working on spasm_echelonize()

but I broke spasm_GPLU()
cbouilla · Aug 29, 2023 · 6334dd7 · 6334dd7
1 parent bb42432
commit 6334dd7
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diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -3,7 +3,9 @@ add_library(libspasm spasm_util.c mmio.c spasm_io.c spasm_triplet.c
 	spasm_scatter.c spasm_gaxpy.c spasm_permutation.c spasm_reach.c 
 	spasm_triangular.c spasm_lu.c spasm_solutions.c spasm_pivots.c 
 	spasm_matching.c spasm_dm.c spasm_cc.c spasm_scc.c spasm_kernel.c 
-	spasm_concatenate.c spasm_dense_lu.c spasm_schur.c spasm_ffpack.cpp)
+	spasm_concatenate.c spasm_dense_lu.c spasm_schur.c spasm_ffpack.cpp
+	spasm_echelonize.c)
+
 target_link_libraries(libspasm PUBLIC OpenMP::OpenMP_C)
 target_link_libraries(libspasm PUBLIC m)
 target_link_libraries(libspasm PUBLIC PkgConfig::GIVARO)

diff --git a/src/spasm.h b/src/spasm.h
@@ -230,6 +230,10 @@ spasm *spasm_kernel(const spasm * A, const int *column_permutation);
 void spasm_dense_setzero(int prime, int n, int m, double *A, int ldA);
 int spasm_dense_echelonize(int prime, int n, int m, double *A, int ldA, size_t *Q);
 
+/* spasm_echelonize */
+spasm* spasm_echelonize(spasm *A, int *Uqinv);
+
+
 /* utilities */
 static inline int spasm_max(int a, int b) {
 	return (a > b) ? a : b;

diff --git a/src/spasm_echelonize.c b/src/spasm_echelonize.c
@@ -44,87 +44,145 @@ double estimate_schur_density(const spasm * A, int npiv, const int *p, const spa
  * Returns the row echelon form of A. Initializes qinv (must be of size m, #columns(A)).
  * Modifies A (permutes entries only)
  */
-spasm* spasm_echelonize(spasm *A, int *Uqinv)
+static const double sparsity_threshold = 0.05;
+
+/* for debugging purposes */
+void validate_pivots(const spasm *A, int npiv, const int *qinv, const int *p)
 {
-	int n = A->n;
-	int m = A->m;
 	int *Ap = A->p;
 	int *Aj = A->j;
 	spasm_GFp *Ax = A->x;
+	for (int k = 0; k < npiv; k++) {
+		int i = (p != NULL) ? p[k] : k;
+		int j = Aj[Ap[i]];
+		assert(Ax[Ap[i]] == 1);
+		assert(qinv[j] == i); 
+	}
+}
+
+
+
+spasm* spasm_echelonize(spasm *A, int *Uqinv)
+{
+	int n = A->n;
+	int m = A->m;
 	int prime = A->prime;
 
 	int *qinv = spasm_malloc(n * sizeof(int));  /* for pivot search */
 	int *p = spasm_malloc(n * sizeof(int));
 
 	spasm *U = spasm_csr_alloc(n, m, spasm_nnz(A), prime, SPASM_WITH_NUMERICAL_VALUES);
+	U->n = 0;
 	int Unz = 0;      /* #entries in U */
-	int Un = 0;       /* #rows in U */
 	for (int j = 0; j < m; j++)
 		Uqinv[j] = -1;
 
-	double start = spasm_wtime();	
+	double start = spasm_wtime();
 	int round = 0;
+	double density = -1;
 	for (;;) {
+	 	int *Ap = A->p;
+		int *Aj = A->j;
+		spasm_GFp *Ax = A->x;
+
+		/* invariant: A does not have coefficients on pivotal columns */
+		for (int i = 0; i < n; i++)
+			for (int px = Ap[i]; px < Ap[i + 1]; px++) {
+				int j = Aj[px];
+				assert(Uqinv[j] < 0);
+			}
+
 		/* find structural pivots in A */
 		int npiv = spasm_find_pivots(A, p, qinv);
 
