Annotation of /trunk/gadget/ecosystem.cc

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Revision 24 - (view) (download)

1 :	agomez	1	#include "ecosystem.h"
2 :			#include "runid.h"
3 :			#include "global.h"
4 :	ulcessvp	19	#include <ctime>
5 :	ulcessvp	16	#ifdef _OPENMP
6 :	ulcessvp	11	#include <omp.h>
7 :			#endif
8 :	agomez	1
9 :	ulcessvp	16	#ifdef _OPENMP
10 :	ulcessvp	11	extern Ecosystem** EcoSystems;
11 :			//extern StochasticData* data;
12 :			#endif
13 :	ulcessvp	17	extern volatile int interrupted_print;
14 :	ulcessvp	11
15 :	ulcessvp	19	time_t starttime, stoptime;
16 :
17 :	agomez	1	Ecosystem::Ecosystem(const MainInfo& main) : printinfo(main.getPI()) {
18 :
19 :			funceval = 0;
20 :	ulcessvp	17	//interrupted = 0;
21 :	agomez	1	likelihood = 0.0;
22 :			keeper = new Keeper;
23 :
24 :			// initialise counter used when printing output files
25 :			printcount = printinfo.getPrintIteration() - 1;
26 :
27 :			// read the model specification from the main file
28 :			char* filename = main.getMainGadgetFile();
29 :			ifstream infile;
30 :			infile.open(filename, ios::in);
31 :			CommentStream commin(infile);
32 :			handle.checkIfFailure(infile, filename);
33 :			handle.Open(filename);
34 :			this->readMain(commin, main);
35 :			handle.Close();
36 :			infile.close();
37 :			infile.clear();
38 :
39 :			// if this is an optimising run then read the optimisation parameters from file
40 :			if (main.runOptimise()) {
41 :			handle.logMessage(LOGMESSAGE, ""); //write blank line to log file
42 :			if (main.getOptInfoGiven()) {
43 :			filename = main.getOptInfoFile();
44 :			infile.open(filename, ios::in);
45 :			handle.checkIfFailure(infile, filename);
46 :			handle.Open(filename);
47 :	ulcessvp	11	unsigned seed;
48 :			main.getForcePrint();
49 :			this->readOptimisation(commin, main.getSeed());
50 :	agomez	1	handle.Close();
51 :			infile.close();
52 :			infile.clear();
53 :			} else {
54 :			handle.logMessage(LOGINFO, "Warning - no optimisation file specified, using default values");
55 :			optvec.resize(new OptInfoHooke());
56 :			}
57 :			}
58 :	agomez	20	#ifdef _OPENMP
59 :			runParallel=main.runParallel();
60 :			if (!omp_in_parallel()){
61 :			if (main.runOptimise())
62 :			{
63 :			switch(runParallel){
64 :			case SPECULATIVE:
65 :			handle.logMessage(LOGINFO, "\nFinished reading model data files, starting to run parallel speculative optimisation with ", omp_get_max_threads(), " threads");
66 :			break;
67 :			case REPRODUCIBLE:
68 :			handle.logMessage(LOGINFO, "\nFinished reading model data files, starting to run parallel reproducible optimisation with ", omp_get_max_threads(), " threads");
69 :			break;
70 :			default:
71 :			handle.logMessage(LOGINFO, "\nFinished reading model data files, starting to serial optimisation with ", omp_get_num_threads() , "threads");
72 :			}
73 :			}
74 :			else
75 :			handle.logMessage(LOGINFO, "\nFinished reading model data files, starting to run simulation ", omp_get_num_threads(), " threads");
76 :			handle.logMessage(LOGMESSAGE, ""); //write blank line to log file
77 :			}
78 :			#else
79 :	agomez	1	if (main.runOptimise())
