| 1 : |
agomez |
1 |
#include "maininfo.h" |
| 2 : |
|
|
#include "errorhandler.h" |
| 3 : |
|
|
#include "gadget.h" |
| 4 : |
|
|
#include "runid.h" |
| 5 : |
|
|
#include "global.h" |
| 6 : |
|
|
|
| 7 : |
|
|
void MainInfo::showCorrectUsage(char* error) {
|
| 8 : |
|
|
RUNID.Print(cerr);
|
| 9 : |
|
|
cerr << "\nError in command line value - unrecognised option " << error << endl
|
| 10 : |
|
|
<< "Common options are -l or -s, -i <filename> -o <filename>\n"
|
| 11 : |
|
|
<< "For more information try running Gadget with the -h switch\n";
|
| 12 : |
|
|
exit(EXIT_FAILURE);
|
| 13 : |
|
|
}
|
| 14 : |
|
|
|
| 15 : |
|
|
void MainInfo::showUsage() {
|
| 16 : |
|
|
RUNID.Print(cout);
|
| 17 : |
|
|
cout << "\nOptions for running Gadget:\n"
|
| 18 : |
|
|
<< " -l perform a likelihood (optimising) model run\n"
|
| 19 : |
|
|
<< " -s perform a single (simulation) model run\n"
|
| 20 : |
|
|
<< " -n perform a network run (using paramin)\n"
|
| 21 : |
|
|
<< " -v --version display version information and exit\n"
|
| 22 : |
|
|
<< " -h --help display this help screen and exit\n"
|
| 23 : |
agomez |
20 |
#ifdef _OPENMP
|
| 24 : |
|
|
<< " -parallel <option> run in parallel <option> == [spe, rep]. spe=speculative, rep=reproducible. Defaull spe\n"
|
| 25 : |
|
|
#endif
|
| 26 : |
agomez |
1 |
<< "\nOptions for specifying the input to Gadget models:\n"
|
| 27 : |
|
|
<< " -i <filename> read model parameters from <filename>\n"
|
| 28 : |
|
|
<< " -opt <filename> read optimising parameters from <filename>\n"
|
| 29 : |
|
|
<< " -main <filename> read model information from <filename>\n"
|
| 30 : |
|
|
<< " (default filename is 'main')\n"
|
| 31 : |
|
|
<< " -m <filename> read other commandline parameters from <filename>\n"
|
| 32 : |
|
|
<< "\nOptions for specifying the output from Gadget models:\n"
|
| 33 : |
|
|
<< " -p <filename> print final model parameters to <filename>\n"
|
| 34 : |
|
|
<< " (default filename is 'params.out')\n"
|
| 35 : |
|
|
<< " -o <filename> print likelihood output to <filename>\n"
|
| 36 : |
|
|
<< " -print <number> print -o output every <number> iterations\n"
|
| 37 : |
|
|
<< " -precision <number> set the precision to <number> in output files\n"
|
| 38 : |
|
|
<< "\nOptions for debugging Gadget models:\n"
|
| 39 : |
|
|
<< " -log <filename> print logging information to <filename>\n"
|
| 40 : |
|
|
<< " -printinitial <filename> print initial model information to <filename>\n"
|
| 41 : |
|
|
<< " -printfinal <filename> print final model information to <filename>\n"
|
| 42 : |
|
|
<< "\nFor more information see the Gadget web page at http://www.hafro.is/gadget\n\n";
|
| 43 : |
|
|
exit(EXIT_SUCCESS);
|
| 44 : |
|
|
}
|
| 45 : |
|
|
|
| 46 : |
|
|
MainInfo::MainInfo()
|
| 47 : |
agomez |
20 |
#ifdef _OPENMP
|
| 48 : |
|
|
: givenOptInfo(0), givenInitialParam(0), runoptimise(0), runparallel(0),
|
| 49 : |
|
|
#else
|
| 50 : |
|
|
: givenOptInfo(0), givenInitialParam(0), runoptimise(0),
|
| 51 : |
|
|
#endif
|
| 52 : |
agomez |
1 |
runstochastic(0), runnetwork(0), runprint(1), forceprint(0),
|
| 53 : |
|
|
printInitialInfo(0), printFinalInfo(0), printLogLevel(0), maxratio(0.95) {
|
| 54 : |
|
|
|
