void MatrixMarketReader<FloatType>::MMGenerateCOOFromFile( FILE *infile, cl_bool read_explicit_zeroes )
{
clsparseIdx_t unsym_actual_nnz = 0;
FloatType val;
clsparseIdx_t ir, ic;
const int exp_zeroes = read_explicit_zeroes;
//silence warnings from fscanf (-Wunused-result)
clsparseIdx_t rv = 0;
for ( clsparseIdx_t i = 0; i < nNZ; i++)
{
if( mm_is_real( Typecode ) )
{
fscanf(infile, "%" SIZET "u", &ir);
fscanf(infile, "%" SIZET "u", &ic);
if (typeid(FloatType) == typeid(float))
rv = fscanf(infile, "%f\n", (float*)(&val));
else if( typeid( FloatType ) == typeid( double ) )
rv = fscanf( infile, "%lf\n", (double*)( &val ) );
if( exp_zeroes == 0 && val == 0 )
continue;
else
FillCoordData( Typecode, unsym_coords, unsym_actual_nnz, ir, ic, val );
}
else if( mm_is_integer( Typecode ) )
{
fscanf(infile, "%" SIZET "u", &ir);
fscanf(infile, "%" SIZET "u", &ic);
if(typeid(FloatType) == typeid(float))
rv = fscanf(infile, "%f\n", (float*)( &val ) );
else if(typeid(FloatType) == typeid(double))
rv = fscanf(infile, "%lf\n", (double*)( &val ) );
if( exp_zeroes == 0 && val == 0 )
continue;
else
FillCoordData( Typecode, unsym_coords, unsym_actual_nnz, ir, ic, val );
}
else if( mm_is_pattern( Typecode ) )
{
rv = fscanf(infile, "%" SIZET "u", &ir);
rv = fscanf(infile, "%" SIZET "u", &ic);
val = static_cast<FloatType>( MAX_RAND_VAL * ( rand( ) / ( RAND_MAX + 1.0 ) ) );
if( exp_zeroes == 0 && val == 0 )
continue;
else
FillCoordData( Typecode, unsym_coords, unsym_actual_nnz, ir, ic, val );
}
}
nNZ = unsym_actual_nnz;
}
int mm_read_mtx_crd_entry(FILE *f, int *I, int *J,
double *real, double *imag, MM_typecode matcode)
{
if (mm_is_complex(matcode))
{
if (fscanf(f, "%d %d %lg %lg", I, J, real, imag)
!= 4) return MM_PREMATURE_EOF;
}
else if (mm_is_real(matcode))
{
if (fscanf(f, "%d %d %lg\n", I, J, real)
!= 3) return MM_PREMATURE_EOF;
}
/** ADDITION: Integer format, just parse as double */
else if (mm_is_integer(matcode))
{
if (fscanf(f, "%d %d %lg\n", I, J, real)
!= 3) return MM_PREMATURE_EOF;
}
else if (mm_is_pattern(matcode))
{
if (fscanf(f, "%d %d", I, J) != 2) return MM_PREMATURE_EOF;
}
else
return MM_UNSUPPORTED_TYPE;
return 0;
}
char *mm_typecode_to_str(MM_typecode matcode)
{
char buffer[MM_MAX_LINE_LENGTH];
char *types[4];
int error =0;
int i;
/* check for MTX type */
if (mm_is_matrix(matcode))
types[0] = MM_MTX_STR;
else
error=1;
/* check for CRD or ARR matrix */
if (mm_is_sparserow(matcode))
types[1] = MM_SPARSEROW_STR;
else
if (mm_is_coordinate(matcode))
types[1] = MM_COORDINATE_STR;
else
if (mm_is_dense(matcode))
types[1] = MM_DENSE_STR;
else
return NULL;
/* check for element data type */
if (mm_is_real(matcode))
types[2] = MM_REAL_STR;
else
if (mm_is_complex(matcode))
types[2] = MM_COMPLEX_STR;
else
if (mm_is_pattern(matcode))
types[2] = MM_PATTERN_STR;
else
if (mm_is_integer(matcode))
types[2] = MM_INT_STR;
else
return NULL;
/* check for symmetry type */
if (mm_is_general(matcode))
types[3] = MM_GENERAL_STR;
else
if (mm_is_symmetric(matcode))
types[3] = MM_SYMM_STR;
else
if (mm_is_hermitian(matcode))
types[3] = MM_HERM_STR;
else
if (mm_is_skew(matcode))
types[3] = MM_SKEW_STR;
else
return NULL;
sprintf(buffer,"%s %s %s %s", types[0], types[1], types[2], types[3]);
return strdup(buffer);
}
void mm_typecode_to_str(MM_typecode matcode, char * buffer)
{
char type0[20];
char type1[20];
char type2[20];
char type3[20];
int error =0;
/* check for MTX type */
if (mm_is_matrix(matcode))
strcpy(type0, MM_MTX_STR);
else
error=1;
/* check for CRD or ARR matrix */
if (mm_is_sparse(matcode))
strcpy(type1, MM_SPARSE_STR);
else
if (mm_is_dense(matcode))
strcpy(type1, MM_DENSE_STR);
else
return;
/* check for element data type */
if (mm_is_real(matcode))
strcpy(type2, MM_REAL_STR);
else
if (mm_is_complex(matcode))
strcpy(type2, MM_COMPLEX_STR);
else
if (mm_is_pattern(matcode))
strcpy(type2, MM_PATTERN_STR);
else
if (mm_is_integer(matcode))
strcpy(type2, MM_INT_STR);
else
return;
/* check for symmetry type */
if (mm_is_general(matcode))
strcpy(type3, MM_GENERAL_STR);
else
if (mm_is_symmetric(matcode))
strcpy(type3, MM_SYMM_STR);
else
if (mm_is_hermitian(matcode))
strcpy(type3, MM_HERM_STR);
else
if (mm_is_skew(matcode))
strcpy(type3, MM_SKEW_STR);
else
return;
sprintf(buffer,"%s %s %s %s", type0, type1, type2, type3);
return;
}
void MatrixMarketReader<FloatType>::MMGenerateCOOFromFile( FILE *infile )
{
int unsym_actual_nnz = 0;
FloatType val;
int ir, ic;
const int exp_zeroes = 0;
for( int i = 0; i < nNZ; i++ )
{
