ModelGeneratorContext::ModelGeneratorContext(libsbml::SBMLDocument const *doc,
unsigned options) :
ownedDoc(0),
doc(0),
symbols(new LLVMModelDataSymbols(doc->getModel(), options)),
modelSymbols(new LLVMModelSymbols(getModel(), *symbols)),
errString(new string()),
context(0),
executionEngine(0),
module(0),
builder(0),
functionPassManager(0),
options(options),
moietyConverter(0)
{
try
{
if (options & rr::ModelGenerator::CONSERVED_MOIETIES)
{
Log(Logger::LOG_NOTICE) << "performing conserved moiety conversion";
moietyConverter = new rr::conservation::ConservedMoietyConverter();
if (moietyConverter->setDocument(doc) != LIBSBML_OPERATION_SUCCESS)
{
throw_llvm_exception("error setting conserved moiety converter document");
}
if (moietyConverter->convert() != LIBSBML_OPERATION_SUCCESS)
{
throw_llvm_exception("error converting document to conserved moieties");
}
this->doc = moietyConverter->getDocument();
SBMLWriter sw;
char* convertedStr = sw.writeToString(doc);
Log(Logger::LOG_INFORMATION) << "***************** Conserved Moiety Converted Document ***************";
Log(Logger::LOG_INFORMATION) << convertedStr;
Log(Logger::LOG_INFORMATION) << "*********************************************************************";
delete convertedStr;
}
else
{
this->doc = doc;
}
symbols = new LLVMModelDataSymbols(doc->getModel(), options);
modelSymbols = new LLVMModelSymbols(getModel(), *symbols);
// initialize LLVM
// TODO check result
InitializeNativeTarget();
context = new LLVMContext();
// Make the module, which holds all the code.
module = new Module("LLVM Module", *context);
builder = new IRBuilder<>(*context);
// engine take ownership of module
EngineBuilder engineBuilder(module);
//engineBuilder.setEngineKind(EngineKind::JIT);
engineBuilder.setErrorStr(errString);
executionEngine = engineBuilder.create();
addGlobalMappings();
createLibraryFunctions(module);
ModelDataIRBuilder::createModelDataStructType(module, executionEngine, *symbols);
initFunctionPassManager();
}
catch(const std::exception&)
{
cleanup();
throw;
}
}
ModelGeneratorContext::ModelGeneratorContext(std::string const &sbml,
unsigned options) :
ownedDoc(0),
doc(0),
symbols(0),
modelSymbols(0),
errString(new string()),
context(0),
executionEngine(0),
module(0),
builder(0),
functionPassManager(0),
options(options),
moietyConverter(0)
{
try
{
ownedDoc = checkedReadSBMLFromString(sbml.c_str());
if (options & rr::ModelGenerator::CONSERVED_MOIETIES)
{
if ((rr::Config::getInt(rr::Config::ROADRUNNER_DISABLE_WARNINGS) &
rr::Config::ROADRUNNER_DISABLE_WARNINGS_CONSERVED_MOIETY) == 0)
{
Log(Logger::LOG_NOTICE) << "performing conserved moiety conversion";
}
// check if already conserved doc
if (rr::conservation::ConservationExtension::isConservedMoietyDocument(ownedDoc))
{
doc = ownedDoc;
}
else
{
moietyConverter = new rr::conservation::ConservedMoietyConverter();
if (moietyConverter->setDocument(ownedDoc) != LIBSBML_OPERATION_SUCCESS)
{
throw_llvm_exception("error setting conserved moiety converter document");
}
if (moietyConverter->convert() != LIBSBML_OPERATION_SUCCESS)
{
throw_llvm_exception("error converting document to conserved moieties");
}
doc = moietyConverter->getDocument();
SBMLWriter sw;
char* convertedStr = sw.writeToString(doc);
Log(Logger::LOG_INFORMATION) << "***************** Conserved Moiety Converted Document ***************";
Log(Logger::LOG_INFORMATION) << convertedStr;
Log(Logger::LOG_INFORMATION) << "*********************************************************************";
free(convertedStr);
}
}
else
{
doc = ownedDoc;
}
symbols = new LLVMModelDataSymbols(doc->getModel(), options);
modelSymbols = new LLVMModelSymbols(getModel(), *symbols);
// initialize LLVM
// TODO check result
InitializeNativeTarget();
context = new LLVMContext();
// Make the module, which holds all the code.
module = new Module("LLVM Module", *context);
builder = new IRBuilder<>(*context);
// engine take ownership of module
EngineBuilder engineBuilder(module);
engineBuilder.setErrorStr(errString);
executionEngine = engineBuilder.create();
addGlobalMappings();
createLibraryFunctions(module);
ModelDataIRBuilder::createModelDataStructType(module, executionEngine, *symbols);
initFunctionPassManager();
}
catch(const std::exception&)
{
// we might have allocated memory in a failed ctor,
// clean it up here.
