int main()
{
RoadRunner lRR;
LogOutput::mLogToConsole = true;
gLog.SetCutOffLogLevel(lInfo);
Log(lInfo)<<"======================";
Log(lInfo)<<lRR.getInfo();
Log(lInfo)<<"======================";
LoadModelThread load(JoinPath("..", "models", "feedback.xml"), &lRR);
load.start();
load.waitForFinish();
SimulateThread sim(&lRR);
sim.start();
sim.waitForFinish();
Log(lInfo)<<lRR.getSimulationResult();
for(int i = 0; i < 2; i++)
{
lRR.setNumPoints(10);
sim.addJob(&lRR);
sim.start();
sim.waitForFinish();
Log(lInfo)<<lRR.getSimulationResult();
}
return 0;
}
void LoadModelThread::worker()
{
RoadRunner *rri = NULL;
mWasStarted = true;
mIsWorking = true;
//Any thread working on this Job list need to increment this one
Mutex::ScopedLock lock(mNrOfWorkersMutex);
mNrOfWorkers++;
mNrOfWorkersMutex.unlock();
while(!mIsTimeToDie)
{
{ //Scope for scoped lock
Mutex::ScopedLock lock(mJobsMutex);
if(mJobs.size() == 0)
{
RRPLOG(tlp::lDebug5)<<"Waiting for jobs in loadSBML worker";
//mJobsCondition.wait(mJobsMutex);
break;
}
if(mIsTimeToDie)
{
break; //ends the life of the thread..
}
else
{
//Get a job
rri = mJobs.front();
mJobs.pop_front();
}
} //Causes the scoped lock to unlock
//Do the job
if(rri)
{
RRPLOG(lDebug2)<<"Loading model into instance: "<<rri->getInstanceID();
if(mModelFileName.size())
{
rri->load(mModelFileName, &mLoadSBMLOptions);
}
else if(mSBML.size())
{
rri->load(mSBML, &mLoadSBMLOptions);
}
}
else
{
RRPLOG(lError)<<"Null job pointer...!";
}
}
RRPLOG(lDebug)<<"Exiting Load Model thread: "<<mThread.id();
mIsWorking = false;
Mutex::ScopedLock lock2(mNrOfWorkersMutex);
mNrOfWorkers--;
}
void TestRoadRunner::steadyState(const std::string& uri)
{
Logger::setLevel(Logger::LOG_DEBUG);
RoadRunner r;
r.load(uri);
r.steadyState();
}
void TestRoadRunner::testRead(const std::string &fname)
{
Logger::enableConsoleLogging(Logger::LOG_DEBUG);
//const char* fname = "/Users/andy/src/sbml_test/cases/semantic/00001/00001-sbml-l2v4.xml";
libsbml::SBMLReader reader;
SBMLDocument *doc = reader.readSBML(fname);
Model *m = doc->getModel();
const ListOfParameters *params = m->getListOfParameters();
for(int i = 0; i < params->size(); ++i)
{
const Parameter *p = params->get(i);
cout << "param \'" << p->getId() << "\', conservedMoiety: "
<< ConservationExtension::getConservedMoiety(*p) << endl;
}
const ListOfSpecies *species = m->getListOfSpecies();
for(int i = 0; i < species->size(); ++i)
{
const Species *s = species->get(i);
cout << "species \'" << s->getId() << "\', conservedMoiety: "
<< ConservationExtension::getConservedMoiety(*s) << endl;
}
delete doc;
Logger::setLevel(Logger::LOG_TRACE);
RoadRunner r;
r.load(fname, 0);
rr::ExecutableModel *model = r.getModel();
int len = model->getNumIndFloatingSpecies();
double *buffer = new double[len];
model->getFloatingSpeciesAmountRates(len, 0, buffer);
delete[] buffer;
cout << "its all good" << endl;
}
bool TestCapabilities::test()
{
RoadRunner rr;
std::string caps = rr.getConfigurationXML();
Log(Logger::PRIO_INFORMATION) << caps;
return true;
}
void ParameterScanWorker::run()
{
workerStarted();
//The user may have aborted the minization... check here..
if(mHost.isBeingTerminated())
{
//user did set the terminate flag to true.. discard any data and get out of the
//plugin execute code..