if( mm_is_real( Typecode ) )
{
if( typeid( FloatType ) == typeid( float ) )
fscanf( infile, "%d %d %f\n", &ir, &ic, &val );
else if( typeid( FloatType ) == typeid( double ) )
fscanf( infile, "%d %d %lf\n", &ir, &ic, &val );
if( exp_zeroes == 0 && val == 0 )
continue;
else
FillCoordData( Typecode, unsym_coords, unsym_actual_nnz, ir, ic, val );
}
else if( mm_is_integer( Typecode ) )
{
if(typeid(FloatType) == typeid(float))
fscanf(infile, "%d %d %f\n", &ir, &ic, &val);
else if(typeid(FloatType) == typeid(double))
fscanf(infile, "%d %d %lf\n", &ir, &ic, &val);
if( exp_zeroes == 0 && val == 0 )
continue;
else
FillCoordData( Typecode, unsym_coords, unsym_actual_nnz, ir, ic, val );
}
else if( mm_is_pattern( Typecode ) )
{
fscanf( infile, "%d %d", &ir, &ic );
val = static_cast<FloatType>( MAX_RAND_VAL * ( rand( ) / ( RAND_MAX + 1.0 ) ) );
if( exp_zeroes == 0 && val == 0 )
continue;
else
FillCoordData( Typecode, unsym_coords, unsym_actual_nnz, ir, ic, val );
}
}
nNZ = unsym_actual_nnz;
}
/* mm_real supports real symmetric/general sparse/dense matrix */
static bool
is_type_supported (const MM_typecode typecode)
{
// invalid type
if (!mm_is_valid (typecode)) return false;
// pattern is not supported
if (mm_is_pattern (typecode)) return false;
// integer and complex matrix are not supported
if (mm_is_integer (typecode) || mm_is_complex (typecode)) return false;
// skew and hermitian are not supported
if (mm_is_skew (typecode) || mm_is_hermitian (typecode)) return false;
return true;
}
bool loadMmProperties(int *rowsCount,
int *columnsCount,
int *nonZerosCount,
bool *isStoredSparse,
int* matrixStorage,
int* matrixType,
FILE *file)
{
MM_typecode matcode;
// supports only valid matrices
if ((mm_read_banner(file, &matcode) != 0)
|| (!mm_is_matrix(matcode))
|| (!mm_is_valid(matcode)))
return false;
if ( mm_read_mtx_crd_size(file, rowsCount, columnsCount, nonZerosCount) != 0 )
return false;
// is it stored sparse?
if (mm_is_sparse(matcode))
*isStoredSparse = true;
else
*isStoredSparse = false;
if (mm_is_integer(matcode))
*matrixStorage = MATRIX_STORAGE_INTEGER;
else if (mm_is_real(matcode))
*matrixStorage = MATRIX_STORAGE_REAL;
else if (mm_is_complex(matcode))
*matrixStorage = MATRIX_STORAGE_COMPLEX;
else if (mm_is_pattern(matcode))
*matrixStorage = MATRIX_STORAGE_PATTERN;
if (mm_is_general(matcode))
*matrixType = MATRIX_TYPE_GENERAL;
else if (mm_is_symmetric(matcode))
*matrixType = MATRIX_TYPE_SYMMETRIC;
else if (mm_is_skew(matcode))
*matrixType = MATRIX_TYPE_SKEW;
else if (mm_is_hermitian(matcode))
*matrixType = MATRIX_TYPE_HERMITIAN;
return true;
}
int get_mm_info(const char *file, int *m, int *n, int *nz)
{
FILE *fp;
MM_typecode matcode;
if ((fp = fopen(file, "r")) == NULL)
{
fprintf(stderr,"ERROR: Could not open file: %s\n",file);
exit(1);
}
if (mm_read_banner(fp, &matcode) != 0)
{
fprintf(stderr,"ERROR: Could not process Matrix Market banner.\n");
exit(1);
}
if (!(mm_is_real(matcode) || mm_is_integer(matcode)))
{
fprintf(stderr,"ERROR: Market Market type: [%s] not supported\n",
mm_typecode_to_str(matcode));
exit(1);
}
if (mm_is_sparse(matcode))
{
if (mm_read_mtx_crd_size(fp, m, n, nz) !=0)
{ /* find out size of sparse matrix */
exit(1);
}
}
else
{
if (mm_read_mtx_array_size(fp, m, n) !=0)
{ /* find out size of dense matrix */
exit(1);
}
*nz = -1;
}
fclose(fp);
return 0;
}
magma_int_t
magma_d_csr_mtx(
magma_d_matrix *A,
const char *filename,
magma_queue_t queue )
{
char buffer[ 1024 ];
magma_int_t info = 0;
int csr_compressor = 0; // checks for zeros in original file
magma_d_matrix B={Magma_CSR};
magma_index_t *coo_col = NULL;
magma_index_t *coo_row = NULL;
double *coo_val = NULL;
double *new_val = NULL;
magma_index_t* new_row = NULL;
magma_index_t* new_col = NULL;
magma_int_t symmetric = 0;
std::vector< std::pair< magma_index_t, double > > rowval;
FILE *fid = NULL;
MM_typecode matcode;
fid = fopen(filename, "r");
if (fid == NULL) {
printf("%% Unable to open file %s\n", filename);
info = MAGMA_ERR_NOT_FOUND;
goto cleanup;
}
printf("%% Reading sparse matrix from file (%s):", filename);
fflush(stdout);
if (mm_read_banner(fid, &matcode) != 0) {
printf("\n%% Could not process Matrix Market banner: %s.\n", matcode);
info = MAGMA_ERR_NOT_SUPPORTED;
goto cleanup;
}
if (!mm_is_valid(matcode)) {
printf("\n%% Invalid Matrix Market file.\n");
info = MAGMA_ERR_NOT_SUPPORTED;
goto cleanup;
}
if ( ! ( ( mm_is_real(matcode) ||
mm_is_integer(matcode) ||
mm_is_pattern(matcode) ||
mm_is_real(matcode) ) &&
mm_is_coordinate(matcode) &&