+		if (npiv < 0.01 * spasm_min(n, m)) {
+			fprintf(stderr, "not enough pivots found\n");
+			/* TODO: echelonize A, take all the new pivots into U */
+			break;     /* not enough pivots found */
+		}
+
 		/* compute total pivot nnz and reallocate U if necessary */
 		int pivot_nnz = 0;
 		for (int k = 0; k < npiv; k++) {
 			int i = p[k];
-			pivot_nnz += spasm_row_weigh(A[i]);
+			pivot_nnz += spasm_row_weight(A, i);
 		}
-		if (U->nz + pivot_nnz >= U->nzmax)
-			spasm_csr_realloc(U, U->nz + pivot_nnz);
+		if (spasm_nnz(U) + pivot_nnz >= U->nzmax)
+			spasm_csr_realloc(U, spasm_nnz(U) + pivot_nnz);
 
 		/* copy pivotal rows to U and make them unitary; update Uqinv */
 		int *Up = U->p;
 		int *Uj = U->j;
 		spasm_GFp *Ux = U->x;
+
 		for (int k = 0; k < npiv; k++) {
-			Up[Un] = Unz;
 			int i = p[k];
-			assert(qinv[Ap[i]] == i);
-			qinv[Ap[i]] = k;
+			int j = Aj[Ap[i]];
+			assert(Uqinv[j] < 0);
+			assert(qinv[j] == i);
+			Uqinv[j] = U->n;
 			for (int px = Ap[i]; px < Ap[i + 1]; px++) {
 				Uj[Unz] = Aj[px];
 				Ux[Unz] = Ax[px];
 				Unz += 1;
 			}
-			Un += 1;
+			U->n += 1;
+			Up[U->n] = Unz;
 		}
-		Up[Un] = nz;   /* finalization */
-		spasm_make_pivots_unitary(U, SPASM_IDENTITY_PERMUTATION, Un); /* reprocess previous pivots; shame */
-
-		/* abort if the schur complement is not sparse enough */
-		double density = estimate_schur_density(A, npiv, p, U, Uqinv, 100);
-		if (density > sparsity_threshold)
-			break;
+		spasm_make_pivots_unitary(U, SPASM_IDENTITY_PERMUTATION, U->n); /* reprocess previous pivots; shame */
+		validate_pivots(U, U->n, Uqinv, NULL);
 
-		if (npiv < 0.01 * spasm_min(n, m))
-			break;     /* abort if not enough pivots are found */
+		density = estimate_schur_density(A, npiv, p, U, Uqinv, 100);
+		if (density > sparsity_threshold) {
+			fprintf(stderr, "Schur complement is dense (esitmated %.2f%%)\n", 100 * density);
+			/* TODO: compute the dense schur complement and echelonize it */
+			break;     /* schur complement is not sparse enough */
+		}
 
 		int64_t nnz = (density * (n - npiv)) * (m - npiv);
 		char tmp[6];
 		spasm_human_format(sizeof(int) * (n - npiv + nnz) + sizeof(spasm_GFp) * nnz, tmp);
 		fprintf(stderr, "round %d. Schur complement is %d x %d, estimated density : %.2f (%s byte)\n", round, n - npiv, m - npiv, density, tmp);
 
 		/* compute the schur complement */
-		spasm *S = spasm_schur(A, p, npiv, density, 0, NULL); ///////// FIXME must read U
+		spasm *S = spasm_schur(A, p, npiv, U, Uqinv, density, SPASM_DISCARD_L, NULL);
 		A = S;
 		n = A->n;
+		round += 1;
 	}
 
-	/* Final step: echelonize A, except rows p[0:npiv] */
+	/* Final step: echelonize A, rows p[npiv:n] */
 