| 55 : |
|
|
char tmpname[10];
|
| 56 : |
|
|
strncpy(tmpname, "", 10);
|
| 57 : |
|
|
strcpy(tmpname, "main");
|
| 58 : |
|
|
|
| 59 : |
|
|
strOptInfoFile = NULL;
|
| 60 : |
|
|
strInitialParamFile = NULL;
|
| 61 : |
|
|
strPrintInitialFile = NULL;
|
| 62 : |
|
|
strPrintFinalFile = NULL;
|
| 63 : |
|
|
strMainGadgetFile = NULL;
|
| 64 : |
|
|
setMainGadgetFile(tmpname);
|
| 65 : |
|
|
}
|
| 66 : |
|
|
|
| 67 : |
|
|
MainInfo::~MainInfo() {
|
| 68 : |
|
|
if (strOptInfoFile != NULL) {
|
| 69 : |
|
|
delete[] strOptInfoFile;
|
| 70 : |
|
|
strOptInfoFile = NULL;
|
| 71 : |
|
|
}
|
| 72 : |
|
|
if (strInitialParamFile != NULL) {
|
| 73 : |
|
|
delete[] strInitialParamFile;
|
| 74 : |
|
|
strInitialParamFile = NULL;
|
| 75 : |
|
|
}
|
| 76 : |
|
|
if (strPrintInitialFile != NULL) {
|
| 77 : |
|
|
delete[] strPrintInitialFile;
|
| 78 : |
|
|
strPrintInitialFile = NULL;
|
| 79 : |
|
|
}
|
| 80 : |
|
|
if (strPrintFinalFile != NULL) {
|
| 81 : |
|
|
delete[] strPrintFinalFile;
|
| 82 : |
|
|
strPrintFinalFile = NULL;
|
| 83 : |
|
|
}
|
| 84 : |
|
|
if (strMainGadgetFile != NULL) {
|
| 85 : |
|
|
delete[] strMainGadgetFile;
|
| 86 : |
|
|
strMainGadgetFile = NULL;
|
| 87 : |
|
|
}
|
| 88 : |
ulcessvp |
11 |
if (seed != NULL) {
|
| 89 : |
|
|
delete[] seed;
|
| 90 : |
|
|
seed = NULL;
|
| 91 : |
|
|
}
|
| 92 : |
agomez |
1 |
}
|
| 93 : |
|
|
|
| 94 : |
|
|
void MainInfo::read(int aNumber, char* const aVector[]) {
|
| 95 : |
|
|
|
| 96 : |
|
|
if (aNumber == 1) {
|
| 97 : |
|
|
handle.logMessage(LOGWARN, "Warning - no command line options specified, using default values");
|
| 98 : |
|
|
return;
|
| 99 : |
|
|
}
|
| 100 : |
|
|
|
| 101 : |
ulcessvp |
11 |
seed = new unsigned[3];
|
| 102 : |
|
|
seed[0] = 0;
|
| 103 : |
|
|
seed[1] = 0;
|
| 104 : |
|
|
seed[2] = 0;
|
| 105 : |
agomez |
1 |
int k = 1;
|
| 106 : |
|
|
while (k < aNumber) {
|
| 107 : |
|
|
if (strcasecmp(aVector[k], "-l") == 0) {
|
| 108 : |
|
|
runoptimise = 1;
|
| 109 : |
|
|
|
| 110 : |
|
|
} else if (strcasecmp(aVector[k], "-n") == 0) {
|
| 111 : |
|
|
runnetwork = 1;
|
| 112 : |
|
|
|
| 113 : |
|
|
#ifndef GADGET_NETWORK
|
| 114 : |
|
|
handle.logMessage(LOGFAIL, "Error - Gadget cannot currently run in network mode for paramin\nGadget must be recompiled to enable the network communication");
|
| 115 : |
|
|
#endif
|
| 116 : |
|
|
|
| 117 : |
|
|
} else if (strcasecmp(aVector[k], "-s") == 0) {
|
| 118 : |
ulcessvp |
11 |
runstochastic = 1;
|
| 119 : |
agomez |
1 |
} else if (strcasecmp(aVector[k], "-m") == 0) {
|
| 120 : |
|
|
ifstream infile;
|
| 121 : |
|
|
CommentStream incomment(infile);
|
| 122 : |
|
|
if (k == aNumber - 1)
|
| 123 : |
|
|
this->showCorrectUsage(aVector[k]);
|
| 124 : |
|
|
k++;
|
| 125 : |
|
|
infile.open(aVector[k], ios::in);
|
| 126 : |
|
|
handle.checkIfFailure(infile, aVector[k]);
|
| 127 : |
|
|
if (infile.fail())
|
| 128 : |
|
|
this->showCorrectUsage(aVector[k]);
|
| 129 : |
|
|
this->read(incomment);
|
| 130 : |
|
|
infile.close();
|
| 131 : |
|
|
infile.clear();
|
| 132 : |
|
|
|
| 133 : |
|
|
} else if (strcasecmp(aVector[k], "-i") == 0) {
|
| 134 : |
|
|
if (k == aNumber - 1)
|
| 135 : |
|
|
this->showCorrectUsage(aVector[k]);
