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 const 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 const 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 = VecGetArrayRead(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 = VecGetArrayRead(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 = VecRestoreArrayRead(xcoorl,&zctx.xy);CHKERRQ(ierr); 324 ierr = VecRestoreArrayRead(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,PetscMin(max_chunk_size,PetscMax(avg_local_vec_size,PetscMax(ceil(vec_size*1.0/max_chunks),min_size))))); 347 /* following line uses sizeof(PetscReal) instead of sizeof(PetscScalar) because the last dimension of chunkDims[] captures the 2* when complex numbers are being used */ 348 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); 349 350 /* 351 if size/rank > max_chunk_size, we need radical measures: even going down to 352 avg_local_vec_size is not enough, so we simply use chunk size of 4 GiB no matter 353 what, composed in the most efficient way possible. 354 N.B. this minimises the number of chunks, which may or may not be the optimal 355 solution. In a BG, for example, the optimal solution is probably to make # chunks = # 356 IO nodes involved, but this author has no access to a BG to figure out how to 357 reliably find the right number. And even then it may or may not be enough. 358 */ 359 if (avg_local_vec_size > max_chunk_size) { 360 /* check if we can just split local z-axis: is that enough? */ 361 zslices = (PetscInt)ceil(vec_size*1.0/(da->p*max_chunk_size))*zslices; 362 if (zslices > da->P) { 363 /* lattice is too large in xy-directions, splitting z only is not enough */ 364 zslices = da->P; 365 yslices= (PetscInt)ceil(vec_size*1.0/(zslices*da->n*max_chunk_size))*yslices; 366 if (yslices > da->N) { 367 /* lattice is too large in x-direction, splitting along z, y is not enough */ 368 yslices = da->N; 369 xslices= (PetscInt)ceil(vec_size*1.0/(zslices*yslices*da->m*max_chunk_size))*xslices; 370 } 371 } 372 dim = 0; 373 if (timestep >= 0) { 374 ++dim; 375 } 376 /* prefer to split z-axis, even down to planar slices */ 377 if (dimension == 3) { 378 chunkDims[dim++] = (hsize_t) da->P/zslices; 379 chunkDims[dim++] = (hsize_t) da->N/yslices; 380 chunkDims[dim++] = (hsize_t) da->M/xslices; 381 } else { 382 /* This is a 2D world exceeding 4GiB in size; yes, I've seen them, even used myself */ 383 chunkDims[dim++] = (hsize_t) da->N/yslices; 384 chunkDims[dim++] = (hsize_t) da->M/xslices; 385 } 386 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); 387 } else { 388 if (target_size < chunk_size) { 389 /* only change the defaults if target_size < chunk_size */ 390 dim = 0; 391 if (timestep >= 0) { 392 ++dim; 393 } 394 /* prefer to split z-axis, even down to planar slices */ 395 if (dimension == 3) { 396 /* try splitting the z-axis to core-size bits, i.e. divide chunk size by # comm_size in z-direction */ 397 if (target_size >= chunk_size/da->p) { 398 /* just make chunks the size of <local_z>x<whole_world_y>x<whole_world_x>x<dof> */ 399 chunkDims[dim] = (hsize_t) ceil(da->P*1.0/da->p); 400 } else { 401 /* oops, just splitting the z-axis is NOT ENOUGH, need to split more; let's be 402 radical and let everyone write all they've got */ 403 chunkDims[dim++] = (hsize_t) ceil(da->P*1.0/da->p); 404 chunkDims[dim++] = (hsize_t) ceil(da->N*1.0/da->n); 405 chunkDims[dim++] = (hsize_t) ceil(da->M*1.0/da->m); 406 } 407 } else { 408 /* This is a 2D world exceeding 4GiB in size; yes, I've seen them, even used myself */ 409 if (target_size >= chunk_size/da->n) { 410 /* just make chunks the size of <local_z>x<whole_world_y>x<whole_world_x>x<dof> */ 411 chunkDims[dim] = (hsize_t) ceil(da->N*1.0/da->n); 412 } else { 413 /* oops, just splitting the z-axis is NOT ENOUGH, need to split more; let's be 414 radical and let everyone write all they've got */ 415 chunkDims[dim++] = (hsize_t) ceil(da->N*1.0/da->n); 416 chunkDims[dim++] = (hsize_t) ceil(da->M*1.0/da->m); 417 } 418 419 } 420 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); 421 } else { 422 /* precomputed chunks are fine, we don't need to do anything */ 423 } 424 } 425 PetscFunctionReturn(0); 426 } 427 #endif 428 429 #if defined(PETSC_HAVE_HDF5) 430 #undef __FUNCT__ 431 #define __FUNCT__ "VecView_MPI_HDF5_DA" 432 PetscErrorCode VecView_MPI_HDF5_DA(Vec xin,PetscViewer viewer) 433 { 434 DM dm; 435 DM_DA *da; 436 hid_t filespace; /* file dataspace identifier */ 437 hid_t chunkspace; /* chunk dataset property identifier */ 438 hid_t plist_id; /* property list identifier */ 439 hid_t dset_id; /* dataset identifier */ 440 hid_t memspace; /* memory dataspace identifier */ 441 hid_t file_id; 442 hid_t group; 443 hid_t scalartype; /* scalar type (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */ 444 hsize_t dim; 445 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 */ 446 PetscInt timestep, dimension; 447 const PetscScalar *x; 448 const char *vecname; 449 PetscErrorCode ierr; 450 451 PetscFunctionBegin; 452 ierr = PetscViewerHDF5OpenGroup(viewer, &file_id, &group);CHKERRQ(ierr); 453 ierr = PetscViewerHDF5GetTimestep(viewer, ×tep);CHKERRQ(ierr); 454 455 ierr = VecGetDM(xin,&dm);CHKERRQ(ierr); 456 if (!dm) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA"); 457 da = (DM_DA*)dm->data; 458 ierr = DMGetDimension(dm, &dimension);CHKERRQ(ierr); 459 460 /* Create the dataspace for the dataset. 461 * 462 * dims - holds the current dimensions of the dataset 463 * 464 * maxDims - holds the maximum dimensions of the dataset (unlimited 465 * for the number of time steps with the current dimensions for the 466 * other dimensions; so only additional time steps can be added). 467 * 468 * chunkDims - holds the size of a single time step (required to 469 * permit extending dataset). 