mm_is_sparse(matcode) ) )
{
mm_snprintf_typecode( buffer, sizeof(buffer), matcode );
printf("\n%% Sorry, MAGMA-sparse does not support Market Market type: [%s]\n", buffer );
printf("%% Only real-valued or pattern coordinate matrices are supported.\n");
info = MAGMA_ERR_NOT_SUPPORTED;
goto cleanup;
}
magma_index_t num_rows, num_cols, num_nonzeros;
if (mm_read_mtx_crd_size(fid, &num_rows, &num_cols, &num_nonzeros) != 0) {
info = MAGMA_ERR_UNKNOWN;
goto cleanup;
}
A->storage_type = Magma_CSR;
A->memory_location = Magma_CPU;
A->num_rows = num_rows;
A->num_cols = num_cols;
A->nnz = num_nonzeros;
A->fill_mode = MagmaFull;
CHECK( magma_index_malloc_cpu( &coo_col, A->nnz ) );
CHECK( magma_index_malloc_cpu( &coo_row, A->nnz ) );
CHECK( magma_dmalloc_cpu( &coo_val, A->nnz ) );
if (mm_is_real(matcode) || mm_is_integer(matcode)) {
for(magma_int_t i = 0; i < A->nnz; ++i) {
magma_index_t ROW, COL;
double VAL; // always read in a double and convert later if necessary
fscanf(fid, " %d %d %lf \n", &ROW, &COL, &VAL);
if ( VAL == 0 )
csr_compressor = 1;
coo_row[i] = ROW - 1;
coo_col[i] = COL - 1;
coo_val[i] = MAGMA_D_MAKE( VAL, 0.);
}
} else if (mm_is_pattern(matcode) ) {
for(magma_int_t i = 0; i < A->nnz; ++i) {
magma_index_t ROW, COL;
fscanf(fid, " %d %d \n", &ROW, &COL );
coo_row[i] = ROW - 1;
coo_col[i] = COL - 1;
coo_val[i] = MAGMA_D_MAKE( 1.0, 0.);
}
} else if (mm_is_real(matcode) ){
for(magma_int_t i = 0; i < A->nnz; ++i) {
magma_index_t ROW, COL;
double VAL, VALC; // always read in a double and convert later if necessary
fscanf(fid, " %d %d %lf %lf\n", &ROW, &COL, &VAL, &VALC);
coo_row[i] = ROW - 1;
coo_col[i] = COL - 1;
coo_val[i] = MAGMA_D_MAKE( VAL, VALC);
}
// printf(" ...successfully read real matrix... ");
} else {
printf("\n%% Unrecognized data type\n");
info = MAGMA_ERR_NOT_SUPPORTED;
goto cleanup;
}
fclose(fid);
fid = NULL;
printf(" done. Converting to CSR:");
fflush(stdout);
A->sym = Magma_GENERAL;
if( mm_is_symmetric(matcode) ) {
symmetric = 1;
}
if ( mm_is_symmetric(matcode) || mm_is_symmetric(matcode) ) {
// duplicate off diagonal entries
printf("\n%% Detected symmetric case.");
A->sym = Magma_SYMMETRIC;
magma_index_t off_diagonals = 0;
for(magma_int_t i = 0; i < A->nnz; ++i) {
if (coo_row[i] != coo_col[i])
++off_diagonals;
}
magma_index_t true_nonzeros = 2*off_diagonals + (A->nnz - off_diagonals);
//printf("%% total number of nonzeros: %d\n%%", int(A->nnz));
CHECK( magma_index_malloc_cpu( &new_row, true_nonzeros ));
CHECK( magma_index_malloc_cpu( &new_col, true_nonzeros ));
CHECK( magma_dmalloc_cpu( &new_val, true_nonzeros ));
magma_index_t ptr = 0;
for(magma_int_t i = 0; i < A->nnz; ++i) {
if (coo_row[i] != coo_col[i]) {
new_row[ptr] = coo_row[i];
new_col[ptr] = coo_col[i];
new_val[ptr] = coo_val[i];
ptr++;
new_col[ptr] = coo_row[i];
new_row[ptr] = coo_col[i];
new_val[ptr] = (symmetric == 0) ? coo_val[i] : conj(coo_val[i]);
ptr++;
} else {
new_row[ptr] = coo_row[i];
new_col[ptr] = coo_col[i];
new_val[ptr] = coo_val[i];
ptr++;
}
}
magma_free_cpu(coo_row);
magma_free_cpu(coo_col);
magma_free_cpu(coo_val);
coo_row = new_row;
coo_col = new_col;
coo_val = new_val;
A->nnz = true_nonzeros;
//printf("total number of nonzeros: %d\n", A->nnz);
} // end symmetric case
CHECK( magma_dmalloc_cpu( &A->val, A->nnz ));
CHECK( magma_index_malloc_cpu( &A->col, A->nnz ));
CHECK( magma_index_malloc_cpu( &A->row, A->num_rows+1 ));
// original code from Nathan Bell and Michael Garland
for (magma_index_t i = 0; i < num_rows; i++)
(A->row)[i] = 0;
for (magma_index_t i = 0; i < A->nnz; i++)
(A->row)[coo_row[i]]++;
// cumulative sum the nnz per row to get row[]
magma_int_t cumsum;
cumsum = 0;
for(magma_int_t i = 0; i < num_rows; i++) {
magma_index_t temp = (A->row)[i];
(A->row)[i] = cumsum;
cumsum += temp;
}
(A->row)[num_rows] = A->nnz;
// write Aj,Ax into Bj,Bx
for(magma_int_t i = 0; i < A->nnz; i++) {
magma_index_t row_ = coo_row[i];
magma_index_t dest = (A->row)[row_];
(A->col)[dest] = coo_col[i];
(A->val)[dest] = coo_val[i];
(A->row)[row_]++;
}
magma_free_cpu(coo_row);
magma_free_cpu(coo_col);
magma_free_cpu(coo_val);
coo_row = NULL;
coo_col = NULL;
coo_val = NULL;
int last;
last = 0;
for(int i = 0; i <= num_rows; i++) {
int temp = (A->row)[i];
(A->row)[i] = last;
last = temp;
}
(A->row)[A->num_rows] = A->nnz;
// sort column indices within each row
// copy into vector of pairs (column index, value), sort by column index, then copy back
for (magma_index_t k=0; k < A->num_rows; ++k) {
int kk = (A->row)[k];
