1 2 /* 3 Plots vectors obtained with DMDACreate2d() 4 */ 5 6 #include <petsc-private/dmdaimpl.h> /*I "petscdmda.h" I*/ 7 #include <petsc-private/vecimpl.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 PetscInt m,n,step,k; 16 PetscReal min,max,scale; 17 PetscScalar *xy,*v; 18 PetscBool showgrid; 19 const char *name0,*name1; 20 } ZoomCtx; 21 22 /* 23 This does the drawing for one particular field 24 in one particular set of coordinates. It is a callback 25 called from PetscDrawZoom() 26 */ 27 #undef __FUNCT__ 28 #define __FUNCT__ "VecView_MPI_Draw_DA2d_Zoom" 29 PetscErrorCode VecView_MPI_Draw_DA2d_Zoom(PetscDraw draw,void *ctx) 30 { 31 ZoomCtx *zctx = (ZoomCtx*)ctx; 32 PetscErrorCode ierr; 33 PetscInt m,n,i,j,k,step,id,c1,c2,c3,c4; 34 PetscReal s,min,max,x1,x2,x3,x4,y_1,y2,y3,y4,xmin = PETSC_MAX_REAL,xmax = PETSC_MIN_REAL,ymin = PETSC_MAX_REAL,ymax = PETSC_MIN_REAL; 35 PetscReal xminf,xmaxf,yminf,ymaxf,w; 36 PetscScalar *v,*xy; 37 char value[16]; 38 size_t len; 39 40 PetscFunctionBegin; 41 m = zctx->m; 42 n = zctx->n; 43 step = zctx->step; 44 k = zctx->k; 45 v = zctx->v; 46 xy = zctx->xy; 47 s = zctx->scale; 48 min = zctx->min; 49 max = zctx->max; 50 51 /* PetscDraw the contour plot patch */ 52 for (j=0; j<n-1; j++) { 53 for (i=0; i<m-1; i++) { 54 id = i+j*m; 55 x1 = PetscRealPart(xy[2*id]); 56 y_1 = PetscRealPart(xy[2*id+1]); 57 c1 = (int)(PETSC_DRAW_BASIC_COLORS+s*(PetscClipInterval(PetscRealPart(v[k+step*id]),min,max)-min)); 58 xmin = PetscMin(xmin,x1); 59 ymin = PetscMin(ymin,y_1); 60 xmax = PetscMax(xmax,x1); 61 ymax = PetscMax(ymax,y_1); 62 63 id = i+j*m+1; 64 x2 = PetscRealPart(xy[2*id]); 65 y2 = PetscRealPart(xy[2*id+1]); 66 c2 = (int)(PETSC_DRAW_BASIC_COLORS+s*(PetscClipInterval(PetscRealPart(v[k+step*id]),min,max)-min)); 67 xmin = PetscMin(xmin,x2); 68 ymin = PetscMin(ymin,y2); 69 xmax = PetscMax(xmax,x2); 70 ymax = PetscMax(ymax,y2); 71 72 id = i+j*m+1+m; 73 x3 = PetscRealPart(xy[2*id]); 74 y3 = PetscRealPart(xy[2*id+1]); 75 c3 = (int)(PETSC_DRAW_BASIC_COLORS+s*(PetscClipInterval(PetscRealPart(v[k+step*id]),min,max)-min)); 76 xmin = PetscMin(xmin,x3); 77 ymin = PetscMin(ymin,y3); 78 xmax = PetscMax(xmax,x3); 79 ymax = PetscMax(ymax,y3); 80 81 id = i+j*m+m; 82 x4 = PetscRealPart(xy[2*id]); 83 y4 = PetscRealPart(xy[2*id+1]); 84 c4 = (int)(PETSC_DRAW_BASIC_COLORS+s*(PetscClipInterval(PetscRealPart(v[k+step*id]),min,max)-min)); 85 xmin = PetscMin(xmin,x4); 86 ymin = PetscMin(ymin,y4); 87 xmax = PetscMax(xmax,x4); 88 ymax = PetscMax(ymax,y4); 89 90 ierr = PetscDrawTriangle(draw,x1,y_1,x2,y2,x3,y3,c1,c2,c3);CHKERRQ(ierr); 91 ierr = PetscDrawTriangle(draw,x1,y_1,x3,y3,x4,y4,c1,c3,c4);CHKERRQ(ierr); 92 if (zctx->showgrid) { 93 ierr = PetscDrawLine(draw,x1,y_1,x2,y2,PETSC_DRAW_BLACK);CHKERRQ(ierr); 94 ierr = PetscDrawLine(draw,x2,y2,x3,y3,PETSC_DRAW_BLACK);CHKERRQ(ierr); 95 ierr = PetscDrawLine(draw,x3,y3,x4,y4,PETSC_DRAW_BLACK);CHKERRQ(ierr); 96 ierr = PetscDrawLine(draw,x4,y4,x1,y_1,PETSC_DRAW_BLACK);CHKERRQ(ierr); 97 } 98 } 99 } 100 if (zctx->name0) { 101 PetscReal xl,yl,xr,yr,x,y; 102 ierr = PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);CHKERRQ(ierr); 103 x = xl + .3*(xr - xl); 104 xl = xl + .01*(xr - xl); 105 y = yr - .3*(yr - yl); 106 yl = yl + .01*(yr - yl); 107 ierr = PetscDrawString(draw,x,yl,PETSC_DRAW_BLACK,zctx->name0);CHKERRQ(ierr); 108 ierr = PetscDrawStringVertical(draw,xl,y,PETSC_DRAW_BLACK,zctx->name1);CHKERRQ(ierr); 109 } 110 /* 111 Ideally we would use the PetscDrawAxis object to manage displaying the coordinate limits 112 but that may require some refactoring. 113 */ 114 ierr = MPI_Allreduce(&xmin,&xminf,1,MPIU_REAL,MPIU_MIN,PetscObjectComm((PetscObject)draw));CHKERRQ(ierr); 115 ierr = MPI_Allreduce(&xmax,&xmaxf,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)draw));CHKERRQ(ierr); 116 ierr = MPI_Allreduce(&ymin,&yminf,1,MPIU_REAL,MPIU_MIN,PetscObjectComm((PetscObject)draw));CHKERRQ(ierr); 117 ierr = MPI_Allreduce(&ymax,&ymaxf,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)draw));CHKERRQ(ierr); 118 ierr = PetscSNPrintf(value,16,"%f",xminf);CHKERRQ(ierr); 119 ierr = PetscDrawString(draw,xminf,yminf - .05*(ymaxf - yminf),PETSC_DRAW_BLACK,value);CHKERRQ(ierr); 120 ierr = PetscSNPrintf(value,16,"%f",xmaxf);CHKERRQ(ierr); 121 ierr = PetscStrlen(value,&len);CHKERRQ(ierr); 122 ierr = PetscDrawStringGetSize(draw,&w,NULL);CHKERRQ(ierr); 123 ierr = PetscDrawString(draw,xmaxf - len*w,yminf - .05*(ymaxf - yminf),PETSC_DRAW_BLACK,value);CHKERRQ(ierr); 124 ierr = PetscSNPrintf(value,16,"%f",yminf);CHKERRQ(ierr); 125 ierr = PetscDrawString(draw,xminf - .05*(xmaxf - xminf),yminf,PETSC_DRAW_BLACK,value);CHKERRQ(ierr); 126 ierr = PetscSNPrintf(value,16,"%f",ymaxf);CHKERRQ(ierr); 127 ierr = PetscDrawString(draw,xminf - .05*(xmaxf - xminf),ymaxf,PETSC_DRAW_BLACK,value);CHKERRQ(ierr); 128 PetscFunctionReturn(0); 129 } 130 131 #undef __FUNCT__ 132 #define __FUNCT__ "VecView_MPI_Draw_DA2d" 133 PetscErrorCode VecView_MPI_Draw_DA2d(Vec xin,PetscViewer viewer) 134 { 135 DM da,dac,dag; 136 PetscErrorCode ierr; 137 PetscMPIInt rank; 138 PetscInt N,s,M,w,ncoors = 4; 139 const PetscInt *lx,*ly; 140 PetscReal coors[4],ymin,ymax,xmin,xmax; 141 PetscDraw draw,popup; 142 PetscBool isnull,useports = PETSC_FALSE; 143 MPI_Comm comm; 144 Vec xlocal,xcoor,xcoorl; 145 DMBoundaryType bx,by; 146 DMDAStencilType st; 147 ZoomCtx zctx; 148 PetscDrawViewPorts *ports = NULL; 149 PetscViewerFormat format; 150 PetscInt *displayfields; 151 PetscInt ndisplayfields,i,nbounds; 152 const PetscReal *bounds; 153 154 PetscFunctionBegin; 155 zctx.showgrid = PETSC_FALSE; 156 157 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 158 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); if (isnull) PetscFunctionReturn(0); 159 ierr = PetscViewerDrawGetBounds(viewer,&nbounds,&bounds);CHKERRQ(ierr); 160 161 ierr = VecGetDM(xin,&da);CHKERRQ(ierr); 162 if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA"); 163 164 ierr = PetscObjectGetComm((PetscObject)xin,&comm);CHKERRQ(ierr); 165 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 166 167 ierr = DMDAGetInfo(da,0,&M,&N,0,&zctx.m,&zctx.n,0,&w,&s,&bx,&by,0,&st);CHKERRQ(ierr); 168 ierr = DMDAGetOwnershipRanges(da,&lx,&ly,NULL);CHKERRQ(ierr); 169 170 /* 171 Obtain a sequential vector that is going to contain the local values plus ONE layer of 172 ghosted values to draw the graphics from. We also need its corresponding DMDA (dac) that will 173 update the local values pluse ONE layer of ghost values. 174 */ 175 ierr = PetscObjectQuery((PetscObject)da,"GraphicsGhosted",(PetscObject*)&xlocal);CHKERRQ(ierr); 176 if (!xlocal) { 177 if (bx != DM_BOUNDARY_NONE || by != DM_BOUNDARY_NONE || s != 1 || st != DMDA_STENCIL_BOX) { 178 /* 179 if original da is not of stencil width one, or periodic or not a box stencil then 180 create a special DMDA to handle one level of ghost points for graphics 181 */ 182 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); 183 ierr = PetscInfo(da,"Creating auxilary DMDA for managing graphics ghost points\n");CHKERRQ(ierr); 184 } else { 185 /* otherwise we can use the da we already have */ 186 dac = da; 187 } 188 /* create local vector for holding ghosted values used in graphics */ 189 ierr = DMCreateLocalVector(dac,&xlocal);CHKERRQ(ierr); 190 if (dac != da) { 191 /* don't keep any public reference of this DMDA, is is only available through xlocal */ 192 ierr = PetscObjectDereference((PetscObject)dac);CHKERRQ(ierr); 193 } else { 194 /* remove association between xlocal and da, because below we compose in the opposite 195 direction and if we left this connect we'd get a loop, so the objects could 196 never be destroyed */ 197 ierr = PetscObjectRemoveReference((PetscObject)xlocal,"__PETSc_dm");CHKERRQ(ierr); 198 } 199 ierr = PetscObjectCompose((PetscObject)da,"GraphicsGhosted",(PetscObject)xlocal);CHKERRQ(ierr); 200 ierr = PetscObjectDereference((PetscObject)xlocal);CHKERRQ(ierr); 201 } else { 202 if (bx != DM_BOUNDARY_NONE || by != DM_BOUNDARY_NONE || s != 1 || st != DMDA_STENCIL_BOX) { 203 ierr = VecGetDM(xlocal, &dac);CHKERRQ(ierr); 204 } else { 205 dac = da; 206 } 207 } 208 209 /* 210 Get local (ghosted) values of vector 211 */ 212 ierr = DMGlobalToLocalBegin(dac,xin,INSERT_VALUES,xlocal);CHKERRQ(ierr); 213 ierr = DMGlobalToLocalEnd(dac,xin,INSERT_VALUES,xlocal);CHKERRQ(ierr); 214 ierr = VecGetArray(xlocal,&zctx.v);CHKERRQ(ierr); 215 216 /* get coordinates of nodes */ 217 ierr = DMGetCoordinates(da,&xcoor);CHKERRQ(ierr); 218 if (!xcoor) { 219 ierr = DMDASetUniformCoordinates(da,0.0,1.0,0.0,1.0,0.0,0.0);CHKERRQ(ierr); 220 ierr = DMGetCoordinates(da,&xcoor);CHKERRQ(ierr); 221 } 222 223 /* 224 Determine the min and max coordinates in plot 225 */ 226 ierr = VecStrideMin(xcoor,0,NULL,&xmin);CHKERRQ(ierr); 227 ierr = VecStrideMax(xcoor,0,NULL,&xmax);CHKERRQ(ierr); 228 ierr = VecStrideMin(xcoor,1,NULL,&ymin);CHKERRQ(ierr); 229 ierr = VecStrideMax(xcoor,1,NULL,&ymax);CHKERRQ(ierr); 230 coors[0] = xmin - .05*(xmax- xmin); coors[2] = xmax + .05*(xmax - xmin); 231 coors[1] = ymin - .05*(ymax- ymin); coors[3] = ymax + .05*(ymax - ymin); 232 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); 233 234 ierr = PetscOptionsGetRealArray(NULL,"-draw_coordinates",coors,&ncoors,NULL);CHKERRQ(ierr); 235 236 /* 237 get local ghosted version of coordinates 238 */ 239 ierr = PetscObjectQuery((PetscObject)da,"GraphicsCoordinateGhosted",(PetscObject*)&xcoorl);CHKERRQ(ierr); 240 if (!xcoorl) { 241 /* create DMDA to get local version of graphics */ 242 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); 243 