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Bugfix RBF interpolation: do not allocate memory for Phi matrix when …
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…in cpu mode. (#283)

The Phi matrix is only needed when running in memory mode.
Memory gain: matrix of size internal nodes X boundary nodes.
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David Blom committed May 18, 2016
1 parent adfaf34 commit e500130
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Showing 2 changed files with 3 additions and 80 deletions.
79 changes: 0 additions & 79 deletions src/RBFMeshMotionSolver/RBFCoarsening.C
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,6 @@

namespace rbf
{
Foam::debug::debugSwitch RBFCoarsening::debug( "RBFInterpolation", 0 );

RBFCoarsening::RBFCoarsening()
:
rbf( std::shared_ptr<RBFInterpolation> ( new RBFInterpolation() ) ),
Expand Down Expand Up @@ -278,16 +276,10 @@ namespace rbf
// Create RBF interpolator

// Run the greedy algorithm
scalar runTimeInterpolate = 0.0;
scalar runTimeError = 0.0;
scalar runTimeConvergence = 0.0;
bool addedSecondPoint = false;
int counter = selectedPositions.rows();

while ( true )
{
std::clock_t t = std::clock();

// Build the matrices used for the RBF interpolation
rbf::matrix positionsCoarse( counter, positions.cols() );
rbf::matrix valuesCoarse( positionsCoarse.rows(), positionsCoarse.cols() );
Expand All @@ -302,13 +294,6 @@ namespace rbf
// Perform the RBF interpolation.
rbfCoarse->interpolate( positionsCoarse, positionsInterpolationCoarse, valuesCoarse, valuesInterpolationCoarse );

if ( debug > 0 )
{
t = std::clock() - t;
runTimeInterpolate += static_cast<float>(t) / CLOCKS_PER_SEC;
t = std::clock();
}

// Evaluate the error
for ( int j = 0; j < valuesInterpolationCoarse.rows(); j++ )
errorList( j ) = ( valuesInterpolationCoarse.row( j ) - values.row( j ) ).norm();
Expand Down Expand Up @@ -343,13 +328,6 @@ namespace rbf
}
}

if ( debug > 0 )
{
t = std::clock() - t;
runTimeError += static_cast<float>(t) / CLOCKS_PER_SEC;
t = std::clock();
}

scalar epsilon = std::sqrt( SMALL );
error = (errorList).norm() / (values.norm() + epsilon);
errorMax = largestError / ( ( values.rowwise().norm() ).maxCoeff() + epsilon );
Expand Down Expand Up @@ -381,25 +359,10 @@ namespace rbf
// Add second point if possible
if ( twoPointSelection && index2 >= 0 && index != index2 )
{
addedSecondPoint = true;
selectedPositions.conservativeResize( selectedPositions.rows() + 1 );
selectedPositions( selectedPositions.rows() - 1 ) = index2;
counter++;
}

if ( debug > 0 )
{
t = std::clock() - t;
runTimeConvergence += static_cast<float>(t) / CLOCKS_PER_SEC;
t = std::clock();
}
}

if ( debug > 0 )
{
Info << "RBFCoarsening::debug 1. interpolate to surface = " << runTimeInterpolate << " s" << endl;
Info << "RBFCoarsening::debug 2. find largest error = " << runTimeError << " s" << ". Added second point = " << addedSecondPoint << endl;
Info << "RBFCoarsening::debug 3. convergence check = " << runTimeConvergence << " s" << endl;
}

