Actual source code: snesj2.c


  2: #include <petsc/private/snesimpl.h>
  3: #include <petscdm.h>

  5: /*
  6:    MatFDColoringSetFunction() takes a function with four arguments, we want to use SNESComputeFunction()
  7:    since it logs function computation information.
  8: */
  9: static PetscErrorCode SNESComputeFunctionCtx(SNES snes, Vec x, Vec f, void *ctx)
 10: {
 11:   return SNESComputeFunction(snes, x, f);
 12: }
 13: static PetscErrorCode SNESComputeMFFunctionCtx(SNES snes, Vec x, Vec f, void *ctx)
 14: {
 15:   return SNESComputeMFFunction(snes, x, f);
 16: }

 18: /*@C
 19:     SNESComputeJacobianDefaultColor - Computes the Jacobian using
 20:     finite differences and coloring to exploit matrix sparsity.

 22:     Collective

 24:     Input Parameters:
 25: +   snes - nonlinear solver object
 26: .   x1 - location at which to evaluate Jacobian
 27: -   ctx - `MatFDColoring` context or `NULL`

 29:     Output Parameters:
 30: +   J - Jacobian matrix (not altered in this routine)
 31: -   B - newly computed Jacobian matrix to use with preconditioner (generally the same as `J`)

 33:     Level: intermediate

 35:    Options Database Keys:
 36: +  -snes_fd_color_use_mat - use a matrix coloring from the explicit matrix nonzero pattern instead of from the `DM` providing the matrix
 37: .  -snes_fd_color - Activates `SNESComputeJacobianDefaultColor()` in `SNESSetFromOptions()`
 38: .  -mat_fd_coloring_err <err> - Sets <err> (square root of relative error in the function)
 39: .  -mat_fd_coloring_umin <umin> - Sets umin, the minimum allowable u-value magnitude
 40: .  -mat_fd_type - Either wp or ds (see `MATMFFD_WP` or `MATMFFD_DS`)
 41: .  -snes_mf_operator - Use matrix free application of Jacobian
 42: -  -snes_mf - Use matrix free Jacobian with no explicit Jacobian representation

 44:     Notes:
 45:     If the coloring is not provided through the context, this will first try to get the
 46:     coloring from the `DM`.  If the `DM` has no coloring routine, then it will try to
 47:     get the coloring from the matrix.  This requires that the matrix have its nonzero locations already provided.

 49:     `SNES` supports three approaches for computing (approximate) Jacobians: user provided via `SNESSetJacobian()`, matrix-free via `SNESSetUseMatrixFree()`,
 50:     and computing explicitly with finite differences and coloring using `MatFDColoring`. It is also possible to use automatic differentiation
 51:     and the `MatFDColoring` object, see src/ts/tutorials/autodiff/ex16adj_tl.cxx

 53:    This function can be provided to `SNESSetJacobian()` along with an appropriate sparse matrix to hold the Jacobian

 55: .seealso: `SNES`, `SNESSetJacobian()`, `SNESTestJacobian()`, `SNESComputeJacobianDefault()`, `SNESSetUseMatrixFree()`,
 56:           `MatFDColoringCreate()`, `MatFDColoringSetFunction()`
 57: @*/
 58: PetscErrorCode SNESComputeJacobianDefaultColor(SNES snes, Vec x1, Mat J, Mat B, void *ctx)
 59: {
 60:   MatFDColoring color = (MatFDColoring)ctx;
 61:   DM            dm;
 62:   MatColoring   mc;
 63:   ISColoring    iscoloring;
 64:   PetscBool     hascolor;
 65:   PetscBool     solvec, matcolor = PETSC_FALSE;
 66:   DMSNES        dms;

 68:   PetscFunctionBegin;
 70:   if (!color) PetscCall(PetscObjectQuery((PetscObject)B, "SNESMatFDColoring", (PetscObject *)&color));

 72:   if (!color) {
 73:     PetscCall(SNESGetDM(snes, &dm));
 74:     PetscCall(DMHasColoring(dm, &hascolor));
 75:     matcolor = PETSC_FALSE;
 76:     PetscCall(PetscOptionsGetBool(((PetscObject)snes)->options, ((PetscObject)snes)->prefix, "-snes_fd_color_use_mat", &matcolor, NULL));
 77:     if (hascolor && !matcolor) {
 78:       PetscCall(DMCreateColoring(dm, IS_COLORING_GLOBAL, &iscoloring));
 79:     } else {
 80:       PetscCall(MatColoringCreate(B, &mc));
 81:       PetscCall(MatColoringSetDistance(mc, 2));
 82:       PetscCall(MatColoringSetType(mc, MATCOLORINGSL));
 83:       PetscCall(MatColoringSetFromOptions(mc));
 84:       PetscCall(MatColoringApply(mc, &iscoloring));
 85:       PetscCall(MatColoringDestroy(&mc));
 86:     }
 87:     PetscCall(MatFDColoringCreate(B, iscoloring, &color));
 88:     PetscCall(DMGetDMSNES(dm, &dms));
 89:     if (dms->ops->computemffunction) {
 90:       PetscCall(MatFDColoringSetFunction(color, (PetscErrorCode(*)(void))SNESComputeMFFunctionCtx, NULL));
 91:     } else {
 92:       PetscCall(MatFDColoringSetFunction(color, (PetscErrorCode(*)(void))SNESComputeFunctionCtx, NULL));
 93:     }
 94:     PetscCall(MatFDColoringSetFromOptions(color));
 95:     PetscCall(MatFDColoringSetUp(B, iscoloring, color));
 96:     PetscCall(ISColoringDestroy(&iscoloring));
 97:     PetscCall(PetscObjectCompose((PetscObject)B, "SNESMatFDColoring", (PetscObject)color));
 98:     PetscCall(PetscObjectDereference((PetscObject)color));
 99:   }