int len = (A->row)[k+1] - (A->row)[k];
rowval.resize( len );
for( int i=0; i < len; ++i ) {
rowval[i] = std::make_pair( (A->col)[kk+i], (A->val)[kk+i] );
}
std::sort( rowval.begin(), rowval.end(), compare_first );
for( int i=0; i < len; ++i ) {
(A->col)[kk+i] = rowval[i].first;
(A->val)[kk+i] = rowval[i].second;
}
}
if ( csr_compressor > 0) { // run the CSR compressor to remove zeros
//printf("removing zeros: ");
CHECK( magma_dmtransfer( *A, &B, Magma_CPU, Magma_CPU, queue ));
CHECK( magma_d_csr_compressor(
&(A->val), &(A->row), &(A->col),
&B.val, &B.row, &B.col, &B.num_rows, queue ));
B.nnz = B.row[num_rows];
//printf(" remaining nonzeros:%d ", B.nnz);
magma_free_cpu( A->val );
magma_free_cpu( A->row );
magma_free_cpu( A->col );
CHECK( magma_dmtransfer( B, A, Magma_CPU, Magma_CPU, queue ));
//printf("done.\n");
}
A->true_nnz = A->nnz;
printf(" done.\n");
cleanup:
if ( fid != NULL ) {
fclose( fid );
fid = NULL;
}
magma_dmfree( &B, queue );
magma_free_cpu(coo_row);
magma_free_cpu(coo_col);
magma_free_cpu(coo_val);
return info;
}
bool LoadMatrixMarketFile(const std::string& file_path,
SparseMatrix<T>& A,
unsigned int& height,
unsigned int& width,
unsigned int& nnz)
{
std::ifstream infile(file_path);
if (!infile)
return false;
char mm_typecode[4];
// read the matrix market banner (header)
if (0 != mm_read_banner(infile, mm_typecode))
return false;
if (!mm_is_valid(mm_typecode))
return false;
// this reader supports these matrix types:
//
// sparse, real/integer/pattern, general/symm/skew
//
if (!mm_is_sparse(mm_typecode))
{
std::cerr << "Only sparse MatrixMarket files are supported." << std::endl;
return false;
}
if (!mm_is_real(mm_typecode) && !mm_is_integer(mm_typecode) && !mm_is_pattern(mm_typecode))
{
std::cerr << "Only real, integer, and pattern MatrixMarket formats are supported." << std::endl;
return false;
}
if (!mm_is_general(mm_typecode) && !mm_is_symmetric(mm_typecode) && !mm_is_skew(mm_typecode))
{
std::cerr << "Only general, symmetric, and skew-symmetric MatrixMarket formats are supported."
<< std::endl;
return false;
}
// read the number of rows, cols, nonzeros
if (0 != mm_read_mtx_crd_size(infile, height, width, nnz))
{
std::cerr << "could not read matrix coordinate information" << std::endl;
height = width = nnz = 0;
return false;
}
// read the data according to the type
bool is_real = mm_is_real(mm_typecode);
bool is_int = mm_is_integer(mm_typecode);
bool is_symmetric = mm_is_symmetric(mm_typecode);
bool is_skew = mm_is_skew(mm_typecode);
std::string line;
unsigned int reserve_size = nnz;
if (is_symmetric || is_skew)
reserve_size *= 2;
A.Clear();
A.Reserve(height, width, reserve_size);
// load num random entries of A
A.BeginLoad();
unsigned int row, col, count;
if (is_real)
{
double val;
for (count=0; count != nnz; ++count)
{
infile >> row; assert(row >= 1);
infile >> col; assert(col >= 1);
infile >> val;
// convert to 0-based indexing
row -= 1;
col -= 1;
A.Load(row, col, val);
if (row != col)
{
if (is_symmetric)
A.Load(col, row, val);
else if (is_skew)
A.Load(col, row, -val);
}
}
}
else if (is_int)
char *mm_typecode_to_str(MM_typecode matcode)
{
char buffer[MM_MAX_LINE_LENGTH];
const char *types[4];
char *mm_strdup(const char *);
int error =0;
/* check for MTX type */
if (mm_is_matrix(matcode))
types[0] = MM_MTX_STR;
else {
types[0] = NULL;
error=1;
}
/* check for CRD or ARR matrix */
if (mm_is_sparse(matcode))
types[1] = MM_SPARSE_STR;
else
if (mm_is_dense(matcode))
types[1] = MM_DENSE_STR;
else
return NULL;
/* check for element data type */
if (mm_is_real(matcode))
types[2] = MM_REAL_STR;
else
if (mm_is_complex(matcode))
types[2] = MM_COMPLEX_STR;
else
if (mm_is_pattern(matcode))
types[2] = MM_PATTERN_STR;
else
if (mm_is_integer(matcode))
types[2] = MM_INT_STR;
else
return NULL;
/* check for symmetry type */
if (mm_is_general(matcode))
types[3] = MM_GENERAL_STR;
else
if (mm_is_symmetric(matcode))
types[3] = MM_SYMM_STR;
else
if (mm_is_hermitian(matcode))
types[3] = MM_HERM_STR;
else
if (mm_is_skew(matcode))
types[3] = MM_SKEW_STR;
else
return NULL;
if( error == 1 )
sprintf(buffer,"Object to write is not a matrix; this is unsupported by the current mmio code.");
else
sprintf(buffer,"%s %s %s %s", types[0], types[1], types[2], types[3]);
return mm_strdup(buffer);
}
char *mm_typecode_to_str ( MM_typecode matcode )
/******************************************************************************/
/*
Purpose:
MM_TYPECODE_TO_STR converts the internal typecode to an MM header string.
