tapioca.cpp 34.2 KB
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#include "tapioca.hpp"
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Tapioca::Tapioca ()
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{
  this->SetDefaultValues ();
  this->ParseEnvVariables ();
}


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Tapioca::~Tapioca ()
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{
}


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void Tapioca::WriteInitialize (char *filename, int64_t *chunkCount, int *chunkSize, int64_t *chunkOffset,
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			      int nChunks, int64_t offset, MEMORY_LAYOUT layout, MPI_Comm comm)
{
  int chunk;
#ifdef TIMING
  double startInitTime, endInitTime, startElectTime, endElectTime;
  startInitTime = MPI_Wtime();
#endif
  
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  this->filename_ = filename;
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  this->nChunks_ = nChunks;
  this->chunksIndexMatching.resize (this->nChunks_);
  
  this->chunkCount_  = (int64_t *)malloc (this->nChunks_ * sizeof(int64_t));
  this->chunkSize_   = (int *)malloc (this->nChunks_ * sizeof(int));
  this->chunkOffset_ = (int64_t *)malloc (this->nChunks_ * sizeof(int64_t));
  memcpy (this->chunkCount_, chunkCount, this->nChunks_ * sizeof(int64_t));
  memcpy (this->chunkSize_, chunkSize, this->nChunks_ * sizeof(int));
  memcpy (this->chunkOffset_, chunkOffset, this->nChunks_ * sizeof(int64_t));

  for ( chunk = 0; chunk < this->nChunks_; chunk++ )
    this->rankDataSize_ += this->chunkCount_[chunk] * this->chunkSize_[chunk];
  
  this->offsetInFile_ = offset;
  this->layout_ = layout;
  MPI_Comm_dup (comm, &this->subComm_);
  
  this->SetCommValues ();
  this->SetOffsets ();

  if ( this->writeDevNull_ )
    MPI_File_open(MPI_COMM_SELF, "/dev/null",
		  MPI_MODE_WRONLY | MPI_MODE_CREATE,
		  MPI_INFO_NULL, &this->devNullFileHandle_);

#ifdef DEBUG
  if (this->commRank_ == MASTER) {
    fprintf (stdout, "[DEBUG] #Aggr        = %d   \n", this->nAggr_);
    fprintf (stdout, "[DEBUG] bufferSize   = %lld \n", this->bufferSize_);
    fprintf (stdout, "[DEBUG] commDataSize = %lld \n", this->commDataSize_);
    fprintf (stdout, "[DEBUG] strategy     = %s   \n", this->getStrategyName ());
  }
#endif

  this->SetNodesList ();

  this->IdentifyMyAggregators ();

#ifdef TIMING
  startElectTime = MPI_Wtime();
#endif

  this->ElectAggregators ();
  
#ifdef TIMING
  endElectTime = MPI_Wtime();
#endif
  
  this->InitAggregators ();

#ifdef TIMING
  endInitTime = MPI_Wtime();
  this->PrintTime(startInitTime, endInitTime, "Initialize");
  this->PrintTime(startElectTime, endElectTime, " |-> Elect aggregators");
#endif
}


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void Tapioca::ReadInitialize (char *filename, int64_t *chunkCount, int *chunkSize, int64_t *chunkOffset,
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			      int nChunks, int64_t offset, MEMORY_LAYOUT layout, MPI_Comm comm)
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{
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  int chunk;
#ifdef TIMING
  double startInitTime, endInitTime, startElectTime, endElectTime;
  startInitTime = MPI_Wtime();
#endif
  
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  this->filename_ = filename;
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  this->nChunks_ = nChunks;
  this->chunksIndexMatching.resize (this->nChunks_);
  
  this->chunkCount_  = (int64_t *)malloc (this->nChunks_ * sizeof(int64_t));
  this->chunkSize_   = (int *)malloc (this->nChunks_ * sizeof(int));
  this->chunkOffset_ = (int64_t *)malloc (this->nChunks_ * sizeof(int64_t));
  memcpy (this->chunkCount_, chunkCount, this->nChunks_ * sizeof(int64_t));
  memcpy (this->chunkSize_, chunkSize, this->nChunks_ * sizeof(int));
  memcpy (this->chunkOffset_, chunkOffset, this->nChunks_ * sizeof(int64_t));

  for ( chunk = 0; chunk < this->nChunks_; chunk++ )
    this->rankDataSize_ += this->chunkCount_[chunk] * this->chunkSize_[chunk];
  
  this->offsetInFile_ = offset;
  this->layout_ = layout;
  MPI_Comm_dup (comm, &this->subComm_);
  
  this->SetCommValues ();
  this->SetOffsets ();

#ifdef DEBUG
  if (this->commRank_ == MASTER) {
    fprintf (stdout, "[DEBUG] #Aggr        = %d   \n", this->nAggr_);
    fprintf (stdout, "[DEBUG] bufferSize   = %lld \n", this->bufferSize_);
    fprintf (stdout, "[DEBUG] commDataSize = %lld \n", this->commDataSize_);
    fprintf (stdout, "[DEBUG] strategy     = %s   \n", this->getStrategyName ());
  }
#endif

  this->SetNodesList ();

  //this->IdentifyMyAggregators ();

#ifdef TIMING
  startElectTime = MPI_Wtime();
#endif

  //this->ElectAggregators ();
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#ifdef TIMING
  endElectTime = MPI_Wtime();
#endif
  
  this->InitAggregators ();

#ifdef TIMING
  endInitTime = MPI_Wtime();
  this->PrintTime(startInitTime, endInitTime, "Initialize");
  this->PrintTime(startElectTime, endElectTime, " |-> Elect aggregators");
#endif
}


void Tapioca::Finalize ()
{
  this->chunksIndexMatching.clear();
  free (this->chunkCount_);
  free (this->chunkSize_);
  free (this->chunkOffset_);
  this->excludedNode.clear();
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  MPI_Win_free (&this->RMAWin1);
  MPI_Win_free (&this->RMAWin2);

