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authorGravatar Gael Guennebaud <g.gael@free.fr>2015-03-31 22:54:47 +0200
committerGravatar Gael Guennebaud <g.gael@free.fr>2015-03-31 22:54:47 +0200
commit3c38589984b784687944872534f48f4e0ae22d6c (patch)
tree012d54c991e6fbebb5abad7666dbe2b3534a57d2
parent8313fb7df7f5f116834b412d6a6f5aff8862a173 (diff)
Remove most of the dynamic memory allocations that occured in D&C SVD. Still remains the calls to JacobiSVD and UpperBidiagonalization.
-rw-r--r--Eigen/IterativeLinearSolvers2
-rw-r--r--Eigen/src/SVD/BDCSVD.h94
2 files changed, 59 insertions, 37 deletions
diff --git a/Eigen/IterativeLinearSolvers b/Eigen/IterativeLinearSolvers
index 7fab9eed0..f5fdcd9e5 100644
--- a/Eigen/IterativeLinearSolvers
+++ b/Eigen/IterativeLinearSolvers
@@ -17,7 +17,7 @@
*
* These iterative solvers are associated with some preconditioners:
* - IdentityPreconditioner - not really useful
- * - DiagonalPreconditioner - also called JAcobi preconditioner, work very well on diagonal dominant matrices.
+ * - DiagonalPreconditioner - also called Jacobi preconditioner, work very well on diagonal dominant matrices.
* - IncompleteLUT - incomplete LU factorization with dual thresholding
*
* Such problems can also be solved using the direct sparse decomposition modules: SparseCholesky, CholmodSupport, UmfPackSupport, SuperLUSupport.
diff --git a/Eigen/src/SVD/BDCSVD.h b/Eigen/src/SVD/BDCSVD.h
index cace915e7..9b141c8df 100644
--- a/Eigen/src/SVD/BDCSVD.h
+++ b/Eigen/src/SVD/BDCSVD.h
@@ -84,6 +84,8 @@ public:
typedef Matrix<RealScalar, Dynamic, 1> VectorType;
typedef Array<RealScalar, Dynamic, 1> ArrayXr;
typedef Array<Index,1,Dynamic> ArrayXi;
+ typedef Ref<ArrayXr> ArrayRef;
+ typedef Ref<ArrayXi> IndicesRef;
/** \brief Default Constructor.
*
@@ -159,21 +161,23 @@ private:
void allocate(Index rows, Index cols, unsigned int computationOptions);
void divide(Index firstCol, Index lastCol, Index firstRowW, Index firstColW, Index shift);
void computeSVDofM(Index firstCol, Index n, MatrixXr& U, VectorType& singVals, MatrixXr& V);
- void computeSingVals(const ArrayXr& col0, const ArrayXr& diag, const ArrayXi& perm, VectorType& singVals, ArrayXr& shifts, ArrayXr& mus);
- void perturbCol0(const ArrayXr& col0, const ArrayXr& diag, const ArrayXi& perm, const VectorType& singVals, const ArrayXr& shifts, const ArrayXr& mus, ArrayXr& zhat);
- void computeSingVecs(const ArrayXr& zhat, const ArrayXr& diag, const ArrayXi& perm, const VectorType& singVals, const ArrayXr& shifts, const ArrayXr& mus, MatrixXr& U, MatrixXr& V);
+ void computeSingVals(const ArrayRef& col0, const ArrayRef& diag, const IndicesRef& perm, VectorType& singVals, ArrayRef shifts, ArrayRef mus);
+ void perturbCol0(const ArrayRef& col0, const ArrayRef& diag, const IndicesRef& perm, const VectorType& singVals, const ArrayRef& shifts, const ArrayRef& mus, ArrayRef zhat);
+ void computeSingVecs(const ArrayRef& zhat, const ArrayRef& diag, const IndicesRef& perm, const VectorType& singVals, const ArrayRef& shifts, const ArrayRef& mus, MatrixXr& U, MatrixXr& V);
void deflation43(Index firstCol, Index shift, Index i, Index size);
void deflation44(Index firstColu , Index firstColm, Index firstRowW, Index firstColW, Index i, Index j, Index size);
void deflation(Index firstCol, Index lastCol, Index k, Index firstRowW, Index firstColW, Index shift);