Modified:
31 October 2008
*/
{
char buffer[MM_MAX_LINE_LENGTH];
char *types[4];
char *mm_strdup(const char *);
//int error =0;
/*
check for MTX type
*/
if (mm_is_matrix(matcode))
types[0] = MM_MTX_STR;
// else
// error=1;
/*
check for CRD or ARR matrix
*/
if (mm_is_sparse(matcode))
types[1] = MM_SPARSE_STR;
else
if (mm_is_dense(matcode))
types[1] = MM_DENSE_STR;
else
return NULL;
/*
check for element data type
*/
if (mm_is_real(matcode))
types[2] = MM_REAL_STR;
else
if (mm_is_complex(matcode))
types[2] = MM_COMPLEX_STR;
else
if (mm_is_pattern(matcode))
types[2] = MM_PATTERN_STR;
else
if (mm_is_integer(matcode))
types[2] = MM_INT_STR;
else
return NULL;
/*
check for symmetry type
*/
if (mm_is_general(matcode))
types[3] = MM_GENERAL_STR;
else
if (mm_is_symmetric(matcode))
types[3] = MM_SYMM_STR;
else
if (mm_is_hermitian(matcode))
types[3] = MM_HERM_STR;
else
if (mm_is_skew(matcode))
types[3] = MM_SKEW_STR;
else
return NULL;
sprintf(buffer,"%s %s %s %s", types[0], types[1], types[2], types[3]);
return mm_strdup(buffer);
}
int main(int argc, char ** argv)
{
// report precision of floating-point
printf("---------------------------------------------------------------------------------------------\n");
char *precision;
if (sizeof(VALUE_TYPE) == 4)
{
precision = (char *)"32-bit Single Precision";
}
else if (sizeof(VALUE_TYPE) == 8)
{
precision = (char *)"64-bit Double Precision";
}
else
{
printf("Wrong precision. Program exit!\n");
return 0;
}
printf("PRECISION = %s\n", precision);
printf("Benchmark REPEAT = %i\n", BENCH_REPEAT);
printf("---------------------------------------------------------------------------------------------\n");
int m, n, nnzA;
int *csrRowPtrA;
int *csrColIdxA;
VALUE_TYPE *csrValA;
//ex: ./spmv webbase-1M.mtx
int argi = 1;
char *filename;
if(argc > argi)
{
filename = argv[argi];
argi++;
}
printf("-------------- %s --------------\n", filename);
// read matrix from mtx file
int ret_code;
MM_typecode matcode;
FILE *f;
int nnzA_mtx_report;
int isInteger = 0, isReal = 0, isPattern = 0, isSymmetric = 0;
// load matrix
if ((f = fopen(filename, "r")) == NULL)
return -1;
if (mm_read_banner(f, &matcode) != 0)
{
printf("Could not process Matrix Market banner.\n");
return -2;
}
if ( mm_is_complex( matcode ) )
{
printf("Sorry, data type 'COMPLEX' is not supported.\n");
return -3;
}
if ( mm_is_pattern( matcode ) ) { isPattern = 1; /*printf("type = Pattern\n");*/ }
if ( mm_is_real ( matcode) ) { isReal = 1; /*printf("type = real\n");*/ }
if ( mm_is_integer ( matcode ) ) { isInteger = 1; /*printf("type = integer\n");*/ }
/* find out size of sparse matrix .... */
ret_code = mm_read_mtx_crd_size(f, &m, &n, &nnzA_mtx_report);
if (ret_code != 0)
return -4;
if ( mm_is_symmetric( matcode ) || mm_is_hermitian( matcode ) )
{
isSymmetric = 1;
printf("input matrix is symmetric = true\n");
}
else
{
printf("input matrix is symmetric = false\n");
}
int *csrRowPtrA_counter = (int *)malloc((m+1) * sizeof(int));
memset(csrRowPtrA_counter, 0, (m+1) * sizeof(int));
int *csrRowIdxA_tmp = (int *)malloc(nnzA_mtx_report * sizeof(int));
int *csrColIdxA_tmp = (int *)malloc(nnzA_mtx_report * sizeof(int));
VALUE_TYPE *csrValA_tmp = (VALUE_TYPE *)malloc(nnzA_mtx_report * sizeof(VALUE_TYPE));
/* NOTE: when reading in doubles, ANSI C requires the use of the "l" */
/* specifier as in "%lg", "%lf", "%le", otherwise errors will occur */
/* (ANSI C X3.159-1989, Sec. 4.9.6.2, p. 136 lines 13-15) */
for (int i = 0; i < nnzA_mtx_report; i++)
{
int idxi, idxj;
double fval;
int ival;
int returnvalue;
if (isReal)
returnvalue = fscanf(f, "%d %d %lg\n", &idxi, &idxj, &fval);
else if (isInteger)
{
returnvalue = fscanf(f, "%d %d %d\n", &idxi, &idxj, &ival);
fval = ival;
}
else if (isPattern)
{
returnvalue = fscanf(f, "%d %d\n", &idxi, &idxj);
fval = 1.0;
}
// adjust from 1-based to 0-based
idxi--;
idxj--;
csrRowPtrA_counter[idxi]++;
csrRowIdxA_tmp[i] = idxi;
csrColIdxA_tmp[i] = idxj;
csrValA_tmp[i] = fval;
}
if (f != stdin)
fclose(f);
if (isSymmetric)
{
for (int i = 0; i < nnzA_mtx_report; i++)
{