RRPLOG(lInfo)<<"The ParameterScanWorker was terminated.. aborting";
workerFinished();
return;
}
//Create arrayed data
ArrayedParameter para(mHost.mParameter.getValueReference());
StringList selList(mHost.mSelectionList.getValue());
RoadRunner rr;
rr.load(mHost.mSBML.getValue());
//Make sure time is the first column in the selectin list
if(selList.size() && compareNoCase(selList[0], "time") != true)
{
selList.InsertAt(0,"time");
}
rr.setSelections(selList);
TelluriumData& data = mHost.mOutputData.getValueReference();
data.clear();
for(int i = 0; i < para.getNumberOfIncrements() + 1; i++)
{
rr::SimulateOptions options;
options.flags |= rr::SimulateOptions::RESET_MODEL;
options.start = mHost.mStartTime.getValue();
options.duration = mHost.mEndTime.getValue() - mHost.mStartTime.getValue();
options.steps = mHost.mNumberOfPointsPerSimulation.getValue() - 1;
//Set parameter
rr.setValue(para.getName(), para.getCurrentValue());
const RoadRunnerData *rrData = rr.simulate(&options);
TelluriumData *temp = new TelluriumData(*rrData);
data.append(*temp);
delete temp;
para.increment();
}
//The Arrayed parameter need to be added to the data.
data.setArrayedParameter(para);
workerFinished();
}
int rrcCallConv getNumberOfRules(RRHandle handle)
{
start_try
RoadRunner* rri = castToRoadRunner(handle);
if(!rri->getModel())
{
Log(Logger::LOG_WARNING)<<"Model is not allocated.";
return -1;
}
int value = rri->getModel()->getNumRules();
return value;
catch_int_macro
}
void SimulateThread::worker()
{
mWasStarted = true;
mIsWorking = true;
Mutex::ScopedLock lock(mNrOfWorkersMutex);
mNrOfWorkers++;
mNrOfWorkersMutex.unlock();
RoadRunner *rri = NULL;
//////////////////////////////////
while(!mIsTimeToDie)
{
{ //Scope for the mutex lock...
Mutex::ScopedLock lock(mJobsMutex);
if(mJobs.size() == 0 )//|| mIsTimeToDie)
{
break; //ends the life of the thread..
}
rri = mJobs.front();
mJobs.pop_front();
} //Causes the scoped lock to unlock
//Do the job
if(rri)
{
Log(lInfo)<<"Simulating RR instance: "<<rri->getInstanceID();
if(!rri->simulate2())
{
Log(lError)<<"Failed simulating instance: "<<rri->getInstanceID();
}
}
else
{
Log(lError)<<"Null job pointer...!";
}
}
Log(lDebug)<<"Exiting Simulate thread: "<<mThread.id();
mIsWorking = false;
Mutex::ScopedLock lock2(mNrOfWorkersMutex);
mNrOfWorkers--;
}
/**
* perform a stochastic ensemble calculation.
*
* :param: r an existing roadrunner obj, loaded with a mode.
* :param: n how many ensembles to run.
* :param: seed the seed value, use None to continue with previous
* random number stream.
* :param: start start time
* :param: stop stop time
* :param: ntps how many points display in the result.
*/
DoubleMatrix ensemble(RoadRunner &r, int n, unsigned long seed, double start, double stop, int npts) {
// set the seed value of the integrator
Integrator *itg = r.getIntegrator(Integrator::GILLESPIE);
itg->setItem("seed", seed);
// setup the simulation
// create a sim opt obj, loads itself with
// default values in ctor.
SimulateOptions o;
o.start = start;
o.duration = stop;
o.steps = npts;
// we should reset the model each time we simulate,
// set the RESET_MODEL bit.
o.flags |= SimulateOptions::RESET_MODEL;
o.integrator = Integrator::GILLESPIE;
// make a result var
DoubleMatrix result(npts+1, n+1);
for (int i = 0; i < n; ++i) {
const DoubleMatrix &sim = *r.simulate(&o);
// copy result data colum
for (int row = 0; row < npts+1; ++row) {
result(row, i+1) = sim(row, 1);
}
}
// copy result time column
const DoubleMatrix &sim = *r.getSimulationData();
// copy result data colum
for (int row = 0; row < npts+1; ++row) {
result(row, 0) = sim(row, 0);
}
return result;
}
void TestRoadRunner::testLoad(const std::string& uri)
{
try
{
Logger::setLevel(Logger::LOG_DEBUG);
//std::string sbml = SBMLReader::read(uri);
RoadRunner r;
r.load(uri);
r.steadyState();
}
catch(std::exception& e)
{
cout << "error: " << e.what() << std::endl;
}
}
void compareJacobians(RRHandle gRR)
{
RoadRunner* rri = castToRoadRunner(gRR);
ls::DoubleMatrix jFull = rri->getFullJacobian();
ls::DoubleMatrix jReduced = rri->getReducedJacobian();
//Check dimensions
if(jFull.RSize() != jReduced.RSize() ||
jFull.CSize() != jReduced.CSize())
{
CHECK(false);
return;
}
for(int row = 0; row < jFull.RSize(); row++)
{
for(int col = 0; col < jFull.CSize(); col++)
{
CHECK_CLOSE(jFull(row, col), jReduced(row, col), 1e-6);
}
}
}
bool SBMLTestSuiteSimulation_CAPI::LoadSBMLFromFile()
{
if(!mRRHandle)
{
return false;
}
try
{
std::string fileName = GetModelsFullFilePath();
//Check first if file exists first
if(!fileExists(fileName))
{
Log(Logger::PRIO_ERROR) << "sbml file " << fileName << " not found";
return false;
}
RoadRunner* rri = (RoadRunner*) mRRHandle;
LoadSBMLOptions opt;
// simulation only, no need for accessor functions.
opt.modelGeneratorOpt |= (LoadSBMLOptions::ReadOnlyModel | LoadSBMLOptions::ForceReCompile);
if(!rri->loadSBMLFromFile(fileName, &opt))
{
Log(Logger::PRIO_ERROR) << "Failed to load SBML";
return false;
}
return true;
}
catch(std::exception& e)
{
Log(Logger::PRIO_ERROR) << "exception while loading sbml: " << e.what();
return false;
}
}
bool TestModel::execute(bool inThread)
{
Log(lDebug)<<"Executing the TestModel plugin by Totte Karlsson";
RoadRunner rr;
rr.load(mModel);
rr::SimulateOptions opt;
opt.start = 0;
opt.duration = 10;
opt.steps = 14;
TelluriumData data(rr.simulate(&opt));
mTestData.setValue(data);
//Add noise
const PluginManager* PM = this->getPluginManager();
Plugin* noise = PM->getPlugin("AddNoise");
if(!noise)
{
stringstream msg;
msg<<"The TestModel plugin dependes on the AddNoise plugin, which is not yet loaded.";
throw(Exception(msg.str()));
}
mTestDataWithNoise.setValue(mTestData.getValue());
noise->setPropertyValue("Sigma", mSigma.getValueHandle());
noise->setPropertyValue("InputData", mTestDataWithNoise.getValueHandle());
noise->execute();
mTestDataWithNoise.setValue(noise->getPropertyValueHandle("InputData"));
//Add weights
addWeights();
return true;
}
int main(int argc, char** argv)
{
std::string in_dir;
std::string out_dir;
std::string test_name;
unsigned int level = 0;
unsigned int version = 0;
double start_time = 0.0;
double duration = 0.0;
std::list<std::string> variables;
std::set<std::string> amounts;
std::set<std::string> concentrations;
