConditionsPtr =
EvalInitialConditionsCodeGen(context).createFunction();
rc->evalReactionRatesPtr =
EvalReactionRatesCodeGen(context).createFunction();
rc->getBoundarySpeciesAmountPtr =
GetBoundarySpeciesAmountCodeGen(context).createFunction();
rc->getFloatingSpeciesAmountPtr =
GetFloatingSpeciesAmountCodeGen(context).createFunction();
rc->getBoundarySpeciesConcentrationPtr =
GetBoundarySpeciesConcentrationCodeGen(context).createFunction();
rc->getFloatingSpeciesConcentrationPtr =
GetFloatingSpeciesConcentrationCodeGen(context).createFunction();
rc->getCompartmentVolumePtr =
GetCompartmentVolumeCodeGen(context).createFunction();
rc->getGlobalParameterPtr =
GetGlobalParameterCodeGen(context).createFunction();
rc->evalRateRuleRatesPtr =
EvalRateRuleRatesCodeGen(context).createFunction();
rc->getEventTriggerPtr =
GetEventTriggerCodeGen(context).createFunction();
rc->getEventPriorityPtr =
GetEventPriorityCodeGen(context).createFunction();
rc->getEventDelayPtr =
GetEventDelayCodeGen(context).createFunction();
rc->eventTriggerPtr =
EventTriggerCodeGen(context).createFunction();
rc->eventAssignPtr =
EventAssignCodeGen(context).createFunction();
rc->evalVolatileStoichPtr =
EvalVolatileStoichCodeGen(context).createFunction();
rc->evalConversionFactorPtr =
EvalConversionFactorCodeGen(context).createFunction();
if (options & LoadSBMLOptions::READ_ONLY)
{
rc->setBoundarySpeciesAmountPtr = 0;
rc->setBoundarySpeciesConcentrationPtr = 0;
rc->setFloatingSpeciesConcentrationPtr = 0;
rc->setCompartmentVolumePtr = 0;
rc->setFloatingSpeciesAmountPtr = 0;
rc->setGlobalParameterPtr = 0;
}
else
{
rc->setBoundarySpeciesAmountPtr = SetBoundarySpeciesAmountCodeGen(
context).createFunction();
rc->setBoundarySpeciesConcentrationPtr =
SetBoundarySpeciesConcentrationCodeGen(context).createFunction();
rc->setFloatingSpeciesConcentrationPtr =
SetFloatingSpeciesConcentrationCodeGen(context).createFunction();
rc->setCompartmentVolumePtr =
SetCompartmentVolumeCodeGen(context).createFunction();
rc->setFloatingSpeciesAmountPtr = SetFloatingSpeciesAmountCodeGen(
context).createFunction();
rc->setGlobalParameterPtr =
SetGlobalParameterCodeGen(context).createFunction();
}
if (options & LoadSBMLOptions::MUTABLE_INITIAL_CONDITIONS)
{
rc->getFloatingSpeciesInitConcentrationsPtr =
GetFloatingSpeciesInitConcentrationCodeGen(context).createFunction();
rc->setFloatingSpeciesInitConcentrationsPtr =
SetFloatingSpeciesInitConcentrationCodeGen(context).createFunction();
rc->getFloatingSpeciesInitAmountsPtr =
GetFloatingSpeciesInitAmountCodeGen(context).createFunction();
rc->setFloatingSpeciesInitAmountsPtr =
SetFloatingSpeciesInitAmountCodeGen(context).createFunction();
rc->getCompartmentInitVolumesPtr =
GetCompartmentInitVolumeCodeGen(context).createFunction();
rc->setCompartmentInitVolumesPtr =
SetCompartmentInitVolumeCodeGen(context).createFunction();
rc->getGlobalParameterInitValuePtr =
GetGlobalParameterInitValueCodeGen(context).createFunction();
rc->setGlobalParameterInitValuePtr =
SetGlobalParameterInitValueCodeGen(context).createFunction();
}
else
{
rc->getFloatingSpeciesInitConcentrationsPtr = 0;
rc->setFloatingSpeciesInitConcentrationsPtr = 0;
rc->getFloatingSpeciesInitAmountsPtr = 0;
rc->setFloatingSpeciesInitAmountsPtr = 0;
rc->getCompartmentInitVolumesPtr = 0;
rc->setCompartmentInitVolumesPtr = 0;
rc->getGlobalParameterInitValuePtr = 0;
rc->setGlobalParameterInitValuePtr = 0;
}
// if anything up to this point throws an exception, thats OK, because
// we have not allocated any memory yet that is not taken care of by
// something else.