|
| 136 : |
|
|
k++;
|
| 137 : |
|
|
this->setInitialParamFile(aVector[k]);
|
| 138 : |
|
|
|
| 139 : |
|
|
} else if (strcasecmp(aVector[k], "-o") == 0) {
|
| 140 : |
|
|
if (k == aNumber - 1)
|
| 141 : |
|
|
this->showCorrectUsage(aVector[k]);
|
| 142 : |
|
|
k++;
|
| 143 : |
|
|
printinfo.setOutputFile(aVector[k]);
|
| 144 : |
|
|
|
| 145 : |
|
|
} else if (strcasecmp(aVector[k], "-p") == 0) {
|
| 146 : |
|
|
if (k == aNumber - 1)
|
| 147 : |
|
|
this->showCorrectUsage(aVector[k]);
|
| 148 : |
|
|
k++;
|
| 149 : |
|
|
printinfo.setParamOutFile(aVector[k]);
|
| 150 : |
|
|
|
| 151 : |
|
|
} else if (strcasecmp(aVector[k], "-forceprint") == 0) {
|
| 152 : |
|
|
forceprint = 1;
|
| 153 : |
|
|
|
| 154 : |
|
|
} else if (strcasecmp(aVector[k], "-co") == 0) {
|
| 155 : |
|
|
handle.logMessage(LOGFAIL, "The -co switch is no longer supported");
|
| 156 : |
agomez |
20 |
#ifdef _OPENMP
|
| 157 : |
|
|
} else if (strcasecmp(aVector[k], "-parallel") == 0) {
|
| 158 : |
|
|
handle.logMessage(LOGINFO, "--------parallel option ", aVector[k]);
|
| 159 : |
agomez |
1 |
if (k == aNumber - 1)
|
| 160 : |
|
|
this->showCorrectUsage(aVector[k]);
|
| 161 : |
|
|
k++;
|
| 162 : |
agomez |
20 |
this->setParallel(aVector[k]);
|
| 163 : |
|
|
#endif
|
| 164 : |
agomez |
1 |
|
| 165 : |
|
|
} else if (strcasecmp(aVector[k], "-printfinal") == 0) {
|
| 166 : |
|
|
if (k == aNumber - 1)
|
| 167 : |
|
|
this->showCorrectUsage(aVector[k]);
|
| 168 : |
|
|
k++;
|
| 169 : |
|
|
this->setPrintFinalFile(aVector[k]);
|
| 170 : |
|
|
|
| 171 : |
|
|
} else if (strcasecmp(aVector[k], "-main") == 0) {
|
| 172 : |
|
|
if (k == aNumber - 1)
|
| 173 : |
|
|
this->showCorrectUsage(aVector[k]);
|
| 174 : |
|
|
k++;
|
| 175 : |
|
|
this->setMainGadgetFile(aVector[k]);
|
| 176 : |
|
|
|
| 177 : |
|
|
} else if (strcasecmp(aVector[k], "-opt") == 0) {
|
| 178 : |
|
|
if (k == aNumber - 1)
|
| 179 : |
|
|
this->showCorrectUsage(aVector[k]);
|
| 180 : |
|
|
k++;
|
| 181 : |
|
|
this->setOptInfoFile(aVector[k]);
|
| 182 : |
|
|
|
| 183 : |
|
|
} else if ((strcasecmp(aVector[k], "-printlikelihood") == 0) || (strcasecmp(aVector[k], "-likelihoodprint") == 0)) {
|
| 184 : |
|
|
handle.logMessage(LOGFAIL, "The -printlikelihood switch is no longer supported\nSpecify a likelihoodprinter class in the model print file instead");
|
| 185 : |
|
|
|
| 186 : |
|
|
} else if (strcasecmp(aVector[k], "-printlikesummary") == 0) {
|
| 187 : |
|
|
handle.logMessage(LOGFAIL, "The -printlikesummary switch is no longer supported\nSpecify a likelihoodsummaryprinter class in the model print file instead");
|
| 188 : |
|
|
|
| 189 : |
|
|
} else if (strcasecmp(aVector[k], "-printonelikelihood") == 0) {
|
| 190 : |
|
|
handle.logMessage(LOGFAIL, "The -printonelikelihood switch is no longer supported\nSpecify a likelihoodprinter class in the model print file instead");
|
| 191 : |
|
|
|
| 192 : |
|
|
} else if ((strcasecmp(aVector[k], "-print") == 0) || (strcasecmp(aVector[k], "-print1") == 0)) {
|
| 193 : |
|
|
if (k == aNumber - 1)
|
| 194 : |
|
|
this->showCorrectUsage(aVector[k]);
|
| 195 : |
|
|
k++;
|
| 196 : |
|
|
printinfo.setPrintIteration(atoi(aVector[k]));
|
