1 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 #include <parmmg/libparmmg.h> 3 4 PETSC_EXTERN PetscErrorCode DMAdaptMetric_ParMmg_Plex(DM dm, Vec vertexMetric, DMLabel bdLabel, DM *dmNew) 5 { 6 MPI_Comm comm, tmpComm; 7 const char *bdName = "_boundary_"; 8 DM udm, cdm; 9 DMLabel bdLabelFull; 10 const char *bdLabelName; 11 IS bdIS, globalVertexNum; 12 PetscSection coordSection; 13 Vec coordinates; 14 PetscSF sf; 15 const PetscScalar *coords, *met; 16 const PetscInt *bdFacesFull; 17 PetscInt *bdFaces, *bdFaceIds; 18 PetscReal *vertices, *metric, *verticesNew; 19 PetscInt *cells; 20 const PetscInt *gV, *ioffset, *irootloc, *roffset, *rmine, *rremote; 21 PetscInt *numVerInterfaces, *ngbRanks, *verNgbRank, *interfaces_lv, *interfaces_gv, *intOffset; 22 PetscInt niranks, nrranks, numNgbRanks, numVerNgbRanksTotal, count, sliceSize; 23 PetscInt *verTags, *cellTags; 24 PetscInt dim, Neq, cStart, cEnd, numCells, coff, vStart, vEnd, numVertices; 25 PetscInt maxConeSize, numBdFaces, bdSize, fStart, fEnd; 26 PetscBool flg, noInsert, noSwap, noMove; 27 DMLabel bdLabelNew; 28 PetscReal *verticesNewLoc, gradationFactor; 29 PetscInt *verTagsNew, *cellsNew, *cellTagsNew, *corners; 30 PetscInt *requiredCells, *requiredVer, *facesNew, *faceTagsNew, *ridges, *requiredFaces; 31 PetscInt *gv_new, *owners, *verticesNewSorted; 32 PetscInt numCellsNew, numVerticesNew, numCornersNew, numFacesNew, numVerticesNewLoc; 33 PetscInt i, j, k, p, r, n, v, c, f, off, lv, gv; 34 PetscInt verbosity, numIter; 35 const PetscMPIInt *iranks, *rranks; 36 PetscMPIInt numProcs, rank; 37 PMMG_pParMesh parmesh = NULL; 38 PetscErrorCode ierr; 39 40 PetscFunctionBegin; 41 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 42 ierr = MPI_Comm_size(comm, &numProcs);CHKERRMPI(ierr); 43 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 44 ierr = MPI_Comm_dup(comm, &tmpComm);CHKERRMPI(ierr); 45 if (bdLabel) { 46 ierr = PetscObjectGetName((PetscObject) bdLabel, &bdLabelName);CHKERRQ(ierr); 47 ierr = PetscStrcmp(bdLabelName, bdName, &flg);CHKERRQ(ierr); 48 if (flg) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "\"%s\" cannot be used as label for boundary facets", bdLabelName); 49 } 50 51 /* Get mesh information */ 52 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 53 if (dim != 3) SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "ParMmg only works in 3D.\n"); 54 Neq = (dim*(dim+1))/2; 55 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 56 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 57 ierr = DMPlexUninterpolate(dm, &udm);CHKERRQ(ierr); 58 ierr = DMPlexGetMaxSizes(udm, &maxConeSize, NULL);CHKERRQ(ierr); 59 numCells = cEnd - cStart; 60 numVertices = vEnd - vStart; 61 62 /* Get cell offsets */ 63 ierr = PetscMalloc1(numCells*maxConeSize, &cells);CHKERRQ(ierr); 64 for (c = 0, coff = 0; c < numCells; ++c) { 65 const PetscInt *cone; 66 PetscInt coneSize, cl; 67 68 ierr = DMPlexGetConeSize(udm, c, &coneSize);CHKERRQ(ierr); 69 ierr = DMPlexGetCone(udm, c, &cone);CHKERRQ(ierr); 70 for (cl = 0; cl < coneSize; ++cl) cells[coff++] = cone[cl] - vStart+1; 71 } 72 73 /* Get vertex coordinate array */ 74 