ierr = PetscInfo(dag,"Creating auxilary DMDA for managing graphics coordinates ghost points\n");CHKERRQ(ierr); 244 ierr = DMCreateLocalVector(dag,&xcoorl);CHKERRQ(ierr); 245 ierr = PetscObjectCompose((PetscObject)da,"GraphicsCoordinateGhosted",(PetscObject)xcoorl);CHKERRQ(ierr); 246 ierr = PetscObjectDereference((PetscObject)dag);CHKERRQ(ierr); 247 ierr = PetscObjectDereference((PetscObject)xcoorl);CHKERRQ(ierr); 248 } else { 249 ierr = VecGetDM(xcoorl,&dag);CHKERRQ(ierr); 250 } 251 ierr = DMGlobalToLocalBegin(dag,xcoor,INSERT_VALUES,xcoorl);CHKERRQ(ierr); 252 ierr = DMGlobalToLocalEnd(dag,xcoor,INSERT_VALUES,xcoorl);CHKERRQ(ierr); 253 ierr = VecGetArray(xcoorl,&zctx.xy);CHKERRQ(ierr); 254 255 /* 256 Get information about size of area each processor must do graphics for 257 */ 258 ierr = DMDAGetInfo(dac,0,&M,&N,0,0,0,0,&zctx.step,0,&bx,&by,0,0);CHKERRQ(ierr); 259 ierr = DMDAGetGhostCorners(dac,0,0,0,&zctx.m,&zctx.n,0);CHKERRQ(ierr); 260 261 ierr = PetscOptionsGetBool(NULL,"-draw_contour_grid",&zctx.showgrid,NULL);CHKERRQ(ierr); 262 263 ierr = DMDASelectFields(da,&ndisplayfields,&displayfields);CHKERRQ(ierr); 264 265 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 266 ierr = PetscOptionsGetBool(NULL,"-draw_ports",&useports,NULL);CHKERRQ(ierr); 267 if (useports || format == PETSC_VIEWER_DRAW_PORTS) { 268 ierr = PetscDrawSynchronizedClear(draw);CHKERRQ(ierr); 269 ierr = PetscDrawViewPortsCreate(draw,ndisplayfields,&ports);CHKERRQ(ierr); 270 zctx.name0 = 0; 271 zctx.name1 = 0; 272 } else { 273 ierr = DMDAGetCoordinateName(da,0,&zctx.name0);CHKERRQ(ierr); 274 ierr = DMDAGetCoordinateName(da,1,&zctx.name1);CHKERRQ(ierr); 275 } 276 277 /* 278 Loop over each field; drawing each in a different window 279 */ 280 for (i=0; i<ndisplayfields; i++) { 281 zctx.k = displayfields[i]; 282 if (useports) { 283 ierr = PetscDrawViewPortsSet(ports,i);CHKERRQ(ierr); 284 } else { 285 ierr = PetscViewerDrawGetDraw(viewer,i,&draw);CHKERRQ(ierr); 286 } 287 288 /* 289 Determine the min and max color in plot 290 */ 291 ierr = VecStrideMin(xin,zctx.k,NULL,&zctx.min);CHKERRQ(ierr); 292 ierr = VecStrideMax(xin,zctx.k,NULL,&zctx.max);CHKERRQ(ierr); 293 if (zctx.k < nbounds) { 294 zctx.min = bounds[2*zctx.k]; 295 zctx.max = bounds[2*zctx.k+1]; 296 } 297 if (zctx.min == zctx.max) { 298 zctx.min -= 1.e-12; 299 zctx.max += 1.e-12; 300 } 301 302 if (!rank) { 303 const char *title; 304 305 ierr = DMDAGetFieldName(da,zctx.k,&title);CHKERRQ(ierr); 306 if (title) { 307 ierr = PetscDrawSetTitle(draw,title);CHKERRQ(ierr); 308 } 309 } 310 ierr = PetscDrawSetCoordinates(draw,coors[0],coors[1],coors[2],coors[3]);CHKERRQ(ierr); 311 ierr = PetscInfo2(da,"DMDA 2d contour plot min %g max %g\n",(double)zctx.min,(double)zctx.max);CHKERRQ(ierr); 312 313 ierr = PetscDrawGetPopup(draw,&popup);CHKERRQ(ierr); 314 if (popup) {ierr = PetscDrawScalePopup(popup,zctx.min,zctx.max);CHKERRQ(ierr);} 315 316 zctx.scale = (245.0 - PETSC_DRAW_BASIC_COLORS)/(zctx.max - zctx.min); 317 318 ierr = PetscDrawZoom(draw,VecView_MPI_Draw_DA2d_Zoom,&zctx);CHKERRQ(ierr); 319 } 320 ierr = PetscFree(displayfields);CHKERRQ(ierr); 321 ierr = PetscDrawViewPortsDestroy(ports);CHKERRQ(ierr); 322 323 ierr = VecRestoreArray(xcoorl,&zctx.xy);CHKERRQ(ierr); 324 ierr = VecRestoreArray(xlocal,&zctx.v);CHKERRQ(ierr); 325 PetscFunctionReturn(0); 326 } 327 328 #if defined(PETSC_HAVE_HDF5) 329 #undef __FUNCT__ 330 #define __FUNCT__ "VecGetHDF5ChunkSize" 331 static PetscErrorCode VecGetHDF5ChunkSize(DM_DA *da, Vec xin, PetscInt dimension, PetscInt timestep, hsize_t *chunkDims) 332 { 333 PetscMPIInt comm_size; 334 PetscErrorCode ierr; 335 hsize_t chunk_size, target_size, dim; 336 hsize_t vec_size = sizeof(PetscScalar)*da->M*da->N*da->P*da->w; 337 hsize_t avg_local_vec_size,KiB = 1024,MiB = KiB*KiB,GiB = MiB*KiB,min_size = MiB; 338 hsize_t max_chunks = 64*KiB; /* HDF5 internal limitation */ 339 hsize_t max_chunk_size = 4*GiB; /* HDF5 internal limitation */ 340 PetscInt zslices=da->p, yslices=da->n, xslices=da->m; 341 342 PetscFunctionBegin; 343 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)xin), &comm_size);CHKERRQ(ierr); 344 avg_local_vec_size = (hsize_t) ceil(vec_size*1.0/comm_size); /* we will attempt to use this as the chunk size */ 345 346 target_size = (hsize_t) ceil(PetscMin(vec_size, 347 PetscMin(max_chunk_size, 348 PetscMax(avg_local_vec_size, 349 PetscMax(ceil(vec_size*1.0/max_chunks), 350 min_size))))); 351 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(PetscScalar); 352 353 /* 354 if size/rank > max_chunk_size, we need radical measures: even going down to 355 avg_local_vec_size is not enough, so we simply use chunk size of 4 GiB no matter 356 what, composed in the most efficient way possible. 