1 2 /* 3 Plots vectors obtