void EventNumberContainer::display_nonzeroEvents(){
unsigned long N = _event_label.size();
cout << "Event Label \t sub-Label \t n Events"<<endl;
coutline(40);
for(int i=0; i<N; i++){
if(_n_event[i]>0) cout << _event_label[i]<<"\t"<<_event_sublabel[i]<<"\t"<<_n_event[i]<<endl;
}
coutline(40);
}
void dcDataFrame::display()
{
unsigned int n = _rowname.size();
unsigned int ncol = _value.getNbCols();
cout << endl << "dcDataFrame Content:"<<endl;
string sep = "\t\t|\t";
if (ncol==0) cout << "EMPTY!"<<endl;
// Print headers
if (ncol>0)
{
cout << "_rowname" << sep;
for (int i=0; i<ncol; i++)
cout << _colname[i] << sep;
cout<<endl;
}
if (ncol==1)
{
coutline(20);
for (int i=0; i<n; i++)
{
cout << _rowname[i] << sep << _value[i] <<endl;
}
coutline(20);
}
if (ncol>1)
{
coutline(80);
for (int i=0; i<n; i++)
{
cout << _rowname[i] << sep;
for (int j=0;j<ncol; j++)
cout << _value(i,j)<<"\t";
cout << endl;
}
coutline(80);
}
}
void simulator::displayInfo()
{
coutline(40);
cout<<" === SIMULATOR INFO ==="<<endl;
cout << "Population size: "<<_indiv.size()<<endl;
cout << "# E compartments: " << _nE <<endl;
cout << "# I compartments: " << _nI <<endl;
cout << "sigma rates:"; displayVector(_sigma);
cout << "gamma rates:"; displayVector(_gamma);
double R0 = _beta/_gamma[0]*_nI;
cout << "R0 = "<<R0<<endl;
cout << "Number of events: "<<_time.size()<<endl;
cout << "Last date: "<<_time[_time.size()-1]<<endl;
cout << "Cumul incidence: "<<_cumIncidence[_cumIncidence.size()-1]<<endl;
coutline(40);
}
int main(int argc, const char * argv[])
{
// UNIT JOB FOR CALIBRATION
// ======================
//
// ARG #1: JOB NUMBER
// ARG #2: NUMBER OF LHS EXECUTIONS PER JOB
// ARG #3: MONTE CARLO RUNS (FOR EACH LHS)
// For performance monitoring
// - do not delete -
timeval tim;
gettimeofday(&tim, NULL);
double t1=tim.tv_sec+(tim.tv_usec/1000000.0);
if (argc<3)
{
cout <<endl << " ERROR in Job Unit ('main_jobUnit.cpp'): not enough arguments" << endl;
exit(1);
}
cout << endl << " === JOB UNIT #"<<argv[1]<<" (nrows="<< argv[2] <<") ==="<<endl;
// Parameters file name
string fname = _DIR_CALIB + "calib_LHS_SF_input_" ;
int i_job = atoi(argv[1]);
int nrows = atoi(argv[2]);
int nMC_calibration = atoi(argv[3]);
// === PRE CALIBRATION ===
// Start from an unpartnered population
// Initialize empty Population object
Population P0(0);
// Read starting population from a file
// output of "generateIndividuals.R"
P0.initFromFile("startPopulation.csv",
"in_STI.csv",
"in_STI_SFincrease.csv",
"in_HIVrebound.csv");
// Set all parameters
P0.setAllParameters();
// Set-up pre-calibration simulation
double horizon_preCalib = 60.0;
double timestep_preCalib = 0.25;
Simulation S_preCalib(horizon_preCalib, timestep_preCalib, P0, 0);
// Pre-calibration run to form partnerships first
bool logIndivInfo = false;
bool doSex = false;
bool traceNetwork = false;
bool displayProgress = 0;
S_preCalib.runAllEvents_horizon(doSex,
logIndivInfo,
traceNetwork,
displayProgress);
// Seed STIs' initial prevalence
S_preCalib.STI_set_initial_prevalence("in_STI_initial_prevalence.csv");
coutline(80);
cout << " PRE CALIBRATION POPULATION:";
S_preCalib.get_population().displayInfo(false);
Population P1 = S_preCalib.get_population();
// == END PRE-CALIBRATION ==