357 N.B. this minimises the number of chunks, which may or may not be the optimal 358 solution. In a BG, for example, the optimal solution is probably to make # chunks = # 359 IO nodes involved, but this author has no access to a BG to figure out how to 360 reliably find the right number. And even then it may or may not be enough. 361 */ 362 if (avg_local_vec_size > max_chunk_size) { 363 /* check if we can just split local z-axis: is that enough? */ 364 zslices = (PetscInt)ceil(vec_size*1.0/(da->p*max_chunk_size))*zslices; 365 if (zslices > da->P) { 366 /* lattice is too large in xy-directions, splitting z only is not enough */ 367 zslices = da->P; 368 yslices= (PetscInt)ceil(vec_size*1.0/(zslices*da->n*max_chunk_size))*yslices; 369 if (yslices > da->N) { 370 /* lattice is too large in x-direction, splitting along z, y is not enough */ 371 yslices = da->N; 372 xslices= (PetscInt)ceil(vec_size*1.0/(zslices*yslices*da->m*max_chunk_size))*xslices; 373 } 374 } 375 dim = 0; 376 if (timestep >= 0) { 377 ++dim; 378 } 379 /* prefer to split z-axis, even down to planar slices */ 380 if (dimension == 3) { 381 chunkDims[dim++] = (hsize_t) da->P/zslices; 382 chunkDims[dim++] = (hsize_t) da->N/yslices; 383 chunkDims[dim++] = (hsize_t) da->M/xslices; 384 } else { 385 /* This is a 2D world exceeding 4GiB in size; yes, I've seen them, even used myself */ 386 chunkDims[dim++] = (hsize_t) da->N/yslices; 387 chunkDims[dim++] = (hsize_t) da->M/xslices; 388 } 389 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); 390 } else { 391 if (target_size < chunk_size) { 392 /* only change the defaults if target_size < chunk_size */ 393 dim = 0; 394 if (timestep >= 0) { 395 ++dim; 396 } 397 /* prefer to split z-axis, even down to planar slices */ 398 if (dimension == 3) { 399 /* try splitting the z-axis to core-size bits, i.e. divide chunk size by # comm_size in z-direction */ 400 if (target_size >= chunk_size/da->p) { 401 /* just make chunks the size of <local_z>x<whole_world_y>x<whole_world_x>x<dof> */ 402 chunkDims[dim] = (hsize_t) ceil(da->P*1.0/da->p); 403 } else { 404 /* oops, just splitting the z-axis is NOT ENOUGH, need to split more; let's be 405 radical and let everyone write all they've got */ 406 chunkDims[dim++] = (hsize_t) ceil(da->P*1.0/da->p); 407 chunkDims[dim++] = (hsize_t) ceil(da->N*1.0/da->n); 408 chunkDims[dim++] = (hsize_t) ceil(da->M*1.0/da->m); 409 } 410 } else { 411 /* This is a 2D world exceeding 4GiB in size; yes, I've seen them, even used myself */ 412 if (target_size >= chunk_size/da->n) { 413 /* just make chunks the size of <local_z>x<whole_world_y>x<whole_world_x>x<dof> */ 414 chunkDims[dim] = (hsize_t) ceil(da->N*1.0/da->n); 415 } else { 416 /* oops, just splitting the z-axis is NOT ENOUGH, need to split more; let's be 417 radical and let everyone write all they've got */ 418 chunkDims[dim++] = (hsize_t) ceil(da->N*1.0/da->n); 419 chunkDims[dim++] = (hsize_t) ceil(da->M*1.0/da->m); 420 } 421 422 } 423 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); 424 } else { 425 /* precomputed chunks are fine, we don't need to do anything */ 426 } 427 } 428 PetscFunctionReturn(0); 429 } 430 #endif 431 432 #if defined(PETSC_HAVE_HDF5) 433 #undef __FUNCT__ 434 #define __FUNCT__ "VecView_MPI_HDF5_DA" 435 PetscErrorCode VecView_MPI_HDF5_DA(Vec xin,PetscViewer viewer) 436 { 437 DM dm; 438 DM_DA *da; 439 hid_t filespace; /* file dataspace identifier */ 440 hid_t chunkspace; /* chunk dataset property identifier */ 441 hid_t plist_id; /* property list identifier */ 442 hid_t dset_id; /* dataset identifier */ 443 hid_t memspace; /* memory dataspace identifier */ 444 hid_t file_id; 445 hid_t group; 446 hid_t scalartype; /* scalar type (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */ 447 herr_t status; 448 hsize_t dim; 449 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 */ 450 PetscInt timestep, dimension; 451 PetscScalar *x; 452 const char *vecname; 453 PetscErrorCode ierr; 454 455 PetscFunctionBegin; 456 ierr = PetscViewerHDF5OpenGroup(viewer, &file_id, &group);CHKERRQ(ierr); 457 ierr = PetscViewerHDF5GetTimestep(viewer, ×tep);CHKERRQ(ierr); 458 459 ierr = VecGetDM(xin,&dm);CHKERRQ(ierr); 460 if (!dm) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA"); 461 da = (DM_DA*)dm->data; 462 ierr = DMGetDimension(dm, &dimension);CHKERRQ(ierr); 463 464 /* Create the dataspace for the dataset. 465 * 466 * dims - holds the current dimensions of the dataset 467 * 468 * maxDims - holds the maximum dimensions of the dataset (unlimited 469 * for the number of time steps with the current dimensions for the 470 * other dimensions; so only additional time steps can be added). 471 * 472 * chunkDims - holds the size of a single time step (required to 473 * permit extending dataset). 