#include "maininfo.h"
#include "errorhandler.h"
#include "gadget.h"
#include "runid.h"
#include "global.h"
void MainInfo::showCorrectUsage(char* error) {
RUNID.Print(cerr);
cerr << "\nError in command line value - unrecognised option " << error << endl
<< "Common options are -l or -s, -i <filename> -o <filename>\n"
<< "For more information try running Gadget with the -h switch\n";
exit(EXIT_FAILURE);
}
void MainInfo::showUsage() {
RUNID.Print(cout);
cout << "\nOptions for running Gadget:\n"
<< " -l perform a likelihood (optimising) model run\n"
<< " -s perform a single (simulation) model run\n"
<< " -n perform a network run (using paramin)\n"
<< " -v --version display version information and exit\n"
<< " -h --help display this help screen and exit\n"
<< "\nOptions for specifying the input to Gadget models:\n"
<< " -i <filename> read model parameters from <filename>\n"
<< " -opt <filename> read optimising parameters from <filename>\n"
<< " -main <filename> read model information from <filename>\n"
<< " (default filename is 'main')\n"
<< " -m <filename> read other commandline parameters from <filename>\n"
<< "\nOptions for specifying the output from Gadget models:\n"
<< " -p <filename> print final model parameters to <filename>\n"
<< " (default filename is 'params.out')\n"
<< " -o <filename> print likelihood output to <filename>\n"
<< " -print <number> print -o output every <number> iterations\n"
<< " -precision <number> set the precision to <number> in output files\n"
<< "\nOptions for debugging Gadget models:\n"
<< " -log <filename> print logging information to <filename>\n"
<< " -printinitial <filename> print initial model information to <filename>\n"
<< " -printfinal <filename> print final model information to <filename>\n"
<< "\nFor more information see the Gadget web page at http://www.hafro.is/gadget\n\n";
exit(EXIT_SUCCESS);
}
MainInfo::MainInfo()
: givenOptInfo(0), givenInitialParam(0), runoptimise(0),
runstochastic(0), runnetwork(0), runprint(1), forceprint(0),
printInitialInfo(0), printFinalInfo(0), printLogLevel(0), maxratio(0.95) {
char tmpname[10];
strncpy(tmpname, "", 10);
strcpy(tmpname, "main");
strOptInfoFile = NULL;
strInitialParamFile = NULL;
strPrintInitialFile = NULL;
strPrintFinalFile = NULL;
strMainGadgetFile = NULL;
setMainGadgetFile(tmpname);
}
MainInfo::~MainInfo() {
if (strOptInfoFile != NULL) {
delete[] strOptInfoFile;
strOptInfoFile = NULL;
}
if (strInitialParamFile != NULL) {
delete[] strInitialParamFile;
strInitialParamFile = NULL;
}
if (strPrintInitialFile != NULL) {
delete[] strPrintInitialFile;
strPrintInitialFile = NULL;
}
if (strPrintFinalFile != NULL) {
delete[] strPrintFinalFile;
strPrintFinalFile = NULL;
}
if (strMainGadgetFile != NULL) {
delete[] strMainGadgetFile;
strMainGadgetFile = NULL;
}
if (seed != NULL) {
delete[] seed;
seed = NULL;
}
}
void MainInfo::read(int aNumber, char* const aVector[]) {
if (aNumber == 1) {
handle.logMessage(LOGWARN, "Warning - no command line options specified, using default values");
return;
}
seed = new unsigned[3];
seed[0] = 0;
seed[1] = 0;
seed[2] = 0;
int k = 1;
while (k < aNumber) {
if (strcasecmp(aVector[k], "-l") == 0) {
runoptimise = 1;
} else if (strcasecmp(aVector[k], "-n") == 0) {
runnetwork = 1;
#ifndef GADGET_NETWORK
