void Sampler::recordingStarted() {
printf("Record start\n");
controlMutex.lock();
recording = true;
recordPos = 0;
controlMutex.unlock();
}
void Sampler::recordingEnded() {
printf("Record end\n");
controlMutex.lock();
recording = false;
sample.load(recordBuffer, recordPos);
printf("Loaded sample of %d length\n", recordPos);
controlMutex.unlock();
noteOffset = -12;
}
void Sampler::soundChanged() {
controlMutex.lock();
string sndUrl = "";//AppSettings::soundFile;
if(sndUrl=="") {
sndUrl = ofToDataPath("sounds/harp.wav");
}
sample.loadFromFile(sndUrl);
controlMutex.unlock();
}
void DoSomethingConcurrently()
{
// Declares a mutex (mutual exclusion)
Poco::Mutex mutex;
// No other thread will be able to execute the next line until the mutex is unlocked by a previous thread
mutex.lock();
::OutputDebugStringW(L"Something done.\n");
mutex.unlock();
}
operator TextCache::Result() const {
#ifdef ENABLE_OPENGL
return texture;
#else
return { data, width, width, height };
#endif
}
void Sampler::audioRequested (float * output, int bufferSize, int nChannels) {
controlMutex.lock();
// if we're recording, we want silence!!
if(recording) {
memset(output, 0, bufferSize*nChannels*sizeof(float));
} else {
// printf("Sound %f\n", playbackSpeed);
// otherwise, maybe we want playback
for(int i = 0; i < bufferSize; i++) {
float s = sample.getSample(playbackSpeed);
for(int channel = 0; channel < nChannels; channel++) {
output[i*nChannels + channel] = s;
}
}
}
controlMutex.unlock();
}
//--------------------------------------------------------------
void Sampler::audioReceived (float * input, int bufferSize, int nChannels){
//if(recording) printf("We're recording\n");
//else printf("Not record\n");
controlMutex.lock();
for(int i = 0; i < bufferSize; i++) {
float inp = input[i*nChannels];
// do the recording
if(recording && recordPos<recordBufferSize) {
recordBuffer[recordPos++] = inp;
}
// do a level meter
if(inputLevel<inp) {
inputLevel = inp;
} else {
inputLevel *= 0.99995;
}
}
controlMutex.unlock();
}
void Unlock() { text_cache_mutex.unlock(); }
void Lock() { text_cache_mutex.lock(); }
//--------------------------------------------------------------
void Sampler::init(){
currTouchId = -1;
//AppSettings::addListener(this);
movementThreshold = 0.02;
//Particle::color = &AppSettings::color3;
recordBufferSize = SAMPLERATE*MAX_RECORD_SECONDS;
recordBuffer = new float[recordBufferSize];
recordPos = 0;
recording = false;
inputLevel = 0;
playbackSpeed = 1;
lastSound = -1;
ofDirectory DIR;
int numFiles = DIR.listDir("sounds");
for(int i = 0; i < numFiles; i++) {
sounds.push_back(DIR.getName(i));
}
// this is the last time that there was a note
noteLastTime = -10;
lastNote = 0;
scales.push_back(PENTATONIC);
scales.push_back(MAJOR);
scales.push_back(MINOR);
scales.push_back(CHROMATIC);
memset(recordBuffer, 0, recordBufferSize*sizeof(float));
// 1 output channels,
// 2 input channels
// 44100 samples per second
// 256 samples per buffer
// 1 num buffers (latency)
controlMutex.lock();
sample.loadFromFile(ofToDataPath("sounds/harp.wav"));
controlMutex.unlock();
//--------- PANEL 1
video.listDevices();
#ifdef TARGET_OF_IPHONE
video.setDeviceID(1);
#endif
video.initGrabber(VISION_WIDTH, VISION_HEIGHT, OF_PIXELS_BGRA);
vision.setup();
gui.setup();
gui.recordButton->recListener = this;
}
void Message::Unlock() {
CritSec_Messages.unlock();
}
void LockComm() {
CritSec_Comm.lock();
}
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 */
void Message::Lock() {
CritSec_Messages.lock();
}
void Sampler::update() {
if(!wasRecording && gui.recording) {
// recording just started.
//ofSoundStreamStop();
//ofSoundStreamSetup(0, 1, ofGetAppPtr(), 44100, 512, 4);
}
wasRecording = gui.recording;
if(gui.input==INPUT_ACCELEROMETER) {
#ifdef TARGET_OF_IPHONE
ofPoint a = ofxAccelerometer.getOrientation();
float ax = a.x;// + a.y;
// printf("%f\n", ax);
float pitch = ofMap(ax, -45, 45, 1, 0);
float vol = 0.8;
if(gui.useYAxisAsVolume) {
vol = ofMap(a.y, -45, 45, 1, 0);
}
if(ax<-45) pitch = 1;
else if(ax>45) {
pitch = 0;
// pitch = ofMap(ax, 45, 135, 0, 1, true);
}
int currNote = pitch*vision.levels.size();
if(currNote!=lastNote) {
playSound(vol, pitch);
}
#endif
}
ofBackground(0,0,0);
vision.numLevels = gui.noteRange;
vision.video = &video;
// the vision code works out how much average change there is in each of
// either vertical or horizontal strips across the screen.
// this bit of code finds out if the strip with the most change
// is a different strip from the last strip, and then triggers that note.
float max = 0;
int currMaxLevel = -1;
for(int i = 0; i < vision.levels.size(); i++) {
if(max<vision.levels[i].second) {
max = vision.levels[i].second;
currMaxLevel = i;
}
}
if(lastMaxLevel!=currMaxLevel) {
//printf("Playing note %d %f\n", currMaxLevel, max);
float volume = ofMap(max, 0, 0.5, 0, 1);
if(volume>1) volume = 1;
if(volume>movementThreshold) { // some threshold
lastMaxLevel = currMaxLevel;
if(gui.input==INPUT_CAMERA) playSound(volume, 1.f - (float)currMaxLevel/vision.levels.size());
} else {
currMaxLevel = -1;
}
}
lastMaxLevel = currMaxLevel;
vision.update();
if(gui.mustLoadSound) {
controlMutex.lock();
sample.loadFromFile(gui.soundFile);
controlMutex.unlock();
gui.mustLoadSound = false;
noteOffset = 0;
}
/*for(int i = 0; i < particles.size(); i++) {
particles[i].update();
if(!particles[i].alive) {
particles.erase(particles.begin()+i);
i--;
}
}*/
}
void unlock() { _mutex.unlock(); }
bool try_lock() { return _mutex.tryLock(); }
void lock() { _mutex.lock(); }
void UnlockComm() {
CritSec_Comm.unlock();
}
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 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);
}
