1 2 /* 3 Plots vectors obtained with DMDACreate2d() 4 */ 5 6 #include <petsc/private/dmdaimpl.h> /*I "petscdmda.h" I*/ 7 #include <petsc/private/glvisvecimpl.h> 8 #include <petscdraw.h> 9 #include <petscviewerhdf5.h> 10 11 /* 12 The data that is passed into the graphics callback 13 */ 14 typedef struct { 15 PetscMPIInt rank; 16 PetscInt m,n,dof,k; 17 PetscReal xmin,xmax,ymin,ymax,min,max; 18 const PetscScalar *xy,*v; 19 PetscBool showaxis,showgrid; 20 const char *name0,*name1; 21 } ZoomCtx; 22 23 /* 24 This does the drawing for one particular field 25 in one particular set of coordinates. It is a callback 26 called from PetscDrawZoom() 27 */ 28 PetscErrorCode VecView_MPI_Draw_DA2d_Zoom(PetscDraw draw,void *ctx) 29 { 30 ZoomCtx *zctx = (ZoomCtx*)ctx; 31 PetscErrorCode ierr; 32 PetscInt m,n,i,j,k,dof,id,c1,c2,c3,c4; 33 PetscReal min,max,x1,x2,x3,x4,y_1,y2,y3,y4; 34 const PetscScalar *xy,*v; 35 36 PetscFunctionBegin; 37 m = zctx->m; 38 n = zctx->n; 39 dof = zctx->dof; 40 k = zctx->k; 41 xy = zctx->xy; 42 v = zctx->v; 43 min = zctx->min; 44 max = zctx->max; 45 46 /* PetscDraw the contour plot patch */ 47 ierr = PetscDrawCollectiveBegin(draw);CHKERRQ(ierr); 48 for (j=0; j<n-1; j++) { 49 for (i=0; i<m-1; i++) { 50 id = i+j*m; 51 x1 = PetscRealPart(xy[2*id]); 52 y_1 = PetscRealPart(xy[2*id+1]); 53 c1 = PetscDrawRealToColor(PetscRealPart(v[k+dof*id]),min,max); 54 55 id = i+j*m+1; 56 x2 = PetscRealPart(xy[2*id]); 57 y2 = PetscRealPart(xy[2*id+1]); 58 c2 = PetscDrawRealToColor(PetscRealPart(v[k+dof*id]),min,max); 59 60 id = i+j*m+1+m; 61 x3 = PetscRealPart(xy[2*id]); 62 y3 = PetscRealPart(xy[2*id+1]); 63 c3 = PetscDrawRealToColor(PetscRealPart(v[k+dof*id]),min,max); 64 65 id = i+j*m+m; 66 x4 = PetscRealPart(xy[2*id]); 67 y4 = PetscRealPart(xy[2*id+1]); 68 c4 = PetscDrawRealToColor(PetscRealPart(v[k+dof*id]),min,max); 69 70 ierr = PetscDrawTriangle(draw,x1,y_1,x2,y2,x3,y3,c1,c2,c3);CHKERRQ(ierr); 71 ierr = PetscDrawTriangle(draw,x1,y_1,x3,y3,x4,y4,c1,c3,c4);CHKERRQ(ierr); 72 if (zctx->showgrid) { 73 ierr = PetscDrawLine(draw,x1,y_1,x2,y2,PETSC_DRAW_BLACK);CHKERRQ(ierr); 74 ierr = PetscDrawLine(draw,x2,y2,x3,y3,PETSC_DRAW_BLACK);CHKERRQ(ierr); 75 ierr = PetscDrawLine(draw,x3,y3,x4,y4,PETSC_DRAW_BLACK);CHKERRQ(ierr); 76 ierr = PetscDrawLine(draw,x4,y4,x1,y_1,PETSC_DRAW_BLACK);CHKERRQ(ierr); 77 } 78 } 79 } 80 if (zctx->showaxis && !zctx->rank) { 81 if (zctx->name0 || zctx->name1) { 82 PetscReal xl,yl,xr,yr,x,y; 83 ierr = PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);CHKERRQ(ierr); 84 x = xl + .30*(xr - xl); 85 xl = xl + .01*(xr - xl); 86 y = yr - .30*(yr - yl); 87 yl = yl + .01*(yr - yl); 88 if (zctx->name0) {ierr = PetscDrawString(draw,x,yl,PETSC_DRAW_BLACK,zctx->name0);CHKERRQ(ierr);} 89 if (zctx->name1) {ierr = PetscDrawStringVertical(draw,xl,y,PETSC_DRAW_BLACK,zctx->name1);CHKERRQ(ierr);} 90 } 91 /* 92 Ideally we would use the PetscDrawAxis object to manage displaying the coordinate limits 93 but that may require some refactoring. 94 */ 95 { 96 double xmin = (double)zctx->xmin, ymin = (double)zctx->ymin; 97 double xmax = (double)zctx->xmax, ymax = (double)zctx->ymax; 98 char value[16]; size_t len; PetscReal w; 99 ierr = PetscSNPrintf(value,16,"%0.2e",xmin);CHKERRQ(ierr); 100 ierr = PetscDrawString(draw,xmin,ymin - .05*(ymax - ymin),PETSC_DRAW_BLACK,value);CHKERRQ(ierr); 101 ierr = PetscSNPrintf(value,16,"%0.2e",xmax);CHKERRQ(ierr); 102 ierr = PetscStrlen(value,&len);CHKERRQ(ierr); 103 ierr = PetscDrawStringGetSize(draw,&w,NULL);CHKERRQ(ierr); 104 ierr = PetscDrawString(draw,xmax - len*w,ymin - .05*(ymax - ymin),PETSC_DRAW_BLACK,value);CHKERRQ(ierr); 105 ierr = PetscSNPrintf(value,16,"%0.2e",ymin);CHKERRQ(ierr); 106 ierr = PetscDrawString(draw,xmin - .05*(xmax - xmin),ymin,PETSC_DRAW_BLACK,value);CHKERRQ(ierr); 107 ierr = PetscSNPrintf(value,16,"%0.2e",ymax);CHKERRQ(ierr); 108 ierr = PetscDrawString(draw,xmin - .05*(xmax - xmin),ymax,PETSC_DRAW_BLACK,value);CHKERRQ(ierr); 109 } 110 } 111 ierr = PetscDrawCollectiveEnd(draw);CHKERRQ(ierr); 112 PetscFunctionReturn(0); 113 } 114 115 PetscErrorCode VecView_MPI_Draw_DA2d(Vec xin,PetscViewer viewer) 116 { 117 DM da,dac,dag; 118 PetscErrorCode ierr; 119 PetscInt N,s,M,w,ncoors = 4; 120 const PetscInt *lx,*ly; 121 PetscReal coors[4]; 122 PetscDraw draw,popup; 123 PetscBool isnull,useports = PETSC_FALSE; 124 MPI_Comm comm; 125 Vec xlocal,xcoor,xcoorl; 126 DMBoundaryType bx,by; 127 DMDAStencilType st; 128 ZoomCtx zctx; 129 PetscDrawViewPorts *ports = NULL; 130 PetscViewerFormat format; 131 PetscInt *displayfields; 132 PetscInt ndisplayfields,i,nbounds; 133 const PetscReal *bounds; 134 135 PetscFunctionBegin; 136 zctx.showgrid = PETSC_FALSE; 137 zctx.showaxis = PETSC_TRUE; 138 139 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 140 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); 141 if (isnull) PetscFunctionReturn(0); 142 143 ierr = PetscViewerDrawGetBounds(viewer,&nbounds,&bounds);CHKERRQ(ierr); 144 145 ierr = VecGetDM(xin,&da);CHKERRQ(ierr); 146 if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA"); 147 148 ierr = PetscObjectGetComm((PetscObject)xin,&comm);CHKERRQ(ierr); 149 ierr = MPI_Comm_rank(comm,&zctx.rank);CHKERRQ(ierr); 150 151 ierr = DMDAGetInfo(da,0,&M,&N,0,&zctx.m,&zctx.n,0,&w,&s,&bx,&by,0,&st);CHKERRQ(ierr); 152 ierr = DMDAGetOwnershipRanges(da,&lx,&ly,NULL);CHKERRQ(ierr); 153 154 /* 155 Obtain a sequential vector that is going to contain the local values plus ONE layer of 156 ghosted values to draw the graphics from. We also need its corresponding DMDA (dac) that will 157 update the local values pluse ONE layer of ghost values. 