xref: /petsc/src/ksp/pc/impls/bddc/bddcschurs.c (revision a7bda6aa3ba235683bad061d22ca55702fa6889c)
1 #include <../src/ksp/pc/impls/bddc/bddc.h>
2 #include <../src/ksp/pc/impls/bddc/bddcprivate.h>
3 #include <../src/mat/impls/dense/seq/dense.h>
4 #include <petscblaslapack.h>
5 
6 PETSC_STATIC_INLINE PetscErrorCode PCBDDCAdjGetNextLayer_Private(PetscInt*,PetscInt,PetscBT,PetscInt*,PetscInt*,PetscInt*);
7 static PetscErrorCode PCBDDCComputeExplicitSchur(Mat,PetscBool,MatReuse,Mat*);
8 static PetscErrorCode PCBDDCReuseSolvers_Interior(PC,Vec,Vec);
9 static PetscErrorCode PCBDDCReuseSolvers_Correction(PC,Vec,Vec);
10 
11 /* if v2 is not present, correction is done in-place */
12 PetscErrorCode PCBDDCReuseSolversBenignAdapt(PCBDDCReuseSolvers ctx, Vec v, Vec v2, PetscBool sol, PetscBool full)
13 {
14   PetscScalar    *array;
15   PetscScalar    *array2;
16   PetscErrorCode ierr;
17 
18   PetscFunctionBegin;
19   if (!ctx->benign_n) PetscFunctionReturn(0);
20   if (sol && full) {
21     PetscInt n_I,size_schur;
22 
23     /* get sizes */
24     ierr = MatGetSize(ctx->benign_csAIB,&size_schur,NULL);CHKERRQ(ierr);
25     ierr = VecGetSize(v,&n_I);CHKERRQ(ierr);
26     n_I = n_I - size_schur;
27     /* get schur sol from array */
28     ierr = VecGetArray(v,&array);CHKERRQ(ierr);
29     ierr = VecPlaceArray(ctx->benign_dummy_schur_vec,array+n_I);CHKERRQ(ierr);
30     ierr = VecRestoreArray(v,&array);CHKERRQ(ierr);
31     /* apply interior sol correction */
32     ierr = MatMultTranspose(ctx->benign_csAIB,ctx->benign_dummy_schur_vec,ctx->benign_corr_work);CHKERRQ(ierr);
33     ierr = VecResetArray(ctx->benign_dummy_schur_vec);CHKERRQ(ierr);
34     ierr = MatMultAdd(ctx->benign_AIIm1ones,ctx->benign_corr_work,v,v);CHKERRQ(ierr);
35   }
36   if (v2) {
37     PetscInt nl;
38 
39     ierr = VecGetArrayRead(v,(const PetscScalar**)&array);CHKERRQ(ierr);
40     ierr = VecGetLocalSize(v2,&nl);CHKERRQ(ierr);
41     ierr = VecGetArray(v2,&array2);CHKERRQ(ierr);
42     ierr = PetscMemcpy(array2,array,nl*sizeof(PetscScalar));CHKERRQ(ierr);
43   } else {
44     ierr = VecGetArray(v,&array);CHKERRQ(ierr);
45     array2 = array;
46   }
47   if (!sol) { /* change rhs */
48     PetscInt n;
49     for (n=0;n<ctx->benign_n;n++) {
50       PetscScalar    sum = 0.;
51       const PetscInt *cols;
52       PetscInt       nz,i;
53 
54       ierr = ISGetLocalSize(ctx->benign_zerodiag_subs[n],&nz);CHKERRQ(ierr);
55       ierr = ISGetIndices(ctx->benign_zerodiag_subs[n],&cols);CHKERRQ(ierr);
56       for (i=0;i<nz-1;i++) sum += array[cols[i]];
57 #if defined(PETSC_USE_COMPLEX)
58       sum = -(PetscRealPart(sum)/nz + PETSC_i*(PetscImaginaryPart(sum)/nz));
59 #else
60       sum = -sum/nz;
61 #endif
62       for (i=0;i<nz-1;i++) array2[cols[i]] += sum;
63       ctx->benign_save_vals[n] = array2[cols[nz-1]];
64       array2[cols[nz-1]] = sum;
65       ierr = ISRestoreIndices(ctx->benign_zerodiag_subs[n],&cols);CHKERRQ(ierr);
66     }
67   } else {
68     PetscInt n;
69     for (n=0;n<ctx->benign_n;n++) {
70       PetscScalar    sum = 0.;
71       const PetscInt *cols;
72       PetscInt       nz,i;
73       ierr = ISGetLocalSize(ctx->benign_zerodiag_subs[n],&nz);CHKERRQ(ierr);
74       ierr = ISGetIndices(ctx->benign_zerodiag_subs[n],&cols);CHKERRQ(ierr);
75       for (i=0;i<nz-1;i++) sum += array[cols[i]];
76 #if defined(PETSC_USE_COMPLEX)
77       sum = -(PetscRealPart(sum)/nz + PETSC_i*(PetscImaginaryPart(sum)/nz));
78 #else
79       sum = -sum/nz;
80 #endif
81       for (i=0;i<nz-1;i++) array2[cols[i]] += sum;
82       array2[cols[nz-1]] = ctx->benign_save_vals[n];
83       ierr = ISRestoreIndices(ctx->benign_zerodiag_subs[n],&cols);CHKERRQ(ierr);
84     }
85   }
86   if (v2) {
87     ierr = VecRestoreArrayRead(v,(const PetscScalar**)&array);CHKERRQ(ierr);
88     ierr = VecRestoreArray(v2,&array2);CHKERRQ(ierr);
89   } else {
90     ierr = VecRestoreArray(v,&array);CHKERRQ(ierr);
91   }
92   if (!sol && full) {
93     Vec      usedv;
94     PetscInt n_I,size_schur;
95 
96     /* get sizes */
97     ierr = MatGetSize(ctx->benign_csAIB,&size_schur,NULL);CHKERRQ(ierr);
98     ierr = VecGetSize(v,&n_I);CHKERRQ(ierr);
99     n_I = n_I - size_schur;
100     /* compute schur rhs correction */
101     if (v2) {
102       usedv = v2;
103     } else {
104       usedv = v;
105     }
106     /* apply schur rhs correction */
107     ierr = MatMultTranspose(ctx->benign_AIIm1ones,usedv,ctx->benign_corr_work);CHKERRQ(ierr);
108     ierr = VecGetArrayRead(usedv,(const PetscScalar**)&array);CHKERRQ(ierr);
109     ierr = VecPlaceArray(ctx->benign_dummy_schur_vec,array+n_I);CHKERRQ(ierr);
110     ierr = VecRestoreArrayRead(usedv,(const PetscScalar**)&array);CHKERRQ(ierr);
111     ierr = MatMultAdd(ctx->benign_csAIB,ctx->benign_corr_work,ctx->benign_dummy_schur_vec,ctx->benign_dummy_schur_vec);CHKERRQ(ierr);
112     ierr = VecResetArray(ctx->benign_dummy_schur_vec);CHKERRQ(ierr);
113   }
114   PetscFunctionReturn(0);
115 }
116 
117 static PetscErrorCode PCBDDCReuseSolvers_Solve_Private(PC pc, Vec rhs, Vec sol, PetscBool transpose, PetscBool full)
118 {
119   PCBDDCReuseSolvers ctx;
120   PetscBool          copy = PETSC_FALSE;
121   PetscErrorCode     ierr;
122 
123   PetscFunctionBegin;
124   ierr = PCShellGetContext(pc,(void **)&ctx);CHKERRQ(ierr);
125   if (full) {
126 #if defined(PETSC_HAVE_MUMPS)
127     ierr = MatMumpsSetIcntl(ctx->F,26,-1);CHKERRQ(ierr);
128 #endif
129 #if defined(PETSC_HAVE_MKL_PARDISO)
130     ierr = MatMkl_PardisoSetCntl(ctx->F,70,0);CHKERRQ(ierr);
131 #endif
132     copy = ctx->has_vertices;
133   } else { /* interior solver */
134 #if defined(PETSC_HAVE_MUMPS)
135     ierr = MatMumpsSetIcntl(ctx->F,26,0);CHKERRQ(ierr);
136 #endif
137 #if defined(PETSC_HAVE_MKL_PARDISO)
138     ierr = MatMkl_PardisoSetCntl(ctx->F,70,1);CHKERRQ(ierr);
139 #endif
140     copy = PETSC_TRUE;
141   }
142   /* copy rhs into factored matrix workspace */
143   if (copy) {
144     PetscInt    n;
145     PetscScalar *array,*array_solver;
146 
147     ierr = VecGetLocalSize(rhs,&n);CHKERRQ(ierr);
148     ierr = VecGetArrayRead(rhs,(const PetscScalar**)&array);CHKERRQ(ierr);
149     ierr = VecGetArray(ctx->rhs,&array_solver);CHKERRQ(ierr);
150     ierr = PetscMemcpy(array_solver,array,n*sizeof(PetscScalar));CHKERRQ(ierr);
151     ierr = VecRestoreArray(ctx->rhs,&array_solver);CHKERRQ(ierr);
152     ierr = VecRestoreArrayRead(rhs,(const PetscScalar**)&array);CHKERRQ(ierr);
153 
154     ierr = PCBDDCReuseSolversBenignAdapt(ctx,ctx->rhs,NULL,PETSC_FALSE,full);CHKERRQ(ierr);
155     if (transpose) {
156       ierr = MatSolveTranspose(ctx->F,ctx->rhs,ctx->sol);CHKERRQ(ierr);
157     } else {
158       ierr = MatSolve(ctx->F,ctx->rhs,ctx->sol);CHKERRQ(ierr);
159     }
160     ierr = PCBDDCReuseSolversBenignAdapt(ctx,ctx->sol,NULL,PETSC_TRUE,full);CHKERRQ(ierr);
161 
162     /* get back data to caller worskpace */
163     ierr = VecGetArrayRead(ctx->sol,(const PetscScalar**)&array_solver);CHKERRQ(ierr);
164     ierr = VecGetArray(sol,&array);CHKERRQ(ierr);
165     ierr = PetscMemcpy(array,array_solver,n*sizeof(PetscScalar));CHKERRQ(ierr);
166     ierr = VecRestoreArray(sol,&array);CHKERRQ(ierr);
167     ierr = VecRestoreArrayRead(ctx->sol,(const PetscScalar**)&array_solver);CHKERRQ(ierr);
168   } else {
169     if (ctx->benign_n) {
170       ierr = PCBDDCReuseSolversBenignAdapt(ctx,rhs,ctx->rhs,PETSC_FALSE,full);CHKERRQ(ierr);
171       if (transpose) {
172         ierr = MatSolveTranspose(ctx->F,ctx->rhs,sol);CHKERRQ(ierr);
173       } else {
174         ierr = MatSolve(ctx->F,ctx->rhs,sol);CHKERRQ(ierr);
175       }
176       ierr = PCBDDCReuseSolversBenignAdapt(ctx,sol,NULL,PETSC_TRUE,full);CHKERRQ(ierr);
177     } else {
178       if (transpose) {
179         ierr = MatSolveTranspose(ctx->F,rhs,sol);CHKERRQ(ierr);
180       } else {
181         ierr = MatSolve(ctx->F,rhs,sol);CHKERRQ(ierr);
182       }
183     }
184   }
185   /* restore defaults */
186 #if defined(PETSC_HAVE_MUMPS)
187   ierr = MatMumpsSetIcntl(ctx->F,26,-1);CHKERRQ(ierr);
188 #endif
189 #if defined(PETSC_HAVE_MKL_PARDISO)
190   ierr = MatMkl_PardisoSetCntl(ctx->F,70,0);CHKERRQ(ierr);
191 #endif
192   PetscFunctionReturn(0);
193 }
194 
195 static PetscErrorCode PCBDDCReuseSolvers_Correction(PC pc, Vec rhs, Vec sol)
196 {
197   PetscErrorCode   ierr;
198 
199   PetscFunctionBegin;
200   ierr = PCBDDCReuseSolvers_Solve_Private(pc,rhs,sol,PETSC_FALSE,PETSC_TRUE);CHKERRQ(ierr);
201   PetscFunctionReturn(0);
202 }
203 
204 static PetscErrorCode PCBDDCReuseSolvers_CorrectionTranspose(PC pc, Vec rhs, Vec sol)
205 {
206   PetscErrorCode   ierr;
207 
208   PetscFunctionBegin;
209   ierr = PCBDDCReuseSolvers_Solve_Private(pc,rhs,sol,PETSC_TRUE,PETSC_TRUE);CHKERRQ(ierr);
210   PetscFunctionReturn(0);
211 }
212 
213 static PetscErrorCode PCBDDCReuseSolvers_Interior(PC pc, Vec rhs, Vec sol)
214 {
215   PetscErrorCode   ierr;
216 
217   PetscFunctionBegin;
218   ierr = PCBDDCReuseSolvers_Solve_Private(pc,rhs,sol,PETSC_FALSE,PETSC_FALSE);CHKERRQ(ierr);
219   PetscFunctionReturn(0);
220 }
221 
222 static PetscErrorCode PCBDDCReuseSolvers_InteriorTranspose(PC pc, Vec rhs, Vec sol)
223 {
224   PetscErrorCode   ierr;
225 
226   PetscFunctionBegin;
227   ierr = PCBDDCReuseSolvers_Solve_Private(pc,rhs,sol,PETSC_TRUE,PETSC_FALSE);CHKERRQ(ierr);
228   PetscFunctionReturn(0);
229 }
230 
231 static PetscErrorCode PCBDDCReuseSolversReset(PCBDDCReuseSolvers reuse)
232 {
233   PetscInt       i;
234   PetscErrorCode ierr;
235 
236   PetscFunctionBegin;
237   ierr = MatDestroy(&reuse->F);CHKERRQ(ierr);
238   ierr = VecDestroy(&reuse->sol);CHKERRQ(ierr);
239   ierr = VecDestroy(&reuse->rhs);CHKERRQ(ierr);
240   ierr = PCDestroy(&reuse->interior_solver);CHKERRQ(ierr);
241   ierr = PCDestroy(&reuse->correction_solver);CHKERRQ(ierr);
242   ierr = ISDestroy(&reuse->is_R);CHKERRQ(ierr);
243   ierr = ISDestroy(&reuse->is_B);CHKERRQ(ierr);
244   ierr = VecScatterDestroy(&reuse->correction_scatter_B);CHKERRQ(ierr);
245   ierr = VecDestroy(&reuse->sol_B);CHKERRQ(ierr);
246   ierr = VecDestroy(&reuse->rhs_B);CHKERRQ(ierr);
247   for (i=0;i<reuse->benign_n;i++) {
248     ierr = ISDestroy(&reuse->benign_zerodiag_subs[i]);CHKERRQ(ierr);
249   }
250   ierr = PetscFree(reuse->benign_zerodiag_subs);CHKERRQ(ierr);
251   ierr = PetscFree(reuse->benign_save_vals);CHKERRQ(ierr);
252   ierr = MatDestroy(&reuse->benign_csAIB);CHKERRQ(ierr);
253   ierr = MatDestroy(&reuse->benign_AIIm1ones);CHKERRQ(ierr);
254   ierr = VecDestroy(&reuse->benign_corr_work);CHKERRQ(ierr);
255   ierr = VecDestroy(&reuse->benign_dummy_schur_vec);CHKERRQ(ierr);
256   PetscFunctionReturn(0);
257 }
258 
259 static PetscErrorCode PCBDDCComputeExplicitSchur(Mat M, PetscBool issym, MatReuse reuse, Mat *S)
260 {
261   Mat            B, C, D, Bd, Cd, AinvBd;
262   KSP            ksp;
263   PC             pc;
264   PetscBool      isLU, isILU, isCHOL, Bdense, Cdense;
265   PetscReal      fill = 2.0;
266   PetscInt       n_I;
267   PetscMPIInt    size;
268   PetscErrorCode ierr;
269 
270   PetscFunctionBegin;
271   ierr = MPI_Comm_size(PetscObjectComm((PetscObject)M),&size);CHKERRQ(ierr);
272   if (size != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Not for parallel matrices");
273   if (reuse == MAT_REUSE_MATRIX) {
274     PetscBool Sdense;
275 
276     ierr = PetscObjectTypeCompare((PetscObject)*S, MATSEQDENSE, &Sdense);CHKERRQ(ierr);
277     if (!Sdense) SETERRQ(PetscObjectComm((PetscObject)M),PETSC_ERR_SUP,"S should dense");
278   }