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  MPI_Comm_free (&this->subComm_);

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  free (this->buffer1);
  free (this->buffer2);
}


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int Tapioca::Write (MPI_File fileHandle, MPI_Offset offset, void *buf, 
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		    int count, MPI_Datatype datatype, MPI_Status *status, char* var, int64_t bufOffset)
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{
  int retval, i, c, targetRoundIdx, targetAggrIdx, targetGlobAggr;
  int typeSize, targetAggr, win, buffer;
  bool multipleRounds = false;
  int64_t chunkDataSize, subChunkDataSize, cumulDataSize = 0, cumulDataSizeInRound;
  int64_t winOffset = 0, rankDataOffset, offsetInAggrData;
  MPI_Status iStatus;
  MPI_Request iRequest = NULL;
  

  MPI_Type_size (datatype, &typeSize);
  c                = this->nCommit_;
  chunkDataSize    = count * typeSize;
  subChunkDataSize = chunkDataSize;
  offsetInAggrData = offset - this->offsetInFile_;
  winOffset        = offsetInAggrData % this->bufferSize_;

  targetRoundIdx   = (*this->chunksIndexMatching[c].begin());
  targetAggrIdx    = (*this->chunksIndexMatching[c].begin());
  if ( this->chunksIndexMatching[c].size() > 1 ) {
    multipleRounds   = true;
    subChunkDataSize = this->dataSize[targetRoundIdx];
    this->chunksIndexMatching[c].erase ( this->chunksIndexMatching[c].begin() );
  }
  
  /*
   *  Wait if it's not the appropriate round
   */
  while ( this->roundsIds[targetRoundIdx] > this->currentRound_ ) {
    for ( i = 0; i < this->nAggr_ ; i++ ) {
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      fprintf (stdout, "[INFO] %d calls 1st GlobalFence, buff %d, dat %s (r: %d, f: %d)\n", this->commRank_, (this->currentRound_ % NBUFFERS), var, this->currentRound_, this->currentFence_);
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      this->GlobalFence (var);
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      fprintf (stdout, "[INFO] %d passes 1st GlobalFence, buff %d, dat %s (r: %d, f: %d)\n", this->commRank_, (this->currentRound_ % NBUFFERS), var, this->currentRound_, this->currentFence_);
      this->currentFence_++;
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      this->roundCounter_++;
    }
    
    if ( this->amAnAggr_ ) {
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      // if (iRequest != NULL)
      //  	MPI_Wait ( &iRequest, &iStatus );
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      fprintf (stdout, "[INFO] %d calls 1st Push (r: %d)\n", this->commRank_, this->currentRound_);
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      this->Push (fileHandle, status);
      //this->iPush (fileHandle, &iRequest);
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    }
    
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    fprintf (stdout, "[INFO] %d increment 1st currentRound (r: %d)\n", this->commRank_, this->currentRound_);
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    this->currentRound_++;
  }

#ifdef TIMING
    this->startAggrTime = MPI_Wtime();
#endif
    

  buffer         = this->currentRound_ % NBUFFERS;
  targetGlobAggr = this->globalAggregatorsRanks[targetAggrIdx];
  targetAggr     = this->aggregatorsRanks[targetAggrIdx];
  
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  fprintf (stdout, "[INFO] %d Put %s data in buffer %d, agg %d (r: %d)\n", this->commRank_, var, buffer, targetGlobAggr, this->currentRound_);
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  switch (buffer)
    {
    case 0:
      retval = MPI_Put (static_cast<char*>(buf) + bufOffset, subChunkDataSize, MPI_BYTE,
			 targetAggr, winOffset, subChunkDataSize, MPI_BYTE, this->RMAWin1);
      this->HandleMPIError (retval);
      break;
    case 1:
      retval = MPI_Put (static_cast<char*>(buf) + bufOffset, subChunkDataSize, MPI_BYTE,
			 targetAggr, winOffset, subChunkDataSize, MPI_BYTE, this->RMAWin2);
      this->HandleMPIError (retval);
      break;
    }
 
  this->currentDataSize_ += subChunkDataSize;

  /*
   *  If all the data have been written, wait
   */
  if ( this->currentDataSize_ == this->rankDataSize_) {
    while ( this->roundCounter_ < this->totalRounds_) {
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      fprintf (stdout, "[INFO] %d calls 2nd GlobalFence, buff %d, dat %s (r: %d, f: %d)\n", this->commRank_, (this->currentRound_ % NBUFFERS), var, this->currentRound_, this->currentFence_);
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      this->GlobalFence (var);
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      fprintf (stdout, "[INFO] %d passes 2nd GlobalFence, buff %d, dat %s (r: %d, f: %d)\n", this->commRank_, (this->currentRound_ % NBUFFERS), var, this->currentRound_, this->currentFence_);
      this->currentFence_++;
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      if ( (this->roundCounter_ % this->nAggr_) == 0 ) {
	if ( this->amAnAggr_ ) {
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	  // if (iRequest != NULL)
	  //   MPI_Wait ( &iRequest, &iStatus );
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	  fprintf (stdout, "[INFO] %d calls 2nd Push (r: %d)\n", this->commRank_, this->currentRound_);
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	  this->Push (fileHandle, status);
	  //this->iPush (fileHandle, &iRequest);
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	}
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	fprintf (stdout, "[INFO] %d increment 2nd currentRound (r: %d, rc: %d, nag: %d)\n", this->commRank_, this->currentRound_, this->roundCounter_, this->nAggr_);
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	this->currentRound_++;
      }

      this->roundCounter_++;
    }
  }
  
  if ( multipleRounds ) {
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    fprintf (stdout, "[INFO] %d has a second round (r: %d)\n", this->commRank_, this->currentRound_);
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    retval = this->Write (fileHandle, offset + subChunkDataSize, buf, 
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			  chunkDataSize - subChunkDataSize, MPI_BYTE, status, var, subChunkDataSize);
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  }
  else {
    this->nCommit_ ++;
  }

