// Perform the MPI scatter
public void Scatter()
{
Stopwatch scatterTimer = Stopwatch.StartNew();
TDistance[][][] sentBlockValues = new TDistance[MPI.Intracommunicator.world.Size][][];
_partialMatrix = _partialMatrix.Transpose();
for (int k = 0; k < _processBlocks[_rank].Length; k++)
{
Block block = _processBlocks[_rank][k].Transpose();
sentBlockValues[k] = _partialMatrix.GetBlockValues(block);
}
_partialMatrix = _partialMatrix.Transpose();
for (int receivedRank = 0; receivedRank < MPI.Intracommunicator.world.Size; receivedRank++)
{
TDistance[][] transposedBlockValues = MPI.Intracommunicator.world.Scatter <TDistance[][]>(sentBlockValues, receivedRank);
int rowIndex = _rank;
int columnIndex = receivedRank;
if ((rowIndex < columnIndex) && !IsOdd(rowIndex + columnIndex))
{
_partialMatrix.SetBlockValues(_processBlocks[rowIndex][columnIndex], transposedBlockValues);
}
if ((rowIndex > columnIndex) && IsOdd(rowIndex + columnIndex))
{
_partialMatrix.SetBlockValues(_processBlocks[rowIndex][columnIndex], transposedBlockValues);
}
}
_mpiScatterTime = scatterTimer.ElapsedMilliseconds;
}
public MPIComputeLowerTriangularBlocked(int size, ComputeBlockHandler blockHandler)
{
_size = size;
_blockHander = blockHandler;
_rank = MPI.Intracommunicator.world.Rank;
_processBlocks = BlockPartitioner.Partition(size, size, MPI.Intracommunicator.world.Size, MPI.Intracommunicator.world.Size);
_processRowRanges = RangePartitioner.Partition(size, MPI.Intracommunicator.world.Size);
_processRowRange = _processRowRanges[MPI.Intracommunicator.world.Rank];
_partialMatrix = new PartialMatrix <TDistance>(_processRowRange.StartIndex, _processRowRange.EndIndex, 0, size - 1);
}
static int ComputeBlock(Block block, PartialMatrix <TDistance> matrix, bool isDiagonal)
{
int count = 0;
SmithWatermanGotoh aligner = new SmithWatermanGotoh(_alignmentType);
ScoringMatrix scoringMatrix = ScoringMatrix.Load(_scoringMatrixName);
if (isDiagonal)
{
for (int i = block.RowRange.StartIndex; i <= block.RowRange.EndIndex; i++)
{
Sequence si = _sequences[i];
for (int j = block.ColumnRange.StartIndex; j < i; j++)
{
Sequence sj = _sequences[j];
PairwiseAlignment alignment = aligner.Align(si, sj, scoringMatrix, _gapOpen, _gapExtension);
if ((_writeAlignments) && (_writeAlignmentsWriter != null))
{
WriteAlignment(_writeAlignmentsWriter, alignment);
}
matrix[i, j] = matrix[j, i] = ComputeDistance(alignment);
count++;
}
}
}
else
{
for (int i = block.RowRange.StartIndex; i <= block.RowRange.EndIndex; i++)
{
Sequence si = _sequences[i];
for (int j = block.ColumnRange.StartIndex; j <= block.ColumnRange.EndIndex; j++)
{
Sequence sj = _sequences[j];
PairwiseAlignment alignment = aligner.Align(si, sj, scoringMatrix, _gapOpen, _gapExtension);
if ((_writeAlignments) && (_writeAlignmentsWriter != null))
{
WriteAlignment(_writeAlignmentsWriter, alignment);
}
matrix[i, j] = ComputeDistance(alignment);
count++;
}
}
}
return(count);
}