279   ierr = MatSchurComplementGetSubMatrices(M, NULL, NULL, &B, &C, &D);CHKERRQ(ierr);
280   ierr = MatSchurComplementGetKSP(M, &ksp);CHKERRQ(ierr);
281   ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr);
282   ierr = PetscObjectTypeCompare((PetscObject) pc, PCLU, &isLU);CHKERRQ(ierr);
283   ierr = PetscObjectTypeCompare((PetscObject) pc, PCILU, &isILU);CHKERRQ(ierr);
284   ierr = PetscObjectTypeCompare((PetscObject) pc, PCCHOLESKY, &isCHOL);CHKERRQ(ierr);
285   ierr = PetscObjectTypeCompare((PetscObject) B, MATSEQDENSE, &Bdense);CHKERRQ(ierr);
286   ierr = PetscObjectTypeCompare((PetscObject) C, MATSEQDENSE, &Cdense);CHKERRQ(ierr);
287   ierr = MatGetSize(B,&n_I,NULL);CHKERRQ(ierr);
288   if (n_I) {
289     if (!Bdense) {
290       ierr = MatConvert(B, MATSEQDENSE, MAT_INITIAL_MATRIX, &Bd);CHKERRQ(ierr);
291     } else {
292       Bd = B;
293     }
294 
295     if (isLU || isILU || isCHOL) {
296       Mat fact;
297       ierr = KSPSetUp(ksp);CHKERRQ(ierr);
298       ierr = PCFactorGetMatrix(pc, &fact);CHKERRQ(ierr);
299       ierr = MatDuplicate(Bd, MAT_DO_NOT_COPY_VALUES, &AinvBd);CHKERRQ(ierr);
300       ierr = MatMatSolve(fact, Bd, AinvBd);CHKERRQ(ierr);
301     } else {
302       PetscBool ex = PETSC_TRUE;
303 
304       if (ex) {
305         Mat Ainvd;
306 
307         ierr = PCComputeExplicitOperator(pc, &Ainvd);CHKERRQ(ierr);
308         ierr = MatMatMult(Ainvd, Bd, MAT_INITIAL_MATRIX, fill, &AinvBd);CHKERRQ(ierr);
309         ierr = MatDestroy(&Ainvd);CHKERRQ(ierr);
310       } else {
311         Vec         sol,rhs;
312         PetscScalar *arrayrhs,*arraysol;
313         PetscInt    i,nrhs,n;
314 
315         ierr = MatDuplicate(Bd, MAT_DO_NOT_COPY_VALUES, &AinvBd);CHKERRQ(ierr);
316         ierr = MatGetSize(Bd,&n,&nrhs);CHKERRQ(ierr);
317         ierr = MatDenseGetArray(Bd,&arrayrhs);CHKERRQ(ierr);
318         ierr = MatDenseGetArray(AinvBd,&arraysol);CHKERRQ(ierr);
319         ierr = KSPGetSolution(ksp,&sol);CHKERRQ(ierr);
320         ierr = KSPGetRhs(ksp,&rhs);CHKERRQ(ierr);
321         for (i=0;i<nrhs;i++) {
322           ierr = VecPlaceArray(rhs,arrayrhs+i*n);CHKERRQ(ierr);
323           ierr = VecPlaceArray(sol,arraysol+i*n);CHKERRQ(ierr);
324           ierr = KSPSolve(ksp,rhs,sol);CHKERRQ(ierr);
325           ierr = VecResetArray(rhs);CHKERRQ(ierr);
326           ierr = VecResetArray(sol);CHKERRQ(ierr);
327         }
328         ierr = MatDenseRestoreArray(Bd,&arrayrhs);CHKERRQ(ierr);
329         ierr = MatDenseRestoreArray(AinvBd,&arrayrhs);CHKERRQ(ierr);
330       }
331     }
332     if (!Bdense & !issym) {
333       ierr = MatDestroy(&Bd);CHKERRQ(ierr);
334     }
335 
336     if (!issym) {
337       if (!Cdense) {
338         ierr = MatConvert(C, MATSEQDENSE, MAT_INITIAL_MATRIX, &Cd);CHKERRQ(ierr);
339       } else {
340         Cd = C;
341       }
342       ierr = MatMatMult(Cd, AinvBd, reuse, fill, S);CHKERRQ(ierr);
343       if (!Cdense) {
344         ierr = MatDestroy(&Cd);CHKERRQ(ierr);
345       }
346     } else {
347       ierr = MatTransposeMatMult(Bd, AinvBd, reuse, fill, S);CHKERRQ(ierr);
348       if (!Bdense) {
349         ierr = MatDestroy(&Bd);CHKERRQ(ierr);
350       }
351     }
352     ierr = MatDestroy(&AinvBd);CHKERRQ(ierr);
353   }
354 
355   if (D) {
356     Mat       Dd;
357     PetscBool Ddense;
358 
359     ierr = PetscObjectTypeCompare((PetscObject)D,MATSEQDENSE,&Ddense);CHKERRQ(ierr);
360     if (!Ddense) {
361       ierr = MatConvert(D, MATSEQDENSE, MAT_INITIAL_MATRIX, &Dd);CHKERRQ(ierr);
362     } else {
363       Dd = D;
364     }
365     if (n_I) {
366       ierr = MatAYPX(*S,-1.0,Dd,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
367     } else {
368       if (reuse == MAT_INITIAL_MATRIX) {
369         ierr = MatDuplicate(Dd,MAT_COPY_VALUES,S);CHKERRQ(ierr);
370       } else {
371         ierr = MatCopy(Dd,*S,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
372       }
373     }
374     if (!Ddense) {
375       ierr = MatDestroy(&Dd);CHKERRQ(ierr);
376     }
377   } else {
378     ierr = MatScale(*S,-1.0);CHKERRQ(ierr);
379   }
380   PetscFunctionReturn(0);
381 }
382 
383 PetscErrorCode PCBDDCSubSchursSetUp(PCBDDCSubSchurs sub_schurs, Mat Ain, Mat Sin, PetscBool exact_schur, PetscInt xadj[], PetscInt adjncy[], PetscInt nlayers, Vec scaling, PetscBool compute_Stilda, PetscBool reuse_solvers, PetscBool benign_trick, PetscInt benign_n, PetscInt benign_p0_lidx[], IS benign_zerodiag_subs[], Mat change, IS change_primal)
384 {
385   Mat                    F,A_II,A_IB,A_BI,A_BB,AE_II;
386   Mat                    S_all;
387   Mat                    global_schur_subsets,work_mat,*submats;
388   ISLocalToGlobalMapping l2gmap_subsets;
389   IS                     is_I,is_I_layer;
390   IS                     all_subsets,all_subsets_mult,all_subsets_n;
391   PetscInt               *nnz,*all_local_idx_N;
392   PetscInt               *auxnum1,*auxnum2;
393   PetscInt               i,subset_size,max_subset_size;
394   PetscInt               n_B,extra,local_size,global_size;
395   PetscBLASInt           B_N,B_ierr,B_lwork,*pivots;
396   PetscScalar            *Bwork;
397   PetscSubcomm           subcomm;
398   PetscMPIInt            color,rank;
399   MPI_Comm               comm_n;
400   PetscBool              deluxe = PETSC_TRUE;
401   PetscBool              use_potr = PETSC_FALSE, use_sytr = PETSC_FALSE;
402   PetscErrorCode         ierr;
403 
404   PetscFunctionBegin;
405   ierr = MatDestroy(&sub_schurs->A);CHKERRQ(ierr);
406   ierr = MatDestroy(&sub_schurs->S);CHKERRQ(ierr);
407   /* convert matrix if needed */
408   if (Ain) {
409     PetscBool isseqaij;
410     ierr = PetscObjectTypeCompare((PetscObject)Ain,MATSEQAIJ,&isseqaij);CHKERRQ(ierr);
411     if (isseqaij) {
412       ierr = PetscObjectReference((PetscObject)Ain);CHKERRQ(ierr);
413       sub_schurs->A = Ain;
414     } else {
415       ierr = MatConvert(Ain,MATSEQAIJ,MAT_INITIAL_MATRIX,&sub_schurs->A);CHKERRQ(ierr);
416     }
417   }
418 
419   ierr = PetscObjectReference((PetscObject)Sin);CHKERRQ(ierr);
420   sub_schurs->S = Sin;
421   if (sub_schurs->schur_explicit) {
422     sub_schurs->schur_explicit = (PetscBool)(!!sub_schurs->A);
423   }
424 
425   /* preliminary checks */
426   if (!sub_schurs->schur_explicit && compute_Stilda) SETERRQ(PetscObjectComm((PetscObject)sub_schurs->l2gmap),PETSC_ERR_SUP,"Adaptive selection of constraints requires MUMPS and/or MKL_PARDISO");
427 
428   if (benign_trick) sub_schurs->is_posdef = PETSC_FALSE;
429 
430   /* restrict work on active processes */
431   color = 0;
432   if (!sub_schurs->n_subs) color = 1; /* this can happen if we are in a multilevel case or if the subdomain is disconnected */
433   ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)sub_schurs->l2gmap),&rank);CHKERRQ(ierr);
434   ierr = PetscSubcommCreate(PetscObjectComm((PetscObject)sub_schurs->l2gmap),&subcomm);CHKERRQ(ierr);
435   ierr = PetscSubcommSetNumber(subcomm,2);CHKERRQ(ierr);
436   ierr = PetscSubcommSetTypeGeneral(subcomm,color,rank);CHKERRQ(ierr);
437   ierr = PetscCommDuplicate(PetscSubcommChild(subcomm),&comm_n,NULL);CHKERRQ(ierr);
438   ierr = PetscSubcommDestroy(&subcomm);CHKERRQ(ierr);
439   if (!sub_schurs->n_subs) {
440     ierr = PetscCommDestroy(&comm_n);CHKERRQ(ierr);
441     PetscFunctionReturn(0);
442   }
443   /* ierr = PetscCommDuplicate(PetscObjectComm((PetscObject)sub_schurs->l2gmap),&comm_n,NULL);CHKERRQ(ierr); */
444 
445   /* get Schur complement matrices */
446   if (!sub_schurs->schur_explicit) {
447     Mat       tA_IB,tA_BI,tA_BB;
448     PetscBool isseqsbaij;
449     ierr = MatSchurComplementGetSubMatrices(sub_schurs->S,&A_II,NULL,&tA_IB,&tA_BI,&tA_BB);CHKERRQ(ierr);
450     ierr = PetscObjectTypeCompare((PetscObject)tA_BB,MATSEQSBAIJ,&isseqsbaij);CHKERRQ(ierr);
451     if (isseqsbaij) {
452       ierr = MatConvert(tA_BB,MATSEQAIJ,MAT_INITIAL_MATRIX,&A_BB);CHKERRQ(ierr);
453       ierr = MatConvert(tA_IB,MATSEQAIJ,MAT_INITIAL_MATRIX,&A_IB);CHKERRQ(ierr);
454       ierr = MatConvert(tA_BI,MATSEQAIJ,MAT_INITIAL_MATRIX,&A_BI);CHKERRQ(ierr);
455     } else {
456       ierr = PetscObjectReference((PetscObject)tA_BB);CHKERRQ(ierr);
457       A_BB = tA_BB;
458       ierr = PetscObjectReference((PetscObject)tA_IB);CHKERRQ(ierr);
459       A_IB = tA_IB;
460       ierr = PetscObjectReference((PetscObject)tA_BI);CHKERRQ(ierr);
461       A_BI = tA_BI;
462     }
463   } else {
464     A_II = NULL;
465     A_IB = NULL;
466     A_BI = NULL;
467     A_BB = NULL;
468   }
469   S_all = NULL;
470 
471   /* determine interior problems */
472   ierr = ISGetLocalSize(sub_schurs->is_I,&i);CHKERRQ(ierr);
473   if (nlayers >= 0 && i) { /* Interior problems can be different from the original one */
474     PetscBT                touched;
475     const PetscInt*        idx_B;
476     PetscInt               n_I,n_B,n_local_dofs,n_prev_added,j,layer,*local_numbering;
477 
478     if (!xadj) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Cannot request layering without adjacency");
479     /* get sizes */
480     ierr = ISGetLocalSize(sub_schurs->is_I,&n_I);CHKERRQ(ierr);
481     ierr = ISGetLocalSize(sub_schurs->is_B,&n_B);CHKERRQ(ierr);
482 
483     ierr = PetscMalloc1(n_I+n_B,&local_numbering);CHKERRQ(ierr);
484     ierr = PetscBTCreate(n_I+n_B,&touched);CHKERRQ(ierr);
485     ierr = PetscBTMemzero(n_I+n_B,touched);CHKERRQ(ierr);
486 
487     /* all boundary dofs must be skipped when adding layers */
488     ierr = ISGetIndices(sub_schurs->is_B,&idx_B);CHKERRQ(ierr);
489     for (j=0;j<n_B;j++) {
490       ierr = PetscBTSet(touched,idx_B[j]);CHKERRQ(ierr);
491     }
492     ierr = PetscMemcpy(local_numbering,idx_B,n_B*sizeof(PetscInt));CHKERRQ(ierr);
493     ierr = ISRestoreIndices(sub_schurs->is_B,&idx_B);CHKERRQ(ierr);
494 
495     /* add prescribed number of layers of dofs */
496     n_local_dofs = n_B;
497     n_prev_added = n_B;
498     for (layer=0;layer<nlayers;layer++) {
499       PetscInt n_added;
500       if (n_local_dofs == n_I+n_B) break;
501       if (n_local_dofs > n_I+n_B) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Error querying layer %D. Out of bound access (%D > %D)",layer,n_local_dofs,n_I+n_B);
502       ierr = PCBDDCAdjGetNextLayer_Private(local_numbering+n_local_dofs,n_prev_added,touched,xadj,adjncy,&n_added);CHKERRQ(ierr);
503       n_prev_added = n_added;
504       n_local_dofs += n_added;
505       if (!n_added) break;
506     }
507     ierr = PetscBTDestroy(&touched);CHKERRQ(ierr);
508 
509     /* IS for I layer dofs in original numbering */
510     ierr = ISCreateGeneral(PetscObjectComm((PetscObject)sub_schurs->is_I),n_local_dofs-n_B,local_numbering+n_B,PETSC_COPY_VALUES,&is_I_layer);CHKERRQ(ierr);
511     ierr = PetscFree(local_numbering);CHKERRQ(ierr);
512     ierr = ISSort(is_I_layer);CHKERRQ(ierr);
513     /* IS for I layer dofs in I numbering */
514     if (!sub_schurs->schur_explicit) {
515       ISLocalToGlobalMapping ItoNmap;
516       ierr = ISLocalToGlobalMappingCreateIS(sub_schurs->is_I,&ItoNmap);CHKERRQ(ierr);
517       ierr = ISGlobalToLocalMappingApplyIS(ItoNmap,IS_GTOLM_DROP,is_I_layer,&is_I);CHKERRQ(ierr);
518       ierr = ISLocalToGlobalMappingDestroy(&ItoNmap);CHKERRQ(ierr);
519 
520       /* II block */
521       ierr = MatCreateSubMatrix(A_II,is_I,is_I,MAT_INITIAL_MATRIX,&AE_II);CHKERRQ(ierr);
522     }
523   } else {
524     PetscInt n_I;
525 
526     /* IS for I dofs in original numbering */
527     ierr = PetscObjectReference((PetscObject)sub_schurs->is_I);CHKERRQ(ierr);