// Now that everything that could have thrown would have thrown, we
// can now create the model and set its fields.
LLVMModelData *modelData = createModelData(context.getModelDataSymbols(),
context.getRandom());
uint llvmsize = ModelDataIRBuilder::getModelDataSize(context.getModule(),
&context.getExecutionEngine());
if (llvmsize != modelData->size)
{
std::stringstream s;
s << "LLVM Model Data size " << llvmsize << " is different from " <<
"C++ size of LLVM ModelData, " << modelData->size;
LLVMModelData_free(modelData);
Log(Logger::LOG_FATAL) << s.str();
throw_llvm_exception(s.str());
}
// * MOVE * the bits over from the context to the exe model.
context.stealThePeach(&rc->symbols, &rc->context,
&rc->executionEngine, &rc->random, &rc->errStr);
if (!forceReCompile)
{
// check for a chached copy, another thread could have
// created one while we were making ours...
ModelPtrMap::const_iterator i;
SharedModelPtr sp;
cachedModelsMutex.lock();
// whilst we have it locked, clear any expired ptrs
for (ModelPtrMap::const_iterator j = cachedModels.begin();
j != cachedModels.end();)
{
if (j->second.expired())
{
Log(Logger::LOG_DEBUG) <<
"removing expired model resource for hash " << md5;
j = cachedModels.erase(j);
}
else
{
++j;
}
}
if ((i = cachedModels.find(md5)) == cachedModels.end())
{
Log(Logger::LOG_DEBUG) << "could not find existing cached resource "
"resources, for hash " << md5 <<
", inserting new resources into cache";
cachedModels[md5] = rc;
}
cachedModelsMutex.unlock();
}
return new LLVMExecutableModel(rc, modelData);
}
ExecutableModel* LLVMModelGenerator::createModel(const std::string& sbml,
uint options)
{
bool computeAndAssignConsevationLaws =
options & ModelGenerator::ComputeAndAssignConsevationLaws;
bool forceReCompile = options & ModelGenerator::ForceReCompile;
string md5;
if (!forceReCompile)
{
// check for a chached copy
md5 = rr::getMD5(sbml);
ModelPtrMap::const_iterator i;
SharedModelPtr sp;
cachedModelsMutex.lock();
if ((i = cachedModels.find(md5)) != cachedModels.end())
{
sp = i->second.lock();
}
cachedModelsMutex.unlock();
// we could have recieved a bad ptr, a model could have been deleted,
// in which case, we should have a bad ptr.
if (sp)
{
Log(Logger::PRIO_DEBUG) << "found a cached model for " << md5;
return new LLVMExecutableModel(sp);
}
else
{
Log(Logger::PRIO_TRACE) << "no cached model found for " << md5
<< ", creating new one";
}
}
SharedModelPtr rc(new ModelResources());
ModelGeneratorContext context(sbml, computeAndAssignConsevationLaws);
rc->evalInitialConditionsPtr =
EvalInitialConditionsCodeGen(context).createFunction();
rc->evalReactionRatesPtr =
EvalReactionRatesCodeGen(context).createFunction();
rc->getBoundarySpeciesAmountPtr =
GetBoundarySpeciesAmountCodeGen(context).createFunction();
rc->getFloatingSpeciesAmountPtr =
GetFloatingSpeciesAmountCodeGen(context).createFunction();
rc->getBoundarySpeciesConcentrationPtr =
GetBoundarySpeciesConcentrationCodeGen(context).createFunction();
rc->getFloatingSpeciesConcentrationPtr =
GetFloatingSpeciesConcentrationCodeGen(context).createFunction();
rc->getCompartmentVolumePtr =
GetCompartmentVolumeCodeGen(context).createFunction();