| 197 : |
|
|
|
| 198 : |
|
|
} else if (strcasecmp(aVector[k], "-precision") == 0) {
|
| 199 : |
|
|
if (k == aNumber - 1)
|
| 200 : |
|
|
this->showCorrectUsage(aVector[k]);
|
| 201 : |
|
|
k++;
|
| 202 : |
|
|
printinfo.setPrecision(atoi(aVector[k]));
|
| 203 : |
|
|
|
| 204 : |
|
|
} else if ((strcasecmp(aVector[k], "-v") == 0) || (strcasecmp(aVector[k], "--version") == 0)) {
|
| 205 : |
|
|
RUNID.Print(cout);
|
| 206 : |
|
|
exit(EXIT_SUCCESS);
|
| 207 : |
|
|
|
| 208 : |
|
|
} else if ((strcasecmp(aVector[k], "-h") == 0) || (strcasecmp(aVector[k], "--help") == 0)) {
|
| 209 : |
|
|
this->showUsage();
|
| 210 : |
|
|
|
| 211 : |
|
|
} else if (strcasecmp(aVector[k], "-log") == 0) {
|
| 212 : |
|
|
if (k == aNumber - 1)
|
| 213 : |
|
|
this->showCorrectUsage(aVector[k]);
|
| 214 : |
|
|
k++;
|
| 215 : |
|
|
handle.setLogFile(aVector[k]);
|
| 216 : |
|
|
printLogLevel = 5;
|
| 217 : |
|
|
|
| 218 : |
|
|
} else if (strcasecmp(aVector[k], "-nowarnings") == 0) {
|
| 219 : |
|
|
//handle.logMessage(LOGWARN, "The -nowarnings switch is no longer supported\nSpecify a logging level using the -loglevel <number> instead");
|
| 220 : |
|
|
printLogLevel = 1;
|
| 221 : |
|
|
|
| 222 : |
|
|
} else if (strcasecmp(aVector[k], "-loglevel") == 0) {
|
| 223 : |
|
|
if (k == aNumber - 1)
|
| 224 : |
|
|
this->showCorrectUsage(aVector[k]);
|
| 225 : |
|
|
k++;
|
| 226 : |
|
|
printLogLevel = atoi(aVector[k]);
|
| 227 : |
|
|
|
| 228 : |
|
|
} else if (strcasecmp(aVector[k], "-noprint") == 0) {
|
| 229 : |
|
|
//JMB disable model printing from the commandline
|
| 230 : |
|
|
runprint = 0;
|
| 231 : |
|
|
|
| 232 : |
|
|
} else if (strcasecmp(aVector[k], "-seed") == 0) {
|
| 233 : |
|
|
//JMB experimental setting of random number seed from the commandline
|
| 234 : |
|
|
//if the "seed" is also specified in the optinfo file then that will override
|
| 235 : |
|
|
//any seed that is specified on the commandline
|
| 236 : |
|
|
if (k == aNumber - 1)
|
| 237 : |
|
|
this->showCorrectUsage(aVector[k]);
|
| 238 : |
|
|
k++;
|
| 239 : |
ulcessvp |
11 |
seed[0] = atoi(aVector[k]);
|
| 240 : |
|
|
srand(seed[0]);
|
| 241 : |
ulcessvp |
12 |
//seedM = seed to set the metropolis acceptance in SA
|
| 242 : |
ulcessvp |
11 |
} else if (strcasecmp(aVector[k], "-seedM") == 0) {
|
| 243 : |
|
|
//JMB experimental setting of random number seed from the commandline
|
| 244 : |
|
|
//if the "seed" is also specified in the optinfo file then that will override
|
| 245 : |
|
|
//any seed that is specified on the commandline
|
| 246 : |
|
|
if (k == aNumber - 1)
|
| 247 : |
|
|
this->showCorrectUsage(aVector[k]);
|
| 248 : |
|
|
k++;
|
| 249 : |
|
|
seed[1] = atoi(aVector[k]);
|
| 250 : |
ulcessvp |
12 |
//seedP = seed to set the orden of evaluation of the parameter in SA
|
| 251 : |
ulcessvp |
11 |
} else if (strcasecmp(aVector[k], "-seedP") == 0) {
|
| 252 : |
|
|
//JMB experimental setting of random number seed from the commandline
|
| 253 : |
|
|
//if the "seed" is also specified in the optinfo file then that will override
|
| 254 : |
|
|
//any seed that is specified on the commandline
|
| 255 : |
|
|
if (k == aNumber - 1)
|
| 256 : |
|
|