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  // if (iRequest != NULL)
  //   MPI_Wait ( &iRequest, &iStatus );
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  return retval;
}


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void Tapioca::Push (MPI_File fileHandle, MPI_Status *status)
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{
  int64_t offset, dataSize;
  int win, buffer;

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  fprintf (stdout, "[DEBUG] Enter Push\n");
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  buffer = this->currentRound_ % NBUFFERS;

  if ( this->amAnAggr_ ) {
#ifdef TIMING
    this->startIOTime = MPI_Wtime();
#endif
    offset   = (this->nAggr_ * this->currentRound_ + this->globalAggrRank_) * this->bufferSize_;
    offset   += this->offsetInFile_;
    
    dataSize = this->bufferSize_;
    if ( this->aggrDataSize_ < this->bufferSize_ )
      dataSize = this->aggrDataSize_;
    
    switch (buffer)
      {
      case 0: 
	if ( this->writeDevNull_ )
	  MPI_File_write_at (this->devNullFileHandle_, 0, buffer1, dataSize, MPI_BYTE, status);
	else
	  MPI_File_write_at (fileHandle, offset, buffer1, dataSize, MPI_BYTE, status);
	break;
      case 1:
	if ( this->writeDevNull_ )
	  MPI_File_write_at (this->devNullFileHandle_, 0, buffer2, dataSize, MPI_BYTE, status);
	else
	  MPI_File_write_at (fileHandle, offset, buffer2, dataSize, MPI_BYTE, status);
	break;
      }

    this->aggrDataSize_ -= dataSize;
#ifdef TIMING
    this->endIOTime = MPI_Wtime();
    this->totIOTime = this->endIOTime - this->startIOTime;
    if ( dataSize > 0 )
      fprintf (stdout, "[TIMING][AGG][IO] Agg. %d, Rnd %d - %.2f ms\n",
	       this->commRank_, this->currentRound_, this->totIOTime * 1000);
#endif
  }    
}

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void Tapioca::iPush (MPI_File fileHandle, MPI_Request *request)
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{
  int64_t offset, dataSize;
  int win, buffer;

  buffer = this->currentRound_ % NBUFFERS;

  if ( this->amAnAggr_ ) {
#ifdef TIMING
    this->startIOTime = MPI_Wtime();
#endif
    offset   = (this->nAggr_ * this->currentRound_ + this->globalAggrRank_) * this->bufferSize_;
    offset   += this->offsetInFile_;
    
    dataSize = this->bufferSize_;
    if ( this->aggrDataSize_ < this->bufferSize_ )
      dataSize = this->aggrDataSize_;
    
    switch (buffer)
      {
      case 0: 
	if ( this->writeDevNull_ )
	  MPI_File_iwrite_at (this->devNullFileHandle_, 0, buffer1, dataSize, MPI_BYTE, request);
	else
	  MPI_File_iwrite_at (fileHandle, offset, buffer1, dataSize, MPI_BYTE, request);
	break;
      case 1:
	if ( this->writeDevNull_ )
	  MPI_File_iwrite_at (this->devNullFileHandle_, 0, buffer2, dataSize, MPI_BYTE, request);
	else
	  MPI_File_iwrite_at (fileHandle, offset, buffer2, dataSize, MPI_BYTE, request);
	break;
      }

    this->aggrDataSize_ -= dataSize;
#ifdef TIMING
    this->endIOTime = MPI_Wtime();
    this->totIOTime = this->endIOTime - this->startIOTime;
    if ( dataSize > 0 )
      fprintf (stdout, "[TIMING][AGG][IO] Agg. %d, Rnd %d - %.2f ms\n",
	       this->commRank_, this->currentRound_, this->totIOTime * 1000);
#endif
  }    
}


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void Tapioca::GlobalFence (char* var) 
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{
  int buffer;

  buffer = this->currentRound_ % NBUFFERS;

  switch (buffer)
    {
    case 0:
      MPI_Win_fence (0, this->RMAWin1);
      break;
    case 1:
      MPI_Win_fence (0, this->RMAWin2);
      break;
    }
  
#ifdef TIMING
  this->endAggrTime = MPI_Wtime();
  
  if ( this->startAggrTime != 0 ) {
    this->totAggrTime = this->endAggrTime - this->startAggrTime;
    // fprintf (stdout, "[TIMING][AGG][AGGR] Rank %d, Rnd %d - %.2f ms\n",
    // 	     this->commRank_, this->currentRound_, this->totAggrTime * 1000);
  }
    
  this->startAggrTime = 0;
#endif

}


/***********************/
/*  INITIALIZATION     */
/***********************/
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void Tapioca::SetDefaultValues ()
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{
  this->rankDataSize_ = 0;
  this->strategy_ = SHORTEST_PATH;
  this->nAggr_ = 8;
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  this->bufferSize_ = 16777216;
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  this->amAnAggr_ = false;
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  this->commSplit_ = true;
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  this->currentRound_ = 0;
  this->roundCounter_ = 0;
  this->currentDataSize_ = 0;
  this->nCommit_ = 0;
  this->writeDevNull_ = false;
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  /* DEBUG */
  this->currentFence_ = 1;
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}