80 :			handle.logMessage(LOGINFO, "\nFinished reading model data files, starting to run optimisation");
81 :			else
82 :			handle.logMessage(LOGINFO, "\nFinished reading model data files, starting to run simulation");
83 :			handle.logMessage(LOGMESSAGE, ""); //write blank line to log file
84 :	agomez	20	#endif
85 :	agomez	1	}
86 :
87 :			Ecosystem::~Ecosystem() {
88 :			int i;
89 :			for (i = 0; i < optvec.Size(); i++)
90 :			delete optvec[i];
91 :			for (i = 0; i < printvec.Size(); i++)
92 :			delete printvec[i];
93 :			for (i = 0; i < likevec.Size(); i++)
94 :			delete likevec[i];
95 :			for (i = 0; i < tagvec.Size(); i++)
96 :			delete tagvec[i];
97 :			for (i = 0; i < basevec.Size(); i++)
98 :			delete basevec[i];
99 :
100 :			delete Area;
101 :			delete TimeInfo;
102 :			delete keeper;
103 :			}
104 :
105 :			void Ecosystem::writeStatus(const char* filename) const {
106 :			ofstream outfile;
107 :			outfile.open(filename, ios::out);
108 :			handle.checkIfFailure(outfile, filename);
109 :			handle.Open(filename);
110 :			RUNID.Print(outfile);
111 :			outfile << "The current simulation time is " << TimeInfo->getYear()
112 :			<< ", step " << TimeInfo->getStep() << endl;
113 :
114 :			int i;
115 :			for (i = 0; i < basevec.Size(); i++)
116 :			basevec[i]->Print(outfile);
117 :			for (i = 0; i < likevec.Size(); i++)
118 :			likevec[i]->Print(outfile);
119 :			for (i = 0; i < tagvec.Size(); i++)
120 :			tagvec[i]->Print(outfile);
121 :
122 :			handle.Close();
123 :			outfile.close();
124 :			outfile.clear();
125 :			}
126 :
127 :			void Ecosystem::Reset() {
128 :			int i;
129 :			TimeInfo->Reset();
130 :			for (i = 0; i < likevec.Size(); i++)
131 :			likevec[i]->Reset(keeper);
132 :			for (i = 0; i < basevec.Size(); i++)
133 :			basevec[i]->Reset(TimeInfo);
134 :			}
135 :
136 :			void Ecosystem::Optimise() {
137 :			int i;
138 :			for (i = 0; i < optvec.Size(); i++) {
139 :	ulcessvp	19	time(&starttime);
140 :	ulcessvp	16	#ifdef _OPENMP
141 :	agomez	20	if (runParallel){
142 :	ulcessvp	24	int j, numThr = omp_get_max_threads ( ); //AGT REMOVED
143 :			DoubleVector v = this->getValues();
144 :			for (j = 0; j < numThr; j++)
145 :			EcoSystems[j]->Update(v);
146 :	agomez	20	if(runParallel==SPECULATIVE)
147 :			{
148 :			handle.logMessage(LOGINFO, "\nCalling Speculative Optimization");
149 :			optvec[i]->OptimiseLikelihoodOMP();
150 :			}
151 :			else
152 :			{
153 :			handle.logMessage(LOGINFO, "\nCalling Reproducible parallel Optimization");
154 :			optvec[i]->OptimiseLikelihoodREP();
155 :			}
156 :			}
157 :			else
158 :			{
159 :			handle.logMessage(LOGINFO, "\nCalling Reproducible serial Optimization");
160 :			optvec[i]->OptimiseLikelihood();
161 :			}
162 :	ulcessvp	12	#else
163 :	agomez	20	//#ifdef SPECULATIVE
164 :			// optvec[i]->OptimiseLikelihoodOMP();
165 :			//#else
166 :	ulcessvp	12	optvec[i]->OptimiseLikelihood();
167 :			#endif
168 :	ulcessvp	19	time(&stoptime);
169 :	ulcessvp	11	this->writeOptValues();
170 :			}
171 :			}
172 :
173 :	agomez	1	double Ecosystem::SimulateAndUpdate(const DoubleVector& x) {
174 :			int i, j;