528     is_I_layer = sub_schurs->is_I;
529 
530     /* IS for I dofs in I numbering (strided 1) */
531     if (!sub_schurs->schur_explicit) {
532       ierr = ISGetSize(sub_schurs->is_I,&n_I);CHKERRQ(ierr);
533       ierr = ISCreateStride(PetscObjectComm((PetscObject)sub_schurs->is_I),n_I,0,1,&is_I);CHKERRQ(ierr);
534 
535       /* II block is the same */
536       ierr = PetscObjectReference((PetscObject)A_II);CHKERRQ(ierr);
537       AE_II = A_II;
538     }
539   }
540 
541   /* Get info on subset sizes and sum of all subsets sizes */
542   max_subset_size = 0;
543   local_size = 0;
544   for (i=0;i<sub_schurs->n_subs;i++) {
545     ierr = ISGetLocalSize(sub_schurs->is_subs[i],&subset_size);CHKERRQ(ierr);
546     max_subset_size = PetscMax(subset_size,max_subset_size);
547     local_size += subset_size;
548   }
549 
550   /* Work arrays for local indices */
551   extra = 0;
552   ierr = ISGetLocalSize(sub_schurs->is_B,&n_B);CHKERRQ(ierr);
553   if (sub_schurs->schur_explicit && is_I_layer) {
554     ierr = ISGetLocalSize(is_I_layer,&extra);CHKERRQ(ierr);
555   }
556   ierr = PetscMalloc1(n_B+extra,&all_local_idx_N);CHKERRQ(ierr);
557   if (extra) {
558     const PetscInt *idxs;
559     ierr = ISGetIndices(is_I_layer,&idxs);CHKERRQ(ierr);
560     ierr = PetscMemcpy(all_local_idx_N,idxs,extra*sizeof(PetscInt));CHKERRQ(ierr);
561     ierr = ISRestoreIndices(is_I_layer,&idxs);CHKERRQ(ierr);
562   }
563   ierr = PetscMalloc1(local_size,&nnz);CHKERRQ(ierr);
564   ierr = PetscMalloc1(sub_schurs->n_subs,&auxnum1);CHKERRQ(ierr);
565   ierr = PetscMalloc1(sub_schurs->n_subs,&auxnum2);CHKERRQ(ierr);
566 
567   /* Get local indices in local numbering */
568   local_size = 0;
569   for (i=0;i<sub_schurs->n_subs;i++) {
570     PetscInt j;
571     const    PetscInt *idxs;
572 
573     ierr = ISGetLocalSize(sub_schurs->is_subs[i],&subset_size);CHKERRQ(ierr);
574     ierr = ISGetIndices(sub_schurs->is_subs[i],&idxs);CHKERRQ(ierr);
575     /* start (smallest in global ordering) and multiplicity */
576     auxnum1[i] = idxs[0];
577     auxnum2[i] = subset_size;
578     /* subset indices in local numbering */
579     ierr = PetscMemcpy(all_local_idx_N+local_size+extra,idxs,subset_size*sizeof(PetscInt));CHKERRQ(ierr);
580     ierr = ISRestoreIndices(sub_schurs->is_subs[i],&idxs);CHKERRQ(ierr);
581     for (j=0;j<subset_size;j++) nnz[local_size+j] = subset_size;
582     local_size += subset_size;
583   }
584 
585   /* allocate extra workspace needed only for GETRI or SYTRF */
586   use_potr = PETSC_TRUE;
587   if (local_size && !benign_trick && (!sub_schurs->is_hermitian || !sub_schurs->is_posdef)) {
588     PetscScalar  lwork,dummyscalar = 0.;
589     PetscBLASInt dummyint = 0;
590 
591     use_potr = PETSC_FALSE;
592     use_sytr = sub_schurs->is_hermitian;
593     B_lwork = -1;
594     ierr = PetscBLASIntCast(local_size,&B_N);CHKERRQ(ierr);
595     ierr = PetscFPTrapPush(PETSC_FP_TRAP_OFF);CHKERRQ(ierr);
596     if (use_sytr) {
597       PetscStackCallBLAS("LAPACKsytrf",LAPACKsytrf_("L",&B_N,&dummyscalar,&B_N,&dummyint,&lwork,&B_lwork,&B_ierr));
598       if (B_ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in query to SYTRF Lapack routine %d",(int)B_ierr);
599     } else {
600       PetscStackCallBLAS("LAPACKgetri",LAPACKgetri_(&B_N,&dummyscalar,&B_N,&dummyint,&lwork,&B_lwork,&B_ierr));
601       if (B_ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in query to GETRI Lapack routine %d",(int)B_ierr);
602     }
603     ierr = PetscFPTrapPop();CHKERRQ(ierr);
604     ierr = PetscBLASIntCast((PetscInt)PetscRealPart(lwork),&B_lwork);CHKERRQ(ierr);
605     ierr = PetscMalloc2(B_lwork,&Bwork,B_N,&pivots);CHKERRQ(ierr);
606   } else {
607     Bwork = NULL;
608     pivots = NULL;
609   }
610 
611   /* prepare parallel matrices for summing up properly schurs on subsets */
612   ierr = ISCreateGeneral(comm_n,sub_schurs->n_subs,auxnum1,PETSC_OWN_POINTER,&all_subsets_n);CHKERRQ(ierr);
613   ierr = ISLocalToGlobalMappingApplyIS(sub_schurs->l2gmap,all_subsets_n,&all_subsets);CHKERRQ(ierr);
614   ierr = ISDestroy(&all_subsets_n);CHKERRQ(ierr);
615   ierr = ISCreateGeneral(comm_n,sub_schurs->n_subs,auxnum2,PETSC_OWN_POINTER,&all_subsets_mult);CHKERRQ(ierr);
616   ierr = ISRenumber(all_subsets,all_subsets_mult,&global_size,&all_subsets_n);CHKERRQ(ierr);
617   ierr = ISDestroy(&all_subsets);CHKERRQ(ierr);
618   ierr = ISDestroy(&all_subsets_mult);CHKERRQ(ierr);
619   ierr = ISGetLocalSize(all_subsets_n,&i);CHKERRQ(ierr);
620   if (i != local_size) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Invalid size of new subset! %D != %D",i,local_size);
621   ierr = ISLocalToGlobalMappingCreateIS(all_subsets_n,&l2gmap_subsets);CHKERRQ(ierr);
622   ierr = MatCreateIS(comm_n,1,PETSC_DECIDE,PETSC_DECIDE,global_size,global_size,l2gmap_subsets,NULL,&work_mat);CHKERRQ(ierr);
623   ierr = ISLocalToGlobalMappingDestroy(&l2gmap_subsets);CHKERRQ(ierr);
624   ierr = MatCreate(PetscObjectComm((PetscObject)work_mat),&global_schur_subsets);CHKERRQ(ierr);
625   ierr = MatSetSizes(global_schur_subsets,PETSC_DECIDE,PETSC_DECIDE,global_size,global_size);CHKERRQ(ierr);
626   ierr = MatSetType(global_schur_subsets,MATMPIAIJ);CHKERRQ(ierr);
627 
628   /* subset indices in local boundary numbering */
629   if (!sub_schurs->is_Ej_all) {
630     PetscInt *all_local_idx_B;
631 
632     ierr = PetscMalloc1(local_size,&all_local_idx_B);CHKERRQ(ierr);
633     ierr = ISGlobalToLocalMappingApply(sub_schurs->BtoNmap,IS_GTOLM_DROP,local_size,all_local_idx_N+extra,&subset_size,all_local_idx_B);CHKERRQ(ierr);
634     if (subset_size != local_size) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Error in sub_schurs serial (BtoNmap)! %D != %D\n",subset_size,local_size);
635     ierr = ISCreateGeneral(PETSC_COMM_SELF,local_size,all_local_idx_B,PETSC_OWN_POINTER,&sub_schurs->is_Ej_all);CHKERRQ(ierr);
636   }
637 
638   if (change) {
639     ISLocalToGlobalMapping BtoS;
640     IS                     change_primal_B;
641     IS                     change_primal_all;
642 
643     if (sub_schurs->change_primal_sub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"This should not happen");
644     if (sub_schurs->change) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"This should not happen");
645     ierr = PetscMalloc1(sub_schurs->n_subs,&sub_schurs->change_primal_sub);CHKERRQ(ierr);
646     for (i=0;i<sub_schurs->n_subs;i++) {
647       ISLocalToGlobalMapping NtoS;
648       ierr = ISLocalToGlobalMappingCreateIS(sub_schurs->is_subs[i],&NtoS);CHKERRQ(ierr);
649       ierr = ISGlobalToLocalMappingApplyIS(NtoS,IS_GTOLM_DROP,change_primal,&sub_schurs->change_primal_sub[i]);CHKERRQ(ierr);
650       ierr = ISLocalToGlobalMappingDestroy(&NtoS);CHKERRQ(ierr);
651     }
652     ierr = ISGlobalToLocalMappingApplyIS(sub_schurs->BtoNmap,IS_GTOLM_DROP,change_primal,&change_primal_B);CHKERRQ(ierr);
653     ierr = ISLocalToGlobalMappingCreateIS(sub_schurs->is_Ej_all,&BtoS);CHKERRQ(ierr);
654     ierr = ISGlobalToLocalMappingApplyIS(BtoS,IS_GTOLM_DROP,change_primal_B,&change_primal_all);CHKERRQ(ierr);
655     ierr = ISLocalToGlobalMappingDestroy(&BtoS);CHKERRQ(ierr);
656     ierr = ISDestroy(&change_primal_B);CHKERRQ(ierr);
657     ierr = PetscMalloc1(sub_schurs->n_subs,&sub_schurs->change);CHKERRQ(ierr);
658     for (i=0;i<sub_schurs->n_subs;i++) {
659       Mat change_sub;
660 
661       ierr = ISGetLocalSize(sub_schurs->is_subs[i],&subset_size);CHKERRQ(ierr);
662       ierr = KSPCreate(PETSC_COMM_SELF,&sub_schurs->change[i]);CHKERRQ(ierr);
663       ierr = KSPSetType(sub_schurs->change[i],KSPPREONLY);CHKERRQ(ierr);
664       if (!sub_schurs->change_with_qr) {
665         ierr = MatCreateSubMatrix(change,sub_schurs->is_subs[i],sub_schurs->is_subs[i],MAT_INITIAL_MATRIX,&change_sub);CHKERRQ(ierr);
666       } else {
667         Mat change_subt;
668         ierr = MatCreateSubMatrix(change,sub_schurs->is_subs[i],sub_schurs->is_subs[i],MAT_INITIAL_MATRIX,&change_subt);CHKERRQ(ierr);
669         ierr = MatConvert(change_subt,MATSEQDENSE,MAT_INITIAL_MATRIX,&change_sub);CHKERRQ(ierr);
670         ierr = MatDestroy(&change_subt);CHKERRQ(ierr);
671       }
672       ierr = KSPSetOperators(sub_schurs->change[i],change_sub,change_sub);CHKERRQ(ierr);
673       ierr = MatDestroy(&change_sub);CHKERRQ(ierr);
674       ierr = KSPSetOptionsPrefix(sub_schurs->change[i],sub_schurs->prefix);CHKERRQ(ierr);
675       ierr = KSPAppendOptionsPrefix(sub_schurs->change[i],"sub_schurs_change_");CHKERRQ(ierr);
676     }
677     ierr = ISDestroy(&change_primal_all);CHKERRQ(ierr);
678   }
679 
680   /* Local matrix of all local Schur on subsets (transposed) */
681   if (!sub_schurs->S_Ej_all) {
682     ierr = MatCreate(PETSC_COMM_SELF,&sub_schurs->S_Ej_all);CHKERRQ(ierr);
683     ierr = MatSetSizes(sub_schurs->S_Ej_all,PETSC_DECIDE,PETSC_DECIDE,local_size,local_size);CHKERRQ(ierr);
684     ierr = MatSetType(sub_schurs->S_Ej_all,MATAIJ);CHKERRQ(ierr);
685     ierr = MatSeqAIJSetPreallocation(sub_schurs->S_Ej_all,0,nnz);CHKERRQ(ierr);
686   }
687 
688   /* Compute Schur complements explicitly */
689   F = NULL;
690   if (!sub_schurs->schur_explicit) { /* this code branch is used when MatFactor with Schur complemnent support is not present; it is not very efficient, unless the economic version of the scaling is required */
691     Mat         S_Ej_expl;
692     PetscScalar *work;
693     PetscInt    j,*dummy_idx;
694     PetscBool   Sdense;
695 
696     ierr = PetscMalloc2(max_subset_size,&dummy_idx,max_subset_size*max_subset_size,&work);CHKERRQ(ierr);
697     local_size = 0;
698     for (i=0;i<sub_schurs->n_subs;i++) {
699       IS  is_subset_B;
700       Mat AE_EE,AE_IE,AE_EI,S_Ej;
701 
702       /* subsets in original and boundary numbering */
703       ierr = ISGlobalToLocalMappingApplyIS(sub_schurs->BtoNmap,IS_GTOLM_DROP,sub_schurs->is_subs[i],&is_subset_B);CHKERRQ(ierr);
704       /* EE block */
705       ierr = MatCreateSubMatrix(A_BB,is_subset_B,is_subset_B,MAT_INITIAL_MATRIX,&AE_EE);CHKERRQ(ierr);
706       /* IE block */
707       ierr = MatCreateSubMatrix(A_IB,is_I,is_subset_B,MAT_INITIAL_MATRIX,&AE_IE);CHKERRQ(ierr);
708       /* EI block */
709       if (sub_schurs->is_hermitian) {
710         ierr = MatCreateTranspose(AE_IE,&AE_EI);CHKERRQ(ierr);
711       } else {
712         ierr = MatCreateSubMatrix(A_BI,is_subset_B,is_I,MAT_INITIAL_MATRIX,&AE_EI);CHKERRQ(ierr);
713       }
714       ierr = ISDestroy(&is_subset_B);CHKERRQ(ierr);
715       ierr = MatCreateSchurComplement(AE_II,AE_II,AE_IE,AE_EI,AE_EE,&S_Ej);CHKERRQ(ierr);
716       ierr = MatDestroy(&AE_EE);CHKERRQ(ierr);
717       ierr = MatDestroy(&AE_IE);CHKERRQ(ierr);
718       ierr = MatDestroy(&AE_EI);CHKERRQ(ierr);
719       if (AE_II == A_II) { /* we can reuse the same ksp */
720         KSP ksp;
721         ierr = MatSchurComplementGetKSP(sub_schurs->S,&ksp);CHKERRQ(ierr);
722         ierr = MatSchurComplementSetKSP(S_Ej,ksp);CHKERRQ(ierr);
723       } else { /* build new ksp object which inherits ksp and pc types from the original one */
724         KSP       origksp,schurksp;
725         PC        origpc,schurpc;
726         KSPType   ksp_type;
727         PetscInt  n_internal;
728         PetscBool ispcnone;
729 
730         ierr = MatSchurComplementGetKSP(sub_schurs->S,&origksp);CHKERRQ(ierr);
731         ierr = MatSchurComplementGetKSP(S_Ej,&schurksp);CHKERRQ(ierr);
732         ierr = KSPGetType(origksp,&ksp_type);CHKERRQ(ierr);
733         ierr = KSPSetType(schurksp,ksp_type);CHKERRQ(ierr);