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void Tapioca::ParseEnvVariables ()
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{
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  char *envStrategy   = getenv("TAPIOCA_STRATEGY");
  char *envNAggr      = getenv("TAPIOCA_NBAGGR");
  char *envBufferSize = getenv("TAPIOCA_BUFFERSIZE");
  char *envSplit      = getenv("TAPIOCA_COMMSPLIT");
  char *envDevNull    = getenv("TAPIOCA_DEVNULL");
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  if (envStrategy != NULL) {
    strcmp(envStrategy, "SHORTEST_PATH")    ? 0 : this->strategy_ = SHORTEST_PATH;
    strcmp(envStrategy, "LONGEST_PATH")     ? 0 : this->strategy_ = LONGEST_PATH;
    strcmp(envStrategy, "TOPOLOGY_AWARE")   ? 0 : this->strategy_ = TOPOLOGY_AWARE;
    strcmp(envStrategy, "CONTENTION_AWARE") ? 0 : this->strategy_ = CONTENTION_AWARE;
    strcmp(envStrategy, "UNIFORM")          ? 0 : this->strategy_ = UNIFORM;
  }

  if (envNAggr != NULL) {
    this->nAggr_ = atoi(envNAggr);
  }

  if (envBufferSize != NULL) {
    this->bufferSize_ = atoi(envBufferSize);
  }

  if (envSplit != NULL) {
    strcmp(envSplit, "true")  ? 0 : this->commSplit_ = true;
    strcmp(envSplit, "false") ? 0 : this->commSplit_ = false;
  }

  if (envDevNull != NULL) {
    strcmp(envDevNull, "true")  ? 0 : this->writeDevNull_ = true;
    strcmp(envDevNull, "false") ? 0 : this->writeDevNull_ = false;
  }
}


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void Tapioca::SetCommValues ()
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{
  MPI_Comm_rank (this->subComm_, &this->commRank_);
  MPI_Comm_size (this->subComm_, &this->commSize_);
  MPI_Comm_rank (MPI_COMM_WORLD, &this->worldRank_);

  MPI_Allreduce (&this->rankDataSize_, &this->commDataSize_, 1, MPI_LONG_LONG, MPI_SUM, this->subComm_);
}


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void Tapioca::SetOffsets ()
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{
  MPI_Exscan (&this->rankDataSize_, &this->offsetInAggrData_, 1, 
	      MPI_LONG_LONG, MPI_SUM, this->subComm_);
  if (this->commRank_ == 0)
    this->offsetInAggrData_ = 0;
}


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void Tapioca::SetNodesList ()
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{
  int *coords, *myCoords, i, worldSize, dimensions;
  
  MPI_Comm_size ( MPI_COMM_WORLD, &worldSize );
  coords = (int *)malloc (worldSize * sizeof (int));

  dimensions = topology.NetworkDimensions () + 1;
  myCoords = (int *)malloc (dimensions * sizeof (int));

  topology.RankToCoordinates (this->worldRank_, myCoords);
  this->intCoords_ = this->CoordsToInt (myCoords, dimensions - 1);
  
  MPI_Allgather(&this->intCoords_, 1, MPI_INT, coords, 1, MPI_INT, MPI_COMM_WORLD);

  for ( i = 0; i < worldSize; i++ )
    this->excludedNode[coords[i]] = false;
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  free (coords);
  free (myCoords);
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}


/***********************/
/*    AGGREGATION      */
/***********************/
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int Tapioca::NumberOfAggregators ()
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{
  return 0;
}


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void Tapioca::IdentifyMyAggregators ()
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{
  int i, j, c, globalRoundId, upperBound, index = 0;
  int64_t remainingData, offsetInAggrData;
  std::vector<Round_t> rounds;
  
  this->totalRounds_  = ceil ( (double)this->commDataSize_ / (double)this->bufferSize_ );

  for ( i = 0; i < this->totalRounds_; i++ ) {
    Round_t r;
    r.aggr = i % this->nAggr_;
    r.round = i / this->nAggr_;
    rounds.push_back(r);
  }

  for ( c = 0; c < this->nChunks_; c++ ) {
    remainingData    = this->chunkCount_[c] * this->chunkSize_[c];
    offsetInAggrData = this->chunkOffset_[c] - this->offsetInFile_;
    globalRoundId = floor ( offsetInAggrData / this->bufferSize_ );
    upperBound = ( offsetInAggrData % this->bufferSize_ ) + remainingData;
    
    while ( remainingData > 0 ) {
      this->globalAggregatorsRanks.push_back ( rounds[globalRoundId].aggr );
      this->roundsIds.push_back ( rounds[globalRoundId].round );
      this->chunksIndexMatching[c].push_back ( index );
      
      if ( upperBound > this->bufferSize_) {
	remainingData = (upperBound - this->bufferSize_);
	this->dataSize.push_back ( this->chunkCount_[c] * this->chunkSize_[c] - remainingData );
      }
      else {
	this->dataSize.push_back ( remainingData );
	remainingData = 0;
      }
      
      upperBound -= this->bufferSize_;
      globalRoundId++;
      index++;
    }
  }
  
#ifdef DEBUG
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  if (this->commRank_ == 4) {
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    fprintf (stdout, "[DEBUG] Rounds distrib. on %d aggregators: AGG ", this->nAggr_);
    for ( i = 0; i < this->totalRounds_; i++ )
      fprintf (stdout, "%d ", rounds[i].aggr);
    fprintf (stdout, "\n                                          RND ");
    for ( i = 0; i < this->totalRounds_; i++ )
      fprintf (stdout, "%d ", rounds[i].round);
    fprintf (stdout, "\n                                          AGG ");
    for ( i = 0; i < this->globalAggregatorsRanks.size(); i++ )
      fprintf (stdout, "%d ", this->globalAggregatorsRanks[i]);
    fprintf (stdout, "\n                                          RID ");
    for ( i = 0; i < this->roundsIds.size(); i++ )
      fprintf (stdout, "%d ", this->roundsIds[i]);
    fprintf (stdout, "\n                                          DAS ");
    for ( i = 0; i < this->dataSize.size(); i++ )
      fprintf (stdout, "%d ", this->dataSize[i]);
    fprintf (stdout, "\n                                          CIM ");
    for ( i = 0; i < this->chunksIndexMatching.size(); i++ ) {
      fprintf (stdout, "{ ");
      for ( j = 0; j < this->chunksIndexMatching[i].size(); j++ )
	fprintf (stdout, "%d ", this->chunksIndexMatching[i][j]);
      fprintf (stdout, "}");
    }
    fprintf (stdout, "\n");
  }
#endif
}