// =================
// Horizon for the calibration
string file_calibration = _DIR_CALIB + "in_calibration.csv";
double horizon_calib = getParameterFromFile("horizon_calib", file_calibration);
double timeStep_calib = getParameterFromFile("timeStep_calib", file_calibration);
// Runs the calibration using the
// parameters limits defined in the files defined by the job number
calibration_LHS_fromFile(_DIR_CALIB + "calibration_filename_wrapper.csv",
// Parameters (pre-sampled)
fname + "DMG_"+int2string(i_job)+".csv",
fname + "FORM_"+int2string(i_job)+".csv",
fname + "SPOUSAL_"+int2string(i_job)+".csv",
fname + "DISSOL_"+int2string(i_job)+".csv",
fname + "SEXACT_"+int2string(i_job)+".csv",
fname + "STIFTR_V_"+int2string(i_job)+".csv",
fname + "STIFTR_B_"+int2string(i_job)+".csv",
fname + "STIFTR_P_"+int2string(i_job)+".csv",
fname + "STIFTR_F_"+int2string(i_job)+".csv",
nrows, i_job,
P1, horizon_calib, timeStep_calib,
nMC_calibration);
// --------------------------------------------------------------
// COMPUTER TIME MONITORING - do not delete!
gettimeofday(&tim, NULL);
double t2=tim.tv_sec+(tim.tv_usec/1000000.0);
int minutes = (int)((t2-t1)/60.0);
double sec = (t2-t1)-minutes*60.0;
// --------------------------------------------------------------
cout << endl << "~~~> JOB UNIT #"<<argv[1]<<" was completed in ";
cout << minutes<<" min "<<sec<<" sec" << endl;
return 0;
}
int main(int argc, const char * argv[])
{
// ==============================================
// SERIAL FARMING WRAPPER FOR MONTE CARLO RUNS
// ==============================================
//
// Integrity checks
stopif(argc<=1,"Serial Farming: not enough arguments!");
// retrieve the type of execution
std::string arg1(argv[1]);
bool doSingleRun = (arg1=="singlerun"?true:false);
bool doScenario = (arg1=="scenario"?true:false);
stopif(!doSingleRun && !doScenario, "Serial Farming: unknown execution type!");
// DEBUG informations
system("date");
system("pwd");
// Clean all previous output files
// (some files are incremental, so can get huge)
system("./cleanout");
// simple time stamp
ofstream fstart("SF_MC_timestamp.txt");
fstart<<"dummy"<<endl;
// retrieve execution parameters
int nMCtotal = getParameterFromFile("MCiter", _DIR_IN + "in_simulation.csv");
int nCPU = getParameterFromFile("nCPU", _DIR_IN + "in_simulation.csv");
int nMCperCPU = nMCtotal/nCPU;
coutline(80);
cout << "*** SINGLE SIMULATION WITH "<<nMCtotal<<" MC ITERATIONS ***"<<endl;
// Mandatory code checks
//CODECHECK_mandatory();
// Launch unit jobs (1 for each CPU)
for (int i_job = 1; i_job <= nCPU; i_job++)
{
// -- for sharcnet --
// string sharc_cmd = "sqsub -o alljobs.out -r 1d --mpp 1G ./stiagent_U "
// + int2string(i_job) + " " + int2string(nrows)+ " " + int2string(nMC_calibration);
// Determine the type of execution
string unit_name;
if (doSingleRun) unit_name = "./tphiv_U_MC ";
if (doScenario) unit_name = "./tphiv_U_SCEN ";
// DEBUG
if (doScenario) cout <<endl<<" SCENARIO MODE"<<endl;
// -----
// Execution
string local_cmd = unit_name + int2string(i_job) + " " + int2string(nMCperCPU) + " &";
string cmd_line = local_cmd;
system(cmd_line.c_str());
cout << "Unit job " + int2string(i_job) + "/"<<nCPU<<" launched..." <<endl;
}
return 0;
}