Info << "RBF interpolation coarsening: selected " << selectedPositions.rows() << "/" << positions.rows() << " points, 2-norm(error) = "
Expand All @@ -411,24 +374,6 @@ namespace rbf
positionsCoarse.row( i ) = positions.row( selectedPositions( i ) );

usedPositions = positionsCoarse;

if ( exportTxt )
{
std::string fileNameTXT = "rbf-coarsening-greedy-selection-" + std::to_string( fileExportIndex ) + ".txt";
std::ofstream fileTXT( fileNameTXT );

if ( fileTXT.is_open() )
fileTXT << usedPositions;

std::string fileNameCSV = "rbf-coarsening-greedy-selection-" + std::to_string( fileExportIndex ) + ".csv";
std::ofstream fileCSV( fileNameCSV );
Eigen::IOFormat CSVFmt( Eigen::FullPrecision, Eigen::DontAlignCols, "," );

if ( fileCSV.is_open() )
fileCSV << usedPositions.format( CSVFmt );

fileExportIndex++;
}
}

rbf->compute( usedPositions, positionsInterpolation );
Expand Down Expand Up @@ -536,7 +481,6 @@ namespace rbf
rbf->Hhat.conservativeResize( rbf->Hhat.rows(), rbf->Hhat.cols() - nbStaticFaceCentersRemove );
}
}

usedValues.conservativeResize( usedValues.rows() - nbStaticFaceCentersRemove, usedValues.cols() );
rbf->interpolate( usedValues, valuesInterpolation );

Expand All @@ -557,19 +501,12 @@ namespace rbf

scalar R = ratioRadiusError * ( errorInterpolationCoarse.rowwise().norm() ).maxCoeff();

if ( debug > 0 )
{
Info << nl << "RBFCoarsening::correctSurface::debug 0: ratioRadiusError = " << ratioRadiusError << ", R = " << R << endl;
}

// Find nearest boundary point for each internal point. Do this only the first time
vector closestBoundaryRadius( positionsInterpolation.rows() );

if ( closestBoundaryIndexCorrection.rows() == 0 )
{
closestBoundaryIndexCorrection.conservativeResize( positionsInterpolation.rows() );
std::clock_t t = std::clock();
scalar runTimeNN = 0;

for ( int i = 0; i < positionsInterpolation.rows(); i++ )
{
Expand All @@ -590,13 +527,6 @@ namespace rbf
closestBoundaryIndexCorrection( i ) = boundaryIndex;
closestBoundaryRadius( i ) = smallestRadius;
}

if ( debug > 0 )
{
t = std::clock() - t;
runTimeNN += static_cast<float>(t) / CLOCKS_PER_SEC;
Info << "RBFCoarsening::correctSurface::debug 1. nearest neighbour selection = " << runTimeNN << " s" << endl;
}
}
else
{
Expand All @@ -607,8 +537,6 @@ namespace rbf
}

// Start doing the correction
std::clock_t t = std::clock();
scalar runTimeCorr = 0;
std::shared_ptr<rbf::RBFFunctionInterface> rbfFunction = std::shared_ptr<rbf::RBFFunctionInterface> ( new rbf::WendlandC2Function( R ) );

for ( int i = 0; i < positionsInterpolation.rows(); i++ )
Expand All @@ -617,13 +545,6 @@ namespace rbf
valuesInterpolation.row( i ) += ( fEval - valuesCorrection.row( i ) );
valuesCorrection.row( i ) = fEval;
}

if ( debug > 0 )
{
t = std::clock() - t;
runTimeCorr += static_cast<float>(t) / CLOCKS_PER_SEC;
Info << "RBFCoarsening::correctSurface::debug 2. correction evaluation = " << runTimeCorr << " s" << endl;
}
}

void RBFCoarsening::setNbMovingAndStaticFaceCenters(
Expand Down
4 changes: 3 additions & 1 deletion src/RBFMeshMotionSolver/RBFInterpolation.C
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Original file line number Diff line number Diff line change
Expand Up @@ -122,7 +122,7 @@ namespace rbf

// Radial basis function interpolation
// Initialize matrices H and Phi
matrix H( n_A, n_A ), Phi( n_B, n_A );
matrix H( n_A, n_A );

if ( polynomialTerm )
{
Expand Down Expand Up @@ -158,6 +158,8 @@ namespace rbf
{
// Evaluate Phi which contains the evaluation of the radial basis function

matrix Phi( n_B, n_A );

if ( polynomialTerm )
Phi.resize( n_B, n_A + dimGrid + 1 );

Expand Down

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