470 */ 471 dim = 0; 472 if (timestep >= 0) { 473 dims[dim] = timestep+1; 474 maxDims[dim] = H5S_UNLIMITED; 475 chunkDims[dim] = 1; 476 ++dim; 477 } 478 if (dimension == 3) { 479 ierr = PetscHDF5IntCast(da->P,dims+dim);CHKERRQ(ierr); 480 maxDims[dim] = dims[dim]; 481 chunkDims[dim] = dims[dim]; 482 ++dim; 483 } 484 if (dimension > 1) { 485 ierr = PetscHDF5IntCast(da->N,dims+dim);CHKERRQ(ierr); 486 maxDims[dim] = dims[dim]; 487 chunkDims[dim] = dims[dim]; 488 ++dim; 489 } 490 ierr = PetscHDF5IntCast(da->M,dims+dim);CHKERRQ(ierr); 491 maxDims[dim] = dims[dim]; 492 chunkDims[dim] = dims[dim]; 493 ++dim; 494 if (da->w > 1) { 495 ierr = PetscHDF5IntCast(da->w,dims+dim);CHKERRQ(ierr); 496 maxDims[dim] = dims[dim]; 497 chunkDims[dim] = dims[dim]; 498 ++dim; 499 } 500 #if defined(PETSC_USE_COMPLEX) 501 dims[dim] = 2; 502 maxDims[dim] = dims[dim]; 503 chunkDims[dim] = dims[dim]; 504 ++dim; 505 #endif 506 507 ierr = VecGetHDF5ChunkSize(da, xin, dimension, timestep, chunkDims); CHKERRQ(ierr); 508 509 PetscStackCallHDF5Return(filespace,H5Screate_simple,(dim, dims, maxDims)); 510 511 #if defined(PETSC_USE_REAL_SINGLE) 512 scalartype = H5T_NATIVE_FLOAT; 513 #elif defined(PETSC_USE_REAL___FLOAT128) 514 #error "HDF5 output with 128 bit floats not supported." 515 #else 516 scalartype = H5T_NATIVE_DOUBLE; 517 #endif 518 519 /* Create the dataset with default properties and close filespace */ 520 ierr = PetscObjectGetName((PetscObject)xin,&vecname);CHKERRQ(ierr); 521 if (!H5Lexists(group, vecname, H5P_DEFAULT)) { 522 /* Create chunk */ 523 PetscStackCallHDF5Return(chunkspace,H5Pcreate,(H5P_DATASET_CREATE)); 524 PetscStackCallHDF5(H5Pset_chunk,(chunkspace, dim, chunkDims)); 525 526 #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800) 527 PetscStackCallHDF5Return(dset_id,H5Dcreate2,(group, vecname, scalartype, filespace, H5P_DEFAULT, chunkspace, H5P_DEFAULT)); 528 #else 529 PetscStackCallHDF5Return(dset_id,H5Dcreate,(group, vecname, scalartype, filespace, H5P_DEFAULT)); 530 #endif 531 } else { 532 PetscStackCallHDF5Return(dset_id,H5Dopen2,(group, vecname, H5P_DEFAULT)); 533 PetscStackCallHDF5(H5Dset_extent,(dset_id, dims)); 534 } 535 PetscStackCallHDF5(H5Sclose,(filespace)); 536 537 /* Each process defines a dataset and writes it to the hyperslab in the file */ 538 dim = 0; 539 if (timestep >= 0) { 540 offset[dim] = timestep; 541 ++dim; 542 } 543 if (dimension == 3) {ierr = PetscHDF5IntCast(da->zs,offset + dim++);CHKERRQ(ierr);} 544 if (dimension > 1) {ierr = PetscHDF5IntCast(da->ys,offset + dim++);CHKERRQ(ierr);} 545 ierr = PetscHDF5IntCast(da->xs/da->w,offset + dim++);CHKERRQ(ierr); 546 if (da->w > 1) offset[dim++] = 0; 547 #if defined(PETSC_USE_COMPLEX) 548 offset[dim++] = 0; 549 #endif 550 dim = 0; 551 if (timestep >= 0) { 552 count[dim] = 1; 553 ++dim; 554 } 555 if (dimension == 3) {ierr = PetscHDF5IntCast(da->ze - da->zs,count + dim++);CHKERRQ(ierr);} 556 if (dimension > 1) {ierr = PetscHDF5IntCast(da->ye - da->ys,count + dim++);CHKERRQ(ierr);} 557 ierr = PetscHDF5IntCast((da->xe - da->xs)/da->w,count + dim++);CHKERRQ(ierr); 558 if (da->w > 1) {ierr = PetscHDF5IntCast(da->w,count + dim++);CHKERRQ(ierr);} 559 #if defined(PETSC_USE_COMPLEX) 560 count[dim++] = 2; 561 #endif 562 PetscStackCallHDF5Return(memspace,H5Screate_simple,(dim, count, NULL)); 563 PetscStackCallHDF5Return(filespace,H5Dget_space,(dset_id)); 564 PetscStackCallHDF5(H5Sselect_hyperslab,(filespace, H5S_SELECT_SET, offset, NULL, count, NULL)); 565 566 /* Create property list for collective dataset write */ 567 PetscStackCallHDF5Return(plist_id,H5Pcreate,(H5P_DATASET_XFER)); 