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void Tapioca::ElectAggregators ()
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{
  int aggr, aggrRank, rankAggrComm, sizeAggrComm, aggrRankAggrComm, i, j, aggrCoords, worldSize;
  int64_t color;
  double startTime, endTime, totTime = 0.0;
  MPI_Comm aggrComm;
  MPI_Request request;
  MPI_Status status;
  /* Groups */
  MPI_Group commGroup, aggrGroup;
  int *ranks, *join, *groupRanks, groupSize, groupRank, joinGroup;

  MPI_Comm_size (MPI_COMM_WORLD, &worldSize);

  this->aggregatorsRanks.resize ( this->globalAggregatorsRanks.size() );
  
  for ( aggr = 0; aggr < this->nAggr_; aggr++ ) {
    color = this->DataSizeSentToAggr (aggr);
    
    startTime = MPI_Wtime();

    if ( this->commSplit_ )
      MPI_Comm_split (this->subComm_, color > 0, this->commRank_, &aggrComm);
    else {
      
      MPI_Comm_group (this->subComm_, &commGroup);

      if ( color > 0 ) {
	joinGroup = 1;
	MPI_Allreduce (&joinGroup, &groupSize, 1, MPI_INT, MPI_SUM, this->subComm_ );
      }
      else {
	joinGroup = 0;
	MPI_Allreduce (&joinGroup, &groupSize, 1, MPI_INT, MPI_SUM, this->subComm_ );
	groupSize = this->commSize_ - groupSize;
      }

      join = (int *)malloc (this->commSize_ * sizeof (int));
      MPI_Allgather(&joinGroup, 1, MPI_INT, join, 1, MPI_INT, this->subComm_);
      groupRanks = (int *)malloc (groupSize * sizeof (int));
      
      j = 0;
      for ( i = 0; i < this->commSize_; i++ ) {
	if (join[i] == joinGroup) {
	  groupRanks[j] = i;
	  j++;
	}
      }

      MPI_Group_incl (commGroup, groupSize, groupRanks, &aggrGroup);
      MPI_Comm_create (this->subComm_, aggrGroup, &aggrComm);
      
      free (join);
      free (groupRanks);
    }
    
    MPI_Comm_rank (aggrComm, &rankAggrComm);
    MPI_Comm_size (aggrComm, &sizeAggrComm);

    endTime = MPI_Wtime();
    totTime += ( endTime - startTime );
    
    if ( color > 0 ) {
      switch ( this->strategy_ )
	{
	case SHORTEST_PATH:
	  aggrRank = this->RankShortestPath (aggrComm, color);
	  break;
	case LONGEST_PATH:
	  aggrRank = this->RankLongestPath (aggrComm, color);
	  break;
	case TOPOLOGY_AWARE:
	  aggrRank = this->RankTopologyAware (aggrComm, color);
	  break;
	case CONTENTION_AWARE:
	  aggrRank = this->RankContentionAware (aggrComm, color);
	  break;
	case UNIFORM:
	  aggrRank = this->RankUniformDistribution (aggrComm, color);
	  break;
	}

      if ( this->commRank_ == aggrRank ) {
	this->totalWrites_     = ceil ( (double)this->aggrDataSize_ / (double)this->bufferSize_);
	this->globalAggrRank_  = aggr;
	aggrCoords             = this->intCoords_;
	MPI_Isend ( &aggrCoords, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &request );
      }

      for ( i = 0; i < this->aggregatorsRanks.size(); i++ )
	if ( this->globalAggregatorsRanks[i] == aggr )
	  this->aggregatorsRanks[i] = aggrRank;

#ifdef DEBUG
      int coords[topology.NetworkDimensions() + 1];
      if ( this->commRank_ == aggrRank ) {
	topology.RankToCoordinates (this->worldRank_, coords);
	fprintf (stdout, "[DEBUG] AggRank %d, (", this->worldRank_);
	for ( i = 0; i < topology.NetworkDimensions() + 1; i++ )
	  fprintf (stdout, "%u ", coords[i]);
	fprintf (stdout, ") -> %d, part %d, %lld B from %d ranks, %d rounds\n",
		 this->intCoords_, topology.BridgeNodeId(), this->aggrDataSize_, sizeAggrComm, this->totalWrites_);
      }
#endif
    }

    /*
     *  TODO: Compute this... 
     *              - Vesta: 16 nodes/bridge node
     *              - Mira : 64 nodes/bridge node
     */
    for ( i = 0; i < ( (worldSize / topology.ProcessPerNode ()) / (this->commSize_ / topology.ProcessPerNode ()) ); i++ ) {
      if ( this->worldRank_ == 0 )
	MPI_Recv ( &aggrCoords, 1, MPI_INT, MPI_ANY_SOURCE, 0, MPI_COMM_WORLD, &status );
      
      MPI_Bcast ( &aggrCoords, 1, MPI_INT, 0, MPI_COMM_WORLD);
      this->excludedNode[aggrCoords] = true;
    }
  }

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#ifdef TIMING
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  this->PrintTime( 0, totTime, " |-> Create subcommunicator");
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#endif
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}


