BinaryDataSaver Class Reference

A class to handle simulation data saving in binary format. More...

#include <binarydatasaver.h>

Inheritance diagram for BinaryDataSaver:

Collaboration diagram for BinaryDataSaver:

Public Member Functions
	BinaryDataSaver ()
	~BinaryDataSaver ()
void	printData ()
virtual bool	setParameters ()
virtual void	execute ()
virtual BinaryDataSaver *	clone ()
virtual vector< string >	ifExist ()
virtual void	FHwrite ()
virtual void	FHread (string &filename)
virtual void	loadFileServices (FileServices *loader)
virtual void	loadStatServices (StatServices *loader)
virtual bool	resetParameterFromSource (std::string param, SimComponent *cmpt)
virtual age_t	removeAgeClass ()
virtual age_t	addAgeClass ()
virtual age_t	requiredAgeClass ()
Public Member Functions inherited from LifeCycleEvent
	LifeCycleEvent (const char *name, const char *trait_link)
	Cstor. More...
virtual	~LifeCycleEvent ()
virtual void	init (Metapop *popPtr)
	Sets the pointer to the current Metapop and the trait link if applicable. More...
virtual bool	attach_trait (string trait)
virtual void	set_paramset (std::string name, bool required, SimComponent *owner)
virtual void	set_event_name (std::string &name)
	Set the name of the event (name of the ParamSet) and add the corresponding parameter to the set. More...
virtual void	set_event_name (const char *name)
virtual string &	get_event_name ()
	Accessor to the LCE's name. More...
virtual int	get_rank ()
	Accessor to the LCE rank in the life cycle. More...
virtual void	set_pop_ptr (Metapop *popPtr)
	Accessors for the population pointer. More...
virtual Metapop *	get_pop_ptr ()
Public Member Functions inherited from SimComponent
	SimComponent ()
virtual	~SimComponent ()
virtual void	loadUpdaters (UpdaterServices *loader)
	Loads the parameters and component updater onto the updater manager. More...
virtual void	set_paramset (ParamSet *paramset)
	Sets the ParamSet member. More...
virtual void	set_paramsetFromCopy (const ParamSet &PSet)
	Reset the set of parameters from a another set. More...
virtual ParamSet *	get_paramset ()
	ParamSet accessor. More...
virtual void	add_parameter (Param *param)
	Interface to add a parameter to the set. More...
virtual void	add_parameter (std::string Name, param_t Type, bool isRequired, bool isBounded, double low_bnd, double up_bnd)
	Interface to add a parameter to the set. More...
virtual void	add_parameter (std::string Name, param_t Type, bool isRequired, bool isBounded, double low_bnd, double up_bnd, ParamUpdaterBase *updater)
	Interface to add a parameter and its updater to the set. More...
virtual Param *	get_parameter (std::string name)
	Param getter. More...
virtual double	get_parameter_value (std::string name)
	Param value getter. More...
virtual string	get_name ()
	Returnd the name of the ParamSet, i.e. More...
virtual bool	has_parameter (std::string name)
	Param getter. More...
Public Member Functions inherited from FileHandler
	FileHandler (const char *ext)
virtual	~FileHandler ()
virtual void	init ()
	Called by notifier during simulation setup, performs file checking. More...
virtual vector< string >	ifExist ()
	Checks if any file associated with the current file name already exists on disk. More...
virtual void	set (bool rpl_per, bool gen_per, int rpl_occ, int gen_occ, int rank, string path)
	Sets the hanlder parameters. More...
virtual void	set_multi (bool rpl_per, bool gen_per, int rpl_occ, TMatrix *Occ, string path)
virtual void	FHwrite ()=0
	Default behavior of the class, called by Handler::update(). More...
virtual void	FHread (string &filename)=0
	Default input function. More...
virtual void	update ()
	Updates the inner replicate and generation counters and calls FHwrite if needed by the the periodicity of the file. More...
Metapop *	get_pop_ptr ()
	Returns the pointer to the current metapop through the FileServices interface. More...
void	set_pop_ptr (Metapop *pop_ptr)
FileServices *	get_service ()
	Returns pointer to the FileServices. More...
void	set_service (FileServices *srv)
std::string &	get_path ()
void	set_path ()
std::string &	get_extension ()
void	set_extension (const char *ext)
std::string &	get_filename ()
	Builds and returns the current file name depending on the periodicity of the file. More...
bool	get_isInputHandler ()
void	set_isInputHandler (bool val)
bool	get_isReplicatePeriodic ()
void	set_isReplicatePeriodic (bool val)
unsigned int	get_ReplicateOccurrence ()
void	set_ReplicateOccurrence (unsigned int val)
bool	get_isGenerationPeriodic ()
void	set_isGenerationPeriodic (bool val)
unsigned int	get_GenerationOccurrence ()
void	set_GenerationOccurrence (unsigned int val)
unsigned int	get_ExecRank ()
	unused yet... More...
void	set_ExecRank (int val)
TMatrix *	get_OccMatrix ()
void	set_OccMatrix (TMatrix *occ)
bool	get_isMasterExec ()
void	set_isMasterExec (bool is)
Public Member Functions inherited from Handler
virtual void	init ()=0
	Inits state. More...
virtual void	update ()=0
	Updates the handler state. More...
virtual	~Handler ()