568 #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO) 569 PetscStackCallHDF5(H5Pset_dxpl_mpio,(plist_id, H5FD_MPIO_COLLECTIVE)); 570 #endif 571 /* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */ 572 573 ierr = VecGetArrayRead(xin, &x);CHKERRQ(ierr); 574 PetscStackCallHDF5(H5Dwrite,(dset_id, scalartype, memspace, filespace, plist_id, x)); 575 PetscStackCallHDF5(H5Fflush,(file_id, H5F_SCOPE_GLOBAL)); 576 ierr = VecRestoreArrayRead(xin, &x);CHKERRQ(ierr); 577 578 /* Close/release resources */ 579 if (group != file_id) { 580 PetscStackCallHDF5(H5Gclose,(group)); 581 } 582 PetscStackCallHDF5(H5Pclose,(plist_id)); 583 PetscStackCallHDF5(H5Sclose,(filespace)); 584 PetscStackCallHDF5(H5Sclose,(memspace)); 585 PetscStackCallHDF5(H5Dclose,(dset_id)); 586 ierr = PetscInfo1(xin,"Wrote Vec object with name %s\n",vecname);CHKERRQ(ierr); 587 PetscFunctionReturn(0); 588 } 589 #endif 590 591 extern PetscErrorCode VecView_MPI_Draw_DA1d(Vec,PetscViewer); 592 593 #if defined(PETSC_HAVE_MPIIO) 594 #undef __FUNCT__ 595 #define __FUNCT__ "DMDAArrayMPIIO" 596 static PetscErrorCode DMDAArrayMPIIO(DM da,PetscViewer viewer,Vec xin,PetscBool write) 597 { 598 PetscErrorCode ierr; 599 MPI_File mfdes; 600 PetscMPIInt gsizes[4],lsizes[4],lstarts[4],asiz,dof; 601 MPI_Datatype view; 602 const PetscScalar *array; 603 MPI_Offset off; 604 MPI_Aint ub,ul; 605 PetscInt type,rows,vecrows,tr[2]; 606 DM_DA *dd = (DM_DA*)da->data; 607 PetscBool skipheader; 608 609 PetscFunctionBegin; 610 ierr = VecGetSize(xin,&vecrows);CHKERRQ(ierr); 611 ierr = PetscViewerBinaryGetSkipHeader(viewer,&skipheader);CHKERRQ(ierr); 612 if (!write) { 613 /* Read vector header. */ 614 if (!skipheader) { 615 ierr = PetscViewerBinaryRead(viewer,tr,2,PETSC_INT);CHKERRQ(ierr); 616 type = tr[0]; 617 rows = tr[1]; 618 if (type != VEC_FILE_CLASSID) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_WRONG,"Not vector next in file"); 619 if (rows != vecrows) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_SIZ,"Vector in file not same size as DMDA vector"); 620 } 621 } else { 622 tr[0] = VEC_FILE_CLASSID; 623 tr[1] = vecrows; 624 if (!skipheader) { 625 ierr = PetscViewerBinaryWrite(viewer,tr,2,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 626 } 627 } 628 629 ierr = PetscMPIIntCast(dd->w,&dof);CHKERRQ(ierr); 630 gsizes[0] = dof; 631 ierr = PetscMPIIntCast(dd->M,gsizes+1);CHKERRQ(ierr); 632 ierr = PetscMPIIntCast(dd->N,gsizes+2);CHKERRQ(ierr); 633 ierr = PetscMPIIntCast(dd->P,gsizes+3);CHKERRQ(ierr); 634 lsizes[0] = dof; 635 ierr = PetscMPIIntCast((dd->xe-dd->xs)/dof,lsizes+1);CHKERRQ(ierr); 636 ierr = PetscMPIIntCast(dd->ye-dd->ys,lsizes+2);CHKERRQ(ierr); 637 ierr = PetscMPIIntCast(dd->ze-dd->zs,lsizes+3);CHKERRQ(ierr); 638 lstarts[0] = 0; 639 ierr = PetscMPIIntCast(dd->xs/dof,lstarts+1);CHKERRQ(ierr); 640 ierr = PetscMPIIntCast(dd->ys,lstarts+2);CHKERRQ(ierr); 641 ierr = PetscMPIIntCast(dd->zs,lstarts+3);CHKERRQ(ierr); 642 ierr = MPI_Type_create_subarray(da->dim+1,gsizes,lsizes,lstarts,MPI_ORDER_FORTRAN,MPIU_SCALAR,&view);CHKERRQ(ierr); 643 ierr = MPI_Type_commit(&view);CHKERRQ(ierr); 