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 75 ierr = DMGetLocalSection(cdm, &coordSection);CHKERRQ(ierr); 76 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 77 ierr = VecGetArrayRead(coordinates, &coords);CHKERRQ(ierr); 78 ierr = PetscMalloc2(numVertices*Neq, &metric, dim*numVertices, &vertices);CHKERRQ(ierr); 79 for (v = 0; v < vEnd-vStart; ++v) { 80 ierr = PetscSectionGetOffset(coordSection, v+vStart, &off);CHKERRQ(ierr); 81 for (i = 0; i < dim; ++i) vertices[dim*v+i] = PetscRealPart(coords[off+i]); 82 } 83 ierr = VecRestoreArrayRead(coordinates, &coords);CHKERRQ(ierr); 84 85 /* Get boundary mesh */ 86 ierr = DMLabelCreate(PETSC_COMM_SELF, bdName, &bdLabelFull);CHKERRQ(ierr); 87 ierr = DMPlexMarkBoundaryFaces(dm, 1, bdLabelFull);CHKERRQ(ierr); 88 ierr = DMLabelGetStratumIS(bdLabelFull, 1, &bdIS);CHKERRQ(ierr); 89 ierr = DMLabelGetStratumSize(bdLabelFull, 1, &numBdFaces);CHKERRQ(ierr); 90 ierr = ISGetIndices(bdIS, &bdFacesFull);CHKERRQ(ierr); 91 for (f = 0, bdSize = 0; f < numBdFaces; ++f) { 92 PetscInt *closure = NULL; 93 PetscInt closureSize, cl; 94 95 ierr = DMPlexGetTransitiveClosure(dm, bdFacesFull[f], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 96 for (cl = 0; cl < closureSize*2; cl += 2) { 97 if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) ++bdSize; 98 } 99 ierr = DMPlexRestoreTransitiveClosure(dm, bdFacesFull[f], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 100 } 101 ierr = PetscMalloc2(bdSize, &bdFaces, numBdFaces, &bdFaceIds);CHKERRQ(ierr); 102 for (f = 0, bdSize = 0; f < numBdFaces; ++f) { 103 PetscInt *closure = NULL; 104 PetscInt closureSize, cl; 105 106 ierr = DMPlexGetTransitiveClosure(dm, bdFacesFull[f], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 107 for (cl = 0; cl < closureSize*2; cl += 2) { 108 if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) bdFaces[bdSize++] = closure[cl] - vStart+1; 109 } 110 ierr = DMPlexRestoreTransitiveClosure(dm, bdFacesFull[f], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 111 if (bdLabel) {ierr = DMLabelGetValue(bdLabel, bdFacesFull[f], &bdFaceIds[f]);CHKERRQ(ierr);} 112 else {bdFaceIds[f] = 1;} 113 } 114 ierr = ISDestroy(&bdIS);CHKERRQ(ierr); 115 ierr = DMLabelDestroy(&bdLabelFull);CHKERRQ(ierr); 116 117 /* Get metric */ 118 ierr = VecViewFromOptions(vertexMetric, NULL, "-adapt_metric_view");CHKERRQ(ierr); 119 ierr = VecGetArrayRead(vertexMetric, &met);CHKERRQ(ierr); 120 for (v = 0; v < (vEnd-vStart); ++v) { 121 for (i = 0, k = 0; i < dim; ++i) { 122 for (j = i; j < dim; ++j) { 123 metric[Neq*v+k] = PetscRealPart(met[dim*dim*v+dim*i+j]); 124 k++; 125 } 126 } 127 } 128 ierr = VecRestoreArrayRead(vertexMetric, &met);CHKERRQ(ierr); 129 130 /* Build ParMMG communicators: the list of vertices between two partitions */ 131 niranks = nrranks = 0; 132 numNgbRanks = 0; 133 if (numProcs > 1) { 134 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 135 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 136 ierr = PetscSFGetLeafRanks(sf, &niranks, &iranks, &ioffset, &irootloc);CHKERRQ(ierr); 137 ierr = PetscSFGetRootRanks(sf, &nrranks, &rranks, &roffset, &rmine, &rremote);CHKERRQ(ierr); 138 ierr = PetscCalloc1(numProcs, &numVerInterfaces);CHKERRQ(ierr); 139 140 /* Counting */ 141 for (r = 0; r < niranks; ++r) { 142 for (i=ioffset[r], count=0; i<ioffset[r+1]; ++i) { 143 if (irootloc[i] >= vStart && irootloc[i] < vEnd) count++; 144 } 145 numVerInterfaces[iranks[r]] += count; 146 } 147 for (r = 0; r < nrranks; ++r) { 148 for (i=roffset[r], count=0; i<roffset[r+1]; ++i) { 149 if (rmine[i] >= vStart && rmine[i] < vEnd) count++; 150 } 151 numVerInterfaces[rranks[r]] += count; 152 } 153 for (p = 0; p < numProcs; ++p) { 154 if (numVerInterfaces[p]) numNgbRanks++; 155 } 156 ierr = PetscMalloc2(numNgbRanks, &ngbRanks, numNgbRanks, &verNgbRank);CHKERRQ(ierr); 157 for (p = 0, n = 0; p < numProcs; ++p) { 158 if (numVerInterfaces[p]) { 159 ngbRanks[n] = p; 160 verNgbRank[n] = numVerInterfaces[p]; 161 n++; 162 } 163 } 164 numVerNgbRanksTotal = 0; 165 for (p = 0; p < numNgbRanks; ++p) numVerNgbRanksTotal += verNgbRank[p]; 166 167 /* For each neighbor, fill in interface arrays */ 168 ierr = PetscMalloc3(numVerNgbRanksTotal, &interfaces_lv, numVerNgbRanksTotal, &interfaces_gv, numNgbRanks+1, &intOffset);CHKERRQ(ierr); 169 intOffset[0] = 0; 170 for (p = 0, r = 0, i = 0; p < numNgbRanks; ++p) { 171 intOffset[p+1] = intOffset[p]; 172 if (iranks && iranks[i] == ngbRanks[p]) { 173 174 /* Add the right slice of irootloc at the right place */ 175 sliceSize = ioffset[i+1]-ioffset[i]; 176 for (j = 0, count = 0; j < sliceSize; ++j) { 177 if (ioffset[i]+j >= ioffset[niranks]) SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Offset out of range"); 178 v = irootloc[ioffset[i]+j]; 179 if (v >= vStart && v < vEnd) { 180 if (intOffset[p+1]+count >= numVerNgbRanksTotal) SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Offset out of range"); 181 interfaces_lv[intOffset[p+1]+count] = v-vStart; 182 count++; 183 } 184 } 185 intOffset[p+1] += count; 186 i++; 187 } 188 if (rranks && rranks[r] == ngbRanks[p]) { 189 190 /* Add the right slice of rmine at the right place */ 191 sliceSize = roffset[r+1]-roffset[r]; 192 for (j = 0, count = 0; j < sliceSize; ++j) { 193 if (roffset[r]+j >= roffset[nrranks]) SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Offset out of range"); 194 v = rmine[roffset[r]+j]; 195 if (v >= vStart && v < vEnd) { 196 if (intOffset[p+1]+count >= numVerNgbRanksTotal) SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Offset out of range"); 197 interfaces_lv[intOffset[p+1]+count] = v-vStart; 198 count++; 199 } 200 } 201 intOffset[p+1] += count; 202 r++; 203 } 204 if (intOffset[p+1] != intOffset[p] + verNgbRank[p]) SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Unequal offsets"); 205 } 206 ierr = DMPlexGetVertexNumbering(udm, &globalVertexNum);CHKERRQ(ierr); 207 ierr = ISGetIndices(globalVertexNum, &gV);CHKERRQ(ierr); 208 for (i = 0; i < numVerNgbRanksTotal; ++i) { 209 v = gV[interfaces_lv[i]]; 210 interfaces_gv[i] = v < 0 ? -v-1 : v; 211 interfaces_lv[i] += 1; 212 interfaces_gv[i] += 1; 213 } 214 ierr = ISRestoreIndices(globalVertexNum, &gV);CHKERRQ(ierr); 215 ierr = PetscFree(numVerInterfaces);CHKERRQ(ierr); 216 } 217 ierr = DMDestroy(&udm);CHKERRQ(ierr); 218 219 /* Send the data to ParMmg and