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Speed up parsing of sparse Market file.

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This commit is contained in:
Gael Guennebaud 2016-12-20 21:56:21 +01:00
parent 684cfc762d
commit e2f4ee1c2b
2 changed files with 66 additions and 37 deletions
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76
unsupported/Eigen/src/SparseExtra/MarketIO.h
View File

@ -12,38 +12,38 @@
#define EIGEN_SPARSE_MARKET_IO_H #define EIGEN_SPARSE_MARKET_IO_H
#include <iostream> #include <iostream>
#include <vector>
namespace Eigen { namespace Eigen {
namespace internal namespace internal
{ {
template <typename Scalar> template <typename Scalar, typename StorageIndex>
inline bool GetMarketLine (std::stringstream& line, Index& M, Index& N, Index& i, Index& j, Scalar& value) inline void GetMarketLine (const char* line, StorageIndex& i, StorageIndex& j, Scalar& value)
{ {
line >> i >> j >> value; std::stringstream sline(line);
i--; sline >> i >> j >> value;
j--;
if(i>=0 && j>=0 && i<M && j<N)
{
return true;
}
else
return false;
} }
template <typename Scalar>
inline bool GetMarketLine (std::stringstream& line, Index& M, Index& N, Index& i, Index& j, std::complex<Scalar>& value) template<> inline void GetMarketLine (const char* line, int& i, int& j, float& value)
{ std::sscanf(line, "%d %d %g", &i, &j, &value); }
template<> inline void GetMarketLine (const char* line, int& i, int& j, double& value)
{ std::sscanf(line, "%d %d %lg", &i, &j, &value); }
template<> inline void GetMarketLine (const char* line, int& i, int& j, std::complex<float>& value)
{ std::sscanf(line, "%d %d %g %g", &i, &j, &numext::real_ref(value), &numext::imag_ref(value)); }
template<> inline void GetMarketLine (const char* line, int& i, int& j, std::complex<double>& value)
{ std::sscanf(line, "%d %d %lg %lg", &i, &j, &numext::real_ref(value), &numext::imag_ref(value)); }
template <typename Scalar, typename StorageIndex>
inline void GetMarketLine (const char* line, StorageIndex& i, StorageIndex& j, std::complex<Scalar>& value)
{ {
std::stringstream sline(line);
Scalar valR, valI; Scalar valR, valI;
line >> i >> j >> valR >> valI; sline >> i >> j >> valR >> valI;
i--; value = std::complex<Scalar>(valR,valI);
j--;
if(i>=0 && j>=0 && i<M && j<N)
{
value = std::complex<Scalar>(valR, valI);
return true;
}
else
return false;
} }
template <typename RealScalar> template <typename RealScalar>
@ -81,13 +81,13 @@ namespace internal
} }
} }
template<typename Scalar> template<typename Scalar, typename StorageIndex>
inline void PutMatrixElt(Scalar value, int row, int col, std::ofstream& out) inline void PutMatrixElt(Scalar value, StorageIndex row, StorageIndex col, std::ofstream& out)
{ {
out << row << " "<< col << " " << value << "\n"; out << row << " "<< col << " " << value << "\n";
} }
template<typename Scalar> template<typename Scalar, typename StorageIndex>
inline void PutMatrixElt(std::complex<Scalar> value, int row, int col, std::ofstream& out) inline void PutMatrixElt(std::complex<Scalar> value, StorageIndex row, StorageIndex col, std::ofstream& out)
{ {
out << row << " " << col << " " << value.real() << " " << value.imag() << "\n"; out << row << " " << col << " " << value.real() << " " << value.imag() << "\n";
} }
@ -133,17 +133,20 @@ template<typename SparseMatrixType>
bool loadMarket(SparseMatrixType& mat, const std::string& filename) bool loadMarket(SparseMatrixType& mat, const std::string& filename)
{ {
typedef typename SparseMatrixType::Scalar Scalar; typedef typename SparseMatrixType::Scalar Scalar;
typedef typename SparseMatrixType::Index Index; typedef typename SparseMatrixType::StorageIndex StorageIndex;
std::ifstream input(filename.c_str(),std::ios::in); std::ifstream input(filename.c_str(),std::ios::in);
if(!input) if(!input)
return false; return false;
char rdbuffer[4096];
input.rdbuf()->pubsetbuf(rdbuffer, 4096);
const int maxBuffersize = 2048; const int maxBuffersize = 2048;
char buffer[maxBuffersize]; char buffer[maxBuffersize];
bool readsizes = false; bool readsizes = false;
typedef Triplet<Scalar,Index> T; typedef Triplet<Scalar,StorageIndex> T;
std::vector<T> elements; std::vector<T> elements;
Index M(-1), N(-1), NNZ(-1); Index M(-1), N(-1), NNZ(-1);
@ -155,32 +158,35 @@ bool loadMarket(SparseMatrixType& mat, const std::string& filename)
if(buffer[0]=='%') if(buffer[0]=='%')
continue; continue;
std::stringstream line(buffer);
if(!readsizes) if(!readsizes)
{ {
std::stringstream line(buffer);
line >> M >> N >> NNZ; line >> M >> N >> NNZ;
if(M > 0 && N > 0 && NNZ > 0) if(M > 0 && N > 0 && NNZ > 0)
{ {
readsizes = true; readsizes = true;
//std::cout << "sizes: " << M << "," << N << "," << NNZ << "\n";
mat.resize(M,N); mat.resize(M,N);
mat.reserve(NNZ); mat.reserve(NNZ);
} }
} }
else else
{ {
Index i(-1), j(-1); StorageIndex i(-1), j(-1);
Scalar value; Scalar value;
if( internal::GetMarketLine(line, M, N, i, j, value) ) internal::GetMarketLine(buffer, i, j, value);
i--;
j--;
if(i>=0 && j>=0 && i<M && j<N)
{ {
++ count; ++count;
elements.push_back(T(i,j,value)); elements.push_back(T(i,j,value));
} }
else else
std::cerr << "Invalid read: " << i << "," << j << "\n"; std::cerr << "Invalid read: " << i << "," << j << "\n";
} }
} }
mat.setFromTriplets(elements.begin(), elements.end()); mat.setFromTriplets(elements.begin(), elements.end());
if(count!=NNZ) if(count!=NNZ)
std::cerr << count << "!=" << NNZ << "\n"; std::cerr << count << "!=" << NNZ << "\n";