handle.logMessage(LOGFAIL, "Error - Gadget cannot currently run in network mode for paramin\nGadget must be recompiled to enable the network communication");
#endif
} else if (strcasecmp(aVector[k], "-s") == 0) {
runstochastic = 1;
} else if (strcasecmp(aVector[k], "-m") == 0) {
ifstream infile;
CommentStream incomment(infile);
if (k == aNumber - 1)
this->showCorrectUsage(aVector[k]);
k++;
infile.open(aVector[k], ios::in);
handle.checkIfFailure(infile, aVector[k]);
if (infile.fail())
this->showCorrectUsage(aVector[k]);
this->read(incomment);
infile.close();
infile.clear();
} else if (strcasecmp(aVector[k], "-i") == 0) {
if (k == aNumber - 1)
this->showCorrectUsage(aVector[k]);
k++;
this->setInitialParamFile(aVector[k]);
} else if (strcasecmp(aVector[k], "-o") == 0) {
if (k == aNumber - 1)
this->showCorrectUsage(aVector[k]);
k++;
printinfo.setOutputFile(aVector[k]);
} else if (strcasecmp(aVector[k], "-p") == 0) {
if (k == aNumber - 1)
this->showCorrectUsage(aVector[k]);
k++;
printinfo.setParamOutFile(aVector[k]);
} else if (strcasecmp(aVector[k], "-forceprint") == 0) {
forceprint = 1;
} else if (strcasecmp(aVector[k], "-co") == 0) {
handle.logMessage(LOGFAIL, "The -co switch is no longer supported");
} else if (strcasecmp(aVector[k], "-printinitial") == 0) {
if (k == aNumber - 1)
this->showCorrectUsage(aVector[k]);
k++;
this->setPrintInitialFile(aVector[k]);
} else if (strcasecmp(aVector[k], "-printfinal") == 0) {
if (k == aNumber - 1)
this->showCorrectUsage(aVector[k]);
k++;
this->setPrintFinalFile(aVector[k]);
} else if (strcasecmp(aVector[k], "-main") == 0) {
if (k == aNumber - 1)
this->showCorrectUsage(aVector[k]);
k++;
this->setMainGadgetFile(aVector[k]);
} else if (strcasecmp(aVector[k], "-opt") == 0) {
if (k == aNumber - 1)
this->showCorrectUsage(aVector[k]);
k++;
this->setOptInfoFile(aVector[k]);
} else if ((strcasecmp(aVector[k], "-printlikelihood") == 0) || (strcasecmp(aVector[k], "-likelihoodprint") == 0)) {
handle.logMessage(LOGFAIL, "The -printlikelihood switch is no longer supported\nSpecify a likelihoodprinter class in the model print file instead");
} else if (strcasecmp(aVector[k], "-printlikesummary") == 0) {
handle.logMessage(LOGFAIL, "The -printlikesummary switch is no longer supported\nSpecify a likelihoodsummaryprinter class in the model print file instead");
} else if (strcasecmp(aVector[k], "-printonelikelihood") == 0) {
handle.logMessage(LOGFAIL, "The -printonelikelihood switch is no longer supported\nSpecify a likelihoodprinter class in the model print file instead");
} else if ((strcasecmp(aVector[k], "-print") == 0) || (strcasecmp(aVector[k], "-print1") == 0)) {
if (k == aNumber - 1)
this->showCorrectUsage(aVector[k]);
k++;
printinfo.setPrintIteration(atoi(aVector[k]));
} else if (strcasecmp(aVector[k], "-precision") == 0) {
if (k == aNumber - 1)
this->showCorrectUsage(aVector[k]);
k++;
printinfo.setPrecision(atoi(aVector[k]));
} else if ((strcasecmp(aVector[k], "-v") == 0) || (strcasecmp(aVector[k], "--version") == 0)) {
RUNID.Print(cout);
exit(EXIT_SUCCESS);
} else if ((strcasecmp(aVector[k], "-h") == 0) || (strcasecmp(aVector[k], "--help") == 0)) {
this->showUsage();
} else if (strcasecmp(aVector[k], "-log") == 0) {
if (k == aNumber - 1)
this->showCorrectUsage(aVector[k]);
k++;
handle.setLogFile(aVector[k]);