rc->getGlobalParameterPtr =
GetGlobalParameterCodeGen(context).createFunction();
rc->evalRateRuleRatesPtr =
EvalRateRuleRatesCodeGen(context).createFunction();
rc->getEventTriggerPtr =
GetEventTriggerCodeGen(context).createFunction();
rc->getEventPriorityPtr =
GetEventPriorityCodeGen(context).createFunction();
rc->getEventDelayPtr =
GetEventDelayCodeGen(context).createFunction();
rc->eventTriggerPtr =
EventTriggerCodeGen(context).createFunction();
rc->eventAssignPtr =
EventAssignCodeGen(context).createFunction();
rc->evalVolatileStoichPtr =
EvalVolatileStoichCodeGen(context).createFunction();
rc->evalConversionFactorPtr =
EvalConversionFactorCodeGen(context).createFunction();
if (options & ModelGenerator::ReadOnlyModel)
{
rc->setBoundarySpeciesAmountPtr = 0;
rc->setBoundarySpeciesConcentrationPtr = 0;
rc->setFloatingSpeciesConcentrationPtr = 0;
rc->setCompartmentVolumePtr = 0;
rc->setFloatingSpeciesAmountPtr = 0;
rc->setGlobalParameterPtr = 0;
}
else
{
rc->setBoundarySpeciesAmountPtr = SetBoundarySpeciesAmountCodeGen(
context).createFunction();
rc->setBoundarySpeciesConcentrationPtr =
SetBoundarySpeciesConcentrationCodeGen(context).createFunction();
rc->setFloatingSpeciesConcentrationPtr =
SetFloatingSpeciesConcentrationCodeGen(context).createFunction();
rc->setCompartmentVolumePtr =
SetCompartmentVolumeCodeGen(context).createFunction();
rc->setFloatingSpeciesAmountPtr = SetFloatingSpeciesAmountCodeGen(
context).createFunction();
rc->setGlobalParameterPtr =
SetGlobalParameterCodeGen(context).createFunction();
}
// if anything up to this point throws an exception, thats OK, because
// we have not allocated any memory yet that is not taken care of by
// something else.
// Now that everything that could have thrown would have thrown, we
// can now create the model and set its fields.
// * MOVE * the bits over from the context to the exe model.
context.stealThePeach(&rc->symbols, &rc->context,
&rc->executionEngine, &rc->errStr);
if (!forceReCompile)
{
// check for a chached copy, another thread could have
// created one while we were making ours...
ModelPtrMap::const_iterator i;
SharedModelPtr sp;
cachedModelsMutex.lock();
// whilst we have it locked, clear any expired ptrs
for (ModelPtrMap::const_iterator j = cachedModels.begin();
j != cachedModels.end();)
{
if (j->second.expired())
{
Log(Logger::PRIO_INFORMATION) <<
"removing expired model resource for hash " << md5;
j = cachedModels.erase(j);
}
else
{
++j;
}
}
if ((i = cachedModels.find(md5)) == cachedModels.end())
{
Log(Logger::PRIO_INFORMATION) << "could not find existing cached resource "
"resources, for hash " << md5 <<
", inserting new resources into cache";
cachedModels[md5] = rc;
}
cachedModelsMutex.unlock();
}
return new LLVMExecutableModel(rc);
}
namespace rrllvm
{
typedef cxx11_ns::weak_ptr<ModelResources> WeakModelPtr;
typedef cxx11_ns::shared_ptr<ModelResources> SharedModelPtr;
typedef cxx11_ns::unordered_map<std::string, WeakModelPtr> ModelPtrMap;
static Poco::Mutex cachedModelsMutex;
static ModelPtrMap cachedModels;
/**
* copy the cached model fields between a cached model, and a
* executable model.