734         ierr = KSPGetPC(schurksp,&schurpc);CHKERRQ(ierr);
735         ierr = KSPGetPC(origksp,&origpc);CHKERRQ(ierr);
736         ierr = PetscObjectTypeCompare((PetscObject)origpc,PCNONE,&ispcnone);CHKERRQ(ierr);
737         if (!ispcnone) {
738           PCType pc_type;
739           ierr = PCGetType(origpc,&pc_type);CHKERRQ(ierr);
740           ierr = PCSetType(schurpc,pc_type);CHKERRQ(ierr);
741         } else {
742           ierr = PCSetType(schurpc,PCLU);CHKERRQ(ierr);
743         }
744         ierr = ISGetSize(is_I,&n_internal);CHKERRQ(ierr);
745         if (n_internal) { /* UMFPACK gives error with 0 sized problems */
746           MatSolverType solver = NULL;
747           ierr = PCFactorGetMatSolverType(origpc,(MatSolverType*)&solver);CHKERRQ(ierr);
748           if (solver) {
749             ierr = PCFactorSetMatSolverType(schurpc,solver);CHKERRQ(ierr);
750           }
751         }
752         ierr = KSPSetUp(schurksp);CHKERRQ(ierr);
753       }
754       ierr = ISGetLocalSize(sub_schurs->is_subs[i],&subset_size);CHKERRQ(ierr);
755       ierr = MatCreateSeqDense(PETSC_COMM_SELF,subset_size,subset_size,work,&S_Ej_expl);CHKERRQ(ierr);
756       ierr = PCBDDCComputeExplicitSchur(S_Ej,sub_schurs->is_hermitian,MAT_REUSE_MATRIX,&S_Ej_expl);CHKERRQ(ierr);
757       ierr = PetscObjectTypeCompare((PetscObject)S_Ej_expl,MATSEQDENSE,&Sdense);CHKERRQ(ierr);
758       if (Sdense) {
759         for (j=0;j<subset_size;j++) {
760           dummy_idx[j]=local_size+j;
761         }
762         ierr = MatSetValues(sub_schurs->S_Ej_all,subset_size,dummy_idx,subset_size,dummy_idx,work,INSERT_VALUES);CHKERRQ(ierr);
763       } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Not yet implemented for sparse matrices");
764       ierr = MatDestroy(&S_Ej);CHKERRQ(ierr);
765       ierr = MatDestroy(&S_Ej_expl);CHKERRQ(ierr);
766       local_size += subset_size;
767     }
768     ierr = PetscFree2(dummy_idx,work);CHKERRQ(ierr);
769     /* free */
770     ierr = ISDestroy(&is_I);CHKERRQ(ierr);
771     ierr = MatDestroy(&AE_II);CHKERRQ(ierr);
772     ierr = PetscFree(all_local_idx_N);CHKERRQ(ierr);
773   } else {
774     Mat         A,cs_AIB_mat = NULL,benign_AIIm1_ones_mat = NULL;
775     Vec         Dall = NULL;
776     IS          is_A_all,*is_p_r = NULL;
777     PetscScalar *work,*S_data,*schur_factor,infty = PETSC_MAX_REAL;
778     PetscInt    n,n_I,*dummy_idx,size_schur,size_active_schur,cum,cum2;
779     PetscBool   economic,solver_S,S_lower_triangular = PETSC_FALSE;
780     PetscBool   schur_has_vertices,factor_workaround;
781 
782     /* get sizes */
783     n_I = 0;
784     if (is_I_layer) {
785       ierr = ISGetLocalSize(is_I_layer,&n_I);CHKERRQ(ierr);
786     }
787     economic = PETSC_FALSE;
788     ierr = ISGetLocalSize(sub_schurs->is_I,&cum);CHKERRQ(ierr);
789     if (cum != n_I) economic = PETSC_TRUE;
790     ierr = MatGetLocalSize(sub_schurs->A,&n,NULL);CHKERRQ(ierr);
791     size_active_schur = local_size;
792 
793     /* import scaling vector (wrong formulation if we have 3D edges) */
794     if (scaling && compute_Stilda) {
795       const PetscScalar *array;
796       PetscScalar       *array2;
797       const PetscInt    *idxs;
798       PetscInt          i;
799 
800       ierr = ISGetIndices(sub_schurs->is_Ej_all,&idxs);CHKERRQ(ierr);
801       ierr = VecCreateSeq(PETSC_COMM_SELF,size_active_schur,&Dall);CHKERRQ(ierr);
802       ierr = VecGetArrayRead(scaling,&array);CHKERRQ(ierr);
803       ierr = VecGetArray(Dall,&array2);CHKERRQ(ierr);
804       for (i=0;i<size_active_schur;i++) array2[i] = array[idxs[i]];
805       ierr = VecRestoreArray(Dall,&array2);CHKERRQ(ierr);
806       ierr = VecRestoreArrayRead(scaling,&array);CHKERRQ(ierr);
807       ierr = ISRestoreIndices(sub_schurs->is_Ej_all,&idxs);CHKERRQ(ierr);
808       deluxe = PETSC_FALSE;
809     }
810 
811     /* size active schurs does not count any dirichlet or vertex dof on the interface */
812     factor_workaround = PETSC_FALSE;
813     schur_has_vertices = PETSC_FALSE;
814     cum = n_I+size_active_schur;
815     if (sub_schurs->is_dir) {
816       const PetscInt* idxs;
817       PetscInt        n_dir;
818 
819       ierr = ISGetLocalSize(sub_schurs->is_dir,&n_dir);CHKERRQ(ierr);
820       ierr = ISGetIndices(sub_schurs->is_dir,&idxs);CHKERRQ(ierr);
821       ierr = PetscMemcpy(all_local_idx_N+cum,idxs,n_dir*sizeof(PetscInt));CHKERRQ(ierr);
822       ierr = ISRestoreIndices(sub_schurs->is_dir,&idxs);CHKERRQ(ierr);
823       cum += n_dir;
824       factor_workaround = PETSC_TRUE;
825     }
826     /* include the primal vertices in the Schur complement */
827     if (exact_schur && sub_schurs->is_vertices && (compute_Stilda || benign_n)) {
828       PetscInt n_v;
829 
830       ierr = ISGetLocalSize(sub_schurs->is_vertices,&n_v);CHKERRQ(ierr);
831       if (n_v) {
832         const PetscInt* idxs;
833 
834         ierr = ISGetIndices(sub_schurs->is_vertices,&idxs);CHKERRQ(ierr);
835         ierr = PetscMemcpy(all_local_idx_N+cum,idxs,n_v*sizeof(PetscInt));CHKERRQ(ierr);
836         ierr = ISRestoreIndices(sub_schurs->is_vertices,&idxs);CHKERRQ(ierr);
837         cum += n_v;
838         factor_workaround = PETSC_TRUE;
839         schur_has_vertices = PETSC_TRUE;
840       }
841     }
842     size_schur = cum - n_I;
843     ierr = ISCreateGeneral(PETSC_COMM_SELF,cum,all_local_idx_N,PETSC_OWN_POINTER,&is_A_all);CHKERRQ(ierr);
844     if (cum == n) {
845       ierr = ISSetPermutation(is_A_all);CHKERRQ(ierr);
846       ierr = MatPermute(sub_schurs->A,is_A_all,is_A_all,&A);CHKERRQ(ierr);
847     } else {
848       ierr = MatCreateSubMatrix(sub_schurs->A,is_A_all,is_A_all,MAT_INITIAL_MATRIX,&A);CHKERRQ(ierr);
849     }
850     ierr = MatSetOptionsPrefix(A,sub_schurs->prefix);CHKERRQ(ierr);
851     ierr = MatAppendOptionsPrefix(A,"sub_schurs_");CHKERRQ(ierr);
852 
853     /* if we actually change the basis for the pressures, LDL^T factors will use a lot of memory
854        n^2 instead of n^1.5 or something. This is a workaround */
855     if (benign_n) {
856       Vec                    v;
857       ISLocalToGlobalMapping N_to_reor;
858       IS                     is_p0,is_p0_p;
859       PetscScalar            *cs_AIB,*AIIm1_data;
860       PetscInt               sizeA;
861 
862       ierr = ISLocalToGlobalMappingCreateIS(is_A_all,&N_to_reor);CHKERRQ(ierr);
863       ierr = ISCreateGeneral(PETSC_COMM_SELF,benign_n,benign_p0_lidx,PETSC_COPY_VALUES,&is_p0);CHKERRQ(ierr);
864       ierr = ISGlobalToLocalMappingApplyIS(N_to_reor,IS_GTOLM_DROP,is_p0,&is_p0_p);CHKERRQ(ierr);
865       ierr = ISDestroy(&is_p0);CHKERRQ(ierr);
866       ierr = MatCreateVecs(A,&v,NULL);CHKERRQ(ierr);
867       ierr = VecGetSize(v,&sizeA);CHKERRQ(ierr);
868       ierr = MatCreateSeqDense(PETSC_COMM_SELF,sizeA,benign_n,NULL,&benign_AIIm1_ones_mat);CHKERRQ(ierr);
869       ierr = MatCreateSeqDense(PETSC_COMM_SELF,size_schur,benign_n,NULL,&cs_AIB_mat);CHKERRQ(ierr);
870       ierr = MatDenseGetArray(cs_AIB_mat,&cs_AIB);CHKERRQ(ierr);
871       ierr = MatDenseGetArray(benign_AIIm1_ones_mat,&AIIm1_data);CHKERRQ(ierr);
872       ierr = PetscMalloc1(benign_n,&is_p_r);CHKERRQ(ierr);
873       /* compute colsum of A_IB restricted to pressures */
874       for (i=0;i<benign_n;i++) {
875         Vec            benign_AIIm1_ones;
876         PetscScalar    *array;
877         const PetscInt *idxs;
878         PetscInt       j,nz;
879 
880         ierr = ISGlobalToLocalMappingApplyIS(N_to_reor,IS_GTOLM_DROP,benign_zerodiag_subs[i],&is_p_r[i]);CHKERRQ(ierr);
881         ierr = ISGetLocalSize(is_p_r[i],&nz);CHKERRQ(ierr);
882         ierr = ISGetIndices(is_p_r[i],&idxs);CHKERRQ(ierr);
883         for (j=0;j<nz;j++) AIIm1_data[idxs[j]+sizeA*i] = 1.;
884         ierr = ISRestoreIndices(is_p_r[i],&idxs);CHKERRQ(ierr);
885         ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,1,sizeA,AIIm1_data+sizeA*i,&benign_AIIm1_ones);CHKERRQ(ierr);
886         ierr = MatMult(A,benign_AIIm1_ones,v);CHKERRQ(ierr);
887         ierr = VecDestroy(&benign_AIIm1_ones);CHKERRQ(ierr);
888         ierr = VecGetArray(v,&array);CHKERRQ(ierr);
889         for (j=0;j<size_schur;j++) {
890 #if defined(PETSC_USE_COMPLEX)
891           cs_AIB[i*size_schur + j] = (PetscRealPart(array[j+n_I])/nz + PETSC_i*(PetscImaginaryPart(array[j+n_I])/nz));
892 #else
893           cs_AIB[i*size_schur + j] = array[j+n_I]/nz;
894 #endif
895         }
896         ierr = VecRestoreArray(v,&array);CHKERRQ(ierr);
897       }
898       ierr = MatDenseRestoreArray(cs_AIB_mat,&cs_AIB);CHKERRQ(ierr);
899       ierr = MatDenseRestoreArray(benign_AIIm1_ones_mat,&AIIm1_data);CHKERRQ(ierr);
900       ierr = VecDestroy(&v);CHKERRQ(ierr);
901       ierr = MatSetOption(A,MAT_KEEP_NONZERO_PATTERN,PETSC_FALSE);CHKERRQ(ierr);
902       ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);
903       ierr = MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);
904       ierr = MatZeroRowsColumnsIS(A,is_p0_p,1.0,NULL,NULL);CHKERRQ(ierr);
905       ierr = ISDestroy(&is_p0_p);CHKERRQ(ierr);
906       ierr = ISLocalToGlobalMappingDestroy(&N_to_reor);CHKERRQ(ierr);
907     }
908     ierr = MatSetOption(A,MAT_SYMMETRIC,sub_schurs->is_hermitian);CHKERRQ(ierr);
909     ierr = MatSetOption(A,MAT_HERMITIAN,sub_schurs->is_hermitian);CHKERRQ(ierr);
910     ierr = MatSetOption(A,MAT_SPD,sub_schurs->is_posdef);CHKERRQ(ierr);
911 
912     /* when using the benign subspace trick, the local Schur complements are SPD */
913     if (benign_trick) sub_schurs->is_posdef = PETSC_TRUE;
914 
915     if (n_I) {
916       IS is_schur;
917 
918       if (sub_schurs->is_hermitian && sub_schurs->is_posdef) {
919         ierr = MatGetFactor(A,sub_schurs->mat_solver_type,MAT_FACTOR_CHOLESKY,&F);CHKERRQ(ierr);
920       } else {
921         ierr = MatGetFactor(A,sub_schurs->mat_solver_type,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
922       }
923       ierr = MatSetErrorIfFailure(A,PETSC_TRUE);CHKERRQ(ierr);
924 
925       /* subsets ordered last */
926       ierr = ISCreateStride(PETSC_COMM_SELF,size_schur,n_I,1,&is_schur);CHKERRQ(ierr);
927       ierr = MatFactorSetSchurIS(F,is_schur);CHKERRQ(ierr);
928       ierr = ISDestroy(&is_schur);CHKERRQ(ierr);
929 
930       /* factorization step */
931       if (sub_schurs->is_hermitian && sub_schurs->is_posdef) {
932         ierr = MatCholeskyFactorSymbolic(F,A,NULL,NULL);CHKERRQ(ierr);
933 #if defined(PETSC_HAVE_MUMPS) /* be sure that icntl 19 is not set by command line */
934         ierr = MatMumpsSetIcntl(F,19,2);CHKERRQ(ierr);
935 #endif
936         ierr = MatCholeskyFactorNumeric(F,A,NULL);CHKERRQ(ierr);
937         S_lower_triangular = PETSC_TRUE;
938       } else {
939         ierr = MatLUFactorSymbolic(F,A,NULL,NULL,NULL);CHKERRQ(ierr);
940 #if defined(PETSC_HAVE_MUMPS) /* be sure that icntl 19 is not set by command line */
941         ierr = MatMumpsSetIcntl(F,19,3);CHKERRQ(ierr);
942 #endif
943         ierr = MatLUFactorNumeric(F,A,NULL);CHKERRQ(ierr);
944       }
945       ierr = MatViewFromOptions(F,(PetscObject)A,"-mat_factor_view");CHKERRQ(ierr);
946 
947       /* get explicit Schur Complement computed during numeric factorization */
948       ierr = MatFactorGetSchurComplement(F,&S_all,NULL);CHKERRQ(ierr);
949       ierr = MatSetOption(S_all,MAT_SPD,sub_schurs->is_posdef);CHKERRQ(ierr);
950       ierr = MatSetOption(S_all,MAT_HERMITIAN,sub_schurs->is_hermitian);CHKERRQ(ierr);
951 
952       /* we can reuse the solvers if we are not using the economic version */