if (csrRowIdxA_tmp[i] != csrColIdxA_tmp[i])
csrRowPtrA_counter[csrColIdxA_tmp[i]]++;
}
}
// exclusive scan for csrRowPtrA_counter
int old_val, new_val;
old_val = csrRowPtrA_counter[0];
csrRowPtrA_counter[0] = 0;
for (int i = 1; i <= m; i++)
{
new_val = csrRowPtrA_counter[i];
csrRowPtrA_counter[i] = old_val + csrRowPtrA_counter[i-1];
old_val = new_val;
}
nnzA = csrRowPtrA_counter[m];
csrRowPtrA = (int *)malloc((m+1) * sizeof(int));
memcpy(csrRowPtrA, csrRowPtrA_counter, (m+1) * sizeof(int));
memset(csrRowPtrA_counter, 0, (m+1) * sizeof(int));
csrColIdxA = (int *)malloc(nnzA * sizeof(int));
csrValA = (VALUE_TYPE *)malloc(nnzA * sizeof(VALUE_TYPE));
if (isSymmetric)
{
for (int i = 0; i < nnzA_mtx_report; i++)
{
if (csrRowIdxA_tmp[i] != csrColIdxA_tmp[i])
{
int offset = csrRowPtrA[csrRowIdxA_tmp[i]] + csrRowPtrA_counter[csrRowIdxA_tmp[i]];
csrColIdxA[offset] = csrColIdxA_tmp[i];
csrValA[offset] = csrValA_tmp[i];
csrRowPtrA_counter[csrRowIdxA_tmp[i]]++;
offset = csrRowPtrA[csrColIdxA_tmp[i]] + csrRowPtrA_counter[csrColIdxA_tmp[i]];
csrColIdxA[offset] = csrRowIdxA_tmp[i];
csrValA[offset] = csrValA_tmp[i];
csrRowPtrA_counter[csrColIdxA_tmp[i]]++;
}
else
{
int offset = csrRowPtrA[csrRowIdxA_tmp[i]] + csrRowPtrA_counter[csrRowIdxA_tmp[i]];
csrColIdxA[offset] = csrColIdxA_tmp[i];
csrValA[offset] = csrValA_tmp[i];
csrRowPtrA_counter[csrRowIdxA_tmp[i]]++;
}
}
}
else
{
for (int i = 0; i < nnzA_mtx_report; i++)
{
int offset = csrRowPtrA[csrRowIdxA_tmp[i]] + csrRowPtrA_counter[csrRowIdxA_tmp[i]];
csrColIdxA[offset] = csrColIdxA_tmp[i];
csrValA[offset] = csrValA_tmp[i];
csrRowPtrA_counter[csrRowIdxA_tmp[i]]++;
}
}
// free tmp space
free(csrColIdxA_tmp);
free(csrValA_tmp);
free(csrRowIdxA_tmp);
free(csrRowPtrA_counter);
/*
// a small matrix
free(csrColIdxA);
free(csrValA);
free(csrRowPtrA);
m = n = 8;
nnzA = 17;
csrRowPtrA = (int *)malloc(sizeof(int) * (m+1));
csrColIdxA = (int *)malloc(sizeof(int) * nnzA);
csrValA = (VALUE_TYPE *)malloc(nnzA * sizeof(VALUE_TYPE));
csrRowPtrA[0] = 0; csrRowPtrA[1] = 1; csrRowPtrA[2] = 2; csrRowPtrA[3] = 4; csrRowPtrA[4] = 6;
csrRowPtrA[5] = 10; csrRowPtrA[6] = 12; csrRowPtrA[7] = 15; csrRowPtrA[8] = nnzA;
csrColIdxA[0] = 0; csrColIdxA[1] = 1; csrColIdxA[2] = 1; csrColIdxA[3] = 2; csrColIdxA[4] = 0;
csrColIdxA[5] = 3; csrColIdxA[6] = 1; csrColIdxA[7] = 2; csrColIdxA[8] = 3; csrColIdxA[9] = 4;
csrColIdxA[10] = 3; csrColIdxA[11] = 5; csrColIdxA[12] = 2; csrColIdxA[13] = 5; csrColIdxA[14] = 6;
csrColIdxA[15] = 6; csrColIdxA[16] = 7;
// a small matrix stop
*/
printf("input matrix A: ( %i, %i ) nnz = %i\n", m, n, nnzA);
// extract L with the unit-lower triangular sparsity structure of A
int nnzL = 0;
int *csrRowPtrL_tmp = (int *)malloc((m+1) * sizeof(int));
int *csrColIdxL_tmp = (int *)malloc(nnzA * sizeof(int));
VALUE_TYPE *csrValL_tmp = (VALUE_TYPE *)malloc(nnzA * sizeof(VALUE_TYPE));
int nnz_pointer = 0;
csrRowPtrL_tmp[0] = 0;
for (int i = 0; i < m; i++)
{
for (int j = csrRowPtrA[i]; j < csrRowPtrA[i+1]; j++)
{
if (csrColIdxA[j] < i)
{
csrColIdxL_tmp[nnz_pointer] = csrColIdxA[j];
csrValL_tmp[nnz_pointer] = 1.0; //csrValA[j];
nnz_pointer++;
}
else
{
break;
}
}
csrColIdxL_tmp[nnz_pointer] = i;
csrValL_tmp[nnz_pointer] = 1.0;
nnz_pointer++;
csrRowPtrL_tmp[i+1] = nnz_pointer;
}
nnzL = csrRowPtrL_tmp[m];
printf("A's unit-lower triangular L: ( %i, %i ) nnz = %i\n", m, n, nnzL);
csrColIdxL_tmp = (int *)realloc(csrColIdxL_tmp, sizeof(int) * nnzL);
csrValL_tmp = (VALUE_TYPE *)realloc(csrValL_tmp, sizeof(VALUE_TYPE) * nnzL);
// run serial syncfree SpTS as a reference
printf("---------------------------------------------------------------------------------------------\n");
spts_syncfree_serialref(csrRowPtrL_tmp, csrColIdxL_tmp, csrValL_tmp, m, n, nnzL);
// run cuda syncfree SpTS
printf("---------------------------------------------------------------------------------------------\n");
spts_syncfree_opencl(csrRowPtrL_tmp, csrColIdxL_tmp, csrValL_tmp, m, n, nnzL);
printf("---------------------------------------------------------------------------------------------\n");
// done!
