1 #include <petsc-private/daimpl.h> 2 3 #undef __FUNCT__ 4 #define __FUNCT__ "DMDACreatePatchIS" 5 6 PetscErrorCode DMDACreatePatchIS(DM da,MatStencil *lower,MatStencil *upper,IS *is) 7 { 8 PetscErrorCode ierr; 9 PetscInt i,j,k,idx; 10 PetscInt ii,jj,kk; 11 Vec v; 12 PetscInt n,pn,bs; 13 PetscMPIInt rank; 14 PetscSF sf,psf; 15 PetscLayout map; 16 MPI_Comm comm; 17 PetscInt *natidx,*globidx,*leafidx; 18 PetscInt *pnatidx,*pleafidx; 19 PetscInt base; 20 PetscInt ox,oy,oz; 21 DM_DA *dd; 22 23 PetscFunctionBegin; 24 comm = ((PetscObject)da)->comm; 25 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 26 dd = (DM_DA *)da->data; 27 28 /* construct the natural mapping */ 29 ierr = DMGetGlobalVector(da,&v);CHKERRQ(ierr); 30 ierr = VecGetLocalSize(v,&n);CHKERRQ(ierr); 31 ierr = VecGetOwnershipRange(v,&base,PETSC_NULL);CHKERRQ(ierr); 32 ierr = VecGetBlockSize(v,&bs);CHKERRQ(ierr); 33 ierr = DMRestoreGlobalVector(da,&v);CHKERRQ(ierr); 34 35 /* construct the layout */ 36 ierr = PetscLayoutCreate(comm,&map);CHKERRQ(ierr); 37 ierr = PetscLayoutSetBlockSize(map,1);CHKERRQ(ierr); 38 ierr = PetscLayoutSetLocalSize(map,n);CHKERRQ(ierr); 39 ierr = PetscLayoutSetUp(map);CHKERRQ(ierr); 40 41 /* construct the list of natural indices on this process when PETSc ordering is considered */ 42 ierr = DMDAGetOffset(da,&ox,&oy,&oz,PETSC_NULL,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr); 43 ierr = PetscMalloc(sizeof(PetscInt)*n,&natidx);CHKERRQ(ierr); 44 ierr = PetscMalloc(sizeof(PetscInt)*n,&globidx);CHKERRQ(ierr); 45 ierr = PetscMalloc(sizeof(PetscInt)*n,&leafidx);CHKERRQ(ierr); 46 idx = 0; 47 for (k=dd->zs;k<dd->ze;k++) { 48 for (j=dd->ys;j<dd->ye;j++) { 49 for (i=dd->xs;i<dd->xe;i++) { 50 natidx[idx] = i + dd->w*(j*dd->M + k*dd->M*dd->N); 51 globidx[idx] = base + idx; 52 leafidx[idx] = 0; 53 idx++; 54 } 55 } 56 } 57 58 if (idx != n) SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE, "for some reason the count is wrong."); 59 60 /* construct the SF going from the natural indices to the local set of PETSc indices */ 61 ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr); 62 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 63 ierr = PetscSFSetGraphLayout(sf,map,n,PETSC_NULL,PETSC_OWN_POINTER,natidx);CHKERRQ(ierr); 64 65 /* broadcast the global indices over to the corresponding natural indices */ 66 ierr = PetscSFGatherBegin(sf,MPIU_INT,globidx,leafidx);CHKERRQ(ierr); 67 ierr = PetscSFGatherEnd(sf,MPIU_INT,globidx,leafidx);CHKERRQ(ierr); 68 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 69 70 71 pn = dd->w*(upper->k - lower->k)*(upper->j - lower->j)*(upper->i - lower->i); 72 ierr = PetscMalloc(sizeof(PetscInt)*pn,&pnatidx);CHKERRQ(ierr); 73 ierr = PetscMalloc(sizeof(PetscInt)*pn,&pleafidx);CHKERRQ(ierr); 74 idx = 0; 75 for (k=lower->k-oz;k<upper->k-oz;k++) { 76 for (j=lower->j-oy;j<upper->j-oy;j++) { 77 for (i=dd->w*(lower->i-ox);i<dd->w*(upper->i-ox);i++) { 78 ii = i % (dd->w*dd->M); 79 jj = j % dd->N; 80 kk = k % dd->P; 81 if (ii < 0) ii = dd->w*dd->M + ii; 82 if (jj < 0) jj = dd->N + jj; 83 if (kk < 0) kk = dd->P + kk; 84 pnatidx[idx] = ii + dd->w*(jj*dd->M + kk*dd->M*dd->N); 85 idx++; 86 } 87 } 88 } 89 90 if (idx != pn) SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE, "for some reason the count is wrong"); 91 92 ierr = PetscSFCreate(comm,&psf);CHKERRQ(ierr); 93 ierr = PetscSFSetFromOptions(psf);CHKERRQ(ierr); 94 ierr = PetscSFSetGraphLayout(psf,map,pn,PETSC_NULL,PETSC_OWN_POINTER,pnatidx);CHKERRQ(ierr); 95 96 /* broadcast the global indices through to the patch */ 97 ierr = PetscSFBcastBegin(psf,MPIU_INT,leafidx,pleafidx);CHKERRQ(ierr); 98 ierr = PetscSFBcastEnd(psf,MPIU_INT,leafidx,pleafidx);CHKERRQ(ierr); 99 100 /* create the IS */ 101 ierr = ISCreateGeneral(comm,pn,pleafidx,PETSC_OWN_POINTER,is);CHKERRQ(ierr); 102 103 ierr = PetscSFDestroy(&psf);CHKERRQ(ierr); 104 105 ierr = PetscLayoutDestroy(&map);CHKERRQ(ierr); 106 107 ierr = PetscFree(globidx);CHKERRQ(ierr); 108 ierr = PetscFree(leafidx);CHKERRQ(ierr); 109 ierr = PetscFree(natidx);CHKERRQ(ierr); 110 ierr = PetscFree(pnatidx);CHKERRQ(ierr); 111 PetscFunctionReturn(0); 112 } 113 114 #undef __FUNCT__ 115 #define __FUNCT__ "DMDASubDomainDA_Private" 116 PetscErrorCode DMDASubDomainDA_Private(DM dm, DM *dddm) 117 { 118 DM da; 119 DM_DA *dd; 120 PetscErrorCode ierr; 121 DMDALocalInfo info; 122 PetscReal lmin[3],lmax[3]; 123 PetscInt xsize,ysize,zsize; 124 PetscInt xo,yo,zo; 125 126 PetscFunctionBegin; 127 ierr = DMDAGetLocalInfo(dm,&info);CHKERRQ(ierr); 128 ierr = DMDACreate(PETSC_COMM_SELF,&da);CHKERRQ(ierr); 129 ierr = DMSetOptionsPrefix(da,"sub_");CHKERRQ(ierr); 130 131 ierr = DMDASetDim(da, info.dim);CHKERRQ(ierr); 132 ierr = DMDASetDof(da, info.dof);CHKERRQ(ierr); 133 134 ierr = DMDASetStencilType(da,info.st);CHKERRQ(ierr); 135 ierr = DMDASetStencilWidth(da,info.sw);CHKERRQ(ierr); 136 137 dd = (DM_DA *)dm->data; 138 139 /* local with overlap */ 140 xsize = info.xm; 141 ysize = info.ym; 142 zsize = info.zm; 143 xo = info.xs; 144 yo = info.ys; 145 zo = info.zs; 146 if (info.bx == DMDA_BOUNDARY_PERIODIC || (info.xs != 0)) { 147 xsize += dd->overlap; 148 xo -= dd->overlap; 149 } 150 if (info.by == DMDA_BOUNDARY_PERIODIC || (info.ys != 0)) { 151 ysize += dd->overlap; 152 yo -= dd->overlap; 153 } 154 if (info.bz == DMDA_BOUNDARY_PERIODIC || (info.zs != 0)) { 