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);
}
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);
}