Static Public Attributes
static pid_t	PID = 0

Private Member Functions
void	setFileDescriptor ()
int	getFileDescriptor ()
void	printHeader ()
void	storeData ()
void	printOffsetTable ()
void	finish ()

Private Attributes
BinaryStorageBuffer	_buff
std::string	_comp_cmd
std::string	_comp_ext
std::string	_uncomp_cmd
std::string	_tar_cmd
std::string	_tar_ext
std::string	_dir
bool	_isPeriodic
unsigned int	_generation
off_t	_offsetDataStart
vector< unsigned int >	_occurrences
vector< unsignedint >::const_iterator	_current_occurrence
int	_fdesc

Additional Inherited Members
Protected Attributes inherited from LifeCycleEvent
std::string	_event_name
	The param name to be read in the init file. More...
Metapop *	_popPtr
	The ptr to the current Metapop. More...
std::string	_LCELinkedTraitType
	The name of the linked trait. More...
int	_LCELinkedTraitIndex
	The index in the individual's trait table of the linked trait. More...
Protected Attributes inherited from SimComponent
ParamSet *	_paramSet
	The parameters container. More...
Protected Attributes inherited from FileHandler
Metapop *	_pop
	Pointer to the current metapop, set during initialization within the init function. More...

Detailed Description

A class to handle simulation data saving in binary format.

It is both an LCE and a FileHandler but the writing is executed through the LCE interface (i.e. LifeCycleEvent::execute()). Its inheritance from the FileHandler class is used to access the basic file services (i.e. basename and current replicate filename, etc.).

Constructor & Destructor Documentation

BinaryDataSaver()

BinaryDataSaver::BinaryDataSaver

(

)

: LifeCycleEvent("store",""), FileHandler(".bin"), _isPeriodic(0)
{
  ParamUpdater< BinaryDataSaver > * updater =
  new ParamUpdater< BinaryDataSaver > (&BinaryDataSaver::setParameters);
 
  add_parameter("store_generation",INT,true,false,0,0,updater);
  add_parameter("store_recursive",BOOL,false,false,0,0,updater);
  add_parameter("store_dir",STR,false,false,0,0,updater);
  add_parameter("store_nocompress",BOOL,false,false,0,0,updater);
  add_parameter("store_noarchive",BOOL,false,false,0,0,updater);
  add_parameter("store_compress_cmde",STR,false,false,0,0,updater);
  add_parameter("store_compress_extension",STR,false,false,0,0,updater);
  add_parameter("store_uncompress_cmde",STR,false,false,0,0,updater);
  add_parameter("store_archive_cmde",STR,false,false,0,0,updater);
  add_parameter("store_archive_extension",STR,false,false,0,0,updater);
}

References SimComponent::add_parameter(), BOOL, INT, setParameters(), and STR.

Referenced by clone().