158 */ 159 ierr = PetscObjectQuery((PetscObject)da,"GraphicsGhosted",(PetscObject*)&xlocal);CHKERRQ(ierr); 160 if (!xlocal) { 161 if (bx != DM_BOUNDARY_NONE || by != DM_BOUNDARY_NONE || s != 1 || st != DMDA_STENCIL_BOX) { 162 /* 163 if original da is not of stencil width one, or periodic or not a box stencil then 164 create a special DMDA to handle one level of ghost points for graphics 165 */ 166 ierr = DMDACreate2d(comm,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,N,zctx.m,zctx.n,w,1,lx,ly,&dac);CHKERRQ(ierr); 167 ierr = DMSetUp(dac);CHKERRQ(ierr); 168 ierr = PetscInfo(da,"Creating auxilary DMDA for managing graphics ghost points\n");CHKERRQ(ierr); 169 } else { 170 /* otherwise we can use the da we already have */ 171 dac = da; 172 } 173 /* create local vector for holding ghosted values used in graphics */ 174 ierr = DMCreateLocalVector(dac,&xlocal);CHKERRQ(ierr); 175 if (dac != da) { 176 /* don't keep any public reference of this DMDA, is is only available through xlocal */ 177 ierr = PetscObjectDereference((PetscObject)dac);CHKERRQ(ierr); 178 } else { 179 /* remove association between xlocal and da, because below we compose in the opposite 180 direction and if we left this connect we'd get a loop, so the objects could 181 never be destroyed */ 182 ierr = PetscObjectRemoveReference((PetscObject)xlocal,"__PETSc_dm");CHKERRQ(ierr); 183 } 184 ierr = PetscObjectCompose((PetscObject)da,"GraphicsGhosted",(PetscObject)xlocal);CHKERRQ(ierr); 185 ierr = PetscObjectDereference((PetscObject)xlocal);CHKERRQ(ierr); 186 } else { 187 if (bx != DM_BOUNDARY_NONE || by != DM_BOUNDARY_NONE || s != 1 || st != DMDA_STENCIL_BOX) { 188 ierr = VecGetDM(xlocal, &dac);CHKERRQ(ierr); 189 } else { 190 dac = da; 191 } 192 } 193 194 /* 195 Get local (ghosted) values of vector 196 */ 197 ierr = DMGlobalToLocalBegin(dac,xin,INSERT_VALUES,xlocal);CHKERRQ(ierr); 198 ierr = DMGlobalToLocalEnd(dac,xin,INSERT_VALUES,xlocal);CHKERRQ(ierr); 199 ierr = VecGetArrayRead(xlocal,&zctx.v);CHKERRQ(ierr); 200 201 /* 202 Get coordinates of nodes 203 */ 204 ierr = DMGetCoordinates(da,&xcoor);CHKERRQ(ierr); 205 if (!xcoor) { 206 ierr = DMDASetUniformCoordinates(da,0.0,1.0,0.0,1.0,0.0,0.0);CHKERRQ(ierr); 207 ierr = DMGetCoordinates(da,&xcoor);CHKERRQ(ierr); 208 } 209 210 /* 211 Determine the min and max coordinates in plot 212 */ 213 ierr = VecStrideMin(xcoor,0,NULL,&zctx.xmin);CHKERRQ(ierr); 214 ierr = VecStrideMax(xcoor,0,NULL,&zctx.xmax);CHKERRQ(ierr); 215 ierr = VecStrideMin(xcoor,1,NULL,&zctx.ymin);CHKERRQ(ierr); 216 ierr = VecStrideMax(xcoor,1,NULL,&zctx.ymax);CHKERRQ(ierr); 217 ierr = PetscOptionsGetBool(NULL,NULL,"-draw_contour_axis",&zctx.showaxis,NULL);CHKERRQ(ierr); 218 if (zctx.showaxis) { 219 coors[0] = zctx.xmin - .05*(zctx.xmax - zctx.xmin); coors[1] = zctx.ymin - .05*(zctx.ymax - zctx.ymin); 220 coors[2] = zctx.xmax + .05*(zctx.xmax - zctx.xmin); coors[3] = zctx.ymax + .05*(zctx.ymax - zctx.ymin); 221 } else { 222 coors[0] = zctx.xmin; coors[1] = zctx.ymin; coors[2] = zctx.xmax; coors[3] = zctx.ymax; 223 } 224 ierr = PetscOptionsGetRealArray(NULL,NULL,"-draw_coordinates",coors,&ncoors,NULL);CHKERRQ(ierr); 225 ierr = PetscInfo4(da,"Preparing DMDA 2d contour plot coordinates %g %g %g %g\n",(double)coors[0],(double)coors[1],(double)coors[2],(double)coors[3]);CHKERRQ(ierr); 226 227 /* 228 Get local ghosted version of coordinates 229 */ 230 ierr = PetscObjectQuery((PetscObject)da,"GraphicsCoordinateGhosted",(PetscObject*)&xcoorl);CHKERRQ(ierr); 231 if (!xcoorl) { 232 /* create DMDA to get local version of graphics */ 233 ierr = DMDACreate2d(comm,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,N,zctx.m,zctx.n,2,1,lx,ly,&dag);CHKERRQ(ierr); 234 ierr = DMSetUp(dag);CHKERRQ(ierr); 235 ierr = PetscInfo(dag,"Creating auxilary DMDA for managing graphics coordinates ghost points\n");CHKERRQ(ierr); 236 ierr = DMCreateLocalVector(dag,&xcoorl);CHKERRQ(ierr); 237 ierr = PetscObjectCompose((PetscObject)da,"GraphicsCoordinateGhosted",(PetscObject)xcoorl);CHKERRQ(ierr); 238 ierr = PetscObjectDereference((PetscObject)dag);CHKERRQ(ierr); 239 ierr = PetscObjectDereference((PetscObject)xcoorl);CHKERRQ(ierr); 240 } else { 241 ierr = VecGetDM(xcoorl,&dag);CHKERRQ(ierr); 242 } 243 ierr = DMGlobalToLocalBegin(dag,xcoor,INSERT_VALUES,xcoorl);CHKERRQ(ierr); 244 ierr = DMGlobalToLocalEnd(dag,xcoor,INSERT_VALUES,xcoorl);CHKERRQ(ierr); 245 ierr = VecGetArrayRead(xcoorl,&zctx.xy);CHKERRQ(ierr); 246 ierr = DMDAGetCoordinateName(da,0,&zctx.name0);CHKERRQ(ierr); 247 ierr = DMDAGetCoordinateName(da,1,&zctx.name1);CHKERRQ(ierr); 