474 */ 475 dim = 0; 476 if (timestep >= 0) { 477 dims[dim] = timestep+1; 478 maxDims[dim] = H5S_UNLIMITED; 479 chunkDims[dim] = 1; 480 ++dim; 481 } 482 if (dimension == 3) { 483 ierr = PetscHDF5IntCast(da->P,dims+dim);CHKERRQ(ierr); 484 maxDims[dim] = dims[dim]; 485 chunkDims[dim] = dims[dim]; 486 ++dim; 487 } 488 if (dimension > 1) { 489 ierr = PetscHDF5IntCast(da->N,dims+dim);CHKERRQ(ierr); 490 maxDims[dim] = dims[dim]; 491 chunkDims[dim] = dims[dim]; 492 ++dim; 493 } 494 ierr = PetscHDF5IntCast(da->M,dims+dim);CHKERRQ(ierr); 495 maxDims[dim] = dims[dim]; 496 chunkDims[dim] = dims[dim]; 497 ++dim; 498 if (da->w > 1) { 499 ierr = PetscHDF5IntCast(da->w,dims+dim);CHKERRQ(ierr); 500 maxDims[dim] = dims[dim]; 501 chunkDims[dim] = dims[dim]; 502 ++dim; 503 } 504 #if defined(PETSC_USE_COMPLEX) 505 dims[dim] = 2; 506 maxDims[dim] = dims[dim]; 507 chunkDims[dim] = dims[dim]; 508 ++dim; 509 #endif 510 511 ierr = VecGetHDF5ChunkSize(da, xin, dimension, timestep, chunkDims); CHKERRQ(ierr); 512 513 filespace = H5Screate_simple(dim, dims, maxDims); 514 if (filespace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Screate_simple()"); 515 516 #if defined(PETSC_USE_REAL_SINGLE) 517 scalartype = H5T_NATIVE_FLOAT; 518 #elif defined(PETSC_USE_REAL___FLOAT128) 519 #error "HDF5 output with 128 bit floats not supported." 520 #else 521 scalartype = H5T_NATIVE_DOUBLE; 522 #endif 523 524 /* Create the dataset with default properties and close filespace */ 525 ierr = PetscObjectGetName((PetscObject)xin,&vecname);CHKERRQ(ierr); 526 if (!H5Lexists(group, vecname, H5P_DEFAULT)) { 527 /* Create chunk */ 528 chunkspace = H5Pcreate(H5P_DATASET_CREATE); 529 if (chunkspace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Pcreate()"); 530 status = H5Pset_chunk(chunkspace, dim, chunkDims);CHKERRQ(status); 531 532 #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800) 533 dset_id = H5Dcreate2(group, vecname, scalartype, filespace, H5P_DEFAULT, chunkspace, H5P_DEFAULT); 534 #else 535 dset_id = H5Dcreate(group, vecname, scalartype, filespace, H5P_DEFAULT); 536 #endif 537 if (dset_id == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Dcreate2()"); 538 } else { 539 dset_id = H5Dopen2(group, vecname, H5P_DEFAULT); 540 status = H5Dset_extent(dset_id, dims);CHKERRQ(status); 541 } 542 status = H5Sclose(filespace);CHKERRQ(status); 543 544 /* Each process defines a dataset and writes it to the hyperslab in the file */ 545 dim = 0; 546 if (timestep >= 0) { 547 offset[dim] = timestep; 548 ++dim; 549 } 550 if (dimension == 3) {ierr = PetscHDF5IntCast(da->zs,offset + dim++);CHKERRQ(ierr);} 551 if (dimension > 1) {ierr = PetscHDF5IntCast(da->ys,offset + dim++);CHKERRQ(ierr);} 552 ierr = PetscHDF5IntCast(da->xs/da->w,offset + dim++);CHKERRQ(ierr); 553 if (da->w > 1) offset[dim++] = 0; 554 #if defined(PETSC_USE_COMPLEX) 555 offset[dim++] = 0; 556 #endif 557 dim = 0; 558 if (timestep >= 0) { 559 count[dim] = 1; 560 ++dim; 561 } 562 if (dimension == 3) {ierr = PetscHDF5IntCast(da->ze - da->zs,count + dim++);CHKERRQ(ierr);} 563 if (dimension > 1) {ierr = PetscHDF5IntCast(da->ye - da->ys,count + dim++);CHKERRQ(ierr);} 564 ierr = PetscHDF5IntCast((da->xe - da->xs)/da->w,count + dim++);CHKERRQ(ierr); 565 if (da->w > 1) {ierr = PetscHDF5IntCast(da->w,count + dim++);CHKERRQ(ierr);} 566 #if defined(PETSC_USE_COMPLEX) 567 count[dim++] = 2; 568 #endif 569 memspace = H5Screate_simple(dim, count, NULL); 570 if (memspace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Screate_simple()"); 571 572 filespace = H5Dget_space(dset_id); 573 if (filespace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Dget_space()"); 574 status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, count, NULL);CHKERRQ(status); 575 576 /* Create property list for collective dataset write */ 577 plist_id = H5Pcreate(H5P_DATASET_XFER); 578 if (plist_id == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Pcreate()"); 579 #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO) 580 status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);CHKERRQ(status); 581 #endif 582 /* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */ 583 584 ierr = VecGetArray(xin, &x);CHKERRQ(ierr); 585 status = H5Dwrite(dset_id, scalartype, memspace, filespace, plist_id, x);CHKERRQ(status); 586 status = H5Fflush(file_id, H5F_SCOPE_GLOBAL);CHKERRQ(status); 587 ierr = VecRestoreArray(xin, &x);CHKERRQ(ierr); 588 589 /* Close/release resources */ 590 if (group != file_id) { 591 status = H5Gclose(group);CHKERRQ(status); 592 } 593 status = H5Pclose(plist_id);CHKERRQ(status); 594 status = H5Sclose(filespace);CHKERRQ(status); 595 status = H5Sclose(memspace);CHKERRQ(status); 596 status = H5Dclose(dset_id);CHKERRQ(status); 597 ierr = PetscInfo1(xin,"Wrote Vec object with name %s\n",vecname);CHKERRQ(ierr); 598 PetscFunctionReturn(0); 