155 zsize += dd->overlap; 156 zo -= dd->overlap; 157 } 158 159 if (info.bx == DMDA_BOUNDARY_PERIODIC || (info.xs+info.xm != info.mx)) { 160 xsize += dd->overlap; 161 } 162 if (info.by == DMDA_BOUNDARY_PERIODIC || (info.ys+info.ym != info.my)) { 163 ysize += dd->overlap; 164 } 165 if (info.bz == DMDA_BOUNDARY_PERIODIC || (info.zs+info.zm != info.mz)) { 166 zsize += dd->overlap; 167 } 168 ierr = DMDASetSizes(da, xsize, ysize, zsize);CHKERRQ(ierr); 169 ierr = DMDASetNumProcs(da, 1, 1, 1);CHKERRQ(ierr); 170 ierr = DMDASetBoundaryType(da, DMDA_BOUNDARY_GHOSTED, DMDA_BOUNDARY_GHOSTED, DMDA_BOUNDARY_GHOSTED);CHKERRQ(ierr); 171 172 /* set up as a block instead */ 173 ierr = DMSetUp(da);CHKERRQ(ierr); 174 175 /* todo - nonuniform coordinates */ 176 ierr = DMDAGetLocalBoundingBox(dm,lmin,lmax);CHKERRQ(ierr); 177 ierr = DMDASetUniformCoordinates(da,lmin[0],lmax[0],lmin[1],lmax[1],lmin[2],lmax[2]);CHKERRQ(ierr); 178 179 /* this alters the behavior of DMDAGetInfo, DMDAGetLocalInfo, DMDAGetCorners, and DMDAGetGhostedCorners and should be used with care */ 180 ierr = DMDASetOffset(da,xo,yo,zo,info.mx,info.my,info.mz);CHKERRQ(ierr); 181 182 *dddm = da; 183 PetscFunctionReturn(0); 184 } 185 186 #undef __FUNCT__ 187 #define __FUNCT__ "DMCreateDomainDecompositionScatters_DA" 188 /* 189 Fills the local vector problem on the subdomain from the global problem. 190 191 Right now this assumes one subdomain per processor. 192 193 */ 194 PetscErrorCode DMCreateDomainDecompositionScatters_DA(DM dm,PetscInt nsubdms,DM *subdms,VecScatter **iscat,VecScatter **oscat, VecScatter **lscat) 195 { 196 PetscErrorCode ierr; 197 DMDALocalInfo info,subinfo; 198 DM subdm; 199 MatStencil upper,lower; 200 IS idis,isis,odis,osis,gdis; 201 Vec svec,dvec,slvec; 202 203 PetscFunctionBegin; 204 if (nsubdms != 1) SETERRQ(((PetscObject)dm)->comm,PETSC_ERR_ARG_OUTOFRANGE,"Cannot have more than one subdomain per processor (yet)"); 205 206 /* allocate the arrays of scatters */ 207 if (iscat) {ierr = PetscMalloc(sizeof(VecScatter *),iscat);CHKERRQ(ierr);} 208 if (oscat) {ierr = PetscMalloc(sizeof(VecScatter *),oscat);CHKERRQ(ierr);} 209 if (lscat) {ierr = PetscMalloc(sizeof(VecScatter *),lscat);CHKERRQ(ierr);} 210 211 ierr = DMDAGetLocalInfo(dm,&info);CHKERRQ(ierr); 212 subdm = subdms[0]; 213 ierr = DMDAGetLocalInfo(subdm,&subinfo);CHKERRQ(ierr); 214 215 /* create the global and subdomain index sets for the inner domain */ 216 /* TODO - make this actually support multiple subdomains -- subdomain needs to provide where it's nonoverlapping portion belongs */ 217 lower.i = info.xs; 218 lower.j = info.ys; 219 lower.k = info.zs; 220 upper.i = info.xs+info.xm; 221 upper.j = info.ys+info.ym; 222 upper.k = info.zs+info.zm; 223 ierr = DMDACreatePatchIS(dm,&lower,&upper,&idis);CHKERRQ(ierr); 224 ierr = DMDACreatePatchIS(subdm,&lower,&upper,&isis);CHKERRQ(ierr); 225 226 /* create the global and subdomain index sets for the outer subdomain */ 227 lower.i = subinfo.xs; 228 lower.j = subinfo.ys; 229 lower.k = subinfo.zs; 230 upper.i = subinfo.xs+subinfo.xm; 231 upper.j = subinfo.ys+subinfo.ym; 232 upper.k = subinfo.zs+subinfo.zm; 233 ierr = DMDACreatePatchIS(dm,&lower,&upper,&odis);CHKERRQ(ierr); 234 ierr = DMDACreatePatchIS(subdm,&lower,&upper,&osis);CHKERRQ(ierr); 235 236 /* global and subdomain ISes for the local indices of the subdomain */ 237 /* todo - make this not loop over at nonperiodic boundaries, which will be more involved */ 238 lower.i = subinfo.gxs; 239 lower.j = subinfo.gys; 240 lower.k = subinfo.gzs; 241 upper.i = subinfo.gxs+subinfo.gxm; 242 upper.j = subinfo.gys+subinfo.gym; 243 upper.k = subinfo.gzs+subinfo.gzm; 244 245 ierr = DMDACreatePatchIS(dm,&lower,&upper,&gdis);CHKERRQ(ierr); 246 247 /* form the scatter */ 248 ierr = DMGetGlobalVector(dm,&dvec);CHKERRQ(ierr); 249 ierr = DMGetGlobalVector(subdm,&svec);CHKERRQ(ierr); 250 ierr = DMGetLocalVector(subdm,&slvec);CHKERRQ(ierr); 251 252 if (iscat) {ierr = VecScatterCreate(dvec,idis,svec,isis,&(*iscat)[0]);CHKERRQ(ierr);} 253 if (oscat) {ierr = VecScatterCreate(dvec,odis,svec,osis,&(*oscat)[0]);CHKERRQ(ierr);} 254 if (lscat) {ierr = VecScatterCreate(dvec,gdis,slvec,PETSC_NULL,&(*lscat)[0]);CHKERRQ(ierr);} 255 256 ierr = DMRestoreGlobalVector(dm,&dvec);CHKERRQ(ierr); 257 ierr = DMRestoreGlobalVector(subdm,&svec);CHKERRQ(ierr); 258 ierr = DMRestoreLocalVector(subdm,&slvec);CHKERRQ(ierr); 259 260 ierr = ISDestroy(&idis);CHKERRQ(ierr); 261 ierr = ISDestroy(&isis);CHKERRQ(ierr); 262 263 ierr = ISDestroy(&odis);CHKERRQ(ierr); 264 ierr = ISDestroy(&osis);CHKERRQ(ierr); 265 266 ierr = ISDestroy(&gdis);CHKERRQ(ierr); 267 PetscFunctionReturn(0); 268 } 269 270 #undef __FUNCT__ 271 #define __FUNCT__ "DMDASubDomainIS_Private" 272 /* We have that the interior regions are going to be the same, but the ghost regions might not match up 273 274 ---------- 275 ---------- 276 --++++++o= 277 --++++++o= 278 --++++++o= 279 --++++++o= 280 --ooooooo= 281 --======== 282 283 Therefore, for each point in the overall, we must check if it's: 284 285 1. +: In the interior of the global dm; it lines up 286 2. o: In the overlap region -- for now the same as 1; no overlap 287 3. =: In the shared ghost region -- handled by DMCreateDomainDecompositionLocalScatter() 288 4. -: In the nonshared ghost region 289 */ 290 291 PetscErrorCode DMDASubDomainIS_Private(DM