*
* We don't want to have ExecutableModel inherit from CahcedModel
* because they do compleltly different things, and have completly
* differnt deletion semantics
*/
template <typename a_type, typename b_type>
void copyCachedModel(a_type* src, b_type* dst)
{
dst->symbols = src->symbols;
dst->context = src->context;
dst->executionEngine = src->executionEngine;
dst->errStr = src->errStr;
dst->evalInitialConditionsPtr = src->evalInitialConditionsPtr;
dst->evalReactionRatesPtr = src->evalReactionRatesPtr;
dst->getBoundarySpeciesAmountPtr = src->getBoundarySpeciesAmountPtr;
dst->getFloatingSpeciesAmountPtr = src->getFloatingSpeciesAmountPtr;
dst->getBoundarySpeciesConcentrationPtr = src->getBoundarySpeciesConcentrationPtr;
dst->getFloatingSpeciesConcentrationPtr = src->getFloatingSpeciesConcentrationPtr;
dst->getCompartmentVolumePtr = src->getCompartmentVolumePtr;
dst->getGlobalParameterPtr = src->getGlobalParameterPtr;
dst->evalRateRuleRatesPtr = src->evalRateRuleRatesPtr;
dst->getEventTriggerPtr = src->getEventTriggerPtr;
dst->getEventPriorityPtr = src->getEventPriorityPtr;
dst->getEventDelayPtr = src->getEventDelayPtr;
dst->eventTriggerPtr = src->eventTriggerPtr;
dst->eventAssignPtr = src->eventAssignPtr;
dst->evalVolatileStoichPtr = src->evalVolatileStoichPtr;
dst->evalConversionFactorPtr = src->evalConversionFactorPtr;
}
ExecutableModel* LLVMModelGenerator::createModel(const std::string& sbml,
uint options)
{
bool forceReCompile = options & LoadSBMLOptions::RECOMPILE;
string md5;
if (!forceReCompile)
{
// check for a chached copy
md5 = rr::getMD5(sbml);
if (options & LoadSBMLOptions::CONSERVED_MOIETIES)
{
md5 += "_conserved";
}
ModelPtrMap::const_iterator i;
SharedModelPtr sp;
cachedModelsMutex.lock();
if ((i = cachedModels.find(md5)) != cachedModels.end())
{
sp = i->second.lock();
}
cachedModelsMutex.unlock();
// we could have recieved a bad ptr, a model could have been deleted,
// in which case, we should have a bad ptr.
if (sp)
{
Log(Logger::LOG_DEBUG) << "found a cached model for " << md5;
return new LLVMExecutableModel(sp, createModelData(*sp->symbols, sp->random));
}
else
{
Log(Logger::LOG_TRACE) << "no cached model found for " << md5
<< ", creating new one";
}
}
SharedModelPtr rc(new ModelResources());
ModelGeneratorContext context(sbml, options);
rc->evalInitialConditionsPtr =
EvalInitialConditionsCodeGen(context).createFunction();
rc->evalReactionRatesPtr =
EvalReactionRatesCodeGen(context).createFunction();
rc->getBoundarySpeciesAmountPtr =
GetBoundarySpeciesAmountCodeGen(context).createFunction();
rc->getFloatingSpeciesAmountPtr =
GetFloatingSpeciesAmountCodeGen(context).createFunction();
rc->getBoundarySpeciesConcentrationPtr =
GetBoundarySpeciesConcentrationCodeGen(context).createFunction();
rc->getFloatingSpeciesConcentrationPtr =
GetFloatingSpeciesConcentrationCodeGen(context).createFunction();
rc->getCompartmentVolumePtr =
GetCompartmentVolumeCodeGen(context).createFunction();
rc->getGlobalParameterPtr =
GetGlobalParameterCodeGen(context).createFunction();
rc->evalRateRuleRatesPtr =
EvalRateRuleRatesCodeGen(context).createFunction();
rc->getEventTriggerPtr =
GetEventTriggerCodeGen(context).createFunction();
rc->getEventPriorityPtr =
GetEventPriorityCodeGen(context).createFunction();
rc->getEventDelayPtr =
GetEventDelayCodeGen(context).createFunction();
rc->eventTriggerPtr =