599 } 600 #endif 601 602 extern PetscErrorCode VecView_MPI_Draw_DA1d(Vec,PetscViewer); 603 604 #if defined(PETSC_HAVE_MPIIO) 605 #undef __FUNCT__ 606 #define __FUNCT__ "DMDAArrayMPIIO" 607 static PetscErrorCode DMDAArrayMPIIO(DM da,PetscViewer viewer,Vec xin,PetscBool write) 608 { 609 PetscErrorCode ierr; 610 MPI_File mfdes; 611 PetscMPIInt gsizes[4],lsizes[4],lstarts[4],asiz,dof; 612 MPI_Datatype view; 613 const PetscScalar *array; 614 MPI_Offset off; 615 MPI_Aint ub,ul; 616 PetscInt type,rows,vecrows,tr[2]; 617 DM_DA *dd = (DM_DA*)da->data; 618 619 PetscFunctionBegin; 620 ierr = VecGetSize(xin,&vecrows);CHKERRQ(ierr); 621 if (!write) { 622 /* Read vector header. */ 623 ierr = PetscViewerBinaryRead(viewer,tr,2,PETSC_INT);CHKERRQ(ierr); 624 type = tr[0]; 625 rows = tr[1]; 626 if (type != VEC_FILE_CLASSID) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_WRONG,"Not vector next in file"); 627 if (rows != vecrows) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_SIZ,"Vector in file not same size as DMDA vector"); 628 } else { 629 tr[0] = VEC_FILE_CLASSID; 630 tr[1] = vecrows; 631 ierr = PetscViewerBinaryWrite(viewer,tr,2,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 632 } 633 634 ierr = PetscMPIIntCast(dd->w,&dof);CHKERRQ(ierr); 635 gsizes[0] = dof; 636 ierr = PetscMPIIntCast(dd->M,gsizes+1);CHKERRQ(ierr); 637 ierr = PetscMPIIntCast(dd->N,gsizes+2);CHKERRQ(ierr); 638 ierr = PetscMPIIntCast(dd->P,gsizes+3);CHKERRQ(ierr); 639 lsizes[0] = dof; 640 ierr = PetscMPIIntCast((dd->xe-dd->xs)/dof,lsizes+1);CHKERRQ(ierr); 641 ierr = PetscMPIIntCast(dd->ye-dd->ys,lsizes+2);CHKERRQ(ierr); 642 ierr = PetscMPIIntCast(dd->ze-dd->zs,lsizes+3);CHKERRQ(ierr); 643 lstarts[0] = 0; 644 ierr = PetscMPIIntCast(dd->xs/dof,lstarts+1);CHKERRQ(ierr); 645 ierr = PetscMPIIntCast(dd->ys,lstarts+2);CHKERRQ(ierr); 646 ierr = PetscMPIIntCast(dd->zs,lstarts+3);CHKERRQ(ierr); 647 ierr = MPI_Type_create_subarray(da->dim+1,gsizes,lsizes,lstarts,MPI_ORDER_FORTRAN,MPIU_SCALAR,&view);CHKERRQ(ierr); 648 ierr = MPI_Type_commit(&view);CHKERRQ(ierr); 649 650 ierr = PetscViewerBinaryGetMPIIODescriptor(viewer,&mfdes);CHKERRQ(ierr); 651 ierr = PetscViewerBinaryGetMPIIOOffset(viewer,&off);CHKERRQ(ierr); 652 ierr = MPI_File_set_view(mfdes,off,MPIU_SCALAR,view,(char*)"native",MPI_INFO_NULL);CHKERRQ(ierr); 653 ierr = VecGetArrayRead(xin,&array);CHKERRQ(ierr); 654 asiz = lsizes[1]*(lsizes[2] > 0 ? lsizes[2] : 1)*(lsizes[3] > 0 ? lsizes[3] : 1)*dof; 655 if (write) { 656 ierr = MPIU_File_write_all(mfdes,(PetscScalar*)array,asiz,MPIU_SCALAR,MPI_STATUS_IGNORE);CHKERRQ(ierr); 657 } else { 658 ierr = MPIU_File_read_all(mfdes,(PetscScalar*)array,asiz,MPIU_SCALAR,MPI_STATUS_IGNORE);CHKERRQ(ierr); 659 } 660 ierr = MPI_Type_get_extent(view,&ul,&ub);CHKERRQ(ierr); 661 ierr = PetscViewerBinaryAddMPIIOOffset(viewer,ub);CHKERRQ(ierr); 662 ierr = VecRestoreArrayRead(xin,&array);CHKERRQ(ierr); 663 ierr = MPI_Type_free(&view);CHKERRQ(ierr); 664 PetscFunctionReturn(0); 665 } 666 #endif 667 668 #undef __FUNCT__ 669 #define __FUNCT__ "VecView_MPI_DA" 670 PetscErrorCode VecView_MPI_DA(Vec xin,PetscViewer viewer) 671 { 672 DM da; 673 PetscErrorCode ierr; 674 PetscInt dim; 675 Vec natural; 676 PetscBool isdraw,isvtk; 677 #if defined(PETSC_HAVE_HDF5) 678 PetscBool ishdf5; 679 #endif 680 const char *prefix,*name; 681 PetscViewerFormat format; 682 683 PetscFunctionBegin; 684 ierr = VecGetDM(xin,&da);CHKERRQ(ierr); 685 if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA"); 686 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 687 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERVTK,&isvtk);CHKERRQ(ierr); 688 #if defined(PETSC_HAVE_HDF5) 689 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);CHKERRQ(ierr); 690 #endif 691 if (isdraw) { 692 ierr = DMDAGetInfo(da,&dim,0,0,0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr); 693 if (dim == 1) { 694 ierr = VecView_MPI_Draw_DA1d(xin,viewer);CHKERRQ(ierr); 695 } else if (dim == 2) { 696 ierr = VecView_MPI_Draw_DA2d(xin,viewer);CHKERRQ(ierr); 697 } else SETERRQ1(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Cannot graphically view vector associated with this dimensional DMDA %D",dim); 698 } else if (isvtk) { /* Duplicate the Vec and hold a reference to the DM */ 699 Vec Y; 700 ierr = PetscObjectReference((PetscObject)da);CHKERRQ(ierr); 701 ierr = VecDuplicate(xin,&Y);CHKERRQ(ierr); 702 if (((PetscObject)xin)->name) { 703 /* If xin was named, copy the name over to Y. The duplicate names are safe because nobody else will ever see Y. */ 704 ierr = PetscObjectSetName((PetscObject)Y,((PetscObject)xin)->name);CHKERRQ(ierr); 705 } 706 ierr = VecCopy(xin,Y);CHKERRQ(ierr); 707 ierr = PetscViewerVTKAddField(viewer,(PetscObject)da,DMDAVTKWriteAll,PETSC_VTK_POINT_FIELD,(PetscObject)Y);CHKERRQ(ierr); 