175 :
176 :			if (funceval == 0) {
177 :			// JMB - only need to create these vectors once
178 :			initialval.resize(keeper->numVariables(), 0.0);
179 :			currentval.resize(keeper->numVariables(), 0.0);
180 :			optflag.resize(keeper->numVariables(), 0);
181 :			keeper->getOptFlags(optflag);
182 :	agomez	20
183 :	agomez	1	}
184 :
185 :			j = 0;
186 :			keeper->getCurrentValues(currentval);
187 :			keeper->getInitialValues(initialval);
188 :			for (i = 0; i < currentval.Size(); i++) {
189 :			if (optflag[i]) {
190 :			currentval[i] = x[j] * initialval[i];
191 :			j++;
192 :			}
193 :			}
194 :
195 :			keeper->Update(currentval);
196 :			this->Simulate(0); //dont print whilst optimising
197 :
198 :			if (printinfo.getPrint()) {
199 :			printcount++;
200 :			if (printcount == printinfo.getPrintIteration()) {
201 :			keeper->writeValues(likevec, printinfo.getPrecision());
202 :			printcount = 0;
203 :			}
204 :			}
205 :
206 :			funceval++;
207 :			return likelihood;
208 :			}
209 :
210 :			void Ecosystem::writeOptValues() {
211 :			int i;
212 :			DoubleVector tmpvec(likevec.Size(), 0.0);
213 :			for (i = 0; i < likevec.Size(); i++)
214 :			tmpvec[i] = likevec[i]->getUnweightedLikelihood();
215 :
216 :	ulcessvp	11	int iters = 0;
217 :	ulcessvp	16	#ifdef _OPENMP
218 :	agomez	20	if (runParallel){
219 :			int numThr = omp_get_max_threads ( );
220 :			for (i = 0; i < numThr; i++)
221 :	ulcessvp	11	iters += EcoSystems[i]->getFuncEval();
222 :	agomez	20	}
223 :	ulcessvp	11	#endif
224 :			handle.logMessage(LOGINFO, "\nAfter a total of", funceval+iters, "function evaluations the best point found is");
225 :	agomez	1	keeper->writeBestValues();
226 :			handle.logMessage(LOGINFO, "\nThe scores from each likelihood component are");
227 :			handle.logMessage(LOGINFO, tmpvec);
228 :			if (!isZero(keeper->getBestLikelihoodScore())) // no better point has been found
229 :			handle.logMessage(LOGINFO, "\nThe overall likelihood score is", keeper->getBestLikelihoodScore());
230 :			else
231 :			handle.logMessage(LOGINFO, "\nThe overall likelihood score is", this->getLikelihood());
232 :	ulcessvp	19
233 :			handle.logMessage(LOGINFO, "\n Runtime for the algorithm was ", difftime(stoptime, starttime)," seconds\n");
234 :	agomez	1	}
235 :
236 :			void Ecosystem::writeInitialInformation(const char* const filename) {
237 :			keeper->openPrintFile(filename);
238 :			keeper->writeInitialInformation(likevec);
239 :			}
240 :
241 :			void Ecosystem::writeValues() {
242 :			keeper->writeValues(likevec, printinfo.getPrecision());
243 :			}
244 :
245 :			void Ecosystem::writeParams(const char* const filename, int prec) const {
246 :	ulcessvp	17	if ((funceval > 0) && (interrupted_print == 0)) {
247 :	agomez	1	//JMB - print the final values to any output files specified
248 :			//in case they have been missed by the -print value
249 :			if (printinfo.getPrint())
250 :			keeper->writeValues(likevec, printinfo.getPrecision());
251 :			}
252 :	ulcessvp	17	keeper->writeParams(optvec, filename, prec, interrupted_print);
253 :	agomez	1	}

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