EventTriggerCodeGen(context).createFunction();
rc->eventAssignPtr =
EventAssignCodeGen(context).createFunction();
rc->evalVolatileStoichPtr =
EvalVolatileStoichCodeGen(context).createFunction();
rc->evalConversionFactorPtr =
EvalConversionFactorCodeGen(context).createFunction();
if (options & LoadSBMLOptions::READ_ONLY)
{
rc->setBoundarySpeciesAmountPtr = 0;
rc->setBoundarySpeciesConcentrationPtr = 0;
rc->setFloatingSpeciesConcentrationPtr = 0;
rc->setCompartmentVolumePtr = 0;
rc->setFloatingSpeciesAmountPtr = 0;
rc->setGlobalParameterPtr = 0;
}
else
{
rc->setBoundarySpeciesAmountPtr = SetBoundarySpeciesAmountCodeGen(
context).createFunction();
rc->setBoundarySpeciesConcentrationPtr =
SetBoundarySpeciesConcentrationCodeGen(context).createFunction();
rc->setFloatingSpeciesConcentrationPtr =
SetFloatingSpeciesConcentrationCodeGen(context).createFunction();
rc->setCompartmentVolumePtr =
SetCompartmentVolumeCodeGen(context).createFunction();
rc->setFloatingSpeciesAmountPtr = SetFloatingSpeciesAmountCodeGen(
context).createFunction();
rc->setGlobalParameterPtr =
SetGlobalParameterCodeGen(context).createFunction();
}
if (options & LoadSBMLOptions::MUTABLE_INITIAL_CONDITIONS)
{
rc->getFloatingSpeciesInitConcentrationsPtr =
GetFloatingSpeciesInitConcentrationCodeGen(context).createFunction();
rc->setFloatingSpeciesInitConcentrationsPtr =
SetFloatingSpeciesInitConcentrationCodeGen(context).createFunction();
rc->getFloatingSpeciesInitAmountsPtr =
GetFloatingSpeciesInitAmountCodeGen(context).createFunction();
rc->setFloatingSpeciesInitAmountsPtr =
SetFloatingSpeciesInitAmountCodeGen(context).createFunction();
rc->getCompartmentInitVolumesPtr =
GetCompartmentInitVolumeCodeGen(context).createFunction();
rc->setCompartmentInitVolumesPtr =
SetCompartmentInitVolumeCodeGen(context).createFunction();
rc->getGlobalParameterInitValuePtr =
GetGlobalParameterInitValueCodeGen(context).createFunction();
rc->setGlobalParameterInitValuePtr =
SetGlobalParameterInitValueCodeGen(context).createFunction();
}
else
{
rc->getFloatingSpeciesInitConcentrationsPtr = 0;
rc->setFloatingSpeciesInitConcentrationsPtr = 0;
rc->getFloatingSpeciesInitAmountsPtr = 0;
rc->setFloatingSpeciesInitAmountsPtr = 0;
rc->getCompartmentInitVolumesPtr = 0;
rc->setCompartmentInitVolumesPtr = 0;
rc->getGlobalParameterInitValuePtr = 0;
rc->setGlobalParameterInitValuePtr = 0;
}
// if anything up to this point throws an exception, thats OK, because
// we have not allocated any memory yet that is not taken care of by
// something else.
// Now that everything that could have thrown would have thrown, we
// can now create the model and set its fields.
LLVMModelData *modelData = createModelData(context.getModelDataSymbols(),
context.getRandom());
uint llvmsize = ModelDataIRBuilder::getModelDataSize(context.getModule(),
&context.getExecutionEngine());
if (llvmsize != modelData->size)
{
std::stringstream s;
s << "LLVM Model Data size " << llvmsize << " is different from " <<
"C++ size of LLVM ModelData, " << modelData->size;
LLVMModelData_free(modelData);
Log(Logger::LOG_FATAL) << s.str();
throw_llvm_exception(s.str());
}
// * MOVE * the bits over from the context to the exe model.
context.stealThePeach(&rc->symbols, &rc->context,
&rc->executionEngine, &rc->random, &rc->errStr);
if (!forceReCompile)
{
// check for a chached copy, another thread could have
// created one while we were making ours...