// destructors are not called on *this* class when exception is raised
// in the ctor.
cleanup();
throw;
}
}
JITEngine::JITEngine()
: m_llvmModule(0)
, m_llvmPassManager(0)
, m_llvmFuncPassManager(0)
, m_llvmEngine(0)
, m_eeerror("")
, m_irBuilder(new llvm::IRBuilder<>(llvm::getGlobalContext()))
{
// Init llvm target
llvm::InitializeNativeTarget();
llvm::InitializeNativeTargetAsmPrinter();
llvm::LLVMContext &llvmContext = llvm::getGlobalContext();
m_llvmModule = new llvm::Module("JIT", llvmContext);
// Create a Execution engine via the engine builder
llvm::EngineBuilder engineBuilder(m_llvmModule);
engineBuilder.setUseMCJIT(true);
//engineBuilder.setOptLevel(llvm::CodeGenOpt::Aggressive); // Test gdb
engineBuilder.setErrorStr(&m_eeerror);
engineBuilder.setAllocateGVsWithCode(true); // Global values
m_llvmEngine = engineBuilder.create();
m_llvmPassManager = new llvm::PassManager();
m_llvmPassManager->add(new llvm::DataLayout(*m_llvmEngine->getDataLayout()));
//m_llvmPassManager->add(llvm::createCFGSimplificationPass()); // Merge & remove BBs
//m_llvmPassManager->add(llvm::createInstructionCombiningPass()); // Combine silly seq's
//m_llvmPassManager->add(llvm::createTailCallEliminationPass()); // Eliminate tail calls
//m_llvmPassManager->add(llvm::createCFGSimplificationPass()); // Merge & remove BBs
//m_llvmPassManager->add(llvm::createReassociatePass()); // Reassociate expressions
//m_llvmPassManager->add(llvm::createLoopRotatePass()); // Rotate Loop
//m_llvmPassManager->add(llvm::createLICMPass()); // Hoist loop invariants
//m_llvmPassManager->add(llvm::createInstructionCombiningPass());
//m_llvmPassManager->add(llvm::createIndVarSimplifyPass()); // Canonicalize indvars
//m_llvmPassManager->add(llvm::createLoopIdiomPass()); // Recognize idioms like memset.
//m_llvmPassManager->add(llvm::createLoopDeletionPass()); // Delete dead loops
////m_llvmPassManager->add(llvm::createLoopVectorizePass());
//m_llvmPassManager->add(llvm::createFunctionInliningPass());
////m_llvmPassManager->add(llvm::createBBVectorizePass());
//m_llvmPassManager->add(llvm::createInstructionCombiningPass());
// Function pass manager
m_llvmFuncPassManager = new llvm::FunctionPassManager(m_llvmModule);
// Set up the optimizer pipeline. Start with registering info about how the
// target lays out data structures.
m_llvmFuncPassManager->add(new llvm::DataLayout(*m_llvmEngine->getDataLayout()));
// Promote allocas to registers.
//m_llvmFuncPassManager->add(llvm::createPromoteMemoryToRegisterPass());
//// Provide basic AliasAnalysis support for GVN.
//m_llvmFuncPassManager->add(llvm::createBasicAliasAnalysisPass());
//// Do simple "peephole" optimizations and bit-twiddling optzns.
//m_llvmFuncPassManager->add(llvm::createInstructionCombiningPass());
//// Reassociate expressions.
//m_llvmFuncPassManager->add(llvm::createReassociatePass());
//// Eliminate Common SubExpressions.
//m_llvmFuncPassManager->add(llvm::createGVNPass());
//// Simplify the control flow graph (deleting unreachable blocks, etc).
//m_llvmFuncPassManager->add(llvm::createCFGSimplificationPass());
//// Unroll small loops
//m_llvmFuncPassManager->add(llvm::createLoopInstSimplifyPass());
//m_llvmFuncPassManager->add(llvm::createLoopRotatePass());
//// Recognize idioms like memset.
//m_llvmFuncPassManager->add(llvm::createLoopIdiomPass());
////m_llvmFuncPassManager->add(llvm::createLoopVectorizePass());
//m_llvmFuncPassManager->add(llvm::createLoopUnrollPass());
////m_llvmFuncPassManager->add(llvm::createBBVectorizePass());
//m_llvmFuncPassManager->doInitialization();
//m_nodeCompiler = new NodeCompiler();
}