remesh */ 220 ierr = DMPlexMetricNoInsertion(dm, &noInsert);CHKERRQ(ierr); 221 ierr = DMPlexMetricNoSwapping(dm, &noSwap);CHKERRQ(ierr); 222 ierr = DMPlexMetricNoMovement(dm, &noMove);CHKERRQ(ierr); 223 ierr = DMPlexMetricGetVerbosity(dm, &verbosity);CHKERRQ(ierr); 224 ierr = DMPlexMetricGetNumIterations(dm, &numIter);CHKERRQ(ierr); 225 ierr = DMPlexMetricGetGradationFactor(dm, &gradationFactor);CHKERRQ(ierr); 226 ierr = PetscCalloc2(numVertices, &verTags, numCells, &cellTags);CHKERRQ(ierr); 227 ierr = PMMG_Init_parMesh(PMMG_ARG_start, PMMG_ARG_ppParMesh, &parmesh, PMMG_ARG_pMesh, PMMG_ARG_pMet, PMMG_ARG_dim, 3, PMMG_ARG_MPIComm, tmpComm, PMMG_ARG_end); 228 ierr = PMMG_Set_meshSize(parmesh, numVertices, numCells, 0, numBdFaces, 0, 0); 229 ierr = PMMG_Set_iparameter(parmesh, PMMG_IPARAM_APImode, PMMG_APIDISTRIB_nodes); 230 ierr = PMMG_Set_iparameter(parmesh, PMMG_IPARAM_noinsert, noInsert); 231 ierr = PMMG_Set_iparameter(parmesh, PMMG_IPARAM_noswap, noSwap); 232 ierr = PMMG_Set_iparameter(parmesh, PMMG_IPARAM_nomove, noMove); 233 ierr = PMMG_Set_iparameter(parmesh, PMMG_IPARAM_verbose, verbosity); 234 ierr = PMMG_Set_iparameter(parmesh, PMMG_IPARAM_globalNum, 1); 235 ierr = PMMG_Set_iparameter(parmesh, PMMG_IPARAM_niter, numIter); 236 ierr = PMMG_Set_dparameter(parmesh, PMMG_DPARAM_hgrad, gradationFactor); 237 ierr = PMMG_Set_vertices(parmesh, vertices, verTags); 238 for (i=0; i<numCells; i++) ierr = PMMG_Set_tetrahedron(parmesh, cells[4*i+0], cells[4*i+1], cells[4*i+2], cells[4*i+3], 0, i+1); 239 ierr = PMMG_Set_triangles(parmesh, bdFaces, bdFaceIds); 240 ierr = PMMG_Set_metSize(parmesh, MMG5_Vertex, numVertices, MMG5_Tensor); 241 for (i=0; i<numVertices; i++) { 242 PMMG_Set_tensorMet(parmesh, metric[6*i], metric[6*i+1], metric[6*i+2], metric[6*i+3], metric[6*i+4], metric[6*i+5], i+1); 243 } 244 ierr = PMMG_Set_numberOfNodeCommunicators(parmesh, numNgbRanks); 245 for (c = 0; c < numNgbRanks; ++c) { 246 ierr = PMMG_Set_ithNodeCommunicatorSize(parmesh, c, ngbRanks[c], intOffset[c+1]-intOffset[c]); 247 ierr = PMMG_Set_ithNodeCommunicator_nodes(parmesh, c, &interfaces_lv[intOffset[c]], &interfaces_gv[intOffset[c]], 1); 248 } 249 ierr = PMMG_parmmglib_distributed(parmesh); 250 ierr = PetscFree(cells);CHKERRQ(ierr); 251 ierr = PetscFree2(metric, vertices);CHKERRQ(ierr); 252 ierr = PetscFree2(bdFaces, bdFaceIds);CHKERRQ(ierr); 253 ierr = PetscFree2(verTags, cellTags);CHKERRQ(ierr); 254 if (numProcs > 1) { 255 ierr = PetscFree2(ngbRanks, verNgbRank);CHKERRQ(ierr); 256 ierr = PetscFree3(interfaces_lv, interfaces_gv, intOffset);CHKERRQ(ierr); 257 } 258 259 /* Retrieve mesh from Mmg and create new Plex */ 260 numCornersNew = 4; 261 ierr = PMMG_Get_meshSize(parmesh, &numVerticesNew, &numCellsNew, 0, &numFacesNew, 0, 0); 262 ierr = PetscMalloc4(dim*numVerticesNew, &verticesNew, numVerticesNew, &verTagsNew, numVerticesNew, &corners, numVerticesNew, &requiredVer);CHKERRQ(ierr); 263 ierr = PetscMalloc3((dim+1)*numCellsNew, &cellsNew, numCellsNew, &cellTagsNew, numCellsNew, &requiredCells);CHKERRQ(ierr); 264 ierr = PetscMalloc4(dim*numFacesNew, &facesNew, numFacesNew, &faceTagsNew, numFacesNew, &ridges, numFacesNew, &requiredFaces);CHKERRQ(ierr); 