template<typename HouseholderU, typename HouseholderV, typename NaiveU, typename NaiveV>
void copyUV(const HouseholderU &householderU, const HouseholderV &householderV, const NaiveU &naiveU, const NaiveV &naivev);
- static void structured_update(Block<MatrixXr,Dynamic,Dynamic> A, const MatrixXr &B, Index n1);
- static RealScalar secularEq(RealScalar x, const ArrayXr& col0, const ArrayXr& diag, const ArrayXi &perm, const ArrayXr& diagShifted, RealScalar shift);
+ void structured_update(Block<MatrixXr,Dynamic,Dynamic> A, const MatrixXr &B, Index n1);
+ static RealScalar secularEq(RealScalar x, const ArrayRef& col0, const ArrayRef& diag, const IndicesRef &perm, const ArrayRef& diagShifted, RealScalar shift);
protected:
MatrixXr m_naiveU, m_naiveV;
MatrixXr m_computed;
Index m_nRec;
+ ArrayXr m_workspace;
+ ArrayXi m_workspaceI;
int m_algoswap;
bool m_isTranspose, m_compU, m_compV;
@@ -212,6 +216,9 @@ void BDCSVD<MatrixType>::allocate(Index rows, Index cols, unsigned int computati
else m_naiveU = MatrixXr::Zero(2, m_diagSize + 1 );
if (m_compV) m_naiveV = MatrixXr::Zero(m_diagSize, m_diagSize);
+
+ m_workspace.resize((m_diagSize+1)*(m_diagSize+1)*3);
+ m_workspaceI.resize(3*m_diagSize);
}// end allocate
template<typename MatrixType>
@@ -226,6 +233,7 @@ BDCSVD<MatrixType>& BDCSVD<MatrixType>::compute(const MatrixType& matrix, unsign
//**** step -1 - If the problem is too small, directly falls back to JacobiSVD and return
if(matrix.cols() < m_algoswap)
{
+ // FIXME this line involves temporaries
JacobiSVD<MatrixType> jsvd(matrix,computationOptions);
if(computeU()) m_matrixU = jsvd.matrixU();
if(computeV()) m_matrixV = jsvd.matrixV();
@@ -243,11 +251,13 @@ BDCSVD<MatrixType>& BDCSVD<MatrixType>::compute(const MatrixType& matrix, unsign
else copy = matrix/scale;
//**** step 1 - Bidiagonalization
+ // FIXME this line involves temporaries
internal::UpperBidiagonalization<MatrixX> bid(copy);
//**** step 2 - Divide & Conquer
m_naiveU.setZero();
m_naiveV.setZero();
+ // FIXME this line involves a temporary matrix
m_computed.topRows(m_diagSize) = bid.bidiagonal().toDenseMatrix().transpose();
m_computed.template bottomRows<1>().setZero();
divide(0, m_diagSize - 1, 0, 0, 0);
@@ -292,14 +302,14 @@ void BDCSVD<MatrixType>::copyUV(const HouseholderU &householderU, const Househol
Index Ucols = m_computeThinU ? m_diagSize : householderU.cols();
m_matrixU = MatrixX::Identity(householderU.cols(), Ucols);
m_matrixU.topLeftCorner(m_diagSize, m_diagSize) = naiveV.template cast<Scalar>().topLeftCorner(m_diagSize, m_diagSize);
- householderU.applyThisOnTheLeft(m_matrixU);
+ householderU.applyThisOnTheLeft(m_matrixU); // FIXME this line involves a temporary buffer
}
if (computeV())
{
Index Vcols = m_computeThinV ? m_diagSize : householderV.cols();
m_matrixV = MatrixX::Identity(householderV.cols(), Vcols);
m_matrixV.topLeftCorner(m_diagSize, m_diagSize) = naiveU.template cast<Scalar>().topLeftCorner(m_diagSize, m_diagSize);
- householderV.applyThisOnTheLeft(m_matrixV);
+ householderV.applyThisOnTheLeft(m_matrixV); // FIXME this line involves a temporary buffer
}
}
@@ -320,7 +330,10 @@ void BDCSVD<MatrixType>::structured_update(Block<MatrixXr,Dynamic,Dynamic> A, co
// If the matrices are large enough, let's exploit the sparse structure of A by
// splitting it in half (wrt n1), and packing the non-zero columns.