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~BinaryDataSaver()

BinaryDataSaver::~BinaryDataSaver ( )

inline

{}

Member Function Documentation

addAgeClass()

virtual age_t BinaryDataSaver::addAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

clone()

virtual BinaryDataSaver * BinaryDataSaver::clone ( )

inlinevirtual

Implements LifeCycleEvent.

{return new BinaryDataSaver();}

References BinaryDataSaver().

execute()

void BinaryDataSaver::execute ( )

virtual

Implements LifeCycleEvent.

{
  //set the buffer ready to be filled
  if(_popPtr->getCurrentGeneration() == 1) {
      _current_occurrence = _occurrences.begin();
  }
 
  if( _popPtr->getCurrentGeneration() == *_current_occurrence ) {
 
      _buff.set_buff(this);
      printHeader();
      storeData();
      printOffsetTable();
      finish();
 
      _current_occurrence++;
  }
 
//  //if the generation to store is > than the total nbr of generations,
//  //correct this and store the last one
//  if(!_isPeriodic && _generation == _popPtr->getCurrentGeneration()) {
//    storeData();
//  } else
//        //if periodic, and generation match, store the data in the buffer
//        if( _isPeriodic && !(_popPtr->getCurrentGeneration() % _generation)){
//                storeData();
//        }
//
//  //if reached last generation, write data to file,
//  //this empties the storage buffer with a call to printData() within FHwrite()
//  //thus prevents further calls to FHwrite to rewrite data to disc
//  if (_popPtr->getCurrentGeneration() == _popPtr->getGenerations()) {
//    //make sure the last generation is always stored before writing data to disc:
//    //catch if tot num gene is not a multiple of _generation
//    if( _popPtr->getCurrentGeneration() % _generation ||
//       //catch if tot num gen is a multiple but _generation < num gen and non periodic
//       (!_isPeriodic && _generation != _popPtr->getGenerations() &&
//        !(_popPtr->getCurrentGeneration() % _generation)))
//    {
//      storeData();
//    }
//    printData(); //this calls _buff.clear()
//    finish();  //this should call printOffsetTable()
//  }
}

References _buff, _current_occurrence, _occurrences, LifeCycleEvent::_popPtr, finish(), Metapop::getCurrentGeneration(), printHeader(), printOffsetTable(), BinaryStorageBuffer::set_buff(), and storeData().

FHread()

virtual void BinaryDataSaver::FHread ( string &  filename )

inlinevirtual

Implements FileHandler.

{}

FHwrite()

void BinaryDataSaver::FHwrite ( )

virtual

Implements FileHandler.

{
  //need to make sure data is saved even though last generation has not been reached
  //in case of population extinction, the file manager issues a notify() call after
  //the simulation exited from the generations loop, we try to catch this call here
 
  //keep in mind that this function is always called at the last generation
 
  //if data is already written to disc, the data buffer is empty
  //if the 'store' LCE is after the 'save_files' LCE in the life cycle, we don't write
  //--> issues two calls to printData, this one would be before storing last generation
  //if 'store' is before 'save_files', the data buffer should be empty by now
 
  if(_buff.getBuffLength() > 0 && SIMenv::getCurrentRankInLifeCycle() >= LifeCycleEvent::get_rank()) {
    printHeader();
    printOffsetTable(); //this calls _buff.clear()
    finish();
  }
 
}

References _buff, finish(), LifeCycleEvent::get_rank(), BinaryStorageBuffer::getBuffLength(), SIMenv::getCurrentRankInLifeCycle(), printHeader(), and printOffsetTable().

finish()

void BinaryDataSaver::finish ( )

private

{
  bool doComp = (_comp_cmd.size() > 0), doTar = (_tar_cmd.size() > 0),
  first = (_popPtr->getCurrentReplicate()
           == max((unsigned)1,_myenv->workerRank()));
 
  if (!(doComp || doTar)) return;
 
  stringstream sysCmd;
 
  if (doComp) {
 
    sysCmd << _comp_cmd << " ";
 
    if( get_service()->getMode() == 1 ) // overwrite
      sysCmd<< "--force "; // overwrite existing compressed file
 
    sysCmd << get_filename() << ";";
  }
 
  if (doTar) {
 
    sysCmd << _tar_cmd;
 