ModelPtrMap::const_iterator i;
SharedModelPtr sp;
cachedModelsMutex.lock();
// whilst we have it locked, clear any expired ptrs
for (ModelPtrMap::const_iterator j = cachedModels.begin();
j != cachedModels.end();)
{
if (j->second.expired())
{
Log(Logger::LOG_DEBUG) <<
"removing expired model resource for hash " << md5;
j = cachedModels.erase(j);
}
else
{
++j;
}
}
if ((i = cachedModels.find(md5)) == cachedModels.end())
{
Log(Logger::LOG_DEBUG) << "could not find existing cached resource "
"resources, for hash " << md5 <<
", inserting new resources into cache";
cachedModels[md5] = rc;
}
cachedModelsMutex.unlock();
}
return new LLVMExecutableModel(rc, modelData);
}
/************ LLVM Utility Functions, TODO: Move To Separate File ************/
/**
* C++ 11 style to_string for LLVM types
*/
std::string to_string(const llvm::Value *value)
{
std::string str;
llvm::raw_string_ostream stream(str);
value->print(stream);
return str;
}
LLVMModelData *createModelData(const rrllvm::LLVMModelDataSymbols &symbols,
const Random *random)
{
uint modelDataBaseSize = sizeof(LLVMModelData);
uint numIndCompartments = symbols.getIndependentCompartmentSize();
uint numIndFloatingSpecies = symbols.getIndependentFloatingSpeciesSize();
uint numIndBoundarySpecies = symbols.getIndependentBoundarySpeciesSize();
uint numIndGlobalParameters = symbols.getIndependentGlobalParameterSize();
uint numInitCompartments = symbols.getInitCompartmentSize();
uint numInitFloatingSpecies = symbols.getInitFloatingSpeciesSize();
uint numInitBoundarySpecies = symbols.getInitBoundarySpeciesSize();
uint numInitGlobalParameters = symbols.getInitGlobalParameterSize();
// no initial conditions for these
uint numRateRules = symbols.getRateRuleSize();
uint numReactions = symbols.getReactionSize();
uint modelDataSize = modelDataBaseSize +
sizeof(double) * (
numIndCompartments +
numInitCompartments +
numInitFloatingSpecies +
numIndBoundarySpecies +
numInitBoundarySpecies +
numIndGlobalParameters +
numInitGlobalParameters +
numReactions +
numRateRules +
numIndFloatingSpecies
);
LLVMModelData *modelData = (LLVMModelData*)calloc(
modelDataSize, sizeof(unsigned char));
modelData->size = modelDataSize;
modelData->numIndCompartments = numIndCompartments;
modelData->numIndFloatingSpecies = numIndFloatingSpecies;
modelData->numIndBoundarySpecies = numIndBoundarySpecies;
modelData->numIndGlobalParameters = numIndGlobalParameters;
modelData->numInitCompartments = numInitCompartments;
modelData->numInitFloatingSpecies = numInitFloatingSpecies;
modelData->numInitBoundarySpecies = numInitBoundarySpecies;
modelData->numInitBoundarySpecies = numInitGlobalParameters;
modelData->numRateRules = numRateRules;
modelData->numReactions = numReactions;
modelData->numEvents = symbols.getEventAttributes().size();
// set the aliases to the offsets
uint offset = 0;
modelData->compartmentVolumesAlias = &modelData->data[offset];
offset += numIndCompartments;
modelData->initCompartmentVolumesAlias = &modelData->data[offset];
offset += numInitCompartments;
modelData->initFloatingSpeciesAmountsAlias = &modelData->data[offset];
offset += numInitFloatingSpecies;
modelData->boundarySpeciesAmountsAlias = &modelData->data[offset];
offset += numIndBoundarySpecies;
modelData->initBoundarySpeciesAmountsAlias = &modelData->data[offset];
offset += numInitBoundarySpecies;
modelData->globalParametersAlias = &modelData->data[offset];
offset += numIndGlobalParameters;
modelData->initGlobalParametersAlias = &modelData->data[offset];
offset += numInitGlobalParameters;
modelData->reactionRatesAlias = &modelData->data[offset];
offset += numReactions;
modelData->rateRuleValuesAlias = &modelData->data[offset];
offset += numRateRules;
modelData->floatingSpeciesAmountsAlias = &modelData->data[offset];
offset += numIndFloatingSpecies;
assert (modelDataBaseSize + offset * sizeof(double) == modelDataSize &&
"LLVMModelData size not equal to base size + data");
// allocate the stoichiometry matrix
const std::vector<uint> &stoichRowIndx = symbols.getStoichRowIndx();
const std::vector<uint> &stoichColIndx = symbols.getStoichColIndx();
std::vector<double> stoichValues(stoichRowIndx.size(), 0);
modelData->stoichiometry = rr::csr_matrix_new(numIndFloatingSpecies, numReactions,
stoichRowIndx, stoichColIndx, stoichValues);
// make a copy of the random object
modelData->random = random ? new Random(*random) : 0;
return modelData;
}
} /* namespace rrllvm */