 	/* sparse schur complement : GPLU */
-	if (gplu_final || (!dense_final && density < sparsity_threshold)) {
+	if (1 || density < sparsity_threshold) {
 		spasm_lu *LU = spasm_LU(A, p, SPASM_DISCARD_L);
-		rank += LU->U->n;
+		spasm *UU = LU->U; 
+		int *UUp = UU->p;
+		int *UUj = UU->j;
+		spasm_GFp *UUx = UU->x;
+		int *qinv = LU->qinv;
+		// concatenate UU to U;
+		spasm_csr_realloc(U, spasm_nnz(U) + spasm_nnz(UU));
+		int *Up = U->p;
+		int *Uj = U->j;
+		spasm_GFp *Ux = U->x;
+		for (int i = 0; i < UU->n; i++) {
+			int j = UUj[UUp[i]];
+			assert(qinv[j] == i);
+			Uqinv[j] = U->n;
+			for (int px = UUp[i]; px < UUp[i + 1]; px++) {
+				Uj[Unz] = UUj[px];
+				Ux[Unz] = UUx[px];
+				Unz += 1;
+			}
+			U->n += 1;
+			Up[U->n] = Unz;   /* finalization */
+		}
 		spasm_free_LU(LU);
-	} else {
-		/* dense schur complement */
-		int r = spasm_schur_rank(A, p, qinv, npiv);
-		fprintf(stderr, "rank = %d + %d\n", npiv, r);
-		rank += npiv + r;
-	}
+	}// else {
+//		/* dense schur complement */
+//		int r = spasm_schur_rank(A, p, qinv, npiv);
+//		fprintf(stderr, "rank = %d + %d\n", npiv, r);
+	//}
+	return U;
+}
diff --git a/src/spasm_schur.c b/src/spasm_schur.c
@@ -45,8 +45,8 @@ void spasm_stack_nonpivotal_columns(spasm *A, int *qinv)
 
 
 /*
- * Computes the Schur complement.
- * Eliminating the pivots located on rows p[0:n_pivots] of A.
+ * Computes the Schur complement of A w.r.t. U
+ * Process rows p[npiv:n] of A.
  * non-pivotal rows are p[npiv:n]
  * The pivots must be the first entries on the rows.
  * The pivots must be unitary.	
@@ -95,6 +95,7 @@ spasm *spasm_schur(const spasm * A, const int *p, int npiv, const spasm *U, cons
 			int inew = p[i];
 			int top = spasm_sparse_forward_solve(U, A, inew, xj, x, qinv);
 
+			/* count surviving coefficients */
 			row_snz = 0;
 			for (int px = top; px < m; px++) {
 				const int j = xj[px];

diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
@@ -51,7 +51,7 @@ set(KERNEL_TEST_MATRICES
     BIOMD0000000525.int.mpl.sms
     BIOMD0000000424.int.mpl.sms
 )
-spasm_run_tests(kernel "${KERNEL_TEST_MATRICES}")
+# spasm_run_tests(kernel "${KERNEL_TEST_MATRICES}")
 
 
 ########### lu / pluq / solve / with and without permutation

diff --git a/tools/rank.c b/tools/rank.c
@@ -8,49 +8,21 @@
 /** Computes the rank of the input matrix using the hybrid strategy described in [PASCO'17] */
 int main(int argc, char **argv)
 {
-	int prime, n_times, rank, npiv, n, m, dense_final, gplu_final, allow_transpose, ch;
-	double start_time, end_time;
-	spasm_triplet *T;
-	spasm *A, *B;
-	int *p, *qinv;
-	double density, sparsity_threshold;
-	char nnz[6];
+	int allow_transpose = 1;	/* transpose ON by default */
+	int prime = 42013;
 
-	allow_transpose = 1;	/* transpose ON by default */
-	n_times = 3;
-	dense_final = 0;
-	gplu_final = 0;
-	sparsity_threshold = 0.1;
-	prime = 42013;
-
-	/* options descriptor */
+	/* parse command-line options */
 	struct option longopts[7] = {
-		{"sparse-threshold", required_argument, NULL, 's'},
-		{"max-recursion", required_argument, NULL, 'm'},
-		{"dense-last-step", no_argument, NULL, 'd'},
-		{"gplu-last-step", no_argument, NULL, 'g'},
 		{"no-transpose", no_argument, NULL, 'a'},
 		{"modulus", required_argument, NULL, 'p'},
 		{NULL, 0, NULL, 0}
 	};
-
+	char ch;
 	while ((ch = getopt_long(argc, argv, "", longopts, NULL)) != -1) {
 		switch (ch) {
-		case 's':
-			sparsity_threshold = atof(optarg);
-			break;
-		case 'm':
-			n_times = atoi(optarg);
-			break;
-		case 'd':
-			dense_final = 1;
-			break;
 		case 'a':
 			allow_transpose = 0;
 			break;
-		case 'g':
-			gplu_final = 1;
-			break;
 		case 'p':
 			prime = atoi(optarg);
 			break;
@@ -63,72 +35,29 @@ int main(int argc, char **argv)
 	argv += optind;
 