    if (first) sysCmd << " c"; //first replicate, create the tar archive:
    else             sysCmd << " r"; //next replicates, append files to it:
 
    sysCmd << "f " << get_path() << get_service()->getBaseFileName();
 
    if (!_myenv->isMaster()) sysCmd << _myenv->workerRank();
 
    sysCmd << _tar_ext << " --remove-files " << get_filename() << _comp_ext;
  }
 
 
  //wait for last child:
//  if (!first) waitpid(PID,NULL,0);
//
//  pid_t tPID = fork();
//
//  if (tPID == 0) {
 
    if (system(sysCmd.str().c_str()) < 0)
      error("BinaryDataSaver::finish system cmd \"%s\" failed: %s\n",
            sysCmd.str().c_str(),strerror(errno));
 
//    _exit(EXIT_FAILURE);
 
//  } else if (tPID < 0) //fork failed :
//    error("BinaryDataSaver::finish::could not fork new process: %s\n",
//          strerror(errno));
//
//  PID = tPID;
}

References _comp_cmd, _comp_ext, _myenv, LifeCycleEvent::_popPtr, _tar_cmd, _tar_ext, error(), FileHandler::get_filename(), FileHandler::get_path(), FileHandler::get_service(), FileServices::getBaseFileName(), Metapop::getCurrentReplicate(), FileServices::getMode(), MPIenv::isMaster(), and MPIenv::workerRank().

Referenced by execute(), and FHwrite().

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getFileDescriptor()

int BinaryDataSaver::getFileDescriptor ( )

inlineprivate

{ return _fdesc;}

References _fdesc.

ifExist()

vector< string > BinaryDataSaver::ifExist ( )

virtual

Reimplemented from FileHandler.

{
  ifstream ifExist;
  ifExist.setstate(ios::failbit);
  vector< string > list;
  string filename = get_path() + get_service()->getBaseFileName();
  string testname;
 
  ostringstream rpl, gen;
 
  gen.fill('0');
  gen.width( (int)log10((double)_pop->getGenerations()) + 1);
  gen<<get_GenerationOccurrence();
 
  rpl.fill('0');
  rpl.width( (int)log10((double)_pop->getReplicates()) + 1);
  rpl<<get_ReplicateOccurrence();
 
  if(!_isPeriodic)
    filename += "_" + rpl.str() + get_extension();
  else
    filename += "_" + gen.str() + "_" + rpl.str() + get_extension();
 
  //check if the basefilename is already used on disk:
  ifExist.open(filename.c_str(),ios::in);
  if(ifExist.is_open()) {
    list.push_back(filename);
  }
  ifExist.close();
  ifExist.setstate(ios::failbit);
 
 
  //check if compressed files are present:
  if( _comp_cmd != "" ) {
 
    testname = filename + _comp_ext;
 
    ifExist.open(testname.c_str(),ios::in);
 
    if(ifExist.is_open()) {
      list.push_back(testname);
    }
 
    ifExist.close();
    ifExist.setstate(ios::failbit);
  }
 
  if( _tar_cmd != "" ) {
 
    testname = filename + _tar_ext;
 
    ifExist.open(testname.c_str(),ios::in);
 
    if(ifExist.is_open()) {
      list.push_back(testname);
    }
 
    ifExist.close();
    ifExist.setstate(ios::failbit);
  }
 
  return list;
}

References _comp_cmd, _comp_ext, _isPeriodic, FileHandler::_pop, _tar_cmd, _tar_ext, FileHandler::get_extension(), FileHandler::get_GenerationOccurrence(), FileHandler::get_path(), FileHandler::get_ReplicateOccurrence(), FileHandler::get_service(), FileServices::getBaseFileName(), Metapop::getGenerations(), Metapop::getReplicates(), and ifExist().

Referenced by ifExist().

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loadFileServices()

virtual void BinaryDataSaver::loadFileServices ( FileServices *  loader )

inlinevirtual

Implements SimComponent.

{loader->attach(this);}

References FileServices::attach().

loadStatServices()

virtual void BinaryDataSaver::loadStatServices ( StatServices *  loader )

inlinevirtual

Implements SimComponent.