23
unsupported/test/sparse_extra.cpp
View File

@ -129,6 +129,19 @@ template<typename SparseMatrixType> void sparse_extra(const SparseMatrixType& re
} }
template<typename SparseMatrixType>
void check_marketio()
{
typedef Matrix<typename SparseMatrixType::Scalar, Dynamic, Dynamic> DenseMatrix;
Index rows = internal::random<Index>(1,100);
Index cols = internal::random<Index>(1,100);
SparseMatrixType m1, m2;
m1 = DenseMatrix::Random(rows, cols).sparseView();
saveMarket(m1, "sparse_extra.mtx");
loadMarket(m2, "sparse_extra.mtx");
VERIFY_IS_APPROX(m1,m2);
}
void test_sparse_extra() void test_sparse_extra()
{ {
for(int i = 0; i < g_repeat; i++) { for(int i = 0; i < g_repeat; i++) {
@ -143,5 +156,15 @@ void test_sparse_extra()
CALL_SUBTEST_3( (sparse_product<DynamicSparseMatrix<float, ColMajor> >()) ); CALL_SUBTEST_3( (sparse_product<DynamicSparseMatrix<float, ColMajor> >()) );
CALL_SUBTEST_3( (sparse_product<DynamicSparseMatrix<float, RowMajor> >()) ); CALL_SUBTEST_3( (sparse_product<DynamicSparseMatrix<float, RowMajor> >()) );
CALL_SUBTEST_4( (check_marketio<SparseMatrix<float,ColMajor,int> >()) );
CALL_SUBTEST_4( (check_marketio<SparseMatrix<double,ColMajor,int> >()) );
CALL_SUBTEST_4( (check_marketio<SparseMatrix<std::complex<float>,ColMajor,int> >()) );
CALL_SUBTEST_4( (check_marketio<SparseMatrix<std::complex<double>,ColMajor,int> >()) );
CALL_SUBTEST_4( (check_marketio<SparseMatrix<float,ColMajor,long int> >()) );
CALL_SUBTEST_4( (check_marketio<SparseMatrix<double,ColMajor,long int> >()) );
CALL_SUBTEST_4( (check_marketio<SparseMatrix<std::complex<float>,ColMajor,long int> >()) );
CALL_SUBTEST_4( (check_marketio<SparseMatrix<std::complex<double>,ColMajor,long int> >()) );
TEST_SET_BUT_UNUSED_VARIABLE(s);
} }
} }