free(csrColIdxA);
free(csrValA);
free(csrRowPtrA);
free(csrColIdxL_tmp);
free(csrValL_tmp);
free(csrRowPtrL_tmp);
return 0;
}
/** \brief Read a vector file.
*
* Reads a Matrix Market formatted vector from a file.
* Returns pointer to dense vector.
*
* @param file vector file name
* @param out_vec vector data
*
* @return result
*/
int read_mm_new_vector(const char *file, double **out_vec)
{
double *val;
int i, m, n, nz;
FILE *fp;
MM_typecode matcode;
if ((fp = fopen(file, "r")) == NULL)
{
fprintf(stderr,"ERROR: Could not open file: %s\n",file);
exit(1);
}
if (mm_read_banner(fp, &matcode) != 0)
{
fprintf(stderr,"ERROR: Could not process Matrix Market banner.\n");
exit(1);
}
if (!(mm_is_real(matcode) || mm_is_integer(matcode)))
{
fprintf(stderr,"ERROR: Market Market type: [%s] not supported\n",
mm_typecode_to_str(matcode));
exit(1);
}
if (mm_is_sparse(matcode))
{
if (mm_read_mtx_crd_size(fp, &m, &n, &nz) !=0)
{ /* find out size of sparse matrix */
exit(1);
}
if (n != 1)
{
fprintf(stderr,"ERROR: %s does not contain a column vector\n",file);
exit(1);
}
val = malloc(m*sizeof(double));
memset(val, 0, m*sizeof(double));
for (i = 0; i < nz; i++)
{
int cur_i, cur_j;
double cur_val;
fscanf(fp, "%d %d %lg\n", &cur_i, &cur_j, &cur_val);
val[cur_i-1] = cur_val;
}
}
else
{
if (mm_read_mtx_array_size(fp, &m, &n) !=0)
{ /* find out size of dense matrix */
exit(1);
}
if (n != 1)
{
fprintf(stderr,"ERROR: %s does not contain a column vector\n",file);
exit(1);
}
val = malloc(m*sizeof(double));
for (i = 0; i < m; i++)
{
double cur_val;
fscanf(fp, "%lg\n", &cur_val);
val[i] = cur_val;
}
}
*out_vec = val;
if (fp !=stdin) fclose(fp);
return 0;
}
int read_mm_new_matrix_transpose(const char *file, dmatrix **out_mat)
{
dmatrix *dmat;
int i, j, m, n, nz;
FILE *fp;
MM_typecode matcode;
if ((fp = fopen(file, "r")) == NULL)
{
fprintf(stderr,"ERROR: Could not open file: %s\n",file);
exit(1);
}
if (mm_read_banner(fp, &matcode) != 0)
{
fprintf(stderr,"ERROR: Could not process Matrix Market banner.\n");
exit(1);
}
if (!(mm_is_real(matcode) || mm_is_integer(matcode)))
{
fprintf(stderr,"ERROR: Market Market type: [%s] not supported\n",
mm_typecode_to_str(matcode));
exit(1);
}
if (mm_is_sparse(matcode))
{
int cur_i, cur_j;
double cur_val;
double *val, *vtmp;
int *idx, *jdx, *rdx;
int *itmp, *jtmp, *tmp;
if (mm_read_mtx_crd_size(fp, &n, &m, &nz) !=0)
{ /* find out size of sparse matrix */
exit(1);
}
dmat = malloc(sizeof(dmatrix));
itmp = malloc(nz*sizeof(int));
jtmp = malloc(nz*sizeof(int));
vtmp = malloc(nz*sizeof(double));
rdx = malloc((m+1)*sizeof(int));
idx = malloc(nz*sizeof(int));
jdx = malloc(nz*sizeof(int));
val = malloc(nz*sizeof(double));
tmp = malloc(m*sizeof(int));
memset(tmp, 0, sizeof(int)*m);
for (i = 0; i < nz; i++)
{
fscanf(fp, "%d %d %lg\n", &cur_j, &cur_i, &cur_val);
itmp[i] = --cur_i;
jtmp[i] = --cur_j;
vtmp[i] = cur_val;
tmp[ itmp[i] ]++ ;
}
rdx[0] = 0;
for (i = 0; i < m ; i++)
{
rdx[i+1] = rdx[i] + tmp[i];
tmp[i] = rdx[i];
}
for (i = 0; i < nz; i++)
{
int ii;
ii = tmp[ itmp[i] ]++;
idx[ii] = itmp[i];
jdx[ii] = jtmp[i];
val[ii] = vtmp[i];
}
dmat->n = n;
dmat->m = m;
dmat->nz = nz;
dmat->val = val;
dmat->idx = idx;
dmat->jdx = jdx;
dmat->rdx = rdx;
free(itmp);
free(jtmp);
free(vtmp);
free(tmp);
}
else
{
double *val;
if (mm_read_mtx_array_size(fp, &n, &m) !=0)
{ /* find out size of dense matrix */
exit(1);
}
dmat = malloc(sizeof(dmatrix));
val = malloc((m*n)*sizeof(double));
for (j = 0; j < n*m; j++)
{
fscanf(fp, "%lg\n", &val[j]);
}