double absolute_error = 0.0;
double relative_error = 0.0;
if (argc < 6)
{
std::cerr << "Usage: rr-sbml-benchmrk INPUT_DIRECTORY TESTNAME OUTPUTDIRECTORY SBMLLEVEL SBMLVERSION [steps override] [durration] [compiler] [-stiff]" << std::endl;
exit(1);
}
in_dir = argv[1];
test_name = argv[2];
out_dir = argv[3];
level = strtol(argv[4], NULL, 10);
version = strtol(argv[5], NULL, 10);
if (level < 1 || level > 3)
{
std::cerr << "SBML Level " << level << " Version " << version << " not supported." << std::endl;
exit(1);
}
if (level == 1 && (version < 1 || version > 2))
{
std::cerr << "SBML Level " << level << " Version " << version << " not supported." << std::endl;
exit(1);
}
std::ostringstream os;
os << in_dir << "/" << test_name << "/" << test_name << "-settings.txt";
// open the settings file and parse it
std::cout << "parsing file: " << os.str() << std::endl;
std::ifstream f;
std::string settingsFile = in_dir + "/" + test_name + "/" + test_name + "-settings.txt";
std::string sbmlFile;
{
stringstream os;
os << in_dir << "/" << test_name << "/" << test_name << "-sbml-l" << level << "v" << version << ".xml";
sbmlFile = os.str();
}
std::string output_filename;
if (!out_dir.empty() || out_dir.compare("/dev/null") != 0)
{
stringstream os;
os.str("");
os << out_dir << "/" << test_name << ".csv";
output_filename = os.str();
}
RoadRunner roadRunner;
LoadSBMLOptions opt;
// don't generate cache for models
opt.modelGeneratorOpt = opt.modelGeneratorOpt | LoadSBMLOptions::RECOMPILE;
// no mutable initial conditions
opt.modelGeneratorOpt = opt.modelGeneratorOpt & ~LoadSBMLOptions::MUTABLE_INITIAL_CONDITIONS;
// read only model
opt.modelGeneratorOpt = opt.modelGeneratorOpt | LoadSBMLOptions::READ_ONLY;
opt.modelGeneratorOpt = opt.modelGeneratorOpt | LoadSBMLOptions::OPTIMIZE_CFG_SIMPLIFICATION;
opt.modelGeneratorOpt = opt.modelGeneratorOpt | LoadSBMLOptions::OPTIMIZE_GVN;
std::cout << "loading file: " << sbmlFile << std::endl;
roadRunner.load(sbmlFile, &opt);
SimulateOptions settings;
settings.loadSBMLSettings(settingsFile);
// override steps
if (argc > 6)
{
int steps = strtol(argv[6], NULL, 0);
if (steps > 0) {
settings.steps = steps;
}
}
if (argc > 7)
{
double dur = atof(argv[7]);
if (dur > 0) {
settings.duration = dur;
}
}
for (int i = 0; i < argc; ++i) {
if (string(argv[i]).find("stiff") != string::npos) {
roadRunner.getIntegrator()->setValue("stiff", true);
}
}
std::cout << "running for " << settings.steps << ", duration " << settings.duration << std::endl;
std::cout << "absolute: " << roadRunner.getIntegrator()->getValue("absolute_tolerance").convert<bool>() << std::endl;
std::cout << "relative: " << roadRunner.getIntegrator()->getValue("relative_tolerance").convert<bool>() << std::endl;
std::cout << "stiff: " << (roadRunner.getIntegrator()->getValue("stiff").convert<bool>() ? "True" : "False") << std::endl;
roadRunner.setSimulateOptions(settings);
const DoubleMatrix& result = *roadRunner.simulate(0);
if (!output_filename.empty())
{
ofstream output;
output.open(output_filename.c_str());
int rows = result.numRows();
int cols = result.numCols();
for (int i = 0; i < rows; ++i)
{
for (int j = 0; j < cols; ++j)
{
output << result(i, j);
if (j + 1 < cols)
{
output << ", ";
}
else
{
output << "\n";
}
}
}
}
return 0;
}