644 645 ierr = PetscViewerBinaryGetMPIIODescriptor(viewer,&mfdes);CHKERRQ(ierr); 646 ierr = PetscViewerBinaryGetMPIIOOffset(viewer,&off);CHKERRQ(ierr); 647 ierr = MPI_File_set_view(mfdes,off,MPIU_SCALAR,view,(char*)"native",MPI_INFO_NULL);CHKERRQ(ierr); 648 ierr = VecGetArrayRead(xin,&array);CHKERRQ(ierr); 649 asiz = lsizes[1]*(lsizes[2] > 0 ? lsizes[2] : 1)*(lsizes[3] > 0 ? lsizes[3] : 1)*dof; 650 if (write) { 651 ierr = MPIU_File_write_all(mfdes,(PetscScalar*)array,asiz,MPIU_SCALAR,MPI_STATUS_IGNORE);CHKERRQ(ierr); 652 } else { 653 ierr = MPIU_File_read_all(mfdes,(PetscScalar*)array,asiz,MPIU_SCALAR,MPI_STATUS_IGNORE);CHKERRQ(ierr); 654 } 655 ierr = MPI_Type_get_extent(view,&ul,&ub);CHKERRQ(ierr); 656 ierr = PetscViewerBinaryAddMPIIOOffset(viewer,ub);CHKERRQ(ierr); 657 ierr = VecRestoreArrayRead(xin,&array);CHKERRQ(ierr); 658 ierr = MPI_Type_free(&view);CHKERRQ(ierr); 659 PetscFunctionReturn(0); 660 } 661 #endif 662 663 #undef __FUNCT__ 664 #define __FUNCT__ "VecView_MPI_DA" 665 PetscErrorCode VecView_MPI_DA(Vec xin,PetscViewer viewer) 666 { 667 DM da; 668 PetscErrorCode ierr; 669 PetscInt dim; 670 Vec natural; 671 PetscBool isdraw,isvtk; 672 #if defined(PETSC_HAVE_HDF5) 673 PetscBool ishdf5; 674 #endif 675 const char *prefix,*name; 676 PetscViewerFormat format; 677 678 PetscFunctionBegin; 679 ierr = VecGetDM(xin,&da);CHKERRQ(ierr); 680 if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA"); 681 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 682 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERVTK,&isvtk);CHKERRQ(ierr); 683 #if defined(PETSC_HAVE_HDF5) 684 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);CHKERRQ(ierr); 685 #endif 686 if (isdraw) { 687 ierr = DMDAGetInfo(da,&dim,0,0,0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr); 688 if (dim == 1) { 689 ierr = VecView_MPI_Draw_DA1d(xin,viewer);CHKERRQ(ierr); 690 } else if (dim == 2) { 691 ierr = VecView_MPI_Draw_DA2d(xin,viewer);CHKERRQ(ierr); 692 } else SETERRQ1(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Cannot graphically view vector associated with this dimensional DMDA %D",dim); 693 } else if (isvtk) { /* Duplicate the Vec and hold a reference to the DM */ 694 Vec Y; 695 ierr = PetscObjectReference((PetscObject)da);CHKERRQ(ierr); 696 ierr = VecDuplicate(xin,&Y);CHKERRQ(ierr); 697 if (((PetscObject)xin)->name) { 698 /* If xin was named, copy the name over to Y. The duplicate names are safe because nobody else will ever see Y. */ 699 ierr = PetscObjectSetName((PetscObject)Y,((PetscObject)xin)->name);CHKERRQ(ierr); 700 } 701 ierr = VecCopy(xin,Y);CHKERRQ(ierr); 702 ierr = PetscViewerVTKAddField(viewer,(PetscObject)da,DMDAVTKWriteAll,PETSC_VTK_POINT_FIELD,(PetscObject)Y);CHKERRQ(ierr); 703 #if defined(PETSC_HAVE_HDF5) 704 } else if (ishdf5) { 705 ierr = VecView_MPI_HDF5_DA(xin,viewer);CHKERRQ(ierr); 706 #endif 707 } else { 708 #if defined(PETSC_HAVE_MPIIO) 709 PetscBool isbinary,isMPIIO; 710 711 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 712 if (isbinary) { 713 ierr = PetscViewerBinaryGetUseMPIIO(viewer,&isMPIIO);CHKERRQ(ierr); 714 if (isMPIIO) { 715 ierr = DMDAArrayMPIIO(da,viewer,xin,PETSC_TRUE);CHKERRQ(ierr); 716 PetscFunctionReturn(0); 717 } 718 } 719 #endif 720 721 /* call viewer on natural ordering */ 722 ierr = PetscObjectGetOptionsPrefix((PetscObject)xin,&prefix);CHKERRQ(ierr); 723 ierr = DMDACreateNaturalVector(da,&natural);CHKERRQ(ierr); 724 ierr = PetscObjectSetOptionsPrefix((PetscObject)natural,prefix);CHKERRQ(ierr); 725 ierr = DMDAGlobalToNaturalBegin(da,xin,INSERT_VALUES,natural);CHKERRQ(ierr); 726 ierr = DMDAGlobalToNaturalEnd(da,xin,INSERT_VALUES,natural);CHKERRQ(ierr); 727 ierr = PetscObjectGetName((PetscObject)xin,&name);CHKERRQ(ierr); 728 ierr = PetscObjectSetName((PetscObject)natural,name);CHKERRQ(ierr); 729 730 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 731 if (format == PETSC_VIEWER_BINARY_MATLAB) { 732 /* temporarily remove viewer format so it won't trigger in the VecView() */ 733 ierr = PetscViewerSetFormat(viewer,PETSC_VIEWER_DEFAULT);CHKERRQ(ierr); 734 } 735 736 ierr = VecView(natural,viewer);CHKERRQ(ierr); 737 738 if (format == PETSC_VIEWER_BINARY_MATLAB) { 739 MPI_Comm comm; 740 FILE *info; 741 const char *fieldname; 742 char fieldbuf[256]; 743 PetscInt dim,ni,nj,nk,pi,pj,pk,dof,n; 744 745 /* set the viewer format back into the viewer */ 746 ierr = PetscViewerSetFormat(viewer,format);CHKERRQ(ierr); 747 ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr); 748 ierr = PetscViewerBinaryGetInfoPointer(viewer,&info);CHKERRQ(ierr); 749 ierr = DMDAGetInfo(da,&dim,&ni,&nj,&nk,&pi,&pj,&pk,&dof,0,0,0,0,0);CHKERRQ(ierr); 750 ierr = PetscFPrintf(comm,info,"#--- begin code written by PetscViewerBinary for MATLAB format ---#\n");CHKERRQ(ierr); 751 ierr = PetscFPrintf(comm,info,"#$$ tmp = PetscBinaryRead(fd); \n");CHKERRQ(ierr); 752 if (dim == 1) { ierr = PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d);\n",dof,ni);CHKERRQ(ierr); } 753 if (dim == 2) { ierr = PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d,%d);\n",dof,ni,nj);CHKERRQ(ierr); } 754 if (dim == 3) { ierr = PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d,%d,%d);\n",dof,ni,nj,nk);CHKERRQ(ierr); } 755 756 for (n=0; n<dof; n++) { 757 ierr = DMDAGetFieldName(da,n,&fieldname);CHKERRQ(ierr); 758 if (!fieldname || !fieldname[0]) { 759 ierr = PetscSNPrintf(fieldbuf,sizeof fieldbuf,"field%D",n);CHKERRQ(ierr); 760 fieldname = fieldbuf; 761 } 762 if (dim == 1) { ierr = PetscFPrintf(comm,info,"#$$ Set.%s.%s = squeeze(tmp(%d,:))';\n",name,fieldname,n+1);CHKERRQ(ierr); } 763 if (dim == 2) { ierr = PetscFPrintf(comm,info,"#$$ Set.%s.%s = squeeze(tmp(%d,:,:))';\n",name,fieldname,n+1);CHKERRQ(ierr); } 764 if (dim == 3) { ierr = PetscFPrintf(comm,info,"#$$ Set.%s.