248 249 /* 250 Get information about size of area each processor must do graphics for 251 */ 252 ierr = DMDAGetInfo(dac,NULL,&M,&N,NULL,NULL,NULL,NULL,&zctx.dof,NULL,&bx,&by,NULL,NULL);CHKERRQ(ierr); 253 ierr = DMDAGetGhostCorners(dac,NULL,NULL,NULL,&zctx.m,&zctx.n,NULL);CHKERRQ(ierr); 254 ierr = PetscOptionsGetBool(NULL,NULL,"-draw_contour_grid",&zctx.showgrid,NULL);CHKERRQ(ierr); 255 256 ierr = DMDASelectFields(da,&ndisplayfields,&displayfields);CHKERRQ(ierr); 257 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 258 ierr = PetscOptionsGetBool(NULL,NULL,"-draw_ports",&useports,NULL);CHKERRQ(ierr); 259 if (format == PETSC_VIEWER_DRAW_PORTS) useports = PETSC_TRUE; 260 if (useports) { 261 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 262 ierr = PetscDrawCheckResizedWindow(draw);CHKERRQ(ierr); 263 ierr = PetscDrawClear(draw);CHKERRQ(ierr); 264 ierr = PetscDrawViewPortsCreate(draw,ndisplayfields,&ports);CHKERRQ(ierr); 265 } 266 267 /* 268 Loop over each field; drawing each in a different window 269 */ 270 for (i=0; i<ndisplayfields; i++) { 271 zctx.k = displayfields[i]; 272 273 /* determine the min and max value in plot */ 274 ierr = VecStrideMin(xin,zctx.k,NULL,&zctx.min);CHKERRQ(ierr); 275 ierr = VecStrideMax(xin,zctx.k,NULL,&zctx.max);CHKERRQ(ierr); 276 if (zctx.k < nbounds) { 277 zctx.min = bounds[2*zctx.k]; 278 zctx.max = bounds[2*zctx.k+1]; 279 } 280 if (zctx.min == zctx.max) { 281 zctx.min -= 1.e-12; 282 zctx.max += 1.e-12; 283 } 284 ierr = PetscInfo2(da,"DMDA 2d contour plot min %g max %g\n",(double)zctx.min,(double)zctx.max);CHKERRQ(ierr); 285 286 if (useports) { 287 ierr = PetscDrawViewPortsSet(ports,i);CHKERRQ(ierr); 288 } else { 289 const char *title; 290 ierr = PetscViewerDrawGetDraw(viewer,i,&draw);CHKERRQ(ierr); 291 ierr = DMDAGetFieldName(da,zctx.k,&title);CHKERRQ(ierr); 292 if (title) {ierr = PetscDrawSetTitle(draw,title);CHKERRQ(ierr);} 293 } 294 295 ierr = PetscDrawGetPopup(draw,&popup);CHKERRQ(ierr); 296 ierr = PetscDrawScalePopup(popup,zctx.min,zctx.max);CHKERRQ(ierr); 297 ierr = PetscDrawSetCoordinates(draw,coors[0],coors[1],coors[2],coors[3]);CHKERRQ(ierr); 298 ierr = PetscDrawZoom(draw,VecView_MPI_Draw_DA2d_Zoom,&zctx);CHKERRQ(ierr); 299 if (!useports) {ierr = PetscDrawSave(draw);CHKERRQ(ierr);} 300 } 301 if (useports) { 302 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 303 ierr = PetscDrawSave(draw);CHKERRQ(ierr); 304 } 305 306 ierr = PetscDrawViewPortsDestroy(ports);CHKERRQ(ierr); 307 ierr = PetscFree(displayfields);CHKERRQ(ierr); 308 ierr = VecRestoreArrayRead(xcoorl,&zctx.xy);CHKERRQ(ierr); 309 ierr = VecRestoreArrayRead(xlocal,&zctx.v);CHKERRQ(ierr); 310 PetscFunctionReturn(0); 311 } 312 313 #if defined(PETSC_HAVE_HDF5) 314 static PetscErrorCode VecGetHDF5ChunkSize(DM_DA *da, Vec xin, PetscInt dimension, PetscInt timestep, hsize_t *chunkDims) 315 { 316 PetscMPIInt comm_size; 317 PetscErrorCode ierr; 318 hsize_t chunk_size, target_size, dim; 319 hsize_t vec_size = sizeof(PetscScalar)*da->M*da->N*da->P*da->w; 320 hsize_t avg_local_vec_size,KiB = 1024,MiB = KiB*KiB,GiB = MiB*KiB,min_size = MiB; 321 hsize_t max_chunks = 64*KiB; /* HDF5 internal limitation */ 322 hsize_t max_chunk_size = 4*GiB; /* HDF5 internal limitation */ 323 PetscInt zslices=da->p, yslices=da->n, xslices=da->m; 324 325 PetscFunctionBegin; 326 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)xin), &comm_size);CHKERRQ(ierr); 327 avg_local_vec_size = (hsize_t) ceil(vec_size*1.0/comm_size); /* we will attempt to use this as the chunk size */ 328 329 target_size = (hsize_t) ceil(PetscMin(vec_size,PetscMin(max_chunk_size,PetscMax(avg_local_vec_size,PetscMax(ceil(vec_size*1.0/max_chunks),min_size))))); 330 /* following line uses sizeof(PetscReal) instead of sizeof(PetscScalar) because the last dimension of chunkDims[] captures the 2* when complex numbers are being used */ 331 chunk_size = (hsize_t) PetscMax(1,chunkDims[0])*PetscMax(1,chunkDims[1])*PetscMax(1,chunkDims[2])*PetscMax(1,chunkDims[3])*PetscMax(1,chunkDims[4])*PetscMax(1,chunkDims[5])*sizeof(PetscReal); 332 333 /* 334 if size/rank > max_chunk_size, we need radical measures: even going down to 335 avg_local_vec_size is not enough, so we simply use chunk size of 4 GiB no matter 336 what, composed in the most efficient way possible. 337 N.B. this minimises the number of chunks, which may or may not be the optimal 338 solution. In a BG, for example, the optimal solution is probably to make # chunks = # 339 IO nodes involved, but this author has no access to a BG to figure out how to 340 reliably find the right number. And even then it may or may not be enough. 