Index n2 = n - n1;
- MatrixXr A1(n1,n), A2(n2,n), B1(n,n), B2(n,n);
+ Map<MatrixXr> A1(m_workspace.data() , n1, n);
+ Map<MatrixXr> A2(m_workspace.data()+ n1*n, n2, n);
+ Map<MatrixXr> B1(m_workspace.data()+ n*n, n, n);
+ Map<MatrixXr> B2(m_workspace.data()+2*n*n, n, n);
Index k1=0, k2=0;
for(Index j=0; j<n; ++j)
{
@@ -342,7 +355,11 @@ void BDCSVD<MatrixType>::structured_update(Block<MatrixXr,Dynamic,Dynamic> A, co
A.bottomRows(n2).noalias() = A2.leftCols(k2) * B2.topRows(k2);
}
else
- A *= B; // FIXME this requires a temporary
+ {
+ Map<MatrixXr,Aligned> tmp(m_workspace.data(),n,n);
+ tmp.noalias() = A*B;
+ A = tmp;
+ }
}
// The divide algorithm is done "in place", we are always working on subsets of the same matrix. The divide methods takes as argument the
@@ -373,7 +390,8 @@ void BDCSVD<MatrixType>::divide (Index firstCol, Index lastCol, Index firstRowW,
// matrices.
if (n < m_algoswap)
{
- JacobiSVD<MatrixXr> b(m_computed.block(firstCol, firstCol, n + 1, n), ComputeFullU | (m_compV ? ComputeFullV : 0)) ;
+ // FIXME this line involves temporaries
+ JacobiSVD<MatrixXr> b(m_computed.block(firstCol, firstCol, n + 1, n), ComputeFullU | (m_compV ? ComputeFullV : 0));
if (m_compU)
m_naiveU.block(firstCol, firstCol, n + 1, n + 1).real() = b.matrixU();
else
@@ -504,8 +522,14 @@ void BDCSVD<MatrixType>::divide (Index firstCol, Index lastCol, Index firstRowW,
assert(VofSVD.allFinite());
#endif
- if (m_compU) structured_update(m_naiveU.block(firstCol, firstCol, n + 1, n + 1), UofSVD, (n+2)/2);
- else m_naiveU.middleCols(firstCol, n + 1) *= UofSVD; // FIXME this requires a temporary, and exploit that there are 2 rows at compile time
+ if (m_compU)
+ structured_update(m_naiveU.block(firstCol, firstCol, n + 1, n + 1), UofSVD, (n+2)/2);
+ else
+ {
+ Map<Matrix<RealScalar,2,Dynamic>,Aligned> tmp(m_workspace.data(),2,n+1);
+ tmp.noalias() = m_naiveU.middleCols(firstCol, n+1) * UofSVD;
+ m_naiveU.middleCols(firstCol, n + 1) = tmp;
+ }
if (m_compV) structured_update(m_naiveV.block(firstRowW, firstColW, n, n), VofSVD, (n+1)/2);
@@ -530,10 +554,9 @@ void BDCSVD<MatrixType>::divide (Index firstCol, Index lastCol, Index firstRowW,
template <typename MatrixType>
void BDCSVD<MatrixType>::computeSVDofM(Index firstCol, Index n, MatrixXr& U, VectorType& singVals, MatrixXr& V)
{
- // TODO Get rid of these copies (?)
