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[mareframe] Diff of /trunk/gadget/gadget.cc
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Diff of /trunk/gadget/gadget.cc

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revision 26, Mon May 8 07:59:53 2017 UTC revision 27, Mon May 8 11:58:23 2017 UTC
# Line 13  Line 13 
13  Ecosystem* EcoSystem;  Ecosystem* EcoSystem;
14  StochasticData* data = 0;  StochasticData* data = 0;
15  Ecosystem** EcoSystems;  Ecosystem** EcoSystems;
16    MainInfo _main;
17    
18  volatile int interrupted = 0;  volatile int interrupted = 0;
19  volatile int interrupted_print = 0;  volatile int interrupted_print = 0;
# Line 20  Line 21 
21    
22  int main(int aNumber, char* const aVector[]) {  int main(int aNumber, char* const aVector[]) {
23    
24    MainInfo main;  
25    
26  //  omp_set_num_threads(4);  //  omp_set_num_threads(4);
27    
# Line 53  Line 54 
54    if (chdir(workingdir) != 0) //JMB change back to where we were ...    if (chdir(workingdir) != 0) //JMB change back to where we were ...
55      handle.logMessage(LOGFAIL, "Error - failed to change working directory to", workingdir);      handle.logMessage(LOGFAIL, "Error - failed to change working directory to", workingdir);
56    
57    main.read(aNumber, aVector);    _main.read(aNumber, aVector);
58    main.checkUsage(inputdir, workingdir);    _main.checkUsage(inputdir, workingdir);
59    
60    if (chdir(inputdir) != 0)    if (chdir(inputdir) != 0)
61      handle.logMessage(LOGFAIL, "Error - failed to change input directory to", inputdir);      handle.logMessage(LOGFAIL, "Error - failed to change input directory to", inputdir);
62    EcoSystem = new Ecosystem(main);    EcoSystem = new Ecosystem(_main);
63    
64  #ifdef INTERRUPT_HANDLER  #ifdef INTERRUPT_HANDLER
65    //JMB dont register interrupt if doing a network run    //JMB dont register interrupt if doing a network run
66    if (!(main.runNetwork()))    if (!(_main.runNetwork()))
67      registerInterrupts(&interrupted);      registerInterrupts(&interrupted);
68  #endif  #endif
69    
70    if (chdir(workingdir) != 0)    if (chdir(workingdir) != 0)
71      handle.logMessage(LOGFAIL, "Error - failed to change working directory to", workingdir);      handle.logMessage(LOGFAIL, "Error - failed to change working directory to", workingdir);
72    if ((main.getPI()).getPrint())    if ((_main.getPI()).getPrint())
73      EcoSystem->writeInitialInformation((main.getPI()).getOutputFile());      EcoSystem->writeInitialInformation((_main.getPI()).getOutputFile());
74    
75    if (main.runStochastic()) {    if (_main.runStochastic()) {
76      if (main.runNetwork()) {      if (_main.runNetwork()) {
77  #ifdef GADGET_NETWORK //to help compiling when pvm libraries are unavailable  #ifdef GADGET_NETWORK //to help compiling when pvm libraries are unavailable
78        EcoSystem->Initialise();        EcoSystem->Initialise();
79        data = new StochasticData();        data = new StochasticData();
80        while (data->getDataFromNetwork()) {        while (data->getDataFromNetwork()) {
81          EcoSystem->Update(data);          EcoSystem->Update(data);
82          EcoSystem->Simulate(main.runPrint());          EcoSystem->Simulate(_main.runPrint());
83          data->sendDataToNetwork(EcoSystem->getLikelihood());          data->sendDataToNetwork(EcoSystem->getLikelihood());
84          data->readNextLineFromNetwork();          data->readNextLineFromNetwork();
85        }        }
86        delete data;        delete data;
87  #endif  #endif
88    
89      } else if (main.getInitialParamGiven()) {      } else if (_main.getInitialParamGiven()) {
90        if (chdir(inputdir) != 0) //JMB need to change back to inputdir to read the file        if (chdir(inputdir) != 0) //JMB need to change back to inputdir to read the file
91          handle.logMessage(LOGFAIL, "Error - failed to change input directory to", inputdir);          handle.logMessage(LOGFAIL, "Error - failed to change input directory to", inputdir);
92        data = new StochasticData(main.getInitialParamFile());        data = new StochasticData(_main.getInitialParamFile());
93        if (chdir(workingdir) != 0)        if (chdir(workingdir) != 0)
94          handle.logMessage(LOGFAIL, "Error - failed to change working directory to", workingdir);          handle.logMessage(LOGFAIL, "Error - failed to change working directory to", workingdir);
95    
# Line 96  Line 97 
97        EcoSystem->checkBounds();        EcoSystem->checkBounds();
98    
99        EcoSystem->Initialise();        EcoSystem->Initialise();
100        if (main.printInitial()) {        if (_main.printInitial()) {
101          EcoSystem->Reset();  //JMB only need to call reset() before the print commands          EcoSystem->Reset();  //JMB only need to call reset() before the print commands
102          EcoSystem->writeStatus(main.getPrintInitialFile());          EcoSystem->writeStatus(_main.getPrintInitialFile());
103        }        }
104    
105        EcoSystem->Simulate(main.runPrint());        EcoSystem->Simulate(_main.runPrint());
106        if ((main.getPI()).getPrint())        if ((_main.getPI()).getPrint())
107          EcoSystem->writeValues();          EcoSystem->writeValues();
108    
109        while (data->isDataLeft()) {        while (data->isDataLeft()) {
110          data->readNextLine();          data->readNextLine();
111          EcoSystem->Update(data);          EcoSystem->Update(data);
112          EcoSystem->checkBounds();          EcoSystem->checkBounds();
113          EcoSystem->Simulate(main.runPrint());          EcoSystem->Simulate(_main.runPrint());
114          if ((main.getPI()).getPrint())          if ((_main.getPI()).getPrint())
115            EcoSystem->writeValues();            EcoSystem->writeValues();
116        }        }
117        delete data;        delete data;