341 */ 342 if (avg_local_vec_size > max_chunk_size) { 343 /* check if we can just split local z-axis: is that enough? */ 344 zslices = (PetscInt)ceil(vec_size*1.0/(da->p*max_chunk_size))*zslices; 345 if (zslices > da->P) { 346 /* lattice is too large in xy-directions, splitting z only is not enough */ 347 zslices = da->P; 348 yslices= (PetscInt)ceil(vec_size*1.0/(zslices*da->n*max_chunk_size))*yslices; 349 if (yslices > da->N) { 350 /* lattice is too large in x-direction, splitting along z, y is not enough */ 351 yslices = da->N; 352 xslices= (PetscInt)ceil(vec_size*1.0/(zslices*yslices*da->m*max_chunk_size))*xslices; 353 } 354 } 355 dim = 0; 356 if (timestep >= 0) { 357 ++dim; 358 } 359 /* prefer to split z-axis, even down to planar slices */ 360 if (dimension == 3) { 361 chunkDims[dim++] = (hsize_t) da->P/zslices; 362 chunkDims[dim++] = (hsize_t) da->N/yslices; 363 chunkDims[dim++] = (hsize_t) da->M/xslices; 364 } else { 365 /* This is a 2D world exceeding 4GiB in size; yes, I've seen them, even used myself */ 366 chunkDims[dim++] = (hsize_t) da->N/yslices; 367 chunkDims[dim++] = (hsize_t) da->M/xslices; 368 } 369 chunk_size = (hsize_t) PetscMax(1,chunkDims[0])*PetscMax(1,chunkDims[1])*PetscMax(1,chunkDims[2])*PetscMax(1,chunkDims[3])*PetscMax(1,chunkDims[4])*PetscMax(1,chunkDims[5])*sizeof(double); 370 } else { 371 if (target_size < chunk_size) { 372 /* only change the defaults if target_size < chunk_size */ 373 dim = 0; 374 if (timestep >= 0) { 375 ++dim; 376 } 377 /* prefer to split z-axis, even down to planar slices */ 378 if (dimension == 3) { 379 /* try splitting the z-axis to core-size bits, i.e. divide chunk size by # comm_size in z-direction */ 380 if (target_size >= chunk_size/da->p) { 381 /* just make chunks the size of <local_z>x<whole_world_y>x<whole_world_x>x<dof> */ 382 chunkDims[dim] = (hsize_t) ceil(da->P*1.0/da->p); 383 } else { 384 /* oops, just splitting the z-axis is NOT ENOUGH, need to split more; let's be 385 radical and let everyone write all they've got */ 386 chunkDims[dim++] = (hsize_t) ceil(da->P*1.0/da->p); 387 chunkDims[dim++] = (hsize_t) ceil(da->N*1.0/da->n); 388 chunkDims[dim++] = (hsize_t) ceil(da->M*1.0/da->m); 389 } 390 } else { 391 /* This is a 2D world exceeding 4GiB in size; yes, I've seen them, even used myself */ 392 if (target_size >= chunk_size/da->n) { 393 /* just make chunks the size of <local_z>x<whole_world_y>x<whole_world_x>x<dof> */ 394 chunkDims[dim] = (hsize_t) ceil(da->N*1.0/da->n); 395 } else { 396 /* oops, just splitting the z-axis is NOT ENOUGH, need to split more; let's be 397 radical and let everyone write all they've got */ 398 chunkDims[dim++] = (hsize_t) ceil(da->N*1.0/da->n); 399 chunkDims[dim++] = (hsize_t) ceil(da->M*1.0/da->m); 400 } 401 402 } 403 chunk_size = (hsize_t) PetscMax(1,chunkDims[0])*PetscMax(1,chunkDims[1])*PetscMax(1,chunkDims[2])*PetscMax(1,chunkDims[3])*PetscMax(1,chunkDims[4])*PetscMax(1,chunkDims[5])*sizeof(double); 404 } else { 405 /* precomputed chunks are fine, we don't need to do anything */ 406 } 407 } 408 PetscFunctionReturn(0); 409 } 410 #endif 411 412 #if defined(PETSC_HAVE_HDF5) 413 PetscErrorCode VecView_MPI_HDF5_DA(Vec xin,PetscViewer viewer) 414 { 415 DM dm; 416 DM_DA *da; 417 hid_t filespace; /* file dataspace identifier */ 418 hid_t chunkspace; /* chunk dataset property identifier */ 419 hid_t plist_id; /* property list identifier */ 420 hid_t dset_id; /* dataset identifier */ 421 hid_t memspace; /* memory dataspace identifier */ 422 hid_t file_id; 423 hid_t group; 424 hid_t memscalartype; /* scalar type for mem (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */ 425 hid_t filescalartype; /* scalar type for file (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */ 426 hsize_t dim; 427 hsize_t maxDims[6]={0}, dims[6]={0}, chunkDims[6]={0}, count[6]={0}, offset[6]={0}; /* we depend on these being sane later on */ 428 PetscInt timestep, dimension; 429 const PetscScalar *x; 430 const char *vecname; 431 PetscErrorCode ierr; 432 PetscBool dim2; 433 PetscBool spoutput; 434 435 PetscFunctionBegin; 436 ierr = PetscViewerHDF5OpenGroup(viewer, &file_id, &group);CHKERRQ(ierr); 437 ierr = PetscViewerHDF5GetTimestep(viewer, ×tep);CHKERRQ(ierr); 438 ierr = PetscViewerHDF5GetBaseDimension2(viewer,&dim2);CHKERRQ(ierr); 439 ierr = PetscViewerHDF5GetSPOutput(viewer,&spoutput);CHKERRQ(ierr); 440 441 ierr = VecGetDM(xin,&dm);CHKERRQ(ierr); 442 if (!dm) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA"); 443 da = (DM_DA*)dm->data; 444 ierr = DMGetDimension(dm, &dimension);CHKERRQ(ierr); 445 446 /* Create the dataspace for the dataset. 447 * 448 * dims - holds the current dimensions of the dataset 449 * 450 * maxDims - holds the maximum dimensions of the dataset (unlimited 451 * for the number of time steps with the current dimensions for the 452 * other dimensions; so only additional time steps can be added). 453 * 454 * chunkDims - holds the size of a single time step (required to 455 * permit extending dataset). 