dm,DM subdm,IS *iis,IS *ois) 292 { 293 PetscErrorCode ierr; 294 DMDALocalInfo info,subinfo; 295 MatStencil lower,upper; 296 297 PetscFunctionBegin; 298 ierr = DMDAGetLocalInfo(dm,&info);CHKERRQ(ierr); 299 ierr = DMDAGetLocalInfo(subdm,&subinfo);CHKERRQ(ierr); 300 301 /* create the inner IS */ 302 lower.i = info.xs; 303 lower.j = info.ys; 304 lower.k = info.zs; 305 upper.i = info.xs+info.xm; 306 upper.j = info.ys+info.ym; 307 upper.k = info.zs+info.zm; 308 309 ierr = DMDACreatePatchIS(dm,&lower,&upper,iis);CHKERRQ(ierr); 310 311 /* create the outer IS */ 312 lower.i = subinfo.xs; 313 lower.j = subinfo.ys; 314 lower.k = subinfo.zs; 315 upper.i = subinfo.xs+subinfo.xm; 316 upper.j = subinfo.ys+subinfo.ym; 317 upper.k = subinfo.zs+subinfo.zm; 318 ierr = DMDACreatePatchIS(dm,&lower,&upper,ois);CHKERRQ(ierr); 319 PetscFunctionReturn(0); 320 } 321 322 #undef __FUNCT__ 323 #define __FUNCT__ "DMCreateDomainDecomposition_DA" 324 PetscErrorCode DMCreateDomainDecomposition_DA(DM dm,PetscInt *len,char ***names,IS **iis,IS **ois,DM **subdm) 325 { 326 PetscErrorCode ierr; 327 IS iis0,ois0; 328 DM subdm0; 329 DM_DA *dd = (DM_DA*)dm; 330 331 PetscFunctionBegin; 332 /* fix to enable PCASM default behavior as taking overlap from the matrix */ 333 if (!dd->decompositiondm) { 334 if (len)*len=0; 335 if (names)*names=0; 336 if (iis)*iis=0; 337 if (ois)*ois=0; 338 if (subdm)*subdm=0; 339 PetscFunctionReturn(0); 340 } 341 342 if (len)*len = 1; 343 344 if (iis) {ierr = PetscMalloc(sizeof(IS *),iis);CHKERRQ(ierr);} 345 if (ois) {ierr = PetscMalloc(sizeof(IS *),ois);CHKERRQ(ierr);} 346 if (subdm) {ierr = PetscMalloc(sizeof(DM *),subdm);CHKERRQ(ierr);} 347 if (names) {ierr = PetscMalloc(sizeof(char *),names);CHKERRQ(ierr);} 348 ierr = DMDASubDomainDA_Private(dm,&subdm0);CHKERRQ(ierr); 349 ierr = DMDASubDomainIS_Private(dm,subdm0,&iis0,&ois0);CHKERRQ(ierr); 350 if (iis) { 351 (*iis)[0] = iis0; 352 } else { 353 ierr = ISDestroy(&iis0);CHKERRQ(ierr); 354 } 355 if (ois) { 356 (*ois)[0] = ois0; 357 } else { 358 ierr = ISDestroy(&ois0);CHKERRQ(ierr); 359 } 360 if (subdm) (*subdm)[0] = subdm0; 361 if (names) (*names)[0] = 0; 362 PetscFunctionReturn(0); 363 } 364 365 #undef __FUNCT__ 366 #define __FUNCT__ "DMCreateDomainDecompositionDM_DA" 367 PetscErrorCode DMCreateDomainDecompositionDM_DA(DM dm,const char *name,DM *ddm) 368 { 369 DM_DA *dd = (DM_DA*)dm; 370 PetscBool flg; 371 PetscErrorCode ierr; 372 373 PetscFunctionBegin; 374 ierr = PetscStrcmp(name,"default",&flg);CHKERRQ(ierr); 375 if (flg) { 376 dd->decompositiondm = PETSC_TRUE; 377 *ddm = dm; 378 } else { 379 dd->decompositiondm = PETSC_FALSE; 380 } 381 PetscFunctionReturn(0); 382 } 383