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int64_t Tapioca::DataSizeSentToAggr (int aggrId)
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{
  int i;
  int64_t dataSize = 0;

  for ( i = 0; i < this->aggregatorsRanks.size(); i++ )
    if ( this->globalAggregatorsRanks[i] == aggrId )
      dataSize += this->dataSize[i];

  return dataSize;
}


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void Tapioca::InitAggregators () 
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{
  int aggr, retval;
  
  if ( this->amAnAggr_ ) {
    this->buffer1 = malloc (this->bufferSize_);
    this->buffer2 = malloc (this->bufferSize_);

    retval = MPI_Win_create (this->buffer1, this->bufferSize_, 1, MPI_INFO_NULL, this->subComm_, &this->RMAWin1);
    this->HandleMPIError (retval);
    MPI_Win_create (this->buffer2, this->bufferSize_, 1, MPI_INFO_NULL, this->subComm_, &this->RMAWin2);
    this->HandleMPIError (retval);
  }
  else {
    retval = MPI_Win_create (NULL, 0, 1, MPI_INFO_NULL, this->subComm_, &this->RMAWin1);
    this->HandleMPIError (retval);
    retval = MPI_Win_create (NULL, 0, 1, MPI_INFO_NULL, this->subComm_, &this->RMAWin2);
    this->HandleMPIError (retval);
  }

  retval = MPI_Win_fence (0, this->RMAWin1);
  this->HandleMPIError (retval);
  retval = MPI_Win_fence (0, this->RMAWin2);
  this->HandleMPIError (retval);

#ifdef DEBUG
  if (this->commRank_ == MASTER) {
    fprintf (stdout, "[DEBUG] %d RMA windows created (%d aggr., %d buffers)\n", 
	     NBUFFERS, this->nAggr_, NBUFFERS);
  }
#endif
}


/***********************/
/*     PLACEMENT       */
/***********************/
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int Tapioca::RankShortestPath (MPI_Comm aggrComm, int64_t dataSize)
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{
  int commRank, aggrRank, aggrPrank, ppn, nodeId;
  struct { int hops; int rank; } hopsToIONnode, shortestPath;

  MPI_Comm_rank (aggrComm, &commRank);
  
  hopsToIONnode.hops = topology.DistanceToIONode ( this->worldRank_ );
  hopsToIONnode.rank = commRank;

  if ( this->excludedNode[this->intCoords_] )
    hopsToIONnode.hops = INT_MAX;

  MPI_Allreduce ( &hopsToIONnode, &shortestPath, 1, MPI_2INTEGER, MPI_MINLOC, aggrComm );
  MPI_Reduce ( &dataSize, &this->aggrDataSize_, 1, MPI_LONG_LONG, MPI_SUM, shortestPath.rank, aggrComm );

  if ( shortestPath.rank == commRank ) {
    aggrRank = this->commRank_;
    this->amAnAggr_ = true;
  }

#ifdef DEBUG
  if ( shortestPath.rank == commRank )
    fprintf (stdout, "[DEBUG] Aggr. rank %d in aggrComm, distance to I/O node %d hops\n",
	     shortestPath.rank, shortestPath.hops);
#endif
  
  MPI_Bcast ( &aggrRank, 1, MPI_INT, shortestPath.rank, aggrComm);

  return aggrRank;
}


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int Tapioca::RankLongestPath (MPI_Comm aggrComm, int64_t dataSize)
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{
  int commRank, aggrRank;
  struct { int hops; int rank; } hopsToIONnode, longestPath;

  MPI_Comm_rank (aggrComm, &commRank);
  
  hopsToIONnode.hops = topology.DistanceToIONode ( this->worldRank_ );
  hopsToIONnode.rank = commRank;

  if ( this->excludedNode[this->intCoords_] )
    hopsToIONnode.hops = INT_MIN;
  
  MPI_Allreduce ( &hopsToIONnode, &longestPath, 1, MPI_2INTEGER, MPI_MAXLOC, aggrComm );
  MPI_Reduce ( &dataSize, &this->aggrDataSize_, 1, MPI_LONG_LONG, MPI_SUM, longestPath.rank, aggrComm );

  if ( longestPath.rank == commRank ) {
    aggrRank  = this->commRank_;
    this->amAnAggr_ = true;
  }

#ifdef DEBUG
  if ( longestPath.rank == commRank )
    fprintf (stdout, "[DEBUG] Aggr. rank %d in aggrComm, distance to I/O node %d hops\n",
	     longestPath.rank, longestPath.hops);
#endif
  
  MPI_Bcast ( &aggrRank, 1, MPI_INT, longestPath.rank, aggrComm);

  return aggrRank;
}


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int Tapioca::RankTopologyAware (MPI_Comm aggrComm, int64_t dataSize)
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{
  struct { double cost; int rank; } aggrCost, minCost;
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  int aggrCommRank, aggrCommSize, worldRank, rank, distance, dim, hops, aggrRank, nIOnodes;
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  int64_t *dataDistrib, aggregatedData = 0;
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  int *srcCoords, *destCoords, *globalRanks, *IOnodesList;
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  MPI_Comm_rank (aggrComm, &aggrCommRank);
  MPI_Comm_size (aggrComm, &aggrCommSize);
  MPI_Comm_rank (MPI_COMM_WORLD, &worldRank);

  aggrCost.rank = aggrCommRank;
  aggrCost.cost = 0;

  dataDistrib = (int64_t*) malloc (aggrCommSize * sizeof(int64_t));
  globalRanks = (int *) malloc (aggrCommSize * sizeof(int));
  MPI_Allgather(&worldRank, 1, MPI_INT, globalRanks, 1, MPI_INT, aggrComm);
  MPI_Allgather(&dataSize, 1, MPI_LONG_LONG, dataDistrib, 1, MPI_LONG_LONG, aggrComm);

  for ( rank = 0; rank < aggrCommSize; rank++ ) {
    aggregatedData += dataDistrib[rank];
    if ( rank != aggrCommRank ) {
      distance = topology.DistanceBetweenRanks ( globalRanks[rank], worldRank );