dmat->n = n;
dmat->m = m;
dmat->nz = -1;
dmat->val = val;
dmat->idx = NULL;
dmat->jdx = NULL;
dmat->rdx = NULL;
}
*out_mat = dmat;
if (fp !=stdin) fclose(fp);
return 0;
}
static PetscErrorCode loadmtx(const char* filename, Mat *M, PetscBool *pattern) {
PetscErrorCode ierr;
FILE *f;
MM_typecode type;
int m,n,nz,i,j,k;
PetscInt low,high,lowj,highj,*d_nz,*o_nz;
double re,im;
PetscScalar s;
long pos;
PetscFunctionBegin;
f = fopen(filename,"r");
if (!f) SETERRQ2(PETSC_COMM_SELF,1,"fopen '%s': %s",filename,strerror(errno));
/* first read to set matrix kind and size */
ierr = mm_read_banner(f,&type);CHKERRQ(ierr);
if (!mm_is_valid(type) || !mm_is_sparse(type) ||
!(mm_is_real(type) || mm_is_complex(type) || mm_is_pattern(type) || mm_is_integer(type)))
SETERRQ1(PETSC_COMM_SELF,1,"Matrix format '%s' not supported",mm_typecode_to_str(type));
#if !defined(PETSC_USE_COMPLEX)
if (mm_is_complex(type)) SETERRQ(PETSC_COMM_SELF,1,"Complex matrix not supported in real configuration");
#endif
if (pattern) *pattern = mm_is_pattern(type) ? PETSC_TRUE : PETSC_FALSE;
ierr = mm_read_mtx_crd_size(f,&m,&n,&nz);CHKERRQ(ierr);
pos = ftell(f);
ierr = MatCreate(PETSC_COMM_WORLD,M);CHKERRQ(ierr);
ierr = MatSetSizes(*M,PETSC_DECIDE,PETSC_DECIDE,(PetscInt)m,(PetscInt)n);CHKERRQ(ierr);
ierr = MatSetFromOptions(*M);CHKERRQ(ierr);
ierr = MatSetUp(*M);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(*M,&low,&high);CHKERRQ(ierr);
ierr = MatGetOwnershipRangeColumn(*M,&lowj,&highj);CHKERRQ(ierr);
ierr = PetscMalloc(sizeof(PetscInt)*(high-low),&d_nz);CHKERRQ(ierr);
ierr = PetscMalloc(sizeof(PetscInt)*(high-low),&o_nz);CHKERRQ(ierr);
for (i=0; i<high-low;i++) {
d_nz[i] = (i+low>=lowj && i+low<highj) ? 1 : 0;
o_nz[i] = (i+low>=lowj && i+low<highj) ? 0 : 1;
}
for (k=0;k<nz;k++) {
ierr = mm_read_mtx_crd_entry(f,&i,&j,&re,&im,type);CHKERRQ(ierr);
i--; j--;
if (i!=j) {
if (i>=low && i<high) {
if (j>=lowj && j<highj)
d_nz[i-low]++;
else
o_nz[i-low]++;
}
if (j>=low && j<high && !mm_is_general(type)) {
if (i>=low && i<high)
d_nz[j-low]++;
else
o_nz[j-low]++;
}
}
}
ierr = preallocation(*M,d_nz,o_nz);CHKERRQ(ierr);
ierr = PetscFree(d_nz);CHKERRQ(ierr);
ierr = PetscFree(o_nz);CHKERRQ(ierr);
/* second read to load the values */
ierr = fseek(f, pos, SEEK_SET);
if (ierr) SETERRQ1(PETSC_COMM_SELF,1,"fseek: %s",strerror(errno));
re = 1.0;
im = 0.0;
/* Set the diagonal to zero */
for (i=low; i<PetscMin(high,n); i++) {
ierr = MatSetValue(*M,i,i,0.0,INSERT_VALUES);CHKERRQ(ierr);
}
for (k=0;k<nz;k++) {
ierr = mm_read_mtx_crd_entry(f,&i,&j,&re,&im,type);
i--; j--;
if (i>=low && i<high) {
s = re + IMAGINARY * im;
ierr = MatSetValue(*M,i,j,s,INSERT_VALUES);CHKERRQ(ierr);
}
if (j>=low && j<high && i != j && !mm_is_general(type)) {
if (mm_is_symmetric(type)) s = re + IMAGINARY * im;
else if (mm_is_hermitian(type)) s = re - IMAGINARY * im;
else if (mm_is_skew(type)) s = -re - IMAGINARY * im;
else {
SETERRQ1(PETSC_COMM_SELF,1,"Matrix format '%s' not supported",mm_typecode_to_str(type));
}
ierr = MatSetValue(*M,j,i,s,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(*M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
if (mm_is_symmetric(type)) {
ierr = MatSetOption(*M,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr);
}
if ((mm_is_symmetric(type) && mm_is_real(type)) || mm_is_hermitian(type)) {
ierr = MatSetOption(*M,MAT_HERMITIAN,PETSC_TRUE);CHKERRQ(ierr);
}
ierr = fclose(f);
if (ierr) SETERRQ1(PETSC_COMM_SELF,1,"fclose: %s",strerror(errno));
PetscFunctionReturn(0);
}