%s = permute(squeeze(tmp(%d,:,:,:)),[2 1 3]);\n",name,fieldname,n+1);CHKERRQ(ierr);} 765 } 766 ierr = PetscFPrintf(comm,info,"#$$ clear tmp; \n");CHKERRQ(ierr); 767 ierr = PetscFPrintf(comm,info,"#--- end code written by PetscViewerBinary for MATLAB format ---#\n\n");CHKERRQ(ierr); 768 } 769 770 ierr = VecDestroy(&natural);CHKERRQ(ierr); 771 } 772 PetscFunctionReturn(0); 773 } 774 775 #if defined(PETSC_HAVE_HDF5) 776 #undef __FUNCT__ 777 #define __FUNCT__ "VecLoad_HDF5_DA" 778 PetscErrorCode VecLoad_HDF5_DA(Vec xin, PetscViewer viewer) 779 { 780 DM da; 781 PetscErrorCode ierr; 782 hsize_t dim; 783 hsize_t count[5]; 784 hsize_t offset[5]; 785 PetscInt cnt = 0, dimension; 786 PetscScalar *x; 787 const char *vecname; 788 hid_t filespace; /* file dataspace identifier */ 789 hid_t plist_id; /* property list identifier */ 790 hid_t dset_id; /* dataset identifier */ 791 hid_t memspace; /* memory dataspace identifier */ 792 hid_t file_id,group; 793 hid_t scalartype; /* scalar type (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */ 794 DM_DA *dd; 795 796 PetscFunctionBegin; 797 #if defined(PETSC_USE_REAL_SINGLE) 798 scalartype = H5T_NATIVE_FLOAT; 799 #elif defined(PETSC_USE_REAL___FLOAT128) 800 #error "HDF5 output with 128 bit floats not supported." 801 #else 802 scalartype = H5T_NATIVE_DOUBLE; 803 #endif 804 805 ierr = PetscViewerHDF5OpenGroup(viewer, &file_id, &group);CHKERRQ(ierr); 806 ierr = VecGetDM(xin,&da);CHKERRQ(ierr); 807 dd = (DM_DA*)da->data; 808 ierr = DMGetDimension(da, &dimension);CHKERRQ(ierr); 809 810 /* Create the dataspace for the dataset */ 811 ierr = PetscHDF5IntCast(dimension + ((dd->w == 1) ? 0 : 1),&dim);CHKERRQ(ierr); 812 #if defined(PETSC_USE_COMPLEX) 813 dim++; 814 #endif 815 816 /* Create the dataset with default properties and close filespace */ 817 ierr = PetscObjectGetName((PetscObject)xin,&vecname);CHKERRQ(ierr); 818 #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800) 819 PetscStackCallHDF5Return(dset_id,H5Dopen2,(group, vecname, H5P_DEFAULT)); 820 #else 821 PetscStackCallHDF5Return(dset_id,H5Dopen,(group, vecname)); 822 #endif 823 PetscStackCallHDF5Return(filespace,H5Dget_space,(dset_id)); 824 825 /* Each process defines a dataset and reads it from the hyperslab in the file */ 826 cnt = 0; 827 if (dimension == 3) {ierr = PetscHDF5IntCast(dd->zs,offset + cnt++);CHKERRQ(ierr);} 828 if (dimension > 1) {ierr = PetscHDF5IntCast(dd->ys,offset + cnt++);CHKERRQ(ierr);} 829 ierr = PetscHDF5IntCast(dd->xs/dd->w,offset + cnt++);CHKERRQ(ierr); 830 if (dd->w > 1) offset[cnt++] = 0; 831 #if defined(PETSC_USE_COMPLEX) 832 offset[cnt++] = 0; 833 #endif 834 cnt = 0; 835 if (dimension == 3) {ierr = PetscHDF5IntCast(dd->ze - dd->zs,count + cnt++);CHKERRQ(ierr);} 836 if (dimension > 1) {ierr = PetscHDF5IntCast(dd->ye - dd->ys,count + cnt++);CHKERRQ(ierr);} 837 ierr = PetscHDF5IntCast((dd->xe - dd->xs)/dd->w,count + cnt++);CHKERRQ(ierr); 838 if (dd->w > 1) {ierr = PetscHDF5IntCast(dd->w,count + cnt++);CHKERRQ(ierr);} 839 #if defined(PETSC_USE_COMPLEX) 840 count[cnt++] = 2; 841 #endif 842 PetscStackCallHDF5Return(memspace,H5Screate_simple,(dim, count, NULL)); 843 PetscStackCallHDF5(H5Sselect_hyperslab,(filespace, H5S_SELECT_SET, offset, NULL, count, NULL)); 844 845 /* Create property list for collective dataset write */ 846 PetscStackCallHDF5Return(plist_id,H5Pcreate,(H5P_DATASET_XFER)); 847 #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO) 848 PetscStackCallHDF5(H5Pset_dxpl_mpio,(plist_id, H5FD_MPIO_COLLECTIVE)); 849 #endif 850 /* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */ 851 