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      // aggrCost.cost = std::max ( distance * LATENCY + (double)dataDistrib[rank] / BANDWIDTH,
      // 			 aggrCost.cost );
      aggrCost.cost += (distance * LATENCY + (double)dataDistrib[rank] / BANDWIDTH);
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    }
  }
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  IOnodesList = (int *) malloc ( MAX_IONODES * sizeof ( int ) );
  nIOnodes = topology.IONodesPerFile (this->filename_, IOnodesList);

  if ( this->commRank_ == 0 ) {
    fprintf (stdout, "[LUSTRE] nLnet = %d\n", nIOnodes);
    fprintf (stdout, "[LUSTRE] list = ");
    for ( int i = 0; i < nIOnodes; i++ )
      fprintf (stdout, "%d ", IOnodesList[i]);
    fprintf (stdout, "\n");
  }
    
  //aggrCost.cost += topology.DistanceToIONode ( worldRank ) * LATENCY + (double)aggregatedData / BANDWIDTH;
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  if ( this->excludedNode[this->intCoords_] )
    aggrCost.cost = DBL_MAX;

  MPI_Allreduce ( &aggrCost, &minCost, 1, MPI_DOUBLE_INT, MPI_MINLOC, aggrComm );

  MPI_Reduce ( &dataSize, &this->aggrDataSize_, 1, MPI_LONG_LONG, MPI_SUM, minCost.rank, aggrComm );

  if ( minCost.rank == aggrCommRank ) {
    aggrRank = this->commRank_;
    this->amAnAggr_ = true;
  }

  MPI_Bcast ( &aggrRank, 1, MPI_INT, minCost.rank, aggrComm );

#ifdef DEBUG
  if ( minCost.rank == aggrCommRank )
    fprintf (stdout, "[DEBUG] Aggr. rank %d in aggrComm, distance to I/O node %d hops, cost: %.4f\n",
	     minCost.rank, topology.DistanceToIONode ( worldRank ), minCost.cost );
#endif

  return aggrRank;
}


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int Tapioca::RankUniformDistribution (MPI_Comm aggrComm, int64_t dataSize)
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{
  int aggrRank, aggrCommRank, rootRank = 0, rootCoords;
  
  MPI_Comm_rank (aggrComm, &aggrCommRank);

  if ( aggrCommRank == rootRank )
    rootCoords = this->intCoords_;
  
  MPI_Bcast ( &rootCoords, 1, MPI_INT, rootRank, aggrComm);
  
  while ( this->excludedNode[rootCoords] ) {
    rootRank += topology.ProcessPerNode ();
    if ( aggrCommRank == rootRank )
      rootCoords = this->intCoords_;

    MPI_Bcast ( &rootCoords, 1, MPI_INT, rootRank, aggrComm);
  }

  MPI_Reduce ( &dataSize, &this->aggrDataSize_, 1, MPI_LONG_LONG, MPI_SUM, rootRank, aggrComm );

  if ( aggrCommRank == rootRank ) {
    aggrRank = this->commRank_;
    this->amAnAggr_ = true;
  }    
  
  MPI_Bcast ( &aggrRank, 1, MPI_INT, rootRank, aggrComm);
  
  return aggrRank;
}


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int Tapioca::RankContentionAware (MPI_Comm aggrComm, int64_t dataSize)
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{
  struct { double cost; int rank; } aggrCost, minCost;
  int aggrCommRank, aggrCommSize, worldRank, rank, distance, interRanks;
  int aggrRank, dim, hops, ppn, intaggrRank, node, i;
  int64_t *dataDistrib, aggregatedData = 0;
  int *srcCoords, *destCoords, *globalRanks;
  
  char *split;
  int srcNode, destNode, interNode, srcLink, destLink;
  std::map< int, std::map<int, int> > links;
  std::map< int, std::vector<int> > routes;
  std::map< int, int > routeCost;
  int *path;

  MPI_Comm_rank (aggrComm, &aggrCommRank);
  MPI_Comm_size (aggrComm, &aggrCommSize);
  MPI_Comm_rank (MPI_COMM_WORLD, &worldRank);

  aggrCost.rank = aggrCommRank;
  aggrCost.cost = 0;

  ppn = topology.ProcessPerNode ();

  dataDistrib = (int64_t*) malloc (aggrCommSize * sizeof(int64_t));
  globalRanks = (int *) malloc (aggrCommSize * sizeof(int));
  MPI_Allgather(&worldRank, 1, MPI_INT, globalRanks, 1, MPI_INT, aggrComm);
  MPI_Allgather(&dataSize, 1, MPI_LONG_LONG, dataDistrib, 1, MPI_LONG_LONG, aggrComm);

  destNode = globalRanks[aggrCommRank]/ppn;
  
  /*
   *  Contention:
   *     - routes: map < srcNode, {<intermediate nodes>}
   *     - links: map < node, < node, weight > >
   */
  for ( rank = 0; rank < aggrCommSize; rank++ ) {
    srcNode = globalRanks[rank]/ppn;
    srcLink = srcNode;
    path = (int *)calloc (50, sizeof(int));
    
    if ( srcNode != destNode && routes.find(srcNode) == routes.end() ) {
      interRanks = topology.RouteBetweenRanks (globalRanks[rank], globalRanks[aggrCommRank], path);
      routeCost[srcNode] = 0;
      
      for ( i = 1; i < interRanks; i++ ) {
	interNode = path[i] / ppn;
	routes[srcNode].push_back (interNode);
	links[srcLink][interNode] = 0;
	srcLink = interNode;
      }
    }
    free (path);
  }