708 #if defined(PETSC_HAVE_HDF5) 709 } else if (ishdf5) { 710 ierr = VecView_MPI_HDF5_DA(xin,viewer);CHKERRQ(ierr); 711 #endif 712 } else { 713 #if defined(PETSC_HAVE_MPIIO) 714 PetscBool isbinary,isMPIIO; 715 716 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 717 if (isbinary) { 718 ierr = PetscViewerBinaryGetMPIIO(viewer,&isMPIIO);CHKERRQ(ierr); 719 if (isMPIIO) { 720 ierr = DMDAArrayMPIIO(da,viewer,xin,PETSC_TRUE);CHKERRQ(ierr); 721 PetscFunctionReturn(0); 722 } 723 } 724 #endif 725 726 /* call viewer on natural ordering */ 727 ierr = PetscObjectGetOptionsPrefix((PetscObject)xin,&prefix);CHKERRQ(ierr); 728 ierr = DMDACreateNaturalVector(da,&natural);CHKERRQ(ierr); 729 ierr = PetscObjectSetOptionsPrefix((PetscObject)natural,prefix);CHKERRQ(ierr); 730 ierr = DMDAGlobalToNaturalBegin(da,xin,INSERT_VALUES,natural);CHKERRQ(ierr); 731 ierr = DMDAGlobalToNaturalEnd(da,xin,INSERT_VALUES,natural);CHKERRQ(ierr); 732 ierr = PetscObjectGetName((PetscObject)xin,&name);CHKERRQ(ierr); 733 ierr = PetscObjectSetName((PetscObject)natural,name);CHKERRQ(ierr); 734 735 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 736 if (format == PETSC_VIEWER_BINARY_MATLAB) { 737 /* temporarily remove viewer format so it won't trigger in the VecView() */ 738 ierr = PetscViewerSetFormat(viewer,PETSC_VIEWER_DEFAULT);CHKERRQ(ierr); 739 } 740 741 ierr = VecView(natural,viewer);CHKERRQ(ierr); 742 743 if (format == PETSC_VIEWER_BINARY_MATLAB) { 744 MPI_Comm comm; 745 FILE *info; 746 const char *fieldname; 747 char fieldbuf[256]; 748 PetscInt dim,ni,nj,nk,pi,pj,pk,dof,n; 749 750 /* set the viewer format back into the viewer */ 751 ierr = PetscViewerSetFormat(viewer,format);CHKERRQ(ierr); 752 ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr); 753 ierr = PetscViewerBinaryGetInfoPointer(viewer,&info);CHKERRQ(ierr); 754 ierr = DMDAGetInfo(da,&dim,&ni,&nj,&nk,&pi,&pj,&pk,&dof,0,0,0,0,0);CHKERRQ(ierr); 755 ierr = PetscFPrintf(comm,info,"#--- begin code written by PetscViewerBinary for MATLAB format ---#\n");CHKERRQ(ierr); 756 ierr = PetscFPrintf(comm,info,"#$$ tmp = PetscBinaryRead(fd); \n");CHKERRQ(ierr); 757 if (dim == 1) { ierr = PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d);\n",dof,ni);CHKERRQ(ierr); } 758 if (dim == 2) { ierr = PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d,%d);\n",dof,ni,nj);CHKERRQ(ierr); } 759 if (dim == 3) { ierr = PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d,%d,%d);\n",dof,ni,nj,nk);CHKERRQ(ierr); } 760 761 for (n=0; n<dof; n++) { 762 ierr = DMDAGetFieldName(da,n,&fieldname);CHKERRQ(ierr); 763 if (!fieldname || !fieldname[0]) { 764 ierr = PetscSNPrintf(fieldbuf,sizeof fieldbuf,"field%D",n);CHKERRQ(ierr); 765 fieldname = fieldbuf; 766 } 767 if (dim == 1) { ierr = PetscFPrintf(comm,info,"#$$ Set.%s.%s = squeeze(tmp(%d,:))';\n",name,fieldname,n+1);CHKERRQ(ierr); } 768 if (dim == 2) { ierr = PetscFPrintf(comm,info,"#$$ Set.%s.%s = squeeze(tmp(%d,:,:))';\n",name,fieldname,n+1);CHKERRQ(ierr); } 769 if (dim == 3) { ierr = PetscFPrintf(comm,info,"#$$ Set.%s.%s = permute(squeeze(tmp(%d,:,:,:)),[2 1 3]);\n",name,fieldname,n+1);CHKERRQ(ierr);} 770 } 771 ierr = PetscFPrintf(comm,info,"#$$ clear tmp; \n");CHKERRQ(ierr); 772 ierr = PetscFPrintf(comm,info,"#--- end code written by PetscViewerBinary for MATLAB format ---#\n\n");CHKERRQ(ierr); 773 } 774 775 ierr = VecDestroy(&natural);CHKERRQ(ierr); 776 } 777 PetscFunctionReturn(0); 778 } 779 780 #if defined(PETSC_HAVE_HDF5) 781 #undef __FUNCT__ 782 #define __FUNCT__ "VecLoad_HDF5_DA" 783 PetscErrorCode VecLoad_HDF5_DA(Vec xin, PetscViewer viewer) 784 { 785 DM da; 786 PetscErrorCode ierr; 787 hsize_t dim; 788 hsize_t count[5]; 789 hsize_t offset[5]; 790 PetscInt cnt = 0, dimension; 791 PetscScalar *x; 792 const char *vecname; 793 hid_t filespace; /* file dataspace identifier */ 794 hid_t plist_id; /* property list identifier */ 795 hid_t dset_id; /* dataset identifier */ 796 hid_t memspace; /* memory dataspace identifier */ 797 hid_t file_id; 798 herr_t status; 799 DM_DA *dd; 800 801 PetscFunctionBegin; 802 ierr = PetscViewerHDF5GetFileId(viewer, &file_id);CHKERRQ(ierr); 803 ierr = VecGetDM(xin,&da);CHKERRQ(ierr); 804 dd = (DM_DA*)da->data; 805 ierr = DMGetDimension(da, &dimension);CHKERRQ(ierr); 806 807 /* Create the dataspace for the dataset */ 808 ierr = PetscHDF5IntCast(dimension + ((dd->w == 1) ? 