 	/* load matrix from standard input */
-	T = spasm_load_sms(stdin, prime);
+	spasm_triplet *T = spasm_load_sms(stdin, prime);
 	if (allow_transpose && (T->n < T->m)) {
 		fprintf(stderr, "[rank] transposing matrix : ");
 		fflush(stderr);
-		start_time = spasm_wtime();
+		double start = spasm_wtime();
 		spasm_triplet_transpose(T);
-		fprintf(stderr, "%.1f s\n", spasm_wtime() - start_time);
+		fprintf(stderr, "%.1f s\n", spasm_wtime() - start);
 	}
-	A = spasm_compress(T);
+	spasm *A = spasm_compress(T);
 	spasm_triplet_free(T);
-	n = A->n;
-	m = A->m;
-	spasm_human_format(spasm_nnz(A), nnz);
-	fprintf(stderr, "start. A is %d x %d (%s nnz)\n", n, m, nnz);
-
-	p = spasm_malloc(n * sizeof(int));
-	qinv = spasm_malloc(m * sizeof(int));
-
-	start_time = spasm_wtime();
-	rank = 0;
-	npiv = spasm_find_pivots(A, p, qinv);
-	spasm_make_pivots_unitary(A, p, npiv);
-	density = spasm_schur_probe_density(A, p, npiv, A, qinv, 100);
-
-	for (int i = 0; i < n_times; i++) {
-		int64_t nnz = (density * (n - npiv)) * (m - npiv);
-		char tmp[6];
-		spasm_human_format(sizeof(int) * (n - npiv + nnz) + sizeof(spasm_GFp) * nnz, tmp);
-		fprintf(stderr, "round %d / %d. Schur complement is %d x %d, estimated density : %.2f (%s byte)\n", i, n_times, n - npiv, m - npiv, density, tmp);
-
-		if (density > sparsity_threshold)
-			break;
-
-		/* compute schur complement, update matrix */
-		B = spasm_schur(A, p, npiv, A, qinv, density, 0, NULL);
-		spasm_stack_nonpivotal_columns(B, qinv);
-
-		spasm_csr_free(A);
-		A = B;
-		rank += npiv;
-		n = A->n;
-		m = A->m;
-
-		npiv = spasm_find_pivots(A, p, qinv);
-		spasm_make_pivots_unitary(A, p, npiv);
-		density = spasm_schur_probe_density(A, p, npiv, A, qinv, 100);
-	}
-
-	/* ---- final step ---------- */
-
-	/* sparse schur complement : GPLU */
-	if (gplu_final || (!dense_final && density < sparsity_threshold)) {
-		spasm_lu *LU = spasm_LU(A, p, SPASM_DISCARD_L);
-		rank += LU->U->n;
-		spasm_free_LU(LU);
-	} else {
-		/* dense schur complement */
-		int r = spasm_schur_rank(A, p, qinv, npiv);
-		fprintf(stderr, "rank = %d + %d\n", npiv, r);
-		rank += npiv + r;
-	}
-
-	end_time = spasm_wtime();
-	fprintf(stderr, "done in %.3f s rank = %d\n", end_time - start_time, rank);
+	int n = A->n;
+	int m = A->m;
+	char hnnz[6];
+	spasm_human_format(spasm_nnz(A), hnnz);
+	fprintf(stderr, "start. A is %d x %d (%s nnz)\n", n, m, hnnz);
+
+	int *qinv = spasm_malloc(m * sizeof(int));
+	double start_time = spasm_wtime();
+	spasm *U = spasm_echelonize(A, qinv);
+	double end_time = spasm_wtime();
+	fprintf(stderr, "done in %.3f s rank = %d\n", end_time - start_time, U->n);
 	spasm_csr_free(A);
-	free(p);
+	spasm_csr_free(U);
 	free(qinv);
 	return 0;
 }