953       reuse_solvers = (PetscBool)(reuse_solvers && !economic);
954       factor_workaround = (PetscBool)(reuse_solvers && factor_workaround);
955       if (!sub_schurs->is_posdef && factor_workaround && compute_Stilda && size_active_schur)
956         reuse_solvers = factor_workaround = PETSC_FALSE;
957 
958       solver_S = PETSC_TRUE;
959 
960       /* update the Schur complement with the change of basis on the pressures */
961       if (benign_n) {
962         PetscScalar *S_data,*cs_AIB,*AIIm1_data;
963         Vec         v;
964         PetscInt    sizeA;
965 
966         ierr = MatDenseGetArray(S_all,&S_data);CHKERRQ(ierr);
967         ierr = MatCreateVecs(A,&v,NULL);CHKERRQ(ierr);
968         ierr = VecGetSize(v,&sizeA);CHKERRQ(ierr);
969 #if defined(PETSC_HAVE_MUMPS)
970         ierr = MatMumpsSetIcntl(F,26,0);CHKERRQ(ierr);
971 #endif
972 #if defined(PETSC_HAVE_MKL_PARDISO)
973         ierr = MatMkl_PardisoSetCntl(F,70,1);CHKERRQ(ierr);
974 #endif
975         ierr = MatDenseGetArray(cs_AIB_mat,&cs_AIB);CHKERRQ(ierr);
976         ierr = MatDenseGetArray(benign_AIIm1_ones_mat,&AIIm1_data);CHKERRQ(ierr);
977         for (i=0;i<benign_n;i++) {
978           Vec            benign_AIIm1_ones;
979           PetscScalar    *array,sum = 0.,one = 1.;
980           const PetscInt *idxs;
981           PetscInt       j,nz;
982           PetscBLASInt   B_k,B_n;
983 
984           ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,1,sizeA,AIIm1_data+sizeA*i,&benign_AIIm1_ones);CHKERRQ(ierr);
985           ierr = VecCopy(benign_AIIm1_ones,v);CHKERRQ(ierr);
986           ierr = MatSolve(F,v,benign_AIIm1_ones);CHKERRQ(ierr);
987           ierr = ISGetLocalSize(is_p_r[i],&nz);CHKERRQ(ierr);
988           ierr = ISGetIndices(is_p_r[i],&idxs);CHKERRQ(ierr);
989           /* p0 dof (eliminated) is excluded from the sum */
990           for (j=0;j<nz-1;j++) sum -= AIIm1_data[idxs[j]+sizeA*i];
991           ierr = ISRestoreIndices(is_p_r[i],&idxs);CHKERRQ(ierr);
992           ierr = MatMult(A,benign_AIIm1_ones,v);CHKERRQ(ierr);
993           ierr = VecGetArray(v,&array);CHKERRQ(ierr);
994           /* perform sparse rank updates on symmetric Schur (TODO: move outside of the loop?) */
995           /* cs_AIB already scaled by 1./nz */
996           B_k = 1;
997           ierr = PetscBLASIntCast(size_schur,&B_n);CHKERRQ(ierr);
998           PetscStackCallBLAS("BLASsyrk",BLASsyrk_("L","N",&B_n,&B_k,&sum,cs_AIB+i*size_schur,&B_n,&one,S_data,&B_n));
999           sum  = 1.;
1000           PetscStackCallBLAS("BLASsyr2k",BLASsyr2k_("L","N",&B_n,&B_k,&sum,array+n_I,&B_n,cs_AIB+i*size_schur,&B_n,&one,S_data,&B_n));
1001           ierr = VecRestoreArray(v,&array);CHKERRQ(ierr);
1002           /* set p0 entry of AIIm1_ones to zero */
1003           ierr = ISGetIndices(is_p_r[i],&idxs);CHKERRQ(ierr);
1004           for (j=0;j<benign_n;j++) AIIm1_data[idxs[nz-1]+sizeA*j] = 0.;
1005           ierr = ISRestoreIndices(is_p_r[i],&idxs);CHKERRQ(ierr);
1006           ierr = VecDestroy(&benign_AIIm1_ones);CHKERRQ(ierr);
1007         }
1008         if (!S_lower_triangular) { /* I need to expand the upper triangular data (column oriented) */
1009           PetscInt k,j;
1010           for (k=0;k<size_schur;k++) {
1011             for (j=k;j<size_schur;j++) {
1012               S_data[j*size_schur+k] = PetscConj(S_data[k*size_schur+j]);
1013             }
1014           }
1015         }
1016 
1017         /* restore defaults */
1018 #if defined(PETSC_HAVE_MUMPS)
1019         ierr = MatMumpsSetIcntl(F,26,-1);CHKERRQ(ierr);
1020 #endif
1021 #if defined(PETSC_HAVE_MKL_PARDISO)
1022         ierr = MatMkl_PardisoSetCntl(F,70,0);CHKERRQ(ierr);
1023 #endif
1024         ierr = MatDenseRestoreArray(cs_AIB_mat,&cs_AIB);CHKERRQ(ierr);
1025         ierr = MatDenseRestoreArray(benign_AIIm1_ones_mat,&AIIm1_data);CHKERRQ(ierr);
1026         ierr = VecDestroy(&v);CHKERRQ(ierr);
1027         ierr = MatDenseRestoreArray(S_all,&S_data);CHKERRQ(ierr);
1028       }
1029       if (!reuse_solvers) {
1030         for (i=0;i<benign_n;i++) {
1031           ierr = ISDestroy(&is_p_r[i]);CHKERRQ(ierr);
1032         }
1033         ierr = PetscFree(is_p_r);CHKERRQ(ierr);
1034         ierr = MatDestroy(&cs_AIB_mat);CHKERRQ(ierr);
1035         ierr = MatDestroy(&benign_AIIm1_ones_mat);CHKERRQ(ierr);
1036       }
1037     } else { /* we can't use MatFactor when size_schur == size_of_the_problem */
1038       ierr = MatConvert(A,MATSEQDENSE,MAT_INITIAL_MATRIX,&S_all);CHKERRQ(ierr);
1039       reuse_solvers = PETSC_FALSE; /* TODO: why we can't reuse the solvers here? */
1040       factor_workaround = PETSC_FALSE;
1041       solver_S = PETSC_FALSE;
1042     }
1043 
1044     if (reuse_solvers) {
1045       Mat                A_II,Afake;
1046       Vec                vec1_B;
1047       PCBDDCReuseSolvers msolv_ctx;
1048       PetscInt           n_R;
1049 
1050       if (sub_schurs->reuse_solver) {
1051         ierr = PCBDDCReuseSolversReset(sub_schurs->reuse_solver);CHKERRQ(ierr);
1052       } else {
1053         ierr = PetscNew(&sub_schurs->reuse_solver);CHKERRQ(ierr);
1054       }
1055       msolv_ctx = sub_schurs->reuse_solver;
1056       ierr = MatSchurComplementGetSubMatrices(sub_schurs->S,&A_II,NULL,NULL,NULL,NULL);CHKERRQ(ierr);
1057       ierr = PetscObjectReference((PetscObject)F);CHKERRQ(ierr);
1058       msolv_ctx->F = F;
1059       ierr = MatCreateVecs(F,&msolv_ctx->sol,NULL);CHKERRQ(ierr);
1060       /* currently PETSc has no support for MatSolve(F,x,x), so cheat and let rhs and sol share the same memory */
1061       {
1062         PetscScalar *array;
1063         PetscInt    n;
1064 
1065         ierr = VecGetLocalSize(msolv_ctx->sol,&n);CHKERRQ(ierr);
1066         ierr = VecGetArray(msolv_ctx->sol,&array);CHKERRQ(ierr);
1067         ierr = VecCreateSeqWithArray(PetscObjectComm((PetscObject)msolv_ctx->sol),1,n,array,&msolv_ctx->rhs);CHKERRQ(ierr);
1068         ierr = VecRestoreArray(msolv_ctx->sol,&array);CHKERRQ(ierr);
1069       }
1070       msolv_ctx->has_vertices = schur_has_vertices;
1071 
1072       /* interior solver */
1073       ierr = PCCreate(PetscObjectComm((PetscObject)A_II),&msolv_ctx->interior_solver);CHKERRQ(ierr);
1074       ierr = PCSetOperators(msolv_ctx->interior_solver,A_II,A_II);CHKERRQ(ierr);
1075       ierr = PCSetType(msolv_ctx->interior_solver,PCSHELL);CHKERRQ(ierr);
1076       ierr = PCShellSetContext(msolv_ctx->interior_solver,msolv_ctx);CHKERRQ(ierr);
1077       ierr = PCShellSetApply(msolv_ctx->interior_solver,PCBDDCReuseSolvers_Interior);CHKERRQ(ierr);
1078       ierr = PCShellSetApplyTranspose(msolv_ctx->interior_solver,PCBDDCReuseSolvers_InteriorTranspose);CHKERRQ(ierr);
1079 
1080       /* correction solver */
1081       ierr = PCCreate(PetscObjectComm((PetscObject)A_II),&msolv_ctx->correction_solver);CHKERRQ(ierr);
1082       ierr = PCSetType(msolv_ctx->correction_solver,PCSHELL);CHKERRQ(ierr);
1083       ierr = PCShellSetContext(msolv_ctx->correction_solver,msolv_ctx);CHKERRQ(ierr);
1084       ierr = PCShellSetApply(msolv_ctx->correction_solver,PCBDDCReuseSolvers_Correction);CHKERRQ(ierr);
1085       ierr = PCShellSetApplyTranspose(msolv_ctx->correction_solver,PCBDDCReuseSolvers_CorrectionTranspose);CHKERRQ(ierr);
1086 
1087       /* scatter and vecs for Schur complement solver */
1088       ierr = MatCreateVecs(S_all,&msolv_ctx->sol_B,&msolv_ctx->rhs_B);CHKERRQ(ierr);
1089       ierr = MatCreateVecs(sub_schurs->S,&vec1_B,NULL);CHKERRQ(ierr);
1090       if (!schur_has_vertices) {
1091         ierr = ISGlobalToLocalMappingApplyIS(sub_schurs->BtoNmap,IS_GTOLM_DROP,is_A_all,&msolv_ctx->is_B);CHKERRQ(ierr);
1092         ierr = VecScatterCreate(vec1_B,msolv_ctx->is_B,msolv_ctx->sol_B,NULL,&msolv_ctx->correction_scatter_B);CHKERRQ(ierr);
1093         ierr = PetscObjectReference((PetscObject)is_A_all);CHKERRQ(ierr);
1094         msolv_ctx->is_R = is_A_all;
1095       } else {
1096         IS              is_B_all;
1097         const PetscInt* idxs;
1098         PetscInt        dual,n_v,n;
1099 
1100         ierr = ISGetLocalSize(sub_schurs->is_vertices,&n_v);CHKERRQ(ierr);
1101         dual = size_schur - n_v;
1102         ierr = ISGetLocalSize(is_A_all,&n);CHKERRQ(ierr);
1103         ierr = ISGetIndices(is_A_all,&idxs);CHKERRQ(ierr);
1104         ierr = ISCreateGeneral(PetscObjectComm((PetscObject)is_A_all),dual,idxs+n_I,PETSC_COPY_VALUES,&is_B_all);CHKERRQ(ierr);
1105         ierr = ISGlobalToLocalMappingApplyIS(sub_schurs->BtoNmap,IS_GTOLM_DROP,is_B_all,&msolv_ctx->is_B);CHKERRQ(ierr);
1106         ierr = ISDestroy(&is_B_all);CHKERRQ(ierr);
1107         ierr = ISCreateStride(PetscObjectComm((PetscObject)is_A_all),dual,0,1,&is_B_all);CHKERRQ(ierr);
1108         ierr = VecScatterCreate(vec1_B,msolv_ctx->is_B,msolv_ctx->sol_B,is_B_all,&msolv_ctx->correction_scatter_B);CHKERRQ(ierr);
1109         ierr = ISDestroy(&is_B_all);CHKERRQ(ierr);
1110         ierr = ISCreateGeneral(PetscObjectComm((PetscObject)is_A_all),n-n_v,idxs,PETSC_COPY_VALUES,&msolv_ctx->is_R);CHKERRQ(ierr);
1111         ierr = ISRestoreIndices(is_A_all,&idxs);CHKERRQ(ierr);
1112       }
1113       ierr = ISGetLocalSize(msolv_ctx->is_R,&n_R);CHKERRQ(ierr);
1114       ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,n_R,n_R,0,NULL,&Afake);CHKERRQ(ierr);
1115       ierr = MatAssemblyBegin(Afake,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
1116       ierr = MatAssemblyEnd(Afake,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
1117       ierr = PCSetOperators(msolv_ctx->correction_solver,Afake,Afake);CHKERRQ(ierr);
1118       ierr = MatDestroy(&Afake);CHKERRQ(ierr);
1119       ierr = VecDestroy(&vec1_B);CHKERRQ(ierr);
1120 
1121       /* communicate benign info to solver context */
1122       if (benign_n) {
1123         PetscScalar *array;
1124 
1125         msolv_ctx->benign_n = benign_n;
1126         msolv_ctx->benign_zerodiag_subs = is_p_r;
1127         ierr = PetscMalloc1(benign_n,&msolv_ctx->benign_save_vals);CHKERRQ(ierr);
1128         msolv_ctx->benign_csAIB = cs_AIB_mat;
1129         ierr = MatCreateVecs(cs_AIB_mat,&msolv_ctx->benign_corr_work,NULL);CHKERRQ(ierr);
1130         ierr = VecGetArray(msolv_ctx->benign_corr_work,&array);CHKERRQ(ierr);
1131         ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,1,size_schur,array,&msolv_ctx->benign_dummy_schur_vec);CHKERRQ(ierr);
1132         ierr = VecRestoreArray(msolv_ctx->benign_corr_work,&array);CHKERRQ(ierr);
1133         msolv_ctx->benign_AIIm1ones = benign_AIIm1_ones_mat;
1134       }
1135     } else {
1136       if (sub_schurs->reuse_solver) {
1137         ierr = PCBDDCReuseSolversReset(sub_schurs->reuse_solver);CHKERRQ(ierr);
1138       }
1139       ierr = PetscFree(sub_schurs->reuse_solver);CHKERRQ(ierr);
1140     }
1141     ierr = MatDestroy(&A);CHKERRQ(ierr);
1142     ierr = ISDestroy(&is_A_all);CHKERRQ(ierr);
1143 
1144     /* Work arrays */
1145     ierr = PetscMalloc2(max_subset_size,&dummy_idx,max_subset_size*max_subset_size,&work);CHKERRQ(ierr);
1146 
1147     /* matrices for deluxe scaling and adaptive selection */
1148     if (compute_Stilda) {
1149       if (!sub_schurs->sum_S_Ej_tilda_all) {
1150         ierr = MatDuplicate(sub_schurs->S_Ej_all,MAT_SHARE_NONZERO_PATTERN,&sub_schurs->sum_S_Ej_tilda_all);CHKERRQ(ierr);
1151       }
1152       if (!sub_schurs->sum_S_Ej_inv_all && deluxe) {
1153         ierr = MatDuplicate(sub_schurs->S_Ej_all,MAT_SHARE_NONZERO_PATTERN,&sub_schurs->sum_S_Ej_inv_all);CHKERRQ(ierr);
1154       }
1155     }
1156 
1157     /* S_Ej_all */