- // FIXME at least preallocate them
- ArrayXr col0 = m_computed.col(firstCol).segment(firstCol, n);
- ArrayXr diag = m_computed.block(firstCol, firstCol, n, n).diagonal();
+ ArrayRef col0 = m_computed.col(firstCol).segment(firstCol, n);
+ m_workspace.head(n) = m_computed.block(firstCol, firstCol, n, n).diagonal();
+ ArrayRef diag = m_workspace.head(n);
diag(0) = 0;
// Allocate space for singular values and vectors
@@ -552,13 +575,14 @@ void BDCSVD<MatrixType>::computeSVDofM(Index firstCol, Index n, MatrixXr& U, Vec
Index actual_n = n;
while(actual_n>1 && diag(actual_n-1)==0) --actual_n;
Index m = 0; // size of the deflated problem
- ArrayXi perm(actual_n);
for(Index k=0;k<actual_n;++k)
if(col0(k)!=0)
- perm(m++) = k;
- perm.conservativeResize(m);
+ m_workspaceI(m++) = k;
+ Map<ArrayXi> perm(m_workspaceI.data(),m);
- ArrayXr shifts(n), mus(n), zhat(n);
+ Map<ArrayXr> shifts(m_workspace.data()+1*n, n);
+ Map<ArrayXr> mus(m_workspace.data()+2*n, n);
+ Map<ArrayXr> zhat(m_workspace.data()+3*n, n);
#ifdef EIGEN_BDCSVD_DEBUG_VERBOSE
std::cout << "computeSVDofM using:\n";
@@ -635,8 +659,8 @@ void BDCSVD<MatrixType>::computeSVDofM(Index firstCol, Index n, MatrixXr& U, Vec
// Reverse order so that singular values in increased order
// Because of deflation, the zeros singular-values are already at the end
singVals.head(actual_n).reverseInPlace();
- U.leftCols(actual_n) = U.leftCols(actual_n).rowwise().reverse().eval(); // FIXME this requires a temporary
- if (m_compV) V.leftCols(actual_n) = V.leftCols(actual_n).rowwise().reverse().eval(); // FIXME this requires a temporary
+ U.leftCols(actual_n).rowwise().reverseInPlace();
+ if (m_compV) V.leftCols(actual_n).rowwise().reverseInPlace();
#ifdef EIGEN_BDCSVD_DEBUG_VERBOSE
JacobiSVD<MatrixXr> jsvd(m_computed.block(firstCol, firstCol, n, n) );
@@ -647,7 +671,7 @@ void BDCSVD<MatrixType>::computeSVDofM(Index firstCol, Index n, MatrixXr& U, Vec
}
template <typename MatrixType>
-typename BDCSVD<MatrixType>::RealScalar BDCSVD<MatrixType>::secularEq(RealScalar mu, const ArrayXr& col0, const ArrayXr& diag, const ArrayXi &perm, const ArrayXr& diagShifted, RealScalar shift)
+typename BDCSVD<MatrixType>::RealScalar BDCSVD<MatrixType>::secularEq(RealScalar mu, const ArrayRef& col0, const ArrayRef& diag, const IndicesRef &perm, const ArrayRef& diagShifted, RealScalar shift)
{
Index m = perm.size();
RealScalar res = 1;
@@ -660,8 +684,8 @@ typename BDCSVD<MatrixType>::RealScalar BDCSVD<MatrixType>::secularEq(RealScalar
}
template <typename MatrixType>
-void BDCSVD<MatrixType>::computeSingVals(const ArrayXr& col0, const ArrayXr& diag, const ArrayXi &perm,
- VectorType& singVals, ArrayXr& shifts, ArrayXr& mus)
+void BDCSVD<MatrixType>::computeSingVals(const ArrayRef& col0, const ArrayRef& diag, const IndicesRef &perm,
+ VectorType& singVals, ArrayRef shifts, ArrayRef mus)