101:   /* F is only usable if there is no RHS on the SNES and the full solution corresponds to x1 */
102:   PetscCall(VecEqual(x1, snes->vec_sol, &solvec));
103:   if (!snes->vec_rhs && solvec) {
104:     Vec F;
105:     PetscCall(SNESGetFunction(snes, &F, NULL, NULL));
106:     PetscCall(MatFDColoringSetF(color, F));
107:   }
108:   PetscCall(MatFDColoringApply(B, color, x1, snes));
109:   if (J != B) {
110:     PetscCall(MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY));
111:     PetscCall(MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY));
112:   }
113:   PetscFunctionReturn(PETSC_SUCCESS);
114: }

116: /*@C
117:   SNESPruneJacobianColor - Remove nondiagonal zeros in the Jacobian matrix and update the `MatMFFD` coloring information.

119:   Collective

121:   Input Parameters:
122: + snes - the `SNES` context
123: . J - Jacobian matrix (not altered in this routine)
124: - B - newly computed Jacobian matrix to use with preconditioner (generally the same as `J`)

126:   Level: intermediate

128:   Notes:
129:   This function improves the `MatMFFD` coloring performance when the Jacobian matrix is overallocated or contains
130:   many constant zeros entries, which is typically the case when the matrix is generated by a `DM`
131:   and multiple fields are involved.

133:   Users need to make sure that the Jacobian matrix is properly filled to reflect the sparsity
134:   structure. For `MatMFFD` coloring, the values of nonzero entries are not important. So one can
135:   usually call `SNESComputeJacobian()` with randomized input vectors to generate a dummy Jacobian.
136:   `SNESComputeJacobian()` should be called before `SNESSolve()` but after `SNESSetUp()`.

138: .seealso: `SNESComputeJacobianDefaultColor()`, `MatEliminateZeros()`, `MatFDColoringCreate()`, `MatFDColoringSetFunction()`
139: @*/
140: PetscErrorCode SNESPruneJacobianColor(SNES snes, Mat J, Mat B)
141: {
142:   DM            dm;
143:   DMSNES        dms;
144:   MatColoring   mc;
145:   ISColoring    iscoloring;
146:   MatFDColoring matfdcoloring;

148:   PetscFunctionBegin;
149:   /* Generate new coloring after eliminating zeros in the matrix */
150:   PetscCall(MatEliminateZeros(B));
151:   PetscCall(MatColoringCreate(B, &mc));
152:   PetscCall(MatColoringSetDistance(mc, 2));
153:   PetscCall(MatColoringSetType(mc, MATCOLORINGSL));
154:   PetscCall(MatColoringSetFromOptions(mc));
155:   PetscCall(MatColoringApply(mc, &iscoloring));
156:   PetscCall(MatColoringDestroy(&mc));
157:   /* Replace the old coloring with the new one */
158:   PetscCall(MatFDColoringCreate(B, iscoloring, &matfdcoloring));
159:   PetscCall(SNESGetDM(snes, &dm));
160:   PetscCall(DMGetDMSNES(dm, &dms));
161:   // Comment out the following branch to bypass the coverage test. You can uncomment it when needed.
162:   //if (dms->ops->computemffunction) {
163:   //  PetscCall(MatFDColoringSetFunction(matfdcoloring, (PetscErrorCode(*)(void))SNESComputeMFFunctionCtx, NULL));
164:   //} else {
165:   PetscCall(MatFDColoringSetFunction(matfdcoloring, (PetscErrorCode(*)(void))SNESComputeFunctionCtx, NULL));
166:   //}
167:   PetscCall(MatFDColoringSetFromOptions(matfdcoloring));
168:   PetscCall(MatFDColoringSetUp(B, iscoloring, matfdcoloring));
169:   PetscCall(PetscObjectCompose((PetscObject)B, "SNESMatFDColoring", (PetscObject)matfdcoloring));
170:   PetscCall(PetscObjectDereference((PetscObject)matfdcoloring));
171:   PetscCall(ISColoringDestroy(&iscoloring));
172:   PetscFunctionReturn(PETSC_SUCCESS);
173: }