1158     cum = cum2 = 0;
1159     ierr = MatDenseGetArray(S_all,&S_data);CHKERRQ(ierr);
1160     for (i=0;i<sub_schurs->n_subs;i++) {
1161       PetscInt j;
1162 
1163       /* get S_E */
1164       ierr = ISGetLocalSize(sub_schurs->is_subs[i],&subset_size);CHKERRQ(ierr);
1165       if (S_lower_triangular) { /* I need to expand the upper triangular data (column oriented) */
1166         PetscInt k;
1167         for (k=0;k<subset_size;k++) {
1168           for (j=k;j<subset_size;j++) {
1169             work[k*subset_size+j] = S_data[cum2+k*size_schur+j];
1170             work[j*subset_size+k] = PetscConj(S_data[cum2+k*size_schur+j]);
1171           }
1172         }
1173       } else { /* just copy to workspace */
1174         PetscInt k;
1175         for (k=0;k<subset_size;k++) {
1176           for (j=0;j<subset_size;j++) {
1177             work[k*subset_size+j] = S_data[cum2+k*size_schur+j];
1178           }
1179         }
1180       }
1181       /* insert S_E values */
1182       for (j=0;j<subset_size;j++) dummy_idx[j] = cum+j;
1183       if (sub_schurs->change) {
1184         Mat change_sub,SEj,T;
1185 
1186         /* change basis */
1187         ierr = KSPGetOperators(sub_schurs->change[i],&change_sub,NULL);CHKERRQ(ierr);
1188         ierr = MatCreateSeqDense(PETSC_COMM_SELF,subset_size,subset_size,work,&SEj);CHKERRQ(ierr);
1189         if (!sub_schurs->change_with_qr) { /* currently there's no support for PtAP with P SeqAIJ */
1190           Mat T2;
1191           ierr = MatTransposeMatMult(change_sub,SEj,MAT_INITIAL_MATRIX,1.0,&T2);CHKERRQ(ierr);
1192           ierr = MatMatMult(T2,change_sub,MAT_INITIAL_MATRIX,1.0,&T);CHKERRQ(ierr);
1193           ierr = MatConvert(T,MATSEQDENSE,MAT_INPLACE_MATRIX,&T);CHKERRQ(ierr);
1194           ierr = MatDestroy(&T2);CHKERRQ(ierr);
1195         } else {
1196           ierr = MatPtAP(SEj,change_sub,MAT_INITIAL_MATRIX,1.0,&T);CHKERRQ(ierr);
1197         }
1198         ierr = MatCopy(T,SEj,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
1199         ierr = MatDestroy(&T);CHKERRQ(ierr);
1200         ierr = MatZeroRowsColumnsIS(SEj,sub_schurs->change_primal_sub[i],1.0,NULL,NULL);CHKERRQ(ierr);
1201         ierr = MatDestroy(&SEj);CHKERRQ(ierr);
1202       }
1203       if (deluxe) {
1204         ierr = MatSetValues(sub_schurs->S_Ej_all,subset_size,dummy_idx,subset_size,dummy_idx,work,INSERT_VALUES);CHKERRQ(ierr);
1205         /* if adaptivity is requested, invert S_E blocks */
1206         if (compute_Stilda) {
1207           PetscInt k;
1208 
1209           ierr = PetscBLASIntCast(subset_size,&B_N);CHKERRQ(ierr);
1210           ierr = PetscFPTrapPush(PETSC_FP_TRAP_OFF);CHKERRQ(ierr);
1211           if (use_potr) {
1212             PetscStackCallBLAS("LAPACKpotrf",LAPACKpotrf_("L",&B_N,work,&B_N,&B_ierr));
1213             if (B_ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in POTRF Lapack routine %d",(int)B_ierr);
1214             PetscStackCallBLAS("LAPACKpotri",LAPACKpotri_("L",&B_N,work,&B_N,&B_ierr));
1215             if (B_ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in POTRI Lapack routine %d",(int)B_ierr);
1216             for (k=0;k<subset_size;k++) {
1217               for (j=k;j<subset_size;j++) {
1218                 work[j*subset_size+k] = work[k*subset_size+j];
1219               }
1220             }
1221           } else if (use_sytr) {
1222             PetscStackCallBLAS("LAPACKsytrf",LAPACKsytrf_("L",&B_N,work,&B_N,pivots,Bwork,&B_lwork,&B_ierr));
1223             if (B_ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in SYTRF Lapack routine %d",(int)B_ierr);
1224             PetscStackCallBLAS("LAPACKsytri",LAPACKsytri_("L",&B_N,work,&B_N,pivots,Bwork,&B_ierr));
1225             if (B_ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in SYTRI Lapack routine %d",(int)B_ierr);
1226             for (k=0;k<subset_size;k++) {
1227               for (j=k;j<subset_size;j++) {
1228                 work[j*subset_size+k] = work[k*subset_size+j];
1229               }
1230             }
1231           } else {
1232             PetscStackCallBLAS("LAPACKgetrf",LAPACKgetrf_(&B_N,&B_N,work,&B_N,pivots,&B_ierr));
1233             if (B_ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in GETRF Lapack routine %d",(int)B_ierr);
1234             PetscStackCallBLAS("LAPACKgetri",LAPACKgetri_(&B_N,work,&B_N,pivots,Bwork,&B_lwork,&B_ierr));
1235             if (B_ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in GETRI Lapack routine %d",(int)B_ierr);
1236           }
1237           ierr = PetscFPTrapPop();CHKERRQ(ierr);
1238           ierr = MatSetValues(sub_schurs->sum_S_Ej_inv_all,subset_size,dummy_idx,subset_size,dummy_idx,work,INSERT_VALUES);CHKERRQ(ierr);
1239         }
1240       } else if (compute_Stilda) { /* not using deluxe */
1241         Mat         SEj;
1242         Vec         D;
1243         PetscScalar *array;
1244 
1245         ierr = MatCreateSeqDense(PETSC_COMM_SELF,subset_size,subset_size,work,&SEj);CHKERRQ(ierr);
1246         ierr = VecGetArray(Dall,&array);CHKERRQ(ierr);
1247         ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,1,subset_size,array+cum,&D);CHKERRQ(ierr);
1248         ierr = VecRestoreArray(Dall,&array);CHKERRQ(ierr);
1249         ierr = VecShift(D,-1.);CHKERRQ(ierr);
1250         ierr = MatDiagonalScale(SEj,D,D);CHKERRQ(ierr);
1251         ierr = MatDestroy(&SEj);CHKERRQ(ierr);
1252         ierr = VecDestroy(&D);CHKERRQ(ierr);
1253         ierr = MatSetValues(sub_schurs->S_Ej_all,subset_size,dummy_idx,subset_size,dummy_idx,work,INSERT_VALUES);CHKERRQ(ierr);
1254       }
1255       cum += subset_size;
1256       cum2 += subset_size*(size_schur + 1);
1257     }
1258     ierr = MatDenseRestoreArray(S_all,&S_data);CHKERRQ(ierr);
1259 
1260     if (solver_S) {
1261       ierr = MatFactorRestoreSchurComplement(F,&S_all,MAT_FACTOR_SCHUR_UNFACTORED);CHKERRQ(ierr);
1262     }
1263 
1264     schur_factor = NULL;
1265     if (compute_Stilda && size_active_schur) {
1266 
1267       if (sub_schurs->n_subs == 1 && size_schur == size_active_schur && deluxe) { /* we already computed the inverse */
1268         PetscInt j;
1269         for (j=0;j<size_schur;j++) dummy_idx[j] = j;
1270         ierr = MatSetValues(sub_schurs->sum_S_Ej_tilda_all,size_schur,dummy_idx,size_schur,dummy_idx,work,INSERT_VALUES);CHKERRQ(ierr);
1271       } else {
1272         Mat S_all_inv=NULL;
1273         if (solver_S) {
1274           /* for adaptive selection we need S^-1; for solver reusage we need S_\Delta\Delta^-1.
1275              The latter is not the principal subminor for S^-1. However, the factors can be reused since S_\Delta\Delta is the leading principal submatrix of S */
1276           if (factor_workaround) {/* invert without calling MatFactorInvertSchurComplement, since we are hacking */
1277             PetscScalar *data;
1278             PetscInt     nd = 0;
1279 
1280             if (!use_potr) {
1281               SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Factor update not yet implemented for non SPD matrices");
1282             }
1283             ierr = MatFactorGetSchurComplement(F,&S_all_inv,NULL);CHKERRQ(ierr);
1284             ierr = MatDenseGetArray(S_all_inv,&data);CHKERRQ(ierr);
1285             if (sub_schurs->is_dir) { /* dirichlet dofs could have different scalings */
1286               ierr = ISGetLocalSize(sub_schurs->is_dir,&nd);CHKERRQ(ierr);
1287             }
1288 
1289             /* factor and invert activedofs and vertices (dirichlet dofs does not contribute) */
1290             if (schur_has_vertices) {
1291               Mat          M;
1292               PetscScalar *tdata;
1293               PetscInt     nv = 0, news;
1294 
1295               ierr = ISGetLocalSize(sub_schurs->is_vertices,&nv);CHKERRQ(ierr);
1296               news = size_active_schur + nv;
1297               ierr = PetscCalloc1(news*news,&tdata);CHKERRQ(ierr);
1298               for (i=0;i<size_active_schur;i++) {
1299                 ierr = PetscMemcpy(tdata+i*(news+1),data+i*(size_schur+1),(size_active_schur-i)*sizeof(PetscScalar));CHKERRQ(ierr);
1300                 ierr = PetscMemcpy(tdata+i*(news+1)+size_active_schur-i,data+i*size_schur+size_active_schur+nd,nv*sizeof(PetscScalar));CHKERRQ(ierr);
1301               }
1302               for (i=0;i<nv;i++) {
1303                 PetscInt k = i+size_active_schur;
1304                 ierr = PetscMemcpy(tdata+k*(news+1),data+(k+nd)*(size_schur+1),(nv-i)*sizeof(PetscScalar));CHKERRQ(ierr);
1305               }
1306 
1307               ierr = MatCreateSeqDense(PETSC_COMM_SELF,news,news,tdata,&M);CHKERRQ(ierr);
1308               ierr = MatSetOption(M,MAT_SPD,PETSC_TRUE);CHKERRQ(ierr);
1309               ierr = MatCholeskyFactor(M,NULL,NULL);CHKERRQ(ierr);
1310               /* save the factors */
1311               cum = 0;
1312               ierr = PetscMalloc1((size_active_schur*(size_active_schur +1))/2+nd,&schur_factor);CHKERRQ(ierr);
1313               for (i=0;i<size_active_schur;i++) {
1314                 ierr = PetscMemcpy(schur_factor+cum,tdata+i*(news+1),(size_active_schur-i)*sizeof(PetscScalar));CHKERRQ(ierr);
1315                 cum += size_active_schur - i;
1316               }
1317               for (i=0;i<nd;i++) schur_factor[cum+i] = PetscSqrtReal(PetscRealPart(data[(i+size_active_schur)*(size_schur+1)]));
1318               ierr = MatSeqDenseInvertFactors_Private(M);CHKERRQ(ierr);
1319               /* move back just the active dofs to the Schur complement */
1320               for (i=0;i<size_active_schur;i++) {
1321                 ierr = PetscMemcpy(data+i*size_schur,tdata+i*news,size_active_schur*sizeof(PetscScalar));CHKERRQ(ierr);
1322               }
1323               ierr = PetscFree(tdata);CHKERRQ(ierr);
1324               ierr = MatDestroy(&M);CHKERRQ(ierr);
1325             } else { /* we can factorize and invert just the activedofs */
1326               Mat         M;
1327               PetscScalar *aux;
1328 
1329               ierr = PetscMalloc1(nd,&aux);CHKERRQ(ierr);
1330               for (i=0;i<nd;i++) aux[i] = 1.0/data[(i+size_active_schur)*(size_schur+1)];
1331               ierr = MatCreateSeqDense(PETSC_COMM_SELF,size_active_schur,size_active_schur,data,&M);CHKERRQ(ierr);
1332               ierr = MatSeqDenseSetLDA(M,size_schur);CHKERRQ(ierr);
1333               ierr = MatSetOption(M,MAT_SPD,PETSC_TRUE);CHKERRQ(ierr);
1334               ierr = MatCholeskyFactor(M,NULL,NULL);CHKERRQ(ierr);
1335               ierr = MatSeqDenseInvertFactors_Private(M);CHKERRQ(ierr);
1336               ierr = MatDestroy(&M);CHKERRQ(ierr);
1337               ierr = MatCreateSeqDense(PETSC_COMM_SELF,size_schur,nd,data+size_active_schur*size_schur,&M);CHKERRQ(ierr);
1338               ierr = MatZeroEntries(M);CHKERRQ(ierr);
1339               ierr = MatDestroy(&M);CHKERRQ(ierr);
1340               ierr = MatCreateSeqDense(PETSC_COMM_SELF,nd,size_schur,data+size_active_schur,&M);CHKERRQ(ierr);
1341               ierr = MatSeqDenseSetLDA(M,size_schur);CHKERRQ(ierr);
1342               ierr = MatZeroEntries(M);CHKERRQ(ierr);
1343               ierr = MatDestroy(&M);CHKERRQ(ierr);
1344               for (i=0;i<nd;i++) data[(i+size_active_schur)*(size_schur+1)] = aux[i];
1345               ierr = PetscFree(aux);CHKERRQ(ierr);
1346             }
1347             ierr = MatDenseRestoreArray(S_all_inv,&data);CHKERRQ(ierr);
1348           } else { /* use MatFactor calls to invert S */