  /* I/O Node */
  path = (int *)calloc (50, sizeof(int));
  interRanks = topology.RouteToIONode (this->worldRank_, path );
  srcNode = this->worldRank_ / ppn;
  srcLink = srcNode;

  for ( i = 1; i < interRanks; i++ ) {
    interNode = path[i] / ppn;
    routes[srcNode].push_back (interNode);
    links[srcLink][interNode] = 0;
    srcLink = interNode;
  }
  free (path);

 
  for ( rank = 0; rank < aggrCommSize; rank++ ) {
    srcNode = globalRanks[rank]/ppn;
    srcLink = srcNode;
    
    if ( srcNode != destNode ) {
      for ( node = 0; node < routes[srcNode].size (); node++ ) {
	links[srcLink][routes[srcNode][node]]++;
	routeCost[srcNode] = std::max(routeCost[srcNode], links[srcLink][routes[srcNode][node]]);
	srcLink = routes[srcNode][node];
      }
    }
    else
      routeCost[srcNode] = 1;
  }

  
  for ( rank = 0; rank < aggrCommSize; rank++ ) {
    aggregatedData += dataDistrib[rank];
    srcNode = globalRanks[rank]/ppn;
    
    if ( rank != aggrCommRank ) {
      
      aggrCost.cost = std::max ( (double)dataDistrib[rank] / ( BANDWIDTH / routeCost[srcNode] ),
				 aggrCost.cost );
    }
  }

  /* I/O Node */
  srcNode = this->worldRank_ / ppn;
  aggrCost.cost += aggregatedData / ( BANDWIDTH / routeCost[srcNode] );
 
  
  if ( this->excludedNode[this->intCoords_] )
    aggrCost.cost = DBL_MAX;
  
  MPI_Allreduce ( &aggrCost, &minCost, 1, MPI_DOUBLE_INT, MPI_MINLOC, aggrComm );

  MPI_Reduce ( &dataSize, &this->aggrDataSize_, 1, MPI_LONG_LONG, MPI_SUM, minCost.rank, aggrComm );

  if ( minCost.rank == aggrCommRank ) {
    aggrRank = this->commRank_;
    this->amAnAggr_ = true;
  }

  MPI_Bcast ( &aggrRank, 1, MPI_INT, minCost.rank, aggrComm );

#ifdef DEBUG
  if ( minCost.rank == aggrCommRank )
    fprintf (stdout, "[DEBUG] Aggr. rank %d in aggrComm, distance to I/O node %d hops, cost: %.4f\n",
	     minCost.rank, topology.DistanceToIONode ( this->worldRank_ ), minCost.cost );
#endif

  return aggrRank;
}


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int Tapioca::CoordsToInt (int *coords, int dim)
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{
  int i, res = 0;

  for ( i = 0; i < dim; i++ )
    res += coords[i] * pow (10.0, (double)i);

  return res;
}

/***********************/
/*        MISC.        */
/***********************/
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const char* Tapioca::getStrategyName ()
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{
  switch (this->strategy_)
    {
    case SHORTEST_PATH:    return "Shortest path";
    case LONGEST_PATH:     return "Longest path";
    case TOPOLOGY_AWARE:   return "Topology-aware placement";
    case CONTENTION_AWARE: return "Contention-aware placement";
    case UNIFORM:          return "Uniform placement";
    default:               return "No placement strategy defined!";
    }
}


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void Tapioca::HandleMPIError (int retval) 
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{
#ifdef DEBUG
  char msg[MPI_MAX_ERROR_STRING];
  int resultlen;
  if (retval != MPI_SUCCESS) {
    MPI_Error_string(retval, msg, &resultlen);
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    fprintf(stderr, "[ERR] %s\n", msg);
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  }
#endif

  return;
}


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void Tapioca::PrintTime ( double startTime, double endTime, char* func )
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{
  double totTime, avgTime, minTime, maxTime;
  int commSize, commRank;
  
  MPI_Comm_rank(MPI_COMM_WORLD, &commRank);
  MPI_Comm_size(MPI_COMM_WORLD, &commSize);
  
  totTime = endTime - startTime;
  totTime = totTime * 1000;
  MPI_Reduce(&totTime, &avgTime, 1, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD);
  MPI_Reduce(&totTime, &maxTime, 1, MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);
  MPI_Reduce(&totTime, &minTime, 1, MPI_DOUBLE, MPI_MIN, 0, MPI_COMM_WORLD);
  if (commRank == 0) {
    avgTime = avgTime / commSize;
    fprintf (stdout, "[TIMING][AGG] %s: %.2f ms [%.2f ; %.2f]\n",
             func, avgTime, minTime, maxTime);
  }
}


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Francois Tessier committed
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void Tapioca::MPIIOInfo ( MPI_File fileHandle )
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{
  MPI_Info info;
  int flag;
  char value[1024];

  if ( this->worldRank_ == 0 ) {
    MPI_File_get_info ( fileHandle, &info );
    
    fprintf ( stdout, "[INFO] MPI Two-phases I/O\n");
    
    MPI_Info_get ( info, "cb_buffer_size", 1024, value, &flag );
    fprintf ( stdout, "[INFO] cb_buffer_size = %s\n", value );
    
    MPI_Info_get ( info, "cb_nodes", 1024, value, &flag );
    fprintf ( stdout, "[INFO] cb_nodes = %s\n", value );

    MPI_Info_get ( info, "romio_cb_read", 1024, value, &flag );
    fprintf ( stdout, "[INFO] romio_cb_read = %s\n", value );
    
    MPI_Info_get ( info, "romio_cb_write", 1024, value, &flag );
    fprintf ( stdout, "[INFO] romio_cb_write = %s\n", value );
    
    MPI_Info_get ( info, "romio_no_indep_rw", 1024, value, &flag );
    fprintf ( stdout, "[INFO] romio_no_indep_rw = %s\n", value );
  }
}