{
using std::abs;
using std::swap;
@@ -716,7 +740,8 @@ void BDCSVD<MatrixType>::computeSingVals(const ArrayXr& col0, const ArrayXr& dia
RealScalar shift = (k == actual_n-1 || fMid > 0) ? left : right;
// measure everything relative to shift
- ArrayXr diagShifted = diag - shift;
+ Map<ArrayXr> diagShifted(m_workspace.data()+4*n, n);
+ diagShifted = diag - shift;
// initial guess
RealScalar muPrev, muCur;
@@ -831,8 +856,8 @@ void BDCSVD<MatrixType>::computeSingVals(const ArrayXr& col0, const ArrayXr& dia
// zhat is perturbation of col0 for which singular vectors can be computed stably (see Section 3.1)
template <typename MatrixType>
void BDCSVD<MatrixType>::perturbCol0
- (const ArrayXr& col0, const ArrayXr& diag, const ArrayXi &perm, const VectorType& singVals,
- const ArrayXr& shifts, const ArrayXr& mus, ArrayXr& zhat)
+ (const ArrayRef& col0, const ArrayRef& diag, const IndicesRef &perm, const VectorType& singVals,
+ const ArrayRef& shifts, const ArrayRef& mus, ArrayRef zhat)
{
using std::sqrt;
Index n = col0.size();
@@ -880,8 +905,8 @@ void BDCSVD<MatrixType>::perturbCol0
// compute singular vectors
template <typename MatrixType>
void BDCSVD<MatrixType>::computeSingVecs
- (const ArrayXr& zhat, const ArrayXr& diag, const ArrayXi &perm, const VectorType& singVals,
- const ArrayXr& shifts, const ArrayXr& mus, MatrixXr& U, MatrixXr& V)
+ (const ArrayRef& zhat, const ArrayRef& diag, const IndicesRef &perm, const VectorType& singVals,
+ const ArrayRef& shifts, const ArrayRef& mus, MatrixXr& U, MatrixXr& V)
{
Index n = zhat.size();
Index m = perm.size();
@@ -1062,7 +1087,7 @@ void BDCSVD<MatrixType>::deflation(Index firstCol, Index lastCol, Index k, Index
// Sort the diagonal entries, since diag(1:k-1) and diag(k:length) are already sorted, let's do a sorted merge.
// First, compute the respective permutation.
- Index *permutation = new Index[length]; // FIXME avoid repeated dynamic memory allocation
+ Index *permutation = m_workspaceI.data();
{
permutation[0] = 0;
Index p = 1;
@@ -1099,8 +1124,8 @@ void BDCSVD<MatrixType>::deflation(Index firstCol, Index lastCol, Index k, Index
}
// Current index of each col, and current column of each index
- Index *realInd = new Index[length]; // FIXME avoid repeated dynamic memory allocation
- Index *realCol = new Index[length]; // FIXME avoid repeated dynamic memory allocation
+ Index *realInd = m_workspaceI.data()+length;
+ Index *realCol = m_workspaceI.data()+2*length;
for(int pos = 0; pos< length; pos++)
{
@@ -1130,9 +1155,6 @@ void BDCSVD<MatrixType>::deflation(Index firstCol, Index lastCol, Index k, Index
realInd[J] = realI;
realInd[i] = pi;
}
- delete[] permutation;
- delete[] realInd;
- delete[] realCol;
}
#ifdef EIGEN_BDCSVD_DEBUG_VERBOSE
std::cout << "sorted: " << diag.transpose().format(bdcsvdfmt) << "\n";