this->showCorrectUsage(aVector[k]);
|
| 257 : |
|
|
k++;
|
| 258 : |
|
|
seed[2] = atoi(aVector[k]);
|
| 259 : |
|
|
|
| 260 : |
agomez |
1 |
} else if (strcasecmp(aVector[k], "-maxratio") == 0) {
|
| 261 : |
|
|
//JMB experimental setting of maximum ratio of stock consumed in one timestep
|
| 262 : |
|
|
if (k == aNumber - 1)
|
| 263 : |
|
|
this->showCorrectUsage(aVector[k]);
|
| 264 : |
|
|
k++;
|
| 265 : |
|
|
maxratio = atof(aVector[k]);
|
| 266 : |
|
|
|
| 267 : |
|
|
} else
|
| 268 : |
|
|
this->showCorrectUsage(aVector[k]);
|
| 269 : |
|
|
|
| 270 : |
|
|
k++;
|
| 271 : |
|
|
}
|
| 272 : |
ulcessvp |
11 |
|
| 273 : |
|
|
if (seed[0] == 0) {
|
| 274 : |
|
|
seed[0] = unsigned(time(NULL));
|
| 275 : |
|
|
if (seed[1] == 0)
|
| 276 : |
|
|
seed[1] = unsigned(time(NULL));
|
| 277 : |
|
|
if (seed[2] == 0)
|
| 278 : |
|
|
seed[2] = unsigned(time(NULL));
|
| 279 : |
|
|
} else {
|
| 280 : |
|
|
if (seed[1] == 0)
|
| 281 : |
|
|
seed[1] = seed[0];
|
| 282 : |
|
|
if (seed[2] == 0)
|
| 283 : |
|
|
seed[2] = seed[0];
|
| 284 : |
|
|
}
|
| 285 : |
|
|
|
| 286 : |
|
|
|
| 287 : |
|
|
|
| 288 : |
|
|
|
| 289 : |
agomez |
1 |
}
|
| 290 : |
|
|
|
| 291 : |
|
|
void MainInfo::checkUsage(const char* const inputdir, const char* const workingdir) {
|
| 292 : |
|
|
int check = 0;
|
| 293 : |
|
|
if (runnetwork)
|
| 294 : |
|
|
check = max(0, printLogLevel);
|
| 295 : |
|
|
else if (runstochastic)
|
| 296 : |
|
|
check = max(3, printLogLevel);
|
| 297 : |
|
|
else
|
| 298 : |
|
|
check = max(2, printLogLevel);
|
| 299 : |
|
|
handle.setLogLevel(check);
|
| 300 : |
|
|
|
| 301 : |
|
|
//JMB dont print output if doing a network run
|
| 302 : |
|
|
if (!runnetwork)
|
| 303 : |
|
|
RUNID.Print(cout);
|
| 304 : |
|
|
handle.logMessage(LOGINFO, "Starting Gadget from directory:", workingdir);
|
| 305 : |
|
|
handle.logMessage(LOGINFO, "using data from directory:", inputdir);
|
| 306 : |
|
|
handle.logMessage(LOGMESSAGE, ""); //write a blank line to the log file
|
| 307 : |
|
|
if (strcasecmp(inputdir, workingdir) != 0)
|
| 308 : |
|
|
handle.logMessage(LOGWARN, "Warning - working directory different from input directory");
|
| 309 : |
|
|
|
| 310 : |
|
|
if (runnetwork) {
|
| 311 : |
|
|
handle.logMessage(LOGINFO, "\n** Gadget running in network mode for Paramin **");
|
| 312 : |
|
|
if (printInitialInfo) {
|
| 313 : |
|
|
handle.logMessage(LOGINFO, "Warning - cannot print initial model information");
|
| 314 : |
|
|
printInitialInfo = 0;
|
| 315 : |
|
|
}
|
| 316 : |
|
|
if (printFinalInfo) {
|
| 317 : |
|
|
handle.logMessage(LOGINFO, "Warning - cannot print final model information");
|
| 318 : |
|
|
printFinalInfo = 0;
|
| 319 : |
|
|
}
|
| 320 : |
|
|
}
|
| 321 : |
|
|
|
| 322 : |
|
|
//JMB check to see if we can actually open required files ...
|
| 323 : |
|
|
ifstream tmpin;
|
| 324 : |
|
|
if (chdir(inputdir) != 0)
|
| 325 : |
|
|
handle.logMessage(LOGFAIL, "Error - failed to change input directory to", inputdir);
|
| 326 : |
|
|
if (givenInitialParam) {
|
| 327 : |
|
|
//JMB check to see that the input and output filenames are different
|
| 328 : |
|
|
//Otherwise Gadget will over-write the inputfile with a blank outputfile ...