0 : 1),&dim);CHKERRQ(ierr); 809 #if defined(PETSC_USE_COMPLEX) 810 dim++; 811 #endif 812 813 /* Create the dataset with default properties and close filespace */ 814 ierr = PetscObjectGetName((PetscObject)xin,&vecname);CHKERRQ(ierr); 815 #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800) 816 dset_id = H5Dopen2(file_id, vecname, H5P_DEFAULT); 817 #else 818 dset_id = H5Dopen(file_id, vecname); 819 #endif 820 if (dset_id == -1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Dopen2() with Vec named %s",vecname); 821 filespace = H5Dget_space(dset_id); 822 823 /* Each process defines a dataset and reads it from the hyperslab in the file */ 824 cnt = 0; 825 if (dimension == 3) {ierr = PetscHDF5IntCast(dd->zs,offset + cnt++);CHKERRQ(ierr);} 826 if (dimension > 1) {ierr = PetscHDF5IntCast(dd->ys,offset + cnt++);CHKERRQ(ierr);} 827 ierr = PetscHDF5IntCast(dd->xs/dd->w,offset + cnt++);CHKERRQ(ierr); 828 if (dd->w > 1) offset[cnt++] = 0; 829 #if defined(PETSC_USE_COMPLEX) 830 offset[cnt++] = 0; 831 #endif 832 cnt = 0; 833 if (dimension == 3) {ierr = PetscHDF5IntCast(dd->ze - dd->zs,count + cnt++);CHKERRQ(ierr);} 834 if (dimension > 1) {ierr = PetscHDF5IntCast(dd->ye - dd->ys,count + cnt++);CHKERRQ(ierr);} 835 ierr = PetscHDF5IntCast((dd->xe - dd->xs)/dd->w,count + cnt++);CHKERRQ(ierr); 836 if (dd->w > 1) {ierr = PetscHDF5IntCast(dd->w,count + cnt++);CHKERRQ(ierr);} 837 #if defined(PETSC_USE_COMPLEX) 838 count[cnt++] = 2; 839 #endif 840 memspace = H5Screate_simple(dim, count, NULL); 841 if (memspace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Screate_simple()"); 842 843 status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, count, NULL);CHKERRQ(status); 844 845 /* Create property list for collective dataset write */ 846 plist_id = H5Pcreate(H5P_DATASET_XFER); 847 if (plist_id == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Pcreate()"); 848 #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO) 849 status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);CHKERRQ(status); 850 #endif 851 /* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */ 852 853 ierr = VecGetArray(xin, &x);CHKERRQ(ierr); 854 status = H5Dread(dset_id, H5T_NATIVE_DOUBLE, memspace, filespace, plist_id, x);CHKERRQ(status); 855 ierr = VecRestoreArray(xin, &x);CHKERRQ(ierr); 856 857 /* Close/release resources */ 858 status = H5Pclose(plist_id);CHKERRQ(status); 859 status = H5Sclose(filespace);CHKERRQ(status); 860 status = H5Sclose(memspace);CHKERRQ(status); 861 status = H5Dclose(dset_id);CHKERRQ(status); 862 PetscFunctionReturn(0); 863 } 864 #endif 865 866 #undef __FUNCT__ 867 #define __FUNCT__ "VecLoad_Binary_DA" 868 PetscErrorCode VecLoad_Binary_DA(Vec xin, PetscViewer viewer) 869 { 870 DM da; 871 PetscErrorCode ierr; 872 Vec natural; 873 const char *prefix; 874 PetscInt bs; 875 PetscBool flag; 876 DM_DA *dd; 877 #if defined(PETSC_HAVE_MPIIO) 878 PetscBool isMPIIO; 879 #endif 880 881 PetscFunctionBegin; 882 ierr = VecGetDM(xin,&da);CHKERRQ(ierr); 883 dd = (DM_DA*)da->data; 884 #if defined(PETSC_HAVE_MPIIO) 885 ierr = PetscViewerBinaryGetMPIIO(viewer,&isMPIIO);CHKERRQ(ierr); 886 if (isMPIIO) { 887 ierr = DMDAArrayMPIIO(da,viewer,xin,PETSC_FALSE);CHKERRQ(ierr); 888 PetscFunctionReturn(0); 889 } 890 #endif 891 892 ierr = PetscObjectGetOptionsPrefix((PetscObject)xin,&prefix);CHKERRQ(ierr); 893 ierr = DMDACreateNaturalVector(da,&natural);CHKERRQ(ierr); 894 ierr = PetscObjectSetName((PetscObject)natural,((PetscObject)xin)->name);CHKERRQ(ierr); 895 ierr = PetscObjectSetOptionsPrefix((PetscObject)natural,prefix);CHKERRQ(ierr); 896 ierr = VecLoad(natural,viewer);CHKERRQ(ierr); 897 ierr = DMDANaturalToGlobalBegin(da,natural,INSERT_VALUES,xin);CHKERRQ(ierr); 898 ierr = DMDANaturalToGlobalEnd(da,natural,INSERT_VALUES,xin);CHKERRQ(ierr); 899 ierr = VecDestroy(&natural);CHKERRQ(ierr); 900 ierr = PetscInfo(xin,"Loading vector from natural ordering into DMDA\n");CHKERRQ(ierr); 901 ierr = PetscOptionsGetInt(((PetscObject)xin)->prefix,"-vecload_block_size",&bs,&flag);CHKERRQ(ierr); 902 if (flag && bs != dd->w) { 903 ierr = PetscInfo2(xin,"Block size in file %D not equal to DMDA's dof %D\n",bs,dd->w);CHKERRQ(ierr); 904 } 905 PetscFunctionReturn(0); 906 } 907 908 #undef __FUNCT__ 909 #define __FUNCT__ "VecLoad_Default_DA" 910 PetscErrorCode VecLoad_Default_DA(Vec xin, PetscViewer viewer) 911 { 912 PetscErrorCode ierr; 913 DM da; 914 PetscBool isbinary; 915 #if defined(PETSC_HAVE_HDF5) 916 PetscBool ishdf5; 917 #endif 918 919 PetscFunctionBegin; 920 ierr = VecGetDM(xin,&da);CHKERRQ(ierr); 921 if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA"); 922 923 #if defined(PETSC_HAVE_HDF5) 924 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);CHKERRQ(ierr); 925 #endif 926 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 927 928 if (isbinary) { 929 ierr = VecLoad_Binary_DA(xin,viewer);CHKERRQ(ierr); 930 #if defined(PETSC_HAVE_HDF5) 931 } else if (ishdf5) { 932 ierr = VecLoad_HDF5_DA(xin,viewer);CHKERRQ(ierr); 933 #endif 934 } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Viewer type %s not supported for vector loading", ((PetscObject)viewer)->type_name); 935 PetscFunctionReturn(0); 936 } 937