GrB_Info read_matrix // read a double-precision or boolean matrix ( GrB_Matrix *A_output, // handle of matrix to create FILE *f, // file to read the tuples from bool make_symmetric, // if true, return A as symmetric bool no_self_edges, // if true, then remove self edges from A bool one_based, // if true, input matrix is 1-based bool boolean, // if true, input is GrB_BOOL, otherwise GrB_FP64 bool pr // if true, print status to stdout ) { int64_t len = 256 ; int64_t ntuples = 0 ; double x ; GrB_Index nvals ; //-------------------------------------------------------------------------- // set all pointers to NULL so that FREE_ALL can free everything safely //-------------------------------------------------------------------------- GrB_Matrix C = NULL, A = NULL, B = NULL ; GrB_Descriptor dt1 = NULL, dt2 = NULL ; GrB_UnaryOp scale2_op = NULL ; //-------------------------------------------------------------------------- // allocate initial space for tuples //-------------------------------------------------------------------------- size_t xsize = ((boolean) ? sizeof (bool) : sizeof (double)) ; GrB_Index *I = malloc (len * sizeof (int64_t)), *I2 = NULL ; GrB_Index *J = malloc (len * sizeof (int64_t)), *J2 = NULL ; void *X = malloc (len * xsize) ; bool *Xbool ; double *Xdouble ; void *X2 = NULL ; if (I == NULL || J == NULL || X == NULL) { // out of memory if (pr) printf ("out of memory for initial tuples\n") ; FREE_ALL ; return (GrB_OUT_OF_MEMORY) ; } Xbool = (bool *) X ; Xdouble = (double *) X ; //-------------------------------------------------------------------------- // read in the tuples from stdin, one per line //-------------------------------------------------------------------------- // format warnings vary with compilers, so read in as double double i2, j2 ; while (fscanf (f, "%lg %lg %lg\n", &i2, &j2, &x) != EOF) { int64_t i = (int64_t) i2 ; int64_t j = (int64_t) j2 ; if (ntuples >= len) { I2 = realloc (I, 2 * len * sizeof (int64_t)) ; J2 = realloc (J, 2 * len * sizeof (int64_t)) ; X2 = realloc (X, 2 * len * xsize) ; if (I2 == NULL || J2 == NULL || X2 == NULL) { if (pr) printf ("out of memory for tuples\n") ; FREE_ALL ; return (GrB_OUT_OF_MEMORY) ; } I = I2 ; I2 = NULL ; J = J2 ; J2 = NULL ; X = X2 ; X2 = NULL ; len = len * 2 ; Xbool = (bool *) X ; Xdouble = (double *) X ; } if (one_based) { i-- ; j-- ; } I [ntuples] = i ; J [ntuples] = j ; if (boolean) { Xbool [ntuples] = (x != 0) ; } else { Xdouble [ntuples] = x ; } ntuples++ ; } //-------------------------------------------------------------------------- // find the dimensions //-------------------------------------------------------------------------- if (pr) printf ("ntuples: %.16g\n", (double) ntuples) ; int64_t nrows = 0 ; int64_t ncols = 0 ; for (int64_t k = 0 ; k < ntuples ; k++) { nrows = MAX (nrows, I [k]) ; ncols = MAX (ncols, J [k]) ; } nrows++ ; ncols++ ; if (pr) printf ("nrows %.16g ncols %.16g\n", (double) nrows, (double) ncols) ; //-------------------------------------------------------------------------- // prune self edges //-------------------------------------------------------------------------- // but not if creating the augmented system aka a bipartite graph double tic [2], t1 ; simple_tic (tic) ; if (no_self_edges && ! (make_symmetric && nrows != ncols)) { int64_t ntuples2 = 0 ; for (int64_t k = 0 ; k < ntuples ; k++) { if (I [k] != J [k]) { // keep this off-diagonal edge I [ntuples2] = I [k] ; J [ntuples2] = J [k] ; if (boolean) { Xbool [ntuples2] = Xbool [k] ; } else { Xdouble [ntuples2] = Xdouble [k] ; } ntuples2++ ; } } ntuples = ntuples2 ; } t1 = simple_toc (tic) ; if (pr) printf ("time to prune self-edges: %12.6f\n", t1) ; //-------------------------------------------------------------------------- // build the matrix, summing up duplicates, and then free the tuples //-------------------------------------------------------------------------- GrB_Type xtype ; GrB_BinaryOp xop, xop2 ; if (boolean) { xtype = GrB_BOOL ; xop = GrB_LOR ; xop2 = GrB_FIRST_BOOL ; } else { xtype = GrB_FP64 ; xop = GrB_PLUS_FP64 ; xop2 = GrB_FIRST_FP64 ; } simple_tic (tic) ; GrB_Info info ; OK (GrB_Matrix_new (&C, xtype, nrows, ncols)) ; if (boolean) { OK (GrB_Matrix_build (C, I, J, Xbool, ntuples, xop)) ; } else { OK (GrB_Matrix_build (C, I, J, Xdouble, ntuples, xop)) ; } t1 = simple_toc (tic) ; if (pr) printf ("time to build the graph with GrB_Matrix_build: %12.6f\n", t1) ; #ifdef TEST_SETELEMENT { // This is just for testing performance of GrB_setElement and comparing // with GrB_build. It is not needed if this function is used in // production. // setElement will be just about as fast as build (perhaps 10% to 50% // more time) with non-blocking mode. If blocking mode is enabled, // setElement will be extremely and painfully slow since the matrix is // rebuilt every time a single entry is added. simple_tic (tic) ; OK (GrB_Matrix_new (&B, xtype, nrows, ncols)) ; for (int64_t k = 0 ; k < ntuples ; k++) { // B (I[k], J[k]) = X [k] GrB_Matrix_setElement (B, X [k], I [k], J [k]) ; } // force completion of B GrB_Matrix_nvals (&nvals, B) ; double t2 = simple_toc (tic) ; if (pr) printf ("time to build the graph with GrB_setElement:" " %12.6f\n", t2) ; GrB_free (&B) ; } #endif free (I) ; I = NULL ; free (J) ; J = NULL ; free (X) ; X = NULL ; //-------------------------------------------------------------------------- // construct the descriptors //-------------------------------------------------------------------------- // descriptor dt2: transpose the 2nd input OK (GrB_Descriptor_new (&dt2)) ; OK (GrB_Descriptor_set (dt2, GrB_INP1, GrB_TRAN)) ; // descriptor dt1: transpose the 1st input OK (GrB_Descriptor_new (&dt1)) ; OK (GrB_Descriptor_set (dt1, GrB_INP0, GrB_TRAN)) ; //-------------------------------------------------------------------------- // create the output matrix //-------------------------------------------------------------------------- if (make_symmetric) { //---------------------------------------------------------------------- // ensure the matrix is symmetric //---------------------------------------------------------------------- if (pr) printf ("make symmetric\n") ; if (nrows == ncols) { //------------------------------------------------------------------ // A = (C+C')/2 //------------------------------------------------------------------ if (pr) printf ("A = (C+C')/2\n") ; double tic [2], t ; simple_tic (tic) ; OK (GrB_Matrix_new (&A, xtype, nrows, nrows)) ; OK (GrB_eWiseAdd (A, NULL, NULL, xop, C, C, dt2)) ; OK (GrB_free (&C)) ; if (boolean) { *A_output = A ; A = NULL ; } else { OK (GrB_Matrix_new (&C, xtype, nrows, nrows)) ; OK (GrB_UnaryOp_new (&scale2_op, scale2, xtype, xtype)) ; OK (GrB_apply (C, NULL, NULL, scale2_op, A, NULL)) ; OK (GrB_free (&A)) ; OK (GrB_free (&scale2_op)) ; *A_output = C ; C = NULL ; } t = simple_toc (tic) ; if (pr) printf ("A = (C+C')/2 time %12.6f\n", t) ; } else { //------------------------------------------------------------------ // A = [0 C ; C' 0], a bipartite graph //------------------------------------------------------------------ // no self edges will exist if (pr) printf ("A = [0 C ; C' 0], a bipartite graph\n") ; double tic [2], t ; simple_tic (tic) ; int64_t n = nrows + ncols ; OK (GrB_Matrix_new (&A, xtype, n, n)) ; GrB_Index I_range [3], J_range [3] ; I_range [GxB_BEGIN] = 0 ; I_range [GxB_END ] = nrows-1 ; J_range [GxB_BEGIN] = nrows ; J_range [GxB_END ] = ncols+nrows-1 ; // A (nrows:n-1, 0:nrows-1) += C' OK (GrB_assign (A, NULL, xop2, // or NULL, C, J_range, GxB_RANGE, I_range, GxB_RANGE, dt1)) ; // A (0:nrows-1, nrows:n-1) += C OK (GrB_assign (A, NULL, xop2, // or NULL, C, I_range, GxB_RANGE, J_range, GxB_RANGE, NULL)) ; // force completion; if this statement does not appear, the // timing will not account for the final build, which would be // postponed until A is used by the caller in another GraphBLAS // operation. GrB_Matrix_nvals (&nvals, A) ; t = simple_toc (tic) ; if (pr) printf ("time to construct augmented system: %12.6f\n", t) ; *A_output = A ; // set A to NULL so the FREE_ALL macro does not free *A_output A = NULL ; } } else { //---------------------------------------------------------------------- // return the matrix as-is //---------------------------------------------------------------------- if (pr) printf ("leave A as-is\n") ; *A_output = C ; // set C to NULL so the FREE_ALL macro does not free *A_output C = NULL ; } //-------------------------------------------------------------------------- // success: free everything except the result, and return it to the caller //-------------------------------------------------------------------------- FREE_ALL ; if (pr) printf ("\nMatrix from file:\n") ; GxB_print (*A_output, pr ? GxB_SHORT : GxB_SILENT) ; return (GrB_SUCCESS) ; }
void mexFunction ( int nargout, mxArray *pargout [ ], int nargin, const mxArray *pargin [ ] ) { bool malloc_debug = GB_mx_get_global (true) ; GrB_Matrix C = NULL ; GrB_Descriptor desc = NULL ; GrB_Index *I = NULL, ni = 0, I_range [3] ; GrB_Index *J = NULL, nj = 0, J_range [3] ; bool ignore ; // check inputs GB_WHERE (USAGE) ; if (nargout > 1 || nargin < 2 || nargin > 5) { mexErrMsgTxt ("Usage: " USAGE) ; } // get C (make a deep copy) #define GET_DEEP_COPY \ C = GB_mx_mxArray_to_Matrix (pargin [0], "C input", true, true) ; #define FREE_DEEP_COPY GB_MATRIX_FREE (&C) ; GET_DEEP_COPY ; if (C == NULL) { FREE_ALL ; mexErrMsgTxt ("C failed") ; } mxClassID cclass = GB_mx_Type_to_classID (C->type) ; // get accum; default: NOP, default class is class(C) GrB_BinaryOp accum ; if (!GB_mx_mxArray_to_BinaryOp (&accum, pargin [1], "accum", GB_NOP_opcode, cclass, C->type == Complex, C->type == Complex)) { FREE_ALL ; mexErrMsgTxt ("accum failed") ; } // get I if (!GB_mx_mxArray_to_indices (&I, PARGIN (2), &ni, I_range, &ignore)) { FREE_ALL ; mexErrMsgTxt ("I failed") ; } // get J if (!GB_mx_mxArray_to_indices (&J, PARGIN (3), &nj, J_range, &ignore)) { FREE_ALL ; mexErrMsgTxt ("J failed") ; } // get desc if (!GB_mx_mxArray_to_Descriptor (&desc, PARGIN (4), "desc")) { FREE_ALL ; mexErrMsgTxt ("desc failed") ; } GrB_Index nrows, ncols ; GrB_Matrix_nvals (&nrows, C) ; GrB_Matrix_nvals (&ncols, C) ; // C(I,J) = accum (C(I,J),C) METHOD (GrB_assign (C, NULL, accum, C, I, ni, J, nj, desc)) ; GrB_wait ( ) ; TOC ; // return C to MATLAB as a struct and free the GraphBLAS C pargout [0] = GB_mx_Matrix_to_mxArray (&C, "C output", true) ; FREE_ALL ; }