|
| 329 : |
|
|
if (strcasecmp(strInitialParamFile, printinfo.getParamOutFile()) == 0)
|
| 330 : |
|
|
handle.logFileMessage(LOGFAIL, "the parameter input and output filenames are the same");
|
| 331 : |
|
|
|
| 332 : |
|
|
tmpin.open(strInitialParamFile, ios::in);
|
| 333 : |
|
|
handle.checkIfFailure(tmpin, strInitialParamFile);
|
| 334 : |
|
|
tmpin.close();
|
| 335 : |
|
|
tmpin.clear();
|
| 336 : |
|
|
}
|
| 337 : |
|
|
if (givenOptInfo) {
|
| 338 : |
|
|
tmpin.open(strOptInfoFile, ios::in);
|
| 339 : |
|
|
handle.checkIfFailure(tmpin, strOptInfoFile);
|
| 340 : |
|
|
tmpin.close();
|
| 341 : |
|
|
tmpin.clear();
|
| 342 : |
|
|
}
|
| 343 : |
|
|
ofstream tmpout;
|
| 344 : |
|
|
if (chdir(workingdir) != 0)
|
| 345 : |
|
|
handle.logMessage(LOGFAIL, "Error - failed to change working directory to", workingdir);
|
| 346 : |
|
|
if (printInitialInfo) {
|
| 347 : |
|
|
tmpout.open(strPrintInitialFile, ios::out);
|
| 348 : |
|
|
handle.checkIfFailure(tmpout, strPrintInitialFile);
|
| 349 : |
|
|
tmpout.close();
|
| 350 : |
|
|
tmpout.clear();
|
| 351 : |
|
|
}
|
| 352 : |
|
|
if (printFinalInfo) {
|
| 353 : |
|
|
tmpout.open(strPrintFinalFile, ios::out);
|
| 354 : |
|
|
handle.checkIfFailure(tmpout, strPrintFinalFile);
|
| 355 : |
|
|
tmpout.close();
|
| 356 : |
|
|
tmpout.clear();
|
| 357 : |
|
|
}
|
| 358 : |
|
|
printinfo.checkPrintInfo(runnetwork);
|
| 359 : |
|
|
|
| 360 : |
|
|
//JMB check the value of maxratio
|
| 361 : |
|
|
if ((maxratio < rathersmall) || (maxratio > 1.0)) {
|
| 362 : |
|
|
handle.logMessage(LOGWARN, "Warning - value of maxratio outside bounds", maxratio);
|
| 363 : |
|
|
maxratio = 0.95;
|
| 364 : |
|
|
}
|
| 365 : |
|
|
|
| 366 : |
|
|
if ((!runstochastic) && (runnetwork)) {
|
| 367 : |
|
|
handle.logMessage(LOGWARN, "\nWarning - Gadget for the paramin network should be used with -s option\nGadget will now set the -s switch to perform a simulation run");
|
| 368 : |
|
|
runstochastic = 1;
|
| 369 : |
|
|
}
|
| 370 : |
|
|
|
| 371 : |
|
|
if ((runstochastic) && (runoptimise)) {
|
| 372 : |
|
|
handle.logMessage(LOGWARN, "\nWarning - Gadget has been started with both the -s switch and the -l switch\nHowever, it is not possible to do both a simulation run and a likelihood run!\nGadget will perform only the simulation run (and ignore the -l switch)");
|
| 373 : |
|
|
runoptimise = 0;
|
| 374 : |
|
|
}
|
| 375 : |
|
|
|
| 376 : |
|
|
if ((!runstochastic) && (!runoptimise)) {
|
| 377 : |
|
|
handle.logMessage(LOGWARN, "\nWarning - Gadget has been started without either the -s switch or the -l switch\nGadget will now set the -s switch to perform a simulation run");
|
| 378 : |
|
|
runstochastic = 1;
|
| 379 : |
|
|
}
|
| 380 : |
|
|
|
| 381 : |
|
|
handle.setRunOptimise(runoptimise);
|
| 382 : |
|
|
if ((printLogLevel == 1) && (!runoptimise))
|
| 383 : |
|
|
handle.logMessage(LOGWARN, "\n** Gadget cannot disable warnings for a simulation run **");
|
| 384 : |
|
|
|
| 385 : |
|
|
if ((handle.checkLogFile()) && (runoptimise) && (printLogLevel >= 5))
|
| 386 : |
|
|
handle.logMessage(LOGWARN, "\n** logging model information from a Gadget optimisation is not recommended **");
|
| 387 : |
|
|
|
| 388 : |
|
|
if ((handle.checkLogFile()) && (runnetwork))
|
| 389 : |
|
|
handle.logMessage(LOGWARN, "\n** logging model information from a Gadget network run is not recommended **");
|
| 390 : |
|
|
|
| 391 : |
|
|
//check the printing options
|
| 392 : |
|
|
if (forceprint)
|
| 393 : |
|
|