456 */ 457 dim = 0; 458 if (timestep >= 0) { 459 dims[dim] = timestep+1; 460 maxDims[dim] = H5S_UNLIMITED; 461 chunkDims[dim] = 1; 462 ++dim; 463 } 464 if (dimension == 3) { 465 ierr = PetscHDF5IntCast(da->P,dims+dim);CHKERRQ(ierr); 466 maxDims[dim] = dims[dim]; 467 chunkDims[dim] = dims[dim]; 468 ++dim; 469 } 470 if (dimension > 1) { 471 ierr = PetscHDF5IntCast(da->N,dims+dim);CHKERRQ(ierr); 472 maxDims[dim] = dims[dim]; 473 chunkDims[dim] = dims[dim]; 474 ++dim; 475 } 476 ierr = PetscHDF5IntCast(da->M,dims+dim);CHKERRQ(ierr); 477 maxDims[dim] = dims[dim]; 478 chunkDims[dim] = dims[dim]; 479 ++dim; 480 if (da->w > 1 || dim2) { 481 ierr = PetscHDF5IntCast(da->w,dims+dim);CHKERRQ(ierr); 482 maxDims[dim] = dims[dim]; 483 chunkDims[dim] = dims[dim]; 484 ++dim; 485 } 486 #if defined(PETSC_USE_COMPLEX) 487 dims[dim] = 2; 488 maxDims[dim] = dims[dim]; 489 chunkDims[dim] = dims[dim]; 490 ++dim; 491 #endif 492 493 ierr = VecGetHDF5ChunkSize(da, xin, dimension, timestep, chunkDims); CHKERRQ(ierr); 494 495 PetscStackCallHDF5Return(filespace,H5Screate_simple,(dim, dims, maxDims)); 496 497 #if defined(PETSC_USE_REAL_SINGLE) 498 memscalartype = H5T_NATIVE_FLOAT; 499 filescalartype = H5T_NATIVE_FLOAT; 500 #elif defined(PETSC_USE_REAL___FLOAT128) 501 #error "HDF5 output with 128 bit floats not supported." 502 #elif defined(PETSC_USE_REAL___FP16) 503 #error "HDF5 output with 16 bit floats not supported." 504 #else 505 memscalartype = H5T_NATIVE_DOUBLE; 506 if (spoutput == PETSC_TRUE) filescalartype = H5T_NATIVE_FLOAT; 507 else filescalartype = H5T_NATIVE_DOUBLE; 508 #endif 509 510 /* Create the dataset with default properties and close filespace */ 511 ierr = PetscObjectGetName((PetscObject)xin,&vecname);CHKERRQ(ierr); 512 if (!H5Lexists(group, vecname, H5P_DEFAULT)) { 513 /* Create chunk */ 514 PetscStackCallHDF5Return(chunkspace,H5Pcreate,(H5P_DATASET_CREATE)); 515 PetscStackCallHDF5(H5Pset_chunk,(chunkspace, dim, chunkDims)); 516 517 PetscStackCallHDF5Return(dset_id,H5Dcreate2,(group, vecname, filescalartype, filespace, H5P_DEFAULT, chunkspace, H5P_DEFAULT)); 518 } else { 519 PetscStackCallHDF5Return(dset_id,H5Dopen2,(group, vecname, H5P_DEFAULT)); 520 PetscStackCallHDF5(H5Dset_extent,(dset_id, dims)); 521 } 522 PetscStackCallHDF5(H5Sclose,(filespace)); 523 524 /* Each process defines a dataset and writes it to the hyperslab in the file */ 525 dim = 0; 526 if (timestep >= 0) { 527 offset[dim] = timestep; 528 ++dim; 529 } 530 if (dimension == 3) {ierr = PetscHDF5IntCast(da->zs,offset + dim++);CHKERRQ(ierr);} 531 if (dimension > 1) {ierr = PetscHDF5IntCast(da->ys,offset + dim++);CHKERRQ(ierr);} 532 ierr = PetscHDF5IntCast(da->xs/da->w,offset + dim++);CHKERRQ(ierr); 533 if (da->w > 1 || dim2) offset[dim++] = 0; 534 #if defined(PETSC_USE_COMPLEX) 535 offset[dim++] = 0; 536 #endif 537 dim = 0; 538 if (timestep >= 0) { 539 count[dim] = 1; 540 ++dim; 541 } 542 if (dimension == 3) {ierr = PetscHDF5IntCast(da->ze - da->zs,count + dim++);CHKERRQ(ierr);} 543 if (dimension > 1) {ierr = PetscHDF5IntCast(da->ye - da->ys,count + dim++);CHKERRQ(ierr);} 544 ierr = PetscHDF5IntCast((da->xe - da->xs)/da->w,count + dim++);CHKERRQ(ierr); 545 if (da->w > 1 || dim2) {ierr = PetscHDF5IntCast(da->w,count + dim++);CHKERRQ(ierr);} 546 #if defined(PETSC_USE_COMPLEX) 547 count[dim++] = 2; 548 #endif 549 PetscStackCallHDF5Return(memspace,H5Screate_simple,(dim, count, NULL)); 550 PetscStackCallHDF5Return(filespace,H5Dget_space,(dset_id)); 551 PetscStackCallHDF5(H5Sselect_hyperslab,(filespace, H5S_SELECT_SET, offset, NULL, count, NULL)); 552 553 /* Create property list for collective dataset write */ 554 PetscStackCallHDF5Return(plist_id,H5Pcreate,(H5P_DATASET_XFER)); 555 #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO) 556 PetscStackCallHDF5(H5Pset_dxpl_mpio,(plist_id, H5FD_MPIO_COLLECTIVE)); 557 #endif 558 /* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */ 559 560 ierr = VecGetArrayRead(xin, &x);CHKERRQ(ierr); 561 PetscStackCallHDF5(H5Dwrite,(dset_id, memscalartype, memspace, filespace, plist_id, x)); 562 PetscStackCallHDF5(H5Fflush,(file_id, H5F_SCOPE_GLOBAL)); 563 ierr = VecRestoreArrayRead(xin, &x);CHKERRQ(ierr); 564 565 /* Close/release resources */ 566 if (group != file_id) { 567 PetscStackCallHDF5(H5Gclose,(group)); 568 } 569 PetscStackCallHDF5(H5Pclose,(plist_id)); 570 PetscStackCallHDF5(H5Sclose,(filespace)); 571 PetscStackCallHDF5(H5Sclose,(memspace)); 572 PetscStackCallHDF5(H5Dclose,(dset_id)); 573 ierr = PetscInfo1(xin,"Wrote Vec object with name %s\n",vecname);CHKERRQ(ierr); 574 PetscFunctionReturn(0); 575 } 576 #endif 577 578 extern PetscErrorCode VecView_MPI_Draw_DA1d(Vec,PetscViewer); 579 580 #if defined(PETSC_HAVE_MPIIO) 581 static PetscErrorCode DMDAArrayMPIIO(DM da,PetscViewer viewer,Vec xin,PetscBool write) 582 { 583 PetscErrorCode ierr; 584 MPI_File mfdes; 585 PetscMPIInt gsizes[4],lsizes[4],lstarts[4],asiz,dof; 586 MPI_Datatype view; 587 const PetscScalar *array; 588 MPI_Offset off; 589 MPI_Aint ub,ul; 590 PetscInt type,rows,vecrows,tr[2]; 591 DM_DA *dd = (DM_DA*)da->data; 592 PetscBool skipheader; 593 594 PetscFunctionBegin; 595 ierr = VecGetSize(xin,&vecrows);CHKERRQ(ierr); 596 ierr = PetscViewerBinaryGetSkipHeader(viewer,&skipheader);CHKERRQ(ierr); 597 if (!write) { 598 /* Read vector header. */ 599 if (!skipheader) { 600 ierr = PetscViewerBinaryRead(viewer,tr,2,NULL,PETSC_INT);CHKERRQ(ierr); 601 type = tr[0]; 602 rows = tr[1]; 603 if (type != VEC_FILE_CLASSID) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_WRONG,"Not vector next in file"); 604 if (rows != vecrows) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_SIZ,"Vector