# Line 120  Line 121 
121          handle.logMessage(LOGWARN, "Warning - no parameter input file given, using default values");          handle.logMessage(LOGWARN, "Warning - no parameter input file given, using default values");
122    
123        EcoSystem->Initialise();        EcoSystem->Initialise();
124        if (main.printInitial()) {        if (_main.printInitial()) {
125          EcoSystem->Reset();  //JMB only need to call reset() before the print commands          EcoSystem->Reset();  //JMB only need to call reset() before the print commands
126          EcoSystem->writeStatus(main.getPrintInitialFile());          EcoSystem->writeStatus(_main.getPrintInitialFile());
127        }        }
128    
129        EcoSystem->Simulate(main.runPrint());        EcoSystem->Simulate(_main.runPrint());
130        if ((main.getPI()).getPrint())        if ((_main.getPI()).getPrint())
131          EcoSystem->writeValues();          EcoSystem->writeValues();
132      }      }
133    
134    } else if (main.runOptimise()) {    } else if (_main.runOptimise()) {
135            if (EcoSystem->numVariables() == 0)            if (EcoSystem->numVariables() == 0)
136                    handle.logMessage(LOGFAIL, "Error - no parameters can be optimised");                    handle.logMessage(LOGFAIL, "Error - no parameters can be optimised");
137    
138            if (main.getInitialParamGiven()) {            if (_main.getInitialParamGiven()) {
139                    if (chdir(inputdir) != 0) //JMB need to change back to inputdir to read the file                    if (chdir(inputdir) != 0) //JMB need to change back to inputdir to read the file
140                          handle.logMessage(LOGFAIL, "Error - failed to change input directory to", inputdir);                          handle.logMessage(LOGFAIL, "Error - failed to change input directory to", inputdir);
141                    data = new StochasticData(main.getInitialParamFile());                    data = new StochasticData(_main.getInitialParamFile());
142                    if (chdir(workingdir) != 0)                    if (chdir(workingdir) != 0)
143                          handle.logMessage(LOGFAIL, "Error - failed to change working directory to", workingdir);                          handle.logMessage(LOGFAIL, "Error - failed to change working directory to", workingdir);
144    
# Line 147  Line 148 
148                    handle.logMessage(LOGFAIL, "Error - no parameter input file specified");                    handle.logMessage(LOGFAIL, "Error - no parameter input file specified");
149    
150            EcoSystem->Initialise();            EcoSystem->Initialise();
151            if (main.printInitial()) {            if (_main.printInitial()) {
152                    EcoSystem->Reset();  //JMB only need to call reset() before the print commands                    EcoSystem->Reset();  //JMB only need to call reset() before the print commands
153                    EcoSystem->writeStatus(main.getPrintInitialFile());                    EcoSystem->writeStatus(_main.getPrintInitialFile());
154                    }                    }
155    
156  #ifdef _OPENMP  #ifdef _OPENMP
157            if (main.runParallel()){            if (_main.runParallel()){
158                  int numThr = omp_get_max_threads ( );                  int numThr = omp_get_max_threads ( );
159                  handle.logMessage(LOGINFO, "Info - initialise ", numThr," EcoSystems ");                  handle.logMessage(LOGINFO, "Info - initialise ", numThr," EcoSystems ");
160                  EcoSystems = new Ecosystem*[numThr];                  EcoSystems = new Ecosystem*[numThr];
161                  int i;                  int i;
162  #pragma omp parallel for shared(EcoSystems,main,data,handle)  #pragma omp parallel for shared(EcoSystems,_main,data,handle)
163                  for (i=0; i<numThr; i++)                  for (i=0; i<numThr; i++)
164                  {                  {
165                          handle.logMessage(LOGINFO, "Info - Ecosystem ", i);                          handle.logMessage(LOGINFO, "Info - Ecosystem ", i);
166                          if (main.getInitialParamGiven()) {                          if (_main.getInitialParamGiven()) {
167                              EcoSystems[i] = new Ecosystem(main);                              EcoSystems[i] = new Ecosystem(_main);
168                              EcoSystems[i]->Update(data);                              EcoSystems[i]->Update(data);
169                              EcoSystems[i]->checkBounds();                              EcoSystems[i]->checkBounds();
170                          }                          }
# Line 173  Line 174 
174  #endif  #endif
175            EcoSystem->Optimise();            EcoSystem->Optimise();
176            delete data;            delete data;
177            if (main.getForcePrint())            if (_main.getForcePrint())
178                    EcoSystem->Simulate(main.getForcePrint());                    EcoSystem->Simulate(_main.getForcePrint());
179    }    }
180    
181    handle.logMessage(LOGMESSAGE, "");  //write blank line to log file    handle.logMessage(LOGMESSAGE, "");  //write blank line to log file
182    if (main.printFinal() && !(main.runNetwork()))    if (_main.printFinal() && !(_main.runNetwork()))
183      EcoSystem->writeStatus(main.getPrintFinalFile());      EcoSystem->writeStatus(_main.getPrintFinalFile());
184    
185    //JMB print final values of parameters    //JMB print final values of parameters
186    if (!(main.runNetwork()))    if (!(_main.runNetwork()))
187      EcoSystem->writeParams((main.getPI()).getParamOutFile(), (main.getPI()).getPrecision());      EcoSystem->writeParams((_main.getPI()).getParamOutFile(), (_main.getPI()).getPrecision());
188    
189    if (check)    if (check)
190      free(workingdir);      free(workingdir);
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