handle.logMessage(LOGMESSAGE, "\nPrinting model output has been enabled from the command line");
|
| 394 : |
|
|
if (!runprint)
|
| 395 : |
|
|
handle.logMessage(LOGMESSAGE, "\nPrinting model output has been disabled from the command line");
|
| 396 : |
|
|
|
| 397 : |
|
|
check = runprint;
|
| 398 : |
|
|
if (runnetwork)
|
| 399 : |
|
|
check = 0;
|
| 400 : |
|
|
else if ((runoptimise) && (!forceprint))
|
| 401 : |
|
|
check = 0;
|
| 402 : |
|
|
runprint = check;
|
| 403 : |
|
|
|
| 404 : |
|
|
handle.logMessage(LOGMESSAGE, ""); //write blank line to log file
|
| 405 : |
|
|
}
|
| 406 : |
|
|
|
| 407 : |
|
|
void MainInfo::read(CommentStream& infile) {
|
| 408 : |
|
|
int dummy = 0;
|
| 409 : |
|
|
char text[MaxStrLength];
|
| 410 : |
|
|
strncpy(text, "", MaxStrLength);
|
| 411 : |
|
|
infile >> ws;
|
| 412 : |
|
|
while (!infile.eof()) {
|
| 413 : |
|
|
infile >> text >> ws;
|
| 414 : |
|
|
|
| 415 : |
|
|
if (strcasecmp(text, "-i") == 0) {
|
| 416 : |
|
|
infile >> text >> ws;
|
| 417 : |
|
|
this->setInitialParamFile(text);
|
| 418 : |
|
|
} else if (strcasecmp(text, "-o") == 0) {
|
| 419 : |
|
|
infile >> text >> ws;
|
| 420 : |
|
|
printinfo.setOutputFile(text);
|
| 421 : |
|
|
} else if (strcasecmp(text, "-co") == 0) {
|
| 422 : |
|
|
handle.logMessage(LOGFAIL, "The -co switch is no longer supported");
|
| 423 : |
|
|
} else if (strcasecmp(text, "-p") == 0) {
|
| 424 : |
|
|
infile >> text >> ws;
|
| 425 : |
|
|
printinfo.setParamOutFile(text);
|
| 426 : |
|
|
} else if (strcasecmp(text, "-main") == 0) {
|
| 427 : |
|
|
infile >> text >> ws;
|
| 428 : |
|
|
this->setMainGadgetFile(text);
|
| 429 : |
|
|
} else if (strcasecmp(text, "-printinitial") == 0) {
|
| 430 : |
|
|
infile >> text >> ws;
|
| 431 : |
|
|
this->setPrintInitialFile(text);
|
| 432 : |
|
|
} else if (strcasecmp(text, "-printfinal") == 0) {
|
| 433 : |
|
|
infile >> text >> ws;
|
| 434 : |
|
|
this->setPrintFinalFile(text);
|
| 435 : |
agomez |
20 |
#ifdef _OPENMP
|
| 436 : |
|
|
} else if (strcasecmp(text, "-parallel") == 0) {
|
| 437 : |
|
|
infile >> text >> ws;
|
| 438 : |
|
|
handle.logMessage(LOGINFO, "--------parallel option 222 ", text);
|
| 439 : |
|
|
this->setParallel(text);
|
| 440 : |
|
|
#endif
|
| 441 : |
agomez |
1 |
} else if (strcasecmp(text, "-opt") == 0) {
|
| 442 : |
|
|
infile >> text >> ws;
|
| 443 : |
|
|
this->setOptInfoFile(text);
|
| 444 : |
|
|
} else if (strcasecmp(text, "-forceprint") == 0) {
|
| 445 : |
|
|
forceprint = 1;
|
| 446 : |
|
|
} else if (strcasecmp(text, "-noprint") == 0) {
|
| 447 : |
|
|
runprint = 0;
|
| 448 : |
|
|
} else if ((strcasecmp(text, "-print") == 0) || (strcasecmp(text, "-print1") == 0)) {
|
| 449 : |
|
|
infile >> dummy >> ws;
|
| 450 : |
|
|
printinfo.setPrintIteration(dummy);
|
| 451 : |
|
|
} else if (strcasecmp(text, "-precision") == 0) {
|
| 452 : |
|
|
infile >> dummy >> ws;
|
| 453 : |
|
|
printinfo.setPrecision(dummy);
|
| 454 : |
|
|
} else if (strcasecmp(text, "-log") == 0) {
|
| 455 : |
|
|
infile >> text >> ws;
|
| 456 : |
|
|
handle.setLogFile(text);
|
| 457 : |
|
|
printLogLevel = 5;
|
| 458 : |
|
|
} else if (strcasecmp(text, "-nowarnings") == 0) {
|
| 459 : |
|
|
printLogLevel = 1;
|
| 460 : |
|
|
} else if (strcasecmp(text, "-loglevel") == 0) {
|
| 461 : |
|
|
infile >> printLogLevel >> ws;
|
| 462 : |
|
|
} else if (strcasecmp(text, "-seed") == 0) {
|
| 463 : |
|
|
infile >> dummy >> ws;
|
| 464 : |
|
|
srand(dummy);
|
| 465 : |
|
|
} else if (strcasecmp(text, "-maxratio") == 0) {
|
| 466 : |
|
|
infile >> maxratio >> ws;
|
| 467 : |
|
|