in file not same size as DMDA vector"); 605 } 606 } else { 607 tr[0] = VEC_FILE_CLASSID; 608 tr[1] = vecrows; 609 if (!skipheader) { 610 ierr = PetscViewerBinaryWrite(viewer,tr,2,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 611 } 612 } 613 614 ierr = PetscMPIIntCast(dd->w,&dof);CHKERRQ(ierr); 615 gsizes[0] = dof; 616 ierr = PetscMPIIntCast(dd->M,gsizes+1);CHKERRQ(ierr); 617 ierr = PetscMPIIntCast(dd->N,gsizes+2);CHKERRQ(ierr); 618 ierr = PetscMPIIntCast(dd->P,gsizes+3);CHKERRQ(ierr); 619 lsizes[0] = dof; 620 ierr = PetscMPIIntCast((dd->xe-dd->xs)/dof,lsizes+1);CHKERRQ(ierr); 621 ierr = PetscMPIIntCast(dd->ye-dd->ys,lsizes+2);CHKERRQ(ierr); 622 ierr = PetscMPIIntCast(dd->ze-dd->zs,lsizes+3);CHKERRQ(ierr); 623 lstarts[0] = 0; 624 ierr = PetscMPIIntCast(dd->xs/dof,lstarts+1);CHKERRQ(ierr); 625 ierr = PetscMPIIntCast(dd->ys,lstarts+2);CHKERRQ(ierr); 626 ierr = PetscMPIIntCast(dd->zs,lstarts+3);CHKERRQ(ierr); 627 ierr = MPI_Type_create_subarray(da->dim+1,gsizes,lsizes,lstarts,MPI_ORDER_FORTRAN,MPIU_SCALAR,&view);CHKERRQ(ierr); 628 ierr = MPI_Type_commit(&view);CHKERRQ(ierr); 629 630 ierr = PetscViewerBinaryGetMPIIODescriptor(viewer,&mfdes);CHKERRQ(ierr); 631 ierr = PetscViewerBinaryGetMPIIOOffset(viewer,&off);CHKERRQ(ierr); 632 ierr = MPI_File_set_view(mfdes,off,MPIU_SCALAR,view,(char*)"native",MPI_INFO_NULL);CHKERRQ(ierr); 633 ierr = VecGetArrayRead(xin,&array);CHKERRQ(ierr); 634 asiz = lsizes[1]*(lsizes[2] > 0 ? lsizes[2] : 1)*(lsizes[3] > 0 ? lsizes[3] : 1)*dof; 635 if (write) { 636 ierr = MPIU_File_write_all(mfdes,(PetscScalar*)array,asiz,MPIU_SCALAR,MPI_STATUS_IGNORE);CHKERRQ(ierr); 637 } else { 638 ierr = MPIU_File_read_all(mfdes,(PetscScalar*)array,asiz,MPIU_SCALAR,MPI_STATUS_IGNORE);CHKERRQ(ierr); 639 } 640 ierr = MPI_Type_get_extent(view,&ul,&ub);CHKERRQ(ierr); 641 ierr = PetscViewerBinaryAddMPIIOOffset(viewer,ub);CHKERRQ(ierr); 642 ierr = VecRestoreArrayRead(xin,&array);CHKERRQ(ierr); 643 ierr = MPI_Type_free(&view);CHKERRQ(ierr); 644 PetscFunctionReturn(0); 645 } 646 #endif 647 648 PetscErrorCode VecView_MPI_DA(Vec xin,PetscViewer viewer) 649 { 650 DM da; 651 PetscErrorCode ierr; 652 PetscInt dim; 653 Vec natural; 654 PetscBool isdraw,isvtk,isglvis; 655 #if defined(PETSC_HAVE_HDF5) 656 PetscBool ishdf5; 657 #endif 658 const char *prefix,*name; 659 PetscViewerFormat format; 660 661 PetscFunctionBegin; 662 ierr = VecGetDM(xin,&da);CHKERRQ(ierr); 663 if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA"); 664 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 665 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERVTK,&isvtk);CHKERRQ(ierr); 666 #if defined(PETSC_HAVE_HDF5) 667 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);CHKERRQ(ierr); 668 #endif 669 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERGLVIS,&isglvis);CHKERRQ(ierr); 670 if (isdraw) { 671 ierr = DMDAGetInfo(da,&dim,0,0,0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr); 672 if (dim == 1) { 673 ierr = VecView_MPI_Draw_DA1d(xin,viewer);CHKERRQ(ierr); 674 } else if (dim == 2) { 675 ierr = VecView_MPI_Draw_DA2d(xin,viewer);CHKERRQ(ierr); 676 } else SETERRQ1(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Cannot graphically view vector associated with this dimensional DMDA %D",dim); 677 } else if (isvtk) { /* Duplicate the Vec */ 678 Vec Y; 679 ierr = VecDuplicate(xin,&Y);CHKERRQ(ierr); 680 if (((PetscObject)xin)->name) { 681 /* If xin was named, copy the name over to Y. The duplicate names are safe because nobody else will ever see Y. */ 682 ierr = PetscObjectSetName((PetscObject)Y,((PetscObject)xin)->name);CHKERRQ(ierr); 683 } 684 ierr = VecCopy(xin,Y);CHKERRQ(ierr); 685 { 686 PetscObject dmvtk; 687 PetscBool compatible,compatibleSet; 688 ierr = PetscViewerVTKGetDM(viewer,&dmvtk);CHKERRQ(ierr); 689 if (dmvtk) { 690 PetscValidHeaderSpecific((DM)dmvtk,DM_CLASSID,-1); 691 ierr = DMGetCompatibility(da,(DM)dmvtk,&compatible,&compatibleSet);CHKERRQ(ierr); 692 if (!compatibleSet || !compatible) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_INCOMP,"Cannot confirm compatibility of DMs associated with Vecs viewed in the same VTK file. Check that grids are the same."); 693 } 694 ierr = PetscViewerVTKAddField(viewer,(PetscObject)da,DMDAVTKWriteAll,PETSC_VTK_POINT_FIELD,PETSC_FALSE,(PetscObject)Y);CHKERRQ(ierr); 695 } 696 #if defined(PETSC_HAVE_HDF5) 697 } else if (ishdf5) { 698 ierr = VecView_MPI_HDF5_DA(xin,viewer);CHKERRQ(ierr); 699 #endif 700 } else if (isglvis) { 701 ierr = VecView_GLVis(xin,viewer);CHKERRQ(ierr); 702 } else { 703 #if defined(PETSC_HAVE_MPIIO) 704 PetscBool isbinary,isMPIIO; 705 706 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 707 if (isbinary) { 708 ierr = PetscViewerBinaryGetUseMPIIO(viewer,&isMPIIO);CHKERRQ(ierr); 709 if (isMPIIO) { 710 ierr = DMDAArrayMPIIO(da,viewer,xin,PETSC_TRUE);CHKERRQ(ierr); 711 PetscFunctionReturn(0); 712 } 713 } 714 #endif 715 716 /* call viewer on natural ordering */ 717 ierr = PetscObjectGetOptionsPrefix((PetscObject)xin,&prefix);CHKERRQ(ierr); 718 ierr = DMDACreateNaturalVector(da,&natural);CHKERRQ(ierr); 