printLogLevel = 5;
} else if (strcasecmp(aVector[k], "-nowarnings") == 0) {
//handle.logMessage(LOGWARN, "The -nowarnings switch is no longer supported\nSpecify a logging level using the -loglevel <number> instead");
printLogLevel = 1;
} else if (strcasecmp(aVector[k], "-loglevel") == 0) {
if (k == aNumber - 1)
this->showCorrectUsage(aVector[k]);
k++;
printLogLevel = atoi(aVector[k]);
} else if (strcasecmp(aVector[k], "-noprint") == 0) {
//JMB disable model printing from the commandline
runprint = 0;
} else if (strcasecmp(aVector[k], "-seed") == 0) {
//JMB experimental setting of random number seed from the commandline
//if the "seed" is also specified in the optinfo file then that will override
//any seed that is specified on the commandline
if (k == aNumber - 1)
this->showCorrectUsage(aVector[k]);
k++;
seed[0] = atoi(aVector[k]);
srand(seed[0]);
//seedM = seed to set the metropolis acceptance in SA
} else if (strcasecmp(aVector[k], "-seedM") == 0) {
//JMB experimental setting of random number seed from the commandline
//if the "seed" is also specified in the optinfo file then that will override
//any seed that is specified on the commandline
if (k == aNumber - 1)
this->showCorrectUsage(aVector[k]);
k++;
seed[1] = atoi(aVector[k]);
//seedP = seed to set the orden of evaluation of the parameter in SA
} else if (strcasecmp(aVector[k], "-seedP") == 0) {
//JMB experimental setting of random number seed from the commandline
//if the "seed" is also specified in the optinfo file then that will override
//any seed that is specified on the commandline
if (k == aNumber - 1)
this->showCorrectUsage(aVector[k]);
k++;
seed[2] = atoi(aVector[k]);
} else if (strcasecmp(aVector[k], "-maxratio") == 0) {
//JMB experimental setting of maximum ratio of stock consumed in one timestep
if (k == aNumber - 1)
this->showCorrectUsage(aVector[k]);
k++;
maxratio = atof(aVector[k]);
} else
this->showCorrectUsage(aVector[k]);
k++;
}
if (seed[0] == 0) {
seed[0] = unsigned(time(NULL));
if (seed[1] == 0)
seed[1] = unsigned(time(NULL));
if (seed[2] == 0)
seed[2] = unsigned(time(NULL));
} else {
if (seed[1] == 0)
seed[1] = seed[0];
if (seed[2] == 0)
seed[2] = seed[0];
}
}
void MainInfo::checkUsage(const char* const inputdir, const char* const workingdir) {
int check = 0;
if (runnetwork)
check = max(0, printLogLevel);
else if (runstochastic)
check = max(3, printLogLevel);
else
check = max(2, printLogLevel);
handle.setLogLevel(check);
//JMB dont print output if doing a network run
if (!runnetwork)
RUNID.Print(cout);
handle.logMessage(LOGINFO, "Starting Gadget from directory:", workingdir);
handle.logMessage(LOGINFO, "using data from directory:", inputdir);
handle.logMessage(LOGMESSAGE, ""); //write a blank line to the log file
if (strcasecmp(inputdir, workingdir) != 0)
handle.logMessage(LOGWARN, "Warning - working directory different from input directory");
if (runnetwork) {
handle.logMessage(LOGINFO, "\n** Gadget running in network mode for Paramin **");
if (printInitialInfo) {
handle.logMessage(LOGINFO, "Warning - cannot print initial model information");
printInitialInfo = 0;
}
if (printFinalInfo) {
handle.logMessage(LOGINFO, "Warning - cannot print final model information");
printFinalInfo = 0;
}
}
//JMB check to see if we can actually open required files ...