{}

printData()

void BinaryDataSaver::printData

(

)

{
  //we print what is in the buffer and empty it for the next bucket
  if((write(_fdesc,_buff.getBuffer(),_buff.getBuffLength())) == -1)
    fatal("BinaryDataSaver::printData::write %s\n",strerror(errno));
 
  _buff.emptyBuffer();
}

References _buff, _fdesc, BinaryStorageBuffer::emptyBuffer(), fatal(), BinaryStorageBuffer::getBuffer(), and BinaryStorageBuffer::getBuffLength().

Referenced by BinaryStorageBuffer::store().

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printHeader()

void BinaryDataSaver::printHeader ( )

private

{
  //first, record the parameters in text mode:
  ofstream FILE (get_filename().c_str(), ios::out);
 
  if(!FILE) fatal("could not open Binary output file!!\n");
 
  list< ParamSet* > current_params = get_service()->get_params();
  list< ParamSet* >::iterator Pit = current_params.begin();
 
  FILE<<"#NEMO "<<MAIN_VERSION<<" "<<MINOR_VERSION<<" "<<REVISION<<" "<<RELEASE<<" "<<VERSION_DATE<<endl;
 
#ifdef _DEBUG_
  message("BinaryDataSaver::printHeader:storing parameters\n");
#endif
  while(Pit != current_params.end()) {
    (*Pit)->print(FILE);
    Pit++;
  }
  FILE.close();
}

References fatal(), FileHandler::get_filename(), FileServices::get_params(), FileHandler::get_service(), MAIN_VERSION, message(), MINOR_VERSION, RELEASE, REVISION, and VERSION_DATE.

Referenced by execute(), and FHwrite().

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printOffsetTable()

void BinaryDataSaver::printOffsetTable ( )

private

{
 
  //get the offset position of the EOF, will be the nbr of bytes to add to the generation offsets
  // (data has already been written, the header plus any previous data)
  off_t pos = lseek(_fdesc,0,SEEK_END);
 
  if(pos == -1) fatal("BinaryDataSaver::printOffsetTable::lseek failed %s\n",strerror(errno));
 
//  cout<<"+++BinaryDataSaver::printOffsetTable::EOF at "<<pos;
 
  //offset of the offset table:
//  off_t off_table = _buff.getBuffLength() + pos;
 
//  cout<<"; adding "<<_buff.getBuffLength()<<"B of in-buff data +";
 
  //add the offset info at the end of the _buff:
  unsigned char separator[3] = {'@','O','T'};
  _buff.store(&separator, 3);
 
//  std::map<unsigned int, unsigned int>::iterator IT = _offset_table.begin();
//  while(IT != _offset_table.end()) {
//    IT->second += pos;
//    _buff.store((int*)&IT->first, sizeof(int));
//    _buff.store((int*)&IT->second, sizeof(off_t));
//    IT++;
//  }
 
  //_offset_table = pos; //EOF of current file, position of the start of the generation record
 
  unsigned int dummy = _popPtr->getCurrentGeneration();
 
  _buff.store(&dummy, sizeof(int));
 
  _buff.store(&_offsetDataStart, sizeof(off_t)); //previously stored offset of the generation separator
 
  //finally, record the number of generations recorded and the offset of start of the offset table
//  int nb_recgen = _offset_table.size();
//  int nb_recgen = 1;  //always store only one generation
//  _buff.store(&nb_recgen, sizeof(int));
//  _buff.store(&off_table, sizeof(off_t));
 
//  cout<<" "<<4*sizeof(int)+3<<"B for the offset table = "<<_buff.getBuffLength()<<"B\n";
 
  //now write the data to the file, that is, anything remaining in the buffer:
#ifdef _DEBUG_
  message("BinaryDataSaver::printOffsetTable:writing %iB of data ",_buff.getBuffLength());
#endif
 
  if((write(_fdesc,_buff.getBuffer(),_buff.getBuffLength())) == -1)
    fatal("BinaryDataSaver::printOffsetTable::write %s\n",strerror(errno));
 
  if((close(_fdesc)) == -1)
    error("BinaryDataSaver::printOffsetTable::close %s\n",strerror(errno));
 
  //empty the buffer, get ready for next record
  _buff.clear();
 
#ifdef _DEBUG_
  message(" [ok]\n");
#endif
}

References _buff, _fdesc, _offsetDataStart, LifeCycleEvent::_popPtr, BinaryStorageBuffer::clear(), error(), fatal(), BinaryStorageBuffer::getBuffer(), BinaryStorageBuffer::getBuffLength(), Metapop::getCurrentGeneration(), message(), and BinaryStorageBuffer::store().

