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