852 ierr = VecGetArray(xin, &x);CHKERRQ(ierr); 853 PetscStackCallHDF5(H5Dread,(dset_id, scalartype, memspace, filespace, plist_id, x)); 854 ierr = VecRestoreArray(xin, &x);CHKERRQ(ierr); 855 856 /* Close/release resources */ 857 if (group != file_id) { 858 PetscStackCallHDF5(H5Gclose,(group)); 859 } 860 PetscStackCallHDF5(H5Pclose,(plist_id)); 861 PetscStackCallHDF5(H5Sclose,(filespace)); 862 PetscStackCallHDF5(H5Sclose,(memspace)); 863 PetscStackCallHDF5(H5Dclose,(dset_id)); 864 PetscFunctionReturn(0); 865 } 866 #endif 867 868 #undef __FUNCT__ 869 #define __FUNCT__ "VecLoad_Binary_DA" 870 PetscErrorCode VecLoad_Binary_DA(Vec xin, PetscViewer viewer) 871 { 872 DM da; 873 PetscErrorCode ierr; 874 Vec natural; 875 const char *prefix; 876 PetscInt bs; 877 PetscBool flag; 878 DM_DA *dd; 879 #if defined(PETSC_HAVE_MPIIO) 880 PetscBool isMPIIO; 881 #endif 882 883 PetscFunctionBegin; 884 ierr = VecGetDM(xin,&da);CHKERRQ(ierr); 885 dd = (DM_DA*)da->data; 886 #if defined(PETSC_HAVE_MPIIO) 887 ierr = PetscViewerBinaryGetUseMPIIO(viewer,&isMPIIO);CHKERRQ(ierr); 888 if (isMPIIO) { 889 ierr = DMDAArrayMPIIO(da,viewer,xin,PETSC_FALSE);CHKERRQ(ierr); 890 PetscFunctionReturn(0); 891 } 892 #endif 893 894 ierr = PetscObjectGetOptionsPrefix((PetscObject)xin,&prefix);CHKERRQ(ierr); 895 ierr = DMDACreateNaturalVector(da,&natural);CHKERRQ(ierr); 896 ierr = PetscObjectSetName((PetscObject)natural,((PetscObject)xin)->name);CHKERRQ(ierr); 897 ierr = PetscObjectSetOptionsPrefix((PetscObject)natural,prefix);CHKERRQ(ierr); 898 ierr = VecLoad(natural,viewer);CHKERRQ(ierr); 899 ierr = DMDANaturalToGlobalBegin(da,natural,INSERT_VALUES,xin);CHKERRQ(ierr); 900 ierr = DMDANaturalToGlobalEnd(da,natural,INSERT_VALUES,xin);CHKERRQ(ierr); 901 ierr = VecDestroy(&natural);CHKERRQ(ierr); 902 ierr = PetscInfo(xin,"Loading vector from natural ordering into DMDA\n");CHKERRQ(ierr); 903 ierr = PetscOptionsGetInt(((PetscObject)xin)->prefix,"-vecload_block_size",&bs,&flag);CHKERRQ(ierr); 904 if (flag && bs != dd->w) { 905 ierr = PetscInfo2(xin,"Block size in file %D not equal to DMDA's dof %D\n",bs,dd->w);CHKERRQ(ierr); 906 } 907 PetscFunctionReturn(0); 908 } 909 910 #undef __FUNCT__ 911 #define __FUNCT__ "VecLoad_Default_DA" 912 PetscErrorCode VecLoad_Default_DA(Vec xin, PetscViewer viewer) 913 { 914 PetscErrorCode ierr; 915 DM da; 916 PetscBool isbinary; 917 #if defined(PETSC_HAVE_HDF5) 918 PetscBool ishdf5; 919 #endif 920 921 PetscFunctionBegin; 922 ierr = VecGetDM(xin,&da);CHKERRQ(ierr); 923 if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA"); 924 925 #if defined(PETSC_HAVE_HDF5) 926 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);CHKERRQ(ierr); 927 #endif 928 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 929 930 if (isbinary) { 931 ierr = VecLoad_Binary_DA(xin,viewer);CHKERRQ(ierr); 932 #if defined(PETSC_HAVE_HDF5) 933 } else if (ishdf5) { 934 ierr = VecLoad_HDF5_DA(xin,viewer);CHKERRQ(ierr); 935 #endif 936 } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Viewer type %s not supported for vector loading", ((PetscObject)viewer)->type_name); 937 PetscFunctionReturn(0); 938 } 939