719 ierr = PetscObjectSetOptionsPrefix((PetscObject)natural,prefix);CHKERRQ(ierr); 720 ierr = DMDAGlobalToNaturalBegin(da,xin,INSERT_VALUES,natural);CHKERRQ(ierr); 721 ierr = DMDAGlobalToNaturalEnd(da,xin,INSERT_VALUES,natural);CHKERRQ(ierr); 722 ierr = PetscObjectGetName((PetscObject)xin,&name);CHKERRQ(ierr); 723 ierr = PetscObjectSetName((PetscObject)natural,name);CHKERRQ(ierr); 724 725 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 726 if (format == PETSC_VIEWER_BINARY_MATLAB) { 727 /* temporarily remove viewer format so it won't trigger in the VecView() */ 728 ierr = PetscViewerPushFormat(viewer,PETSC_VIEWER_DEFAULT);CHKERRQ(ierr); 729 } 730 731 ((PetscObject)natural)->donotPetscObjectPrintClassNamePrefixType = PETSC_TRUE; 732 ierr = VecView(natural,viewer);CHKERRQ(ierr); 733 ((PetscObject)natural)->donotPetscObjectPrintClassNamePrefixType = PETSC_FALSE; 734 735 if (format == PETSC_VIEWER_BINARY_MATLAB) { 736 MPI_Comm comm; 737 FILE *info; 738 const char *fieldname; 739 char fieldbuf[256]; 740 PetscInt dim,ni,nj,nk,pi,pj,pk,dof,n; 741 742 /* set the viewer format back into the viewer */ 743 ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr); 744 ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr); 745 ierr = PetscViewerBinaryGetInfoPointer(viewer,&info);CHKERRQ(ierr); 746 ierr = DMDAGetInfo(da,&dim,&ni,&nj,&nk,&pi,&pj,&pk,&dof,0,0,0,0,0);CHKERRQ(ierr); 747 ierr = PetscFPrintf(comm,info,"#--- begin code written by PetscViewerBinary for MATLAB format ---#\n");CHKERRQ(ierr); 748 ierr = PetscFPrintf(comm,info,"#$$ tmp = PetscBinaryRead(fd); \n");CHKERRQ(ierr); 749 if (dim == 1) { ierr = PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d);\n",dof,ni);CHKERRQ(ierr); } 750 if (dim == 2) { ierr = PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d,%d);\n",dof,ni,nj);CHKERRQ(ierr); } 751 if (dim == 3) { ierr = PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d,%d,%d);\n",dof,ni,nj,nk);CHKERRQ(ierr); } 752 753 for (n=0; n<dof; n++) { 754 ierr = DMDAGetFieldName(da,n,&fieldname);CHKERRQ(ierr); 755 if (!fieldname || !fieldname[0]) { 756 ierr = PetscSNPrintf(fieldbuf,sizeof fieldbuf,"field%D",n);CHKERRQ(ierr); 757 fieldname = fieldbuf; 758 } 759 if (dim == 1) { ierr = PetscFPrintf(comm,info,"#$$ Set.%s.%s = squeeze(tmp(%d,:))';\n",name,fieldname,n+1);CHKERRQ(ierr); } 760 if (dim == 2) { ierr = PetscFPrintf(comm,info,"#$$ Set.%s.%s = squeeze(tmp(%d,:,:))';\n",name,fieldname,n+1);CHKERRQ(ierr); } 761 if (dim == 3) { ierr = PetscFPrintf(comm,info,"#$$ Set.%s.%s = permute(squeeze(tmp(%d,:,:,:)),[2 1 3]);\n",name,fieldname,n+1);CHKERRQ(ierr);} 762 } 763 ierr = PetscFPrintf(comm,info,"#$$ clear tmp; \n");CHKERRQ(ierr); 764 ierr = PetscFPrintf(comm,info,"#--- end code written by PetscViewerBinary for MATLAB format ---#\n\n");CHKERRQ(ierr); 765 } 766 767 ierr = VecDestroy(&natural);CHKERRQ(ierr); 768 } 769 PetscFunctionReturn(0); 770 } 771 772 #if defined(PETSC_HAVE_HDF5) 773 PetscErrorCode VecLoad_HDF5_DA(Vec xin, PetscViewer viewer) 774 { 775 DM da; 776 PetscErrorCode ierr; 777 hsize_t dim,rdim; 778 hsize_t dims[6]={0},count[6]={0},offset[6]={0}; 779 PetscInt dimension,timestep,dofInd; 780 PetscScalar *x; 781 const char *vecname; 782 hid_t filespace; /* file dataspace identifier */ 783 hid_t plist_id; /* property list identifier */ 784 hid_t dset_id; /* dataset identifier */ 785 hid_t memspace; /* memory dataspace identifier */ 786 hid_t file_id,group; 787 hid_t scalartype; /* scalar type (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */ 788 DM_DA *dd; 789 PetscBool dim2 = PETSC_FALSE; 790 791 PetscFunctionBegin; 792 #if defined(PETSC_USE_REAL_SINGLE) 793 scalartype = H5T_NATIVE_FLOAT; 794 #elif defined(PETSC_USE_REAL___FLOAT128) 795 #error "HDF5 output with 128 bit floats not supported." 796 #elif defined(PETSC_USE_REAL___FP16) 797 #error "HDF5 output with 16 bit floats not supported." 798 #else 799 scalartype = H5T_NATIVE_DOUBLE; 800 #endif 801 802 ierr = PetscViewerHDF5OpenGroup(viewer, &file_id, &group);CHKERRQ(ierr); 803 ierr = PetscViewerHDF5GetTimestep(viewer, ×tep);CHKERRQ(ierr); 804 ierr = PetscObjectGetName((PetscObject)xin,&vecname);CHKERRQ(ierr); 805 ierr = VecGetDM(xin,&da);CHKERRQ(ierr); 806 dd = (DM_DA*)da->data; 807 ierr = DMGetDimension(da, &dimension);CHKERRQ(ierr); 808 809 /* Open dataset */ 810 PetscStackCallHDF5Return(dset_id,H5Dopen2,(group, vecname, H5P_DEFAULT)); 811 812 /* Retrieve the dataspace for the dataset */ 813 PetscStackCallHDF5Return(filespace,H5Dget_space,(dset_id)); 814 PetscStackCallHDF5Return(rdim,H5Sget_simple_extent_dims,(filespace, dims, NULL)); 815 816 /* Expected dimension for holding the dof's */ 817 #if defined(PETSC_USE_COMPLEX) 818 dofInd = rdim-2; 819 #else 820 dofInd = rdim-1; 821 #endif 822 823 /* The expected number of dimensions, assuming basedimension2 = false */ 824 dim = dimension; 825 if (dd->w > 1) ++dim; 826 if (timestep >= 0) ++dim; 827 #if defined(PETSC_USE_COMPLEX) 828 ++dim; 829 #endif 830 831 /* In this case the input dataset have one extra, unexpected dimension. */ 832 if (rdim == dim+1) { 833 /* In this case the block size unity */ 834 if (dd->w == 1 && dims[dofInd] == 1) dim2 = PETSC_TRUE; 835 836 /* Special error message for the case where dof does not match the input file */ 837 else if (dd->w != (PetscInt) dims[dofInd]) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Number of dofs in file is %D, not %D as expected",(PetscInt)dims[dofInd],dd->w); 838 839 /* Other cases where rdim != dim cannot be handled currently */ 840 } else if (rdim != dim) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Dimension of array in file is %d, not %d as expected with dof = %D",rdim,dim,dd->w); 841 842 /* Set up the hyperslab size */ 843 dim = 0; 844 if (timestep >= 0) { 845 offset[dim] = timestep; 846 count[dim] = 1; 847 ++dim; 848 } 849 if (dimension == 3) { 850 ierr = PetscHDF5IntCast(dd->zs,offset + dim);CHKERRQ(ierr); 851 ierr = PetscHDF5IntCast(dd->ze - dd->zs,count + dim);CHKERRQ(ierr); 852 ++dim; 853 } 854 if (dimension > 1) { 855 ierr = PetscHDF5IntCast(dd->ys,offset + dim);CHKERRQ(ierr); 856 ierr = PetscHDF5IntCast(dd->ye - dd->ys,count + dim);CHKERRQ(ierr); 857 ++dim; 858 } 859 ierr = PetscHDF5IntCast(dd->xs/dd->w,offset + dim);CHKERRQ(ierr); 860 ierr = PetscHDF5IntCast((dd->xe - dd->xs)/dd->w,count + dim);CHKERRQ(ierr); 861 ++dim; 862 if (dd->w > 1 || dim2) { 863 offset[dim] = 0; 864 ierr = PetscHDF5IntCast(dd->w,count + dim);CHKERRQ(ierr); 865 ++dim; 866 } 867 #if defined(PETSC_USE_COMPLEX) 868 offset[dim] = 0; 869 count[dim] = 2; 870 ++dim; 871 #endif 872 873 /* Create the memory and filespace */ 874 PetscStackCallHDF5Return(memspace,H5Screate_simple,(dim, count, NULL)); 875 PetscStackCallHDF5(H5Sselect_hyperslab,(filespace, H5S_SELECT_SET, offset, NULL, count, NULL)); 876 877 /* Create property list for collective dataset write */ 878 PetscStackCallHDF5Return(plist_id,H5Pcreate,(H5P_DATASET_XFER)); 879 #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO) 880 PetscStackCallHDF5(H5Pset_dxpl_mpio,(plist_id, H5FD_MPIO_COLLECTIVE)); 881 #endif 882 /* To read dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */ 883 884 ierr = VecGetArray(xin, &x);CHKERRQ(ierr); 885 PetscStackCallHDF5(H5Dread,(dset_id, scalartype, memspace, filespace, plist_id, x)); 886 ierr = VecRestoreArray(xin, &x);CHKERRQ(ierr); 887 888 /* Close/release resources */ 889 if (group != file_id) { 890 PetscStackCallHDF5(H5Gclose,(group)); 891 } 892 PetscStackCallHDF5(H5Pclose,(plist_id)); 893 PetscStackCallHDF5(H5Sclose,(filespace)); 894 PetscStackCallHDF5(H5Sclose,(memspace)); 895 PetscStackCallHDF5(H5Dclose,(dset_id)); 896 PetscFunctionReturn(0); 897 } 898 #endif 899 900 PetscErrorCode VecLoad_Binary_DA(Vec xin, PetscViewer viewer) 901 { 902 DM da; 903 PetscErrorCode ierr; 904 Vec natural; 905 const char *prefix; 906 PetscInt bs; 907 PetscBool flag; 908 DM_DA *dd; 909 #if defined(PETSC_HAVE_MPIIO) 910 PetscBool isMPIIO; 911 #endif 912 913 PetscFunctionBegin; 914 ierr = VecGetDM(xin,&da);CHKERRQ(ierr); 915 dd = (DM_DA*)da->data; 916 #if defined(PETSC_HAVE_MPIIO) 917 ierr = PetscViewerBinaryGetUseMPIIO(viewer,&isMPIIO);CHKERRQ(ierr); 918 if (isMPIIO) { 919 ierr = DMDAArrayMPIIO(da,viewer,xin,PETSC_FALSE);CHKERRQ(ierr); 920 PetscFunctionReturn(0); 921 } 922 #endif 923 924 ierr = PetscObjectGetOptionsPrefix((PetscObject)xin,&prefix);CHKERRQ(ierr); 925 ierr = DMDACreateNaturalVector(da,&natural);CHKERRQ(ierr); 926 ierr = PetscObjectSetName((PetscObject)natural,((PetscObject)xin)->name);CHKERRQ(ierr); 927 ierr = PetscObjectSetOptionsPrefix((PetscObject)natural,prefix);CHKERRQ(ierr); 928 ierr = VecLoad(natural,viewer);CHKERRQ(ierr); 929 ierr = DMDANaturalToGlobalBegin(da,natural,INSERT_VALUES,xin);CHKERRQ(ierr); 930 ierr = DMDANaturalToGlobalEnd(da,natural,INSERT_VALUES,xin);CHKERRQ(ierr); 931 ierr = VecDestroy(&natural);CHKERRQ(ierr); 932 ierr = PetscInfo(xin,"Loading vector from natural ordering into DMDA\n");CHKERRQ(ierr); 933 ierr = PetscOptionsGetInt(NULL,((PetscObject)xin)->prefix,"-vecload_block_size",&bs,&flag);CHKERRQ(ierr); 934 if (flag && bs != dd->w) { 935 ierr = PetscInfo2(xin,"Block size in file %D not equal to DMDA's dof %D\n",bs,dd->w);CHKERRQ(ierr); 936 } 937 PetscFunctionReturn(0); 938 } 939 940 PetscErrorCode VecLoad_Default_DA(Vec xin, PetscViewer viewer) 941 { 942 PetscErrorCode ierr; 943 DM da; 944 PetscBool isbinary; 945 #if defined(PETSC_HAVE_HDF5) 946 PetscBool ishdf5; 947 #endif 948 949 PetscFunctionBegin; 950 ierr = VecGetDM(xin,&da);CHKERRQ(ierr); 951 if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA"); 952 953 #if defined(PETSC_HAVE_HDF5) 954 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);CHKERRQ(ierr); 955 #endif 956 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 957 958 if (isbinary) { 959 ierr = VecLoad_Binary_DA(xin,viewer);CHKERRQ(ierr); 960 #if defined(PETSC_HAVE_HDF5) 961 } else if (ishdf5) { 962 ierr = VecLoad_HDF5_DA(xin,viewer);CHKERRQ(ierr); 963 #endif 964 } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Viewer type %s not supported for vector loading", ((PetscObject)viewer)->type_name); 965 PetscFunctionReturn(0); 966 } 967