1349             ierr = MatFactorInvertSchurComplement(F);CHKERRQ(ierr);
1350             ierr = MatFactorGetSchurComplement(F,&S_all_inv,NULL);CHKERRQ(ierr);
1351           }
1352         } else { /* we need to invert explicitly since we are not using MatFactor for S */
1353           ierr = PetscObjectReference((PetscObject)S_all);CHKERRQ(ierr);
1354           S_all_inv = S_all;
1355           ierr = MatDenseGetArray(S_all_inv,&S_data);CHKERRQ(ierr);
1356           ierr = PetscBLASIntCast(size_schur,&B_N);CHKERRQ(ierr);
1357           ierr = PetscFPTrapPush(PETSC_FP_TRAP_OFF);CHKERRQ(ierr);
1358           if (use_potr) {
1359             PetscStackCallBLAS("LAPACKpotrf",LAPACKpotrf_("L",&B_N,S_data,&B_N,&B_ierr));
1360             if (B_ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in POTRF Lapack routine %d",(int)B_ierr);
1361             PetscStackCallBLAS("LAPACKpotri",LAPACKpotri_("L",&B_N,S_data,&B_N,&B_ierr));
1362             if (B_ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in POTRI Lapack routine %d",(int)B_ierr);
1363           } else if (use_sytr) {
1364             PetscStackCallBLAS("LAPACKsytrf",LAPACKsytrf_("L",&B_N,S_data,&B_N,pivots,Bwork,&B_lwork,&B_ierr));
1365             if (B_ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in SYTRF Lapack routine %d",(int)B_ierr);
1366             PetscStackCallBLAS("LAPACKsytri",LAPACKsytri_("L",&B_N,S_data,&B_N,pivots,Bwork,&B_ierr));
1367             if (B_ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in SYTRI Lapack routine %d",(int)B_ierr);
1368           } else {
1369             PetscStackCallBLAS("LAPACKgetrf",LAPACKgetrf_(&B_N,&B_N,S_data,&B_N,pivots,&B_ierr));
1370             if (B_ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in GETRF Lapack routine %d",(int)B_ierr);
1371             PetscStackCallBLAS("LAPACKgetri",LAPACKgetri_(&B_N,S_data,&B_N,pivots,Bwork,&B_lwork,&B_ierr));
1372             if (B_ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in GETRI Lapack routine %d",(int)B_ierr);
1373           }
1374           ierr = PetscFPTrapPop();CHKERRQ(ierr);
1375           ierr = MatDenseRestoreArray(S_all_inv,&S_data);CHKERRQ(ierr);
1376         }
1377         /* S_Ej_tilda_all */
1378         cum = cum2 = 0;
1379         ierr = MatDenseGetArray(S_all_inv,&S_data);CHKERRQ(ierr);
1380         for (i=0;i<sub_schurs->n_subs;i++) {
1381           PetscInt j;
1382 
1383           ierr = ISGetLocalSize(sub_schurs->is_subs[i],&subset_size);CHKERRQ(ierr);
1384           /* get (St^-1)_E */
1385           /* Unless we are changing the variables, I don't need to expand to upper triangular since St^-1
1386              will be properly accessed later during adaptive selection */
1387           if (S_lower_triangular) {
1388             PetscInt k;
1389             if (sub_schurs->change) {
1390               for (k=0;k<subset_size;k++) {
1391                 for (j=k;j<subset_size;j++) {
1392                   work[k*subset_size+j] = S_data[cum2+k*size_schur+j];
1393                   work[j*subset_size+k] = work[k*subset_size+j];
1394                 }
1395               }
1396             } else {
1397               for (k=0;k<subset_size;k++) {
1398                 for (j=k;j<subset_size;j++) {
1399                   work[k*subset_size+j] = S_data[cum2+k*size_schur+j];
1400                 }
1401               }
1402             }
1403           } else {
1404             PetscInt k;
1405             for (k=0;k<subset_size;k++) {
1406               for (j=0;j<subset_size;j++) {
1407                 work[k*subset_size+j] = S_data[cum2+k*size_schur+j];
1408               }
1409             }
1410           }
1411           if (sub_schurs->change) {
1412             Mat change_sub,SEj,T;
1413 
1414             /* change basis */
1415             ierr = KSPGetOperators(sub_schurs->change[i],&change_sub,NULL);CHKERRQ(ierr);
1416             ierr = MatCreateSeqDense(PETSC_COMM_SELF,subset_size,subset_size,work,&SEj);CHKERRQ(ierr);
1417             if (!sub_schurs->change_with_qr) { /* currently there's no support for PtAP with P SeqAIJ */
1418               Mat T2;
1419               ierr = MatTransposeMatMult(change_sub,SEj,MAT_INITIAL_MATRIX,1.0,&T2);CHKERRQ(ierr);
1420               ierr = MatMatMult(T2,change_sub,MAT_INITIAL_MATRIX,1.0,&T);CHKERRQ(ierr);
1421               ierr = MatDestroy(&T2);CHKERRQ(ierr);
1422               ierr = MatConvert(T,MATSEQDENSE,MAT_INPLACE_MATRIX,&T);CHKERRQ(ierr);
1423             } else {
1424               ierr = MatPtAP(SEj,change_sub,MAT_INITIAL_MATRIX,1.0,&T);CHKERRQ(ierr);
1425             }
1426             ierr = MatCopy(T,SEj,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
1427             ierr = MatDestroy(&T);CHKERRQ(ierr);
1428             /* set diagonal entry to a very large value to pick the basis we are eliminating as the first eigenvectors with adaptive selection */
1429             ierr = MatZeroRowsColumnsIS(SEj,sub_schurs->change_primal_sub[i],1./PETSC_SMALL,NULL,NULL);CHKERRQ(ierr);
1430             ierr = MatDestroy(&SEj);CHKERRQ(ierr);
1431           }
1432           for (j=0;j<subset_size;j++) dummy_idx[j] = cum+j;
1433           ierr = MatSetValues(sub_schurs->sum_S_Ej_tilda_all,subset_size,dummy_idx,subset_size,dummy_idx,work,INSERT_VALUES);CHKERRQ(ierr);
1434           cum += subset_size;
1435           cum2 += subset_size*(size_schur + 1);
1436         }
1437         ierr = MatDenseRestoreArray(S_all_inv,&S_data);CHKERRQ(ierr);
1438         if (solver_S) {
1439           if (schur_has_vertices) {
1440             ierr = MatFactorRestoreSchurComplement(F,&S_all_inv,MAT_FACTOR_SCHUR_FACTORED);CHKERRQ(ierr);
1441           } else {
1442             ierr = MatFactorRestoreSchurComplement(F,&S_all_inv,MAT_FACTOR_SCHUR_INVERTED);CHKERRQ(ierr);
1443           }
1444         }
1445         ierr = MatDestroy(&S_all_inv);CHKERRQ(ierr);
1446       }
1447 
1448       /* move back factors if needed */
1449       if (schur_has_vertices) {
1450         Mat      S_tmp;
1451         PetscInt nd = 0;
1452 
1453         if (!solver_S) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"This should not happen");
1454         ierr = MatFactorGetSchurComplement(F,&S_tmp,NULL);CHKERRQ(ierr);
1455         if (use_potr) {
1456           PetscScalar *data;
1457 
1458           ierr = MatDenseGetArray(S_tmp,&data);CHKERRQ(ierr);
1459           ierr = PetscMemzero(data,size_schur*size_schur*sizeof(PetscScalar));CHKERRQ(ierr);
1460 
1461           if (S_lower_triangular) {
1462             cum = 0;
1463             for (i=0;i<size_active_schur;i++) {
1464               ierr = PetscMemcpy(data+i*(size_schur+1),schur_factor+cum,(size_active_schur-i)*sizeof(PetscScalar));CHKERRQ(ierr);
1465               cum += size_active_schur-i;
1466 	    }
1467           } else {
1468             ierr = PetscMemcpy(data,schur_factor,size_schur*size_schur*sizeof(PetscScalar));CHKERRQ(ierr);
1469           }
1470           if (sub_schurs->is_dir) {
1471             ierr = ISGetLocalSize(sub_schurs->is_dir,&nd);CHKERRQ(ierr);
1472 	    for (i=0;i<nd;i++) {
1473 	      data[(i+size_active_schur)*(size_schur+1)] = schur_factor[cum+i];
1474 	    }
1475           }
1476           /* workaround: since I cannot modify the matrices used inside the solvers for the forward and backward substitutions,
1477              set the diagonal entry of the Schur factor to a very large value */
1478           for (i=size_active_schur+nd;i<size_schur;i++) {
1479             data[i*(size_schur+1)] = infty;
1480           }
1481           ierr = MatDenseRestoreArray(S_tmp,&data);CHKERRQ(ierr);
1482         } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Factor update not yet implemented for non SPD matrices");
1483         ierr = MatFactorRestoreSchurComplement(F,&S_tmp,MAT_FACTOR_SCHUR_FACTORED);CHKERRQ(ierr);
1484       }
1485     } else if (factor_workaround) { /* we need to eliminate any unneeded coupling */
1486       PetscScalar *data;
1487       PetscInt    nd = 0;
1488 
1489       if (sub_schurs->is_dir) { /* dirichlet dofs could have different scalings */
1490         ierr = ISGetLocalSize(sub_schurs->is_dir,&nd);CHKERRQ(ierr);
1491       }
1492       ierr = MatFactorGetSchurComplement(F,&S_all,NULL);CHKERRQ(ierr);
1493       ierr = MatDenseGetArray(S_all,&data);CHKERRQ(ierr);
1494       for (i=0;i<size_active_schur;i++) {
1495         ierr = PetscMemzero(data+i*size_schur+size_active_schur,(size_schur-size_active_schur)*sizeof(PetscScalar));CHKERRQ(ierr);
1496       }
1497       for (i=size_active_schur+nd;i<size_schur;i++) {
1498         ierr = PetscMemzero(data+i*size_schur+size_active_schur,(size_schur-size_active_schur)*sizeof(PetscScalar));CHKERRQ(ierr);
1499         data[i*(size_schur+1)] = infty;
1500       }
1501       ierr = MatDenseRestoreArray(S_all,&data);CHKERRQ(ierr);
1502       ierr = MatFactorRestoreSchurComplement(F,&S_all,MAT_FACTOR_SCHUR_UNFACTORED);CHKERRQ(ierr);
1503     }
1504     ierr = PetscFree2(dummy_idx,work);CHKERRQ(ierr);
1505     ierr = PetscFree(schur_factor);CHKERRQ(ierr);
1506     ierr = VecDestroy(&Dall);CHKERRQ(ierr);
1507   }
1508   ierr = PetscFree(nnz);CHKERRQ(ierr);
1509   ierr = MatDestroy(&F);CHKERRQ(ierr);
1510   ierr = ISDestroy(&is_I_layer);CHKERRQ(ierr);
1511   ierr = MatDestroy(&S_all);CHKERRQ(ierr);
1512   ierr = MatDestroy(&A_BB);CHKERRQ(ierr);
1513   ierr = MatDestroy(&A_IB);CHKERRQ(ierr);
1514   ierr = MatDestroy(&A_BI);CHKERRQ(ierr);
1515   ierr = MatAssemblyBegin(sub_schurs->S_Ej_all,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
1516   ierr = MatAssemblyEnd(sub_schurs->S_Ej_all,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
1517   if (compute_Stilda) {
1518     ierr = MatAssemblyBegin(sub_schurs->sum_S_Ej_tilda_all,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
1519     ierr = MatAssemblyEnd(sub_schurs->sum_S_Ej_tilda_all,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
1520     if (deluxe) {
1521       ierr = MatAssemblyBegin(sub_schurs->sum_S_Ej_inv_all,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
1522       ierr = MatAssemblyEnd(sub_schurs->sum_S_Ej_inv_all,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
1523     }
1524   }
1525 
1526   /* Global matrix of all assembled Schur on subsets */
1527   ierr = MatISSetLocalMat(work_mat,sub_schurs->S_Ej_all);CHKERRQ(ierr);
1528   ierr = MatISSetMPIXAIJPreallocation_Private(work_mat,global_schur_subsets,PETSC_TRUE);CHKERRQ(ierr);
1529   ierr = MatISGetMPIXAIJ(work_mat,MAT_REUSE_MATRIX,&global_schur_subsets);CHKERRQ(ierr);
1530 
1531   /* Get local part of (\sum_j S_Ej) */
1532   ierr = MatCreateSubMatrices(global_schur_subsets,1,&all_subsets_n,&all_subsets_n,MAT_INITIAL_MATRIX,&submats);CHKERRQ(ierr);
1533   if (!sub_schurs->sum_S_Ej_all) {
1534     ierr = MatDuplicate(submats[0],MAT_COPY_VALUES,&sub_schurs->sum_S_Ej_all);CHKERRQ(ierr);
1535   } else {
1536     ierr = MatCopy(submats[0],sub_schurs->sum_S_Ej_all,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
1537   }
1538 
1539   /* Get local part of (\sum_j S^-1_Ej) (\sum_j St^-1_Ej) */
1540   if (compute_Stilda) {
1541     ierr = MatISSetLocalMat(work_mat,sub_schurs->sum_S_Ej_tilda_all);CHKERRQ(ierr);
1542     ierr = MatISGetMPIXAIJ(work_mat,MAT_REUSE_MATRIX,&global_schur_subsets);CHKERRQ(ierr);
1543     ierr = MatCreateSubMatrices(global_schur_subsets,1,&all_subsets_n,&all_subsets_n,MAT_REUSE_MATRIX,&submats);CHKERRQ(ierr);
1544     ierr = MatCopy(submats[0],sub_schurs->sum_S_Ej_tilda_all,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