} else if (strcasecmp(text, "-printlikesummary") == 0) {
|
| 468 : |
|
|
handle.logMessage(LOGWARN, "The -printlikesummary switch is no longer supported\nSpecify a likelihoodsummaryprinter class in the model print file instead");
|
| 469 : |
|
|
} else if (strcasecmp(text, "-printlikelihood") == 0) {
|
| 470 : |
|
|
handle.logMessage(LOGWARN, "The -printlikelihood switch is no longer supported\nSpecify a likelihoodprinter class in the model print file instead");
|
| 471 : |
|
|
} else if (strcasecmp(text, "-printonelikelihood") == 0) {
|
| 472 : |
|
|
handle.logMessage(LOGWARN, "The -printonelikelihood switch is no longer supported\nSpecify a likelihoodprinter class in the model print file instead");
|
| 473 : |
|
|
} else
|
| 474 : |
|
|
this->showCorrectUsage(text);
|
| 475 : |
|
|
}
|
| 476 : |
|
|
}
|
| 477 : |
|
|
|
| 478 : |
|
|
void MainInfo::setPrintInitialFile(char* filename) {
|
| 479 : |
|
|
if (strPrintInitialFile != NULL) {
|
| 480 : |
|
|
delete[] strPrintInitialFile;
|
| 481 : |
|
|
strPrintInitialFile = NULL;
|
| 482 : |
|
|
}
|
| 483 : |
|
|
strPrintInitialFile = new char[strlen(filename) + 1];
|
| 484 : |
|
|
strcpy(strPrintInitialFile, filename);
|
| 485 : |
|
|
printInitialInfo = 1;
|
| 486 : |
|
|
}
|
| 487 : |
|
|
|
| 488 : |
|
|
void MainInfo::setPrintFinalFile(char* filename) {
|
| 489 : |
|
|
if (strPrintFinalFile != NULL) {
|
| 490 : |
|
|
delete[] strPrintFinalFile;
|
| 491 : |
|
|
strPrintFinalFile = NULL;
|
| 492 : |
|
|
}
|
| 493 : |
|
|
strPrintFinalFile = new char[strlen(filename) + 1];
|
| 494 : |
|
|
strcpy(strPrintFinalFile, filename);
|
| 495 : |
|
|
printFinalInfo = 1;
|
| 496 : |
|
|
}
|
| 497 : |
agomez |
20 |
#ifdef _OPENMP
|
| 498 : |
|
|
void MainInfo::setParallel(char* filename) {
|
| 499 : |
|
|
if (!strcasecmp(filename,"spe")){
|
| 500 : |
|
|
runparallel=1;
|
| 501 : |
|
|
handle.logMessage(LOGINFO, "--------parallel speculative ", filename);
|
| 502 : |
|
|
return;
|
| 503 : |
|
|
}
|
| 504 : |
|
|
if (!strcasecmp(filename,"rep")){
|
| 505 : |
|
|
handle.logMessage(LOGINFO, "--------parallel reproducible ", filename);
|
| 506 : |
|
|
runparallel=2;
|
| 507 : |
|
|
return;
|
| 508 : |
|
|
}
|
| 509 : |
|
|
this->showCorrectUsage("opt");
|
| 510 : |
|
|
|
| 511 : |
|
|
}
|
| 512 : |
|
|
#endif
|
| 513 : |
agomez |
1 |
|
| 514 : |
|
|
void MainInfo::setMainGadgetFile(char* filename) {
|
| 515 : |
|
|
if (strMainGadgetFile != NULL) {
|
| 516 : |
|
|
delete[] strMainGadgetFile;
|
| 517 : |
|
|
strMainGadgetFile = NULL;
|
| 518 : |
|
|
}
|
| 519 : |
|
|
strMainGadgetFile = new char[strlen(filename) + 1];
|
| 520 : |
|
|
strcpy(strMainGadgetFile, filename);
|
| 521 : |
|
|
}
|
| 522 : |
|
|
|
| 523 : |
|
|
void MainInfo::setInitialParamFile(char* filename) {
|
| 524 : |
|
|
if (strInitialParamFile != NULL) {
|
| 525 : |
|
|
delete[] strInitialParamFile;
|
| 526 : |
|
|
strInitialParamFile = NULL;
|
| 527 : |
|
|
}
|
| 528 : |
|
|
strInitialParamFile = new char[strlen(filename) + 1];
|
| 529 : |
|
|
strcpy(strInitialParamFile, filename);
|
| 530 : |
|
|
givenInitialParam = 1;
|
| 531 : |
|
|
}
|
| 532 : |
|
|
|
| 533 : |
|
|
void MainInfo::setOptInfoFile(char* filename) {
|
| 534 : |
|
|
if (strOptInfoFile != NULL) {
|
| 535 : |
|
|
delete[] strOptInfoFile;
|
| 536 : |
|
|
strOptInfoFile = NULL;
|
| 537 : |
|
|
}
|
| 538 : |
|
|
strOptInfoFile = new char[strlen(filename) + 1];
|
| 539 : |
|
|
strcpy(strOptInfoFile, filename);
|
| 540 : |
|
|
givenOptInfo = 1;
|
| 541 : |
|
|
}
|
Parent Directory
Revision Log