Referenced by execute(), and FHwrite().

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removeAgeClass()

virtual age_t BinaryDataSaver::removeAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

requiredAgeClass()

virtual age_t BinaryDataSaver::requiredAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

resetParameterFromSource()

virtual bool BinaryDataSaver::resetParameterFromSource ( std::string  param, SimComponent *  cmpt  )

inlinevirtual

Implements SimComponent.

{return false;}

setFileDescriptor()

void BinaryDataSaver::setFileDescriptor ( )

private

{
  mode_t mode = S_IRUSR | S_IWUSR | S_IRGRP | S_IROTH;
  int flag = O_WRONLY | O_APPEND;
 
  //open in write and append mode with permission flag set to rw-r--r--
  _fdesc = open(get_filename().c_str(), flag, mode);
 
  if(_fdesc == -1)
    fatal("BinaryDataSaver::printData::open %s:%s\n",get_filename().c_str(),strerror(errno));
 
}

References _fdesc, fatal(), and FileHandler::get_filename().

Referenced by storeData().

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setParameters()

bool BinaryDataSaver::setParameters ( )

virtual

Implements SimComponent.

{
  Param* param;
 
  _generation = (unsigned int)get_parameter_value("store_generation");
 
  //make sure we at least save the last generation:
  if(_generation > _popPtr->getGenerations()) _generation = _popPtr->getGenerations();
 
  param = get_parameter("store_dir");
  if(param->isSet())
    _dir = param->getArg();
  else
    _dir = "";
 
  param = get_parameter("store_recursive");
  if(param->isSet())
    _isPeriodic = true;
  else
    _isPeriodic = false;
 
  param = get_parameter("store_compress_cmde");
  if(param->isSet())
    _comp_cmd = param->getArg();
  else
    _comp_cmd = "bzip2"; //default compressor used
 
  param = get_parameter("store_compress_extension");
  if(param->isSet())
    _comp_ext = param->getArg();
  else
    _comp_ext = ".bz2"; //default
 
  param = get_parameter("store_uncompress_cmde");
  if(param->isSet())
    _uncomp_cmd = param->getArg();
  else
    _uncomp_cmd = "unbzip2"; //default
 
  param = get_parameter("store_archive_cmde");
  if(param->isSet())
    _tar_cmd = param->getArg();
  else
    _tar_cmd = "tar"; //default
 
  param = get_parameter("store_archive_extension");
  if(param->isSet())
    _tar_ext = param->getArg();
  else
    _tar_ext = ".tar"; //default
 
  param = get_parameter("store_nocompress");
  if(param->isSet()) {_comp_cmd = ""; _comp_ext ="";} //compression process disabled
 
  param = get_parameter("store_noarchive");
  if(param->isSet()) {_tar_cmd = ""; _tar_ext = "";} //archiving processed disabled
 
  //set the file handler, will be called by FileServices, will output data at each gen
  FileHandler::set(true, _isPeriodic, 1, _generation, get_rank(), _dir);
 
  _offsetDataStart = 0L; //this stores the offset of the stored data in the file, positioned after
                     // the simulation parameters stored in plain text.
 