1545     if (deluxe) {
1546       ierr = MatISSetLocalMat(work_mat,sub_schurs->sum_S_Ej_inv_all);CHKERRQ(ierr);
1547       ierr = MatISGetMPIXAIJ(work_mat,MAT_REUSE_MATRIX,&global_schur_subsets);CHKERRQ(ierr);
1548       ierr = MatCreateSubMatrices(global_schur_subsets,1,&all_subsets_n,&all_subsets_n,MAT_REUSE_MATRIX,&submats);CHKERRQ(ierr);
1549       ierr = MatCopy(submats[0],sub_schurs->sum_S_Ej_inv_all,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
1550     } else {
1551       PetscScalar *array;
1552       PetscInt    cum;
1553 
1554       ierr = MatSeqAIJGetArray(sub_schurs->sum_S_Ej_tilda_all,&array);CHKERRQ(ierr);
1555       cum = 0;
1556       for (i=0;i<sub_schurs->n_subs;i++) {
1557         ierr = ISGetLocalSize(sub_schurs->is_subs[i],&subset_size);CHKERRQ(ierr);
1558         ierr = PetscBLASIntCast(subset_size,&B_N);CHKERRQ(ierr);
1559         ierr = PetscFPTrapPush(PETSC_FP_TRAP_OFF);CHKERRQ(ierr);
1560         if (use_potr) {
1561           PetscStackCallBLAS("LAPACKpotrf",LAPACKpotrf_("L",&B_N,array+cum,&B_N,&B_ierr));
1562           if (B_ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in POTRF Lapack routine %d",(int)B_ierr);
1563           PetscStackCallBLAS("LAPACKpotri",LAPACKpotri_("L",&B_N,array+cum,&B_N,&B_ierr));
1564           if (B_ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in POTRI Lapack routine %d",(int)B_ierr);
1565         } else if (use_sytr) {
1566           PetscStackCallBLAS("LAPACKsytrf",LAPACKsytrf_("L",&B_N,array+cum,&B_N,pivots,Bwork,&B_lwork,&B_ierr));
1567           if (B_ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in SYTRF Lapack routine %d",(int)B_ierr);
1568           PetscStackCallBLAS("LAPACKsytri",LAPACKsytri_("L",&B_N,array+cum,&B_N,pivots,Bwork,&B_ierr));
1569           if (B_ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in SYTRI Lapack routine %d",(int)B_ierr);
1570         } else {
1571           PetscStackCallBLAS("LAPACKgetrf",LAPACKgetrf_(&B_N,&B_N,array+cum,&B_N,pivots,&B_ierr));
1572           if (B_ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in GETRF Lapack routine %d",(int)B_ierr);
1573           PetscStackCallBLAS("LAPACKgetri",LAPACKgetri_(&B_N,array+cum,&B_N,pivots,Bwork,&B_lwork,&B_ierr));
1574           if (B_ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in GETRI Lapack routine %d",(int)B_ierr);
1575         }
1576         ierr = PetscFPTrapPop();CHKERRQ(ierr);
1577         cum += subset_size*subset_size;
1578       }
1579       ierr = MatSeqAIJRestoreArray(sub_schurs->sum_S_Ej_tilda_all,&array);CHKERRQ(ierr);
1580       ierr = PetscObjectReference((PetscObject)sub_schurs->sum_S_Ej_all);CHKERRQ(ierr);
1581       ierr = MatDestroy(&sub_schurs->sum_S_Ej_inv_all);CHKERRQ(ierr);
1582       sub_schurs->sum_S_Ej_inv_all = sub_schurs->sum_S_Ej_all;
1583     }
1584   }
1585   ierr = MatDestroySubMatrices(1,&submats);CHKERRQ(ierr);
1586 
1587   /* free workspace */
1588   ierr = PetscFree(submats);CHKERRQ(ierr);
1589   ierr = PetscFree2(Bwork,pivots);CHKERRQ(ierr);
1590   ierr = MatDestroy(&global_schur_subsets);CHKERRQ(ierr);
1591   ierr = MatDestroy(&work_mat);CHKERRQ(ierr);
1592   ierr = ISDestroy(&all_subsets_n);CHKERRQ(ierr);
1593   ierr = PetscCommDestroy(&comm_n);CHKERRQ(ierr);
1594   PetscFunctionReturn(0);
1595 }
1596 
1597 PetscErrorCode PCBDDCSubSchursInit(PCBDDCSubSchurs sub_schurs, const char* prefix, IS is_I, IS is_B, PCBDDCGraph graph, ISLocalToGlobalMapping BtoNmap, PetscBool copycc)
1598 {
1599   IS              *faces,*edges,*all_cc,vertices;
1600   PetscInt        i,n_faces,n_edges,n_all_cc;
1601   PetscBool       is_sorted,ispetsc;
1602   PetscErrorCode  ierr;
1603 
1604   PetscFunctionBegin;
1605   ierr = ISSorted(is_I,&is_sorted);CHKERRQ(ierr);
1606   if (!is_sorted) SETERRQ(PetscObjectComm((PetscObject)is_I),PETSC_ERR_PLIB,"IS for I dofs should be shorted");
1607   ierr = ISSorted(is_B,&is_sorted);CHKERRQ(ierr);
1608   if (!is_sorted) SETERRQ(PetscObjectComm((PetscObject)is_B),PETSC_ERR_PLIB,"IS for B dofs should be shorted");
1609 
1610   /* reset any previous data */
1611   ierr = PCBDDCSubSchursReset(sub_schurs);CHKERRQ(ierr);
1612 
1613   /* get index sets for faces and edges (already sorted by global ordering) */
1614   ierr = PCBDDCGraphGetCandidatesIS(graph,&n_faces,&faces,&n_edges,&edges,&vertices);CHKERRQ(ierr);
1615   n_all_cc = n_faces+n_edges;
1616   ierr = PetscBTCreate(n_all_cc,&sub_schurs->is_edge);CHKERRQ(ierr);
1617   ierr = PetscMalloc1(n_all_cc,&all_cc);CHKERRQ(ierr);
1618   for (i=0;i<n_faces;i++) {
1619     if (copycc) {
1620       ierr = ISDuplicate(faces[i],&all_cc[i]);CHKERRQ(ierr);
1621     } else {
1622       ierr = PetscObjectReference((PetscObject)faces[i]);CHKERRQ(ierr);
1623       all_cc[i] = faces[i];
1624     }
1625   }
1626   for (i=0;i<n_edges;i++) {
1627     if (copycc) {
1628       ierr = ISDuplicate(edges[i],&all_cc[n_faces+i]);CHKERRQ(ierr);
1629     } else {
1630       ierr = PetscObjectReference((PetscObject)edges[i]);CHKERRQ(ierr);
1631       all_cc[n_faces+i] = edges[i];
1632     }
1633     ierr = PetscBTSet(sub_schurs->is_edge,n_faces+i);CHKERRQ(ierr);
1634   }
1635   ierr = PetscObjectReference((PetscObject)vertices);CHKERRQ(ierr);
1636   sub_schurs->is_vertices = vertices;
1637   ierr = PCBDDCGraphRestoreCandidatesIS(graph,&n_faces,&faces,&n_edges,&edges,&vertices);CHKERRQ(ierr);
1638   sub_schurs->is_dir = NULL;
1639   ierr = PCBDDCGraphGetDirichletDofsB(graph,&sub_schurs->is_dir);CHKERRQ(ierr);
1640 
1641   /* Determine if MatFactor can be used */
1642   ierr = PetscStrallocpy(prefix,&sub_schurs->prefix);CHKERRQ(ierr);
1643 #if defined(PETSC_HAVE_MUMPS)
1644   ierr = PetscStrncpy(sub_schurs->mat_solver_type,MATSOLVERMUMPS,64);CHKERRQ(ierr);
1645 #elif defined(PETSC_HAVE_MKL_PARDISO)
1646   ierr = PetscStrncpy(sub_schurs->mat_solver_type,MATSOLVERMKL_PARDISO,64);CHKERRQ(ierr);
1647 #else
1648   ierr = PetscStrncpy(sub_schurs->mat_solver_type,MATSOLVERPETSC,64);CHKERRQ(ierr);
1649 #endif
1650 #if defined(PETSC_USE_COMPLEX)
1651   sub_schurs->is_hermitian = PETSC_FALSE; /* Hermitian Cholesky is not supported by PETSc and external packages */
1652 #else
1653   sub_schurs->is_hermitian = PETSC_TRUE;
1654 #endif
1655   sub_schurs->is_posdef    = PETSC_TRUE;
1656   ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)graph->l2gmap),sub_schurs->prefix,"BDDC sub_schurs options","PC");CHKERRQ(ierr);
1657   ierr = PetscOptionsString("-sub_schurs_mat_solver_type","Specific direct solver to use",NULL,sub_schurs->mat_solver_type,sub_schurs->mat_solver_type,64,NULL);CHKERRQ(ierr);
1658   ierr = PetscOptionsBool("-sub_schurs_hermitian","Hermitian problem",NULL,sub_schurs->is_hermitian,&sub_schurs->is_hermitian,NULL);CHKERRQ(ierr);
1659   ierr = PetscOptionsBool("-sub_schurs_posdef","Positive definite problem",NULL,sub_schurs->is_posdef,&sub_schurs->is_posdef,NULL);CHKERRQ(ierr);
1660   ierr = PetscOptionsEnd();CHKERRQ(ierr);
1661   ierr = PetscStrcmp(sub_schurs->mat_solver_type,MATSOLVERPETSC,&ispetsc);CHKERRQ(ierr);
1662   sub_schurs->schur_explicit = (PetscBool)!ispetsc;
1663 
1664   ierr = PetscObjectReference((PetscObject)is_I);CHKERRQ(ierr);
1665   sub_schurs->is_I = is_I;
1666   ierr = PetscObjectReference((PetscObject)is_B);CHKERRQ(ierr);
1667   sub_schurs->is_B = is_B;
1668   ierr = PetscObjectReference((PetscObject)graph->l2gmap);CHKERRQ(ierr);
1669   sub_schurs->l2gmap = graph->l2gmap;
1670   ierr = PetscObjectReference((PetscObject)BtoNmap);CHKERRQ(ierr);
1671   sub_schurs->BtoNmap = BtoNmap;
1672   sub_schurs->n_subs = n_all_cc;
1673   sub_schurs->is_subs = all_cc;
1674   if (!sub_schurs->schur_explicit) { /* sort by local ordering if we are not using MatFactor */
1675     for (i=0;i<sub_schurs->n_subs;i++) {
1676       ierr = ISSort(sub_schurs->is_subs[i]);CHKERRQ(ierr);
1677     }
1678   }
1679   sub_schurs->S_Ej_all = NULL;
1680   sub_schurs->sum_S_Ej_all = NULL;
1681   sub_schurs->sum_S_Ej_inv_all = NULL;
1682   sub_schurs->sum_S_Ej_tilda_all = NULL;
1683   sub_schurs->is_Ej_all = NULL;
1684   PetscFunctionReturn(0);
1685 }
1686 
1687 PetscErrorCode PCBDDCSubSchursCreate(PCBDDCSubSchurs *sub_schurs)
1688 {
1689   PCBDDCSubSchurs schurs_ctx;
1690   PetscErrorCode  ierr;
1691 
1692   PetscFunctionBegin;
1693   ierr = PetscNew(&schurs_ctx);CHKERRQ(ierr);
1694   schurs_ctx->n_subs = 0;
1695   *sub_schurs = schurs_ctx;
1696   PetscFunctionReturn(0);
1697 }
1698 
1699 PetscErrorCode PCBDDCSubSchursReset(PCBDDCSubSchurs sub_schurs)
1700 {
1701   PetscInt       i;
1702   PetscErrorCode ierr;
1703 
1704   PetscFunctionBegin;
1705   if (!sub_schurs) PetscFunctionReturn(0);
1706   ierr = PetscFree(sub_schurs->prefix);CHKERRQ(ierr);
1707   ierr = MatDestroy(&sub_schurs->A);CHKERRQ(ierr);
1708   ierr = MatDestroy(&sub_schurs->S);CHKERRQ(ierr);
1709   ierr = ISDestroy(&sub_schurs->is_I);CHKERRQ(ierr);
1710   ierr = ISDestroy(&sub_schurs->is_B);CHKERRQ(ierr);
1711   ierr = ISLocalToGlobalMappingDestroy(&sub_schurs->l2gmap);CHKERRQ(ierr);
1712   ierr = ISLocalToGlobalMappingDestroy(&sub_schurs->BtoNmap);CHKERRQ(ierr);
1713   ierr = MatDestroy(&sub_schurs->S_Ej_all);CHKERRQ(ierr);
1714   ierr = MatDestroy(&sub_schurs->sum_S_Ej_all);CHKERRQ(ierr);
1715   ierr = MatDestroy(&sub_schurs->sum_S_Ej_inv_all);CHKERRQ(ierr);
1716   ierr = MatDestroy(&sub_schurs->sum_S_Ej_tilda_all);CHKERRQ(ierr);
1717   ierr = ISDestroy(&sub_schurs->is_Ej_all);CHKERRQ(ierr);
1718   ierr = ISDestroy(&sub_schurs->is_vertices);CHKERRQ(ierr);
1719   ierr = ISDestroy(&sub_schurs->is_dir);CHKERRQ(ierr);
1720   ierr = PetscBTDestroy(&sub_schurs->is_edge);CHKERRQ(ierr);
1721   for (i=0;i<sub_schurs->n_subs;i++) {
1722     ierr = ISDestroy(&sub_schurs->is_subs[i]);CHKERRQ(ierr);
1723   }
1724   if (sub_schurs->n_subs) {
1725     ierr = PetscFree(sub_schurs->is_subs);CHKERRQ(ierr);
1726   }
1727   if (sub_schurs->reuse_solver) {
1728     ierr = PCBDDCReuseSolversReset(sub_schurs->reuse_solver);CHKERRQ(ierr);
1729   }
1730   ierr = PetscFree(sub_schurs->reuse_solver);CHKERRQ(ierr);
1731   if (sub_schurs->change) {
1732     for (i=0;i<sub_schurs->n_subs;i++) {
1733       ierr = KSPDestroy(&sub_schurs->change[i]);CHKERRQ(ierr);
1734       ierr = ISDestroy(&sub_schurs->change_primal_sub[i]);CHKERRQ(ierr);
1735     }
1736   }
1737   ierr = PetscFree(sub_schurs->change);CHKERRQ(ierr);
1738   ierr = PetscFree(sub_schurs->change_primal_sub);CHKERRQ(ierr);
1739   sub_schurs->n_subs = 0;
1740   PetscFunctionReturn(0);
1741 }
1742 
1743 PetscErrorCode PCBDDCSubSchursDestroy(PCBDDCSubSchurs* sub_schurs)
1744 {
1745   PetscErrorCode ierr;
1746 
1747   PetscFunctionBegin;
1748   ierr = PCBDDCSubSchursReset(*sub_schurs);CHKERRQ(ierr);
1749   ierr = PetscFree(*sub_schurs);CHKERRQ(ierr);
1750   PetscFunctionReturn(0);
1751 }
1752 
1753 PETSC_STATIC_INLINE PetscErrorCode PCBDDCAdjGetNextLayer_Private(PetscInt* queue_tip,PetscInt n_prev,PetscBT touched,PetscInt* xadj,PetscInt* adjncy,PetscInt* n_added)
1754 {
1755   PetscInt       i,j,n;
1756   PetscErrorCode ierr;
1757 
1758   PetscFunctionBegin;
1759   n = 0;
1760   for (i=-n_prev;i<0;i++) {
1761     PetscInt start_dof = queue_tip[i];
1762     for (j=xadj[start_dof];j<xadj[start_dof+1];j++) {
1763       PetscInt dof = adjncy[j];
1764       if (!PetscBTLookup(touched,dof)) {
1765         ierr = PetscBTSet(touched,dof);CHKERRQ(ierr);
1766         queue_tip[n] = dof;
1767         n++;
1768       }
1769     }
1770   }
1771   *n_added = n;
1772   PetscFunctionReturn(0);
1773 }
1774