ifstream tmpin;
if (chdir(inputdir) != 0)
handle.logMessage(LOGFAIL, "Error - failed to change input directory to", inputdir);
if (givenInitialParam) {
//JMB check to see that the input and output filenames are different
//Otherwise Gadget will over-write the inputfile with a blank outputfile ...
if (strcasecmp(strInitialParamFile, printinfo.getParamOutFile()) == 0)
handle.logFileMessage(LOGFAIL, "the parameter input and output filenames are the same");
tmpin.open(strInitialParamFile, ios::in);
handle.checkIfFailure(tmpin, strInitialParamFile);
tmpin.close();
tmpin.clear();
}
if (givenOptInfo) {
tmpin.open(strOptInfoFile, ios::in);
handle.checkIfFailure(tmpin, strOptInfoFile);
tmpin.close();
tmpin.clear();
}
ofstream tmpout;
if (chdir(workingdir) != 0)
handle.logMessage(LOGFAIL, "Error - failed to change working directory to", workingdir);
if (printInitialInfo) {
tmpout.open(strPrintInitialFile, ios::out);
handle.checkIfFailure(tmpout, strPrintInitialFile);
tmpout.close();
tmpout.clear();
}
if (printFinalInfo) {
tmpout.open(strPrintFinalFile, ios::out);
handle.checkIfFailure(tmpout, strPrintFinalFile);
tmpout.close();
tmpout.clear();
}
printinfo.checkPrintInfo(runnetwork);
//JMB check the value of maxratio
if ((maxratio < rathersmall) || (maxratio > 1.0)) {
handle.logMessage(LOGWARN, "Warning - value of maxratio outside bounds", maxratio);
maxratio = 0.95;
}
if ((!runstochastic) && (runnetwork)) {
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");
runstochastic = 1;
}
if ((runstochastic) && (runoptimise)) {
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)");
runoptimise = 0;
}
if ((!runstochastic) && (!runoptimise)) {
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");
runstochastic = 1;
}
handle.setRunOptimise(runoptimise);
if ((printLogLevel == 1) && (!runoptimise))
handle.logMessage(LOGWARN, "\n** Gadget cannot disable warnings for a simulation run **");
if ((handle.checkLogFile()) && (runoptimise) && (printLogLevel >= 5))
handle.logMessage(LOGWARN, "\n** logging model information from a Gadget optimisation is not recommended **");
if ((handle.checkLogFile()) && (runnetwork))
handle.logMessage(LOGWARN, "\n** logging model information from a Gadget network run is not recommended **");
//check the printing options
if (forceprint)
handle.logMessage(LOGMESSAGE, "\nPrinting model output has been enabled from the command line");
if (!runprint)
handle.logMessage(LOGMESSAGE, "\nPrinting model output has been disabled from the command line");
check = runprint;
if (runnetwork)
check = 0;
else if ((runoptimise) && (!forceprint))
check = 0;
runprint = check;
handle.logMessage(LOGMESSAGE, ""); //write blank line to log file
}
void MainInfo::read(CommentStream& infile) {
int dummy = 0;
char text[MaxStrLength];
strncpy(text, "", MaxStrLength);
infile >> ws;
while (!infile.eof()) {
infile >> text >> ws;
if (strcasecmp(text, "-i") == 0) {
infile >> text >> ws;
this->setInitialParamFile(text);
} else if (strcasecmp(text, "-o") == 0) {
infile >> text >> ws;
printinfo.setOutputFile(text);
} else if (strcasecmp(text, "-co") == 0) {
handle.logMessage(LOGFAIL, "The -co switch is no longer supported");
} else if (strcasecmp(text, "-p") == 0) {
infile >> text >> ws;