  _occurrences.clear();
 
  if(_isPeriodic) {
      unsigned int num_occurrences = _popPtr->getGenerations() / _generation;
 
      for(unsigned int i = 1; i <= num_occurrences; ++i)
        _occurrences.push_back( i* _generation);
  } else
    _occurrences.push_back(_generation);
 
  _current_occurrence = _occurrences.begin();
 
 
  return true;
}

References _comp_cmd, _comp_ext, _current_occurrence, _dir, _generation, _isPeriodic, _occurrences, _offsetDataStart, LifeCycleEvent::_popPtr, _tar_cmd, _tar_ext, _uncomp_cmd, SimComponent::get_parameter(), SimComponent::get_parameter_value(), LifeCycleEvent::get_rank(), Param::getArg(), Metapop::getGenerations(), Param::isSet(), and FileHandler::set().

Referenced by BinaryDataSaver().

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storeData()

void BinaryDataSaver::storeData ( )

private

{
#ifdef _DEBUG_
  message("BinaryDataSaver::storeData\n");
  unsigned int byte_count = _buff.getBuffLength();
#endif
 
  unsigned int  generation = _popPtr->getCurrentGeneration();
  unsigned char separator[2] = {'@','G'}; //generation separator = '@G'
 
  //store the data, begin with generation separator and number:
  _buff.store(&separator, 2 * sizeof(unsigned char));
 
  _buff.store(&generation, sizeof(unsigned int));
 
  //open the output file;
  setFileDescriptor();
 
  //store the position of the generation separator in the buffer into the offset table:
  //_offsetDataStart = _buff.getTotByteRecorded();
 
  _offsetDataStart = lseek(_fdesc,0,SEEK_END);
 
//  cout<<"BinaryDataSaver::storeData::offset of start of record: "<<_offsetDataStart
//      <<"; data recorder so far: "<<_buff.getTotByteRecorded()<<"B\n";
  //start storing information, the data buckets will automatically be written to file if >500MB
 
  //Metapop is a StorableComponent, call store_data:
  //stores all individual info, including trait sequences
  _popPtr->store_data(&_buff);
 
#ifdef _DEBUG_
  message("BinaryDataSaver::storeData::stored %iB\n",(_buff.getBuffLength()-byte_count));
  byte_count = _buff.getBuffLength();
#endif
}

References _buff, _fdesc, _offsetDataStart, LifeCycleEvent::_popPtr, BinaryStorageBuffer::getBuffLength(), Metapop::getCurrentGeneration(), message(), setFileDescriptor(), BinaryStorageBuffer::store(), and Metapop::store_data().

Referenced by execute().

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Member Data Documentation

_buff

BinaryStorageBuffer BinaryDataSaver::_buff

private

Referenced by execute(), FHwrite(), printData(), printOffsetTable(), and storeData().

_comp_cmd

std::string BinaryDataSaver::_comp_cmd

private

Referenced by finish(), ifExist(), and setParameters().

_comp_ext

std::string BinaryDataSaver::_comp_ext

private

Referenced by finish(), ifExist(), and setParameters().

_current_occurrence

vector<unsignedint>::const_iterator BinaryDataSaver::_current_occurrence

private

Referenced by execute(), and setParameters().

_dir

std::string BinaryDataSaver::_dir

private

Referenced by setParameters().

_fdesc

int BinaryDataSaver::_fdesc

private

Referenced by getFileDescriptor(), printData(), printOffsetTable(), setFileDescriptor(), and storeData().

_generation

unsigned int BinaryDataSaver::_generation

private

Referenced by setParameters().

_isPeriodic

bool BinaryDataSaver::_isPeriodic

private

Referenced by ifExist(), and setParameters().

_occurrences

vector< unsigned int > BinaryDataSaver::_occurrences

private

Referenced by execute(), and setParameters().

_offsetDataStart

off_t BinaryDataSaver::_offsetDataStart

private

Referenced by printOffsetTable(), setParameters(), and storeData().

_tar_cmd

std::string BinaryDataSaver::_tar_cmd

private

Referenced by finish(), ifExist(), and setParameters().

_tar_ext

std::string BinaryDataSaver::_tar_ext

private

Referenced by finish(), ifExist(), and setParameters().

_uncomp_cmd

std::string BinaryDataSaver::_uncomp_cmd

private

Referenced by setParameters().

PID

pid_t BinaryDataSaver::PID = 0

static

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The documentation for this class was generated from the following files:

• binarydatasaver.h
• binarydatasaver.cc