265 ierr = PMMG_Get_vertices(parmesh, verticesNew, verTagsNew, corners, requiredVer); 266 ierr = PMMG_Get_tetrahedra(parmesh, cellsNew, cellTagsNew, requiredCells); 267 ierr = PMMG_Get_triangles(parmesh, facesNew, faceTagsNew, requiredFaces); 268 ierr = PetscMalloc2(numVerticesNew, &owners, numVerticesNew, &gv_new); 269 ierr = PMMG_Set_iparameter(parmesh, PMMG_IPARAM_globalNum, 1); 270 ierr = PMMG_Get_verticesGloNum(parmesh, gv_new, owners); 271 for (i = 0; i < dim*numFacesNew; ++i) facesNew[i] -= 1; 272 for (i = 0; i < (dim+1)*numCellsNew; ++i) { 273 cellsNew[i] = gv_new[cellsNew[i]-1]-1; 274 } 275 numVerticesNewLoc = 0; 276 for (i = 0; i < numVerticesNew; ++i) { 277 if (owners[i] == rank) numVerticesNewLoc++; 278 } 279 ierr = PetscMalloc2(numVerticesNewLoc*dim, &verticesNewLoc, numVerticesNew, &verticesNewSorted);CHKERRQ(ierr); 280 for (i = 0, c = 0; i < numVerticesNew; i++) { 281 if (owners[i] == rank) { 282 for (j=0; j<dim; ++j) verticesNewLoc[dim*c+j] = verticesNew[dim*i+j]; 283 c++; 284 } 285 } 286 ierr = DMPlexCreateFromCellListParallelPetsc(comm, dim, numCellsNew, numVerticesNewLoc, PETSC_DECIDE, numCornersNew, PETSC_TRUE, cellsNew, dim, verticesNewLoc, NULL, &verticesNewSorted, dmNew);CHKERRQ(ierr); 287 ierr = PMMG_Free_all(PMMG_ARG_start, PMMG_ARG_ppParMesh, &parmesh, PMMG_ARG_end); 288 289 /* Rebuild boundary label*/ 290 ierr = DMPlexGetHeightStratum(*dmNew, 1, &fStart, &fEnd);CHKERRQ(ierr); 291 ierr = DMPlexGetHeightStratum(*dmNew, 0, &cStart, &cEnd);CHKERRQ(ierr); 292 ierr = DMPlexGetDepthStratum(*dmNew, 0, &vStart, &vEnd);CHKERRQ(ierr); 293 ierr = DMCreateLabel(*dmNew, bdLabel ? bdLabelName : bdName);CHKERRQ(ierr); 294 ierr = DMGetLabel(*dmNew, bdLabel ? bdLabelName : bdName, &bdLabelNew);CHKERRQ(ierr); 295 for (i = 0; i < numFacesNew; i++) { 296 PetscInt numCoveredPoints, numFaces = 0, facePoints[3]; 297 const PetscInt *coveredPoints = NULL; 298 299 for (j = 0; j < dim; ++j) { 300 lv = facesNew[i*dim+j]; 301 gv = gv_new[lv]-1; 302 ierr = PetscFindInt(gv, numVerticesNew, verticesNewSorted, &lv);CHKERRQ(ierr); 303 facePoints[j] = lv+vStart; 304 } 305 ierr = DMPlexGetFullJoin(*dmNew, dim, facePoints, &numCoveredPoints, &coveredPoints);CHKERRQ(ierr); 306 for (j = 0; j < numCoveredPoints; ++j) { 307 if (coveredPoints[j] >= fStart && coveredPoints[j] < fEnd) { 308 numFaces++; 309 f = j; 310 } 311 } 312 if (numFaces != 1) SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "%d vertices cannot define more than 1 facet (%d)", dim, numFaces); 313 ierr = DMLabelSetValue(bdLabelNew, coveredPoints[f], faceTagsNew[i]);CHKERRQ(ierr); 314 ierr = DMPlexRestoreJoin(*dmNew, dim, facePoints, &numCoveredPoints, &coveredPoints);CHKERRQ(ierr); 315 } 316 317 /* Clean up */ 318 ierr = PetscFree4(verticesNew, verTagsNew, corners, requiredVer);CHKERRQ(ierr); 319 ierr = PetscFree3(cellsNew, cellTagsNew, requiredCells);CHKERRQ(ierr); 320 ierr = PetscFree4(facesNew, faceTagsNew, ridges, requiredFaces);CHKERRQ(ierr); 321 ierr = PetscFree2(owners, gv_new);CHKERRQ(ierr); 322 ierr = PetscFree2(verticesNewLoc, verticesNewSorted);CHKERRQ(ierr); 323 PetscFunctionReturn(0); 324 } 325