printinfo.setParamOutFile(text);
} else if (strcasecmp(text, "-main") == 0) {
infile >> text >> ws;
this->setMainGadgetFile(text);
} else if (strcasecmp(text, "-printinitial") == 0) {
infile >> text >> ws;
this->setPrintInitialFile(text);
} else if (strcasecmp(text, "-printfinal") == 0) {
infile >> text >> ws;
this->setPrintFinalFile(text);
} else if (strcasecmp(text, "-opt") == 0) {
infile >> text >> ws;
this->setOptInfoFile(text);
} else if (strcasecmp(text, "-forceprint") == 0) {
forceprint = 1;
} else if (strcasecmp(text, "-noprint") == 0) {
runprint = 0;
} else if ((strcasecmp(text, "-print") == 0) || (strcasecmp(text, "-print1") == 0)) {
infile >> dummy >> ws;
printinfo.setPrintIteration(dummy);
} else if (strcasecmp(text, "-precision") == 0) {
infile >> dummy >> ws;
printinfo.setPrecision(dummy);
} else if (strcasecmp(text, "-log") == 0) {
infile >> text >> ws;
handle.setLogFile(text);
printLogLevel = 5;
} else if (strcasecmp(text, "-nowarnings") == 0) {
printLogLevel = 1;
} else if (strcasecmp(text, "-loglevel") == 0) {
infile >> printLogLevel >> ws;
} else if (strcasecmp(text, "-seed") == 0) {
infile >> dummy >> ws;
srand(dummy);
} else if (strcasecmp(text, "-maxratio") == 0) {
infile >> maxratio >> ws;
} else if (strcasecmp(text, "-printlikesummary") == 0) {
handle.logMessage(LOGWARN, "The -printlikesummary switch is no longer supported\nSpecify a likelihoodsummaryprinter class in the model print file instead");
} else if (strcasecmp(text, "-printlikelihood") == 0) {
handle.logMessage(LOGWARN, "The -printlikelihood switch is no longer supported\nSpecify a likelihoodprinter class in the model print file instead");
} else if (strcasecmp(text, "-printonelikelihood") == 0) {
handle.logMessage(LOGWARN, "The -printonelikelihood switch is no longer supported\nSpecify a likelihoodprinter class in the model print file instead");
} else
this->showCorrectUsage(text);
}
}
void MainInfo::setPrintInitialFile(char* filename) {
if (strPrintInitialFile != NULL) {
delete[] strPrintInitialFile;
strPrintInitialFile = NULL;
}
strPrintInitialFile = new char[strlen(filename) + 1];
strcpy(strPrintInitialFile, filename);
printInitialInfo = 1;
}
void MainInfo::setPrintFinalFile(char* filename) {
if (strPrintFinalFile != NULL) {
delete[] strPrintFinalFile;
strPrintFinalFile = NULL;
}
strPrintFinalFile = new char[strlen(filename) + 1];
strcpy(strPrintFinalFile, filename);
printFinalInfo = 1;
}
void MainInfo::setMainGadgetFile(char* filename) {
if (strMainGadgetFile != NULL) {
delete[] strMainGadgetFile;
strMainGadgetFile = NULL;
}
strMainGadgetFile = new char[strlen(filename) + 1];
strcpy(strMainGadgetFile, filename);
}
void MainInfo::setInitialParamFile(char* filename) {
if (strInitialParamFile != NULL) {
delete[] strInitialParamFile;
strInitialParamFile = NULL;
}
strInitialParamFile = new char[strlen(filename) + 1];
strcpy(strInitialParamFile, filename);
givenInitialParam = 1;
}
void MainInfo::setOptInfoFile(char* filename) {
if (strOptInfoFile != NULL) {
delete[] strOptInfoFile;
strOptInfoFile = NULL;
}
strOptInfoFile = new char[strlen(filename) + 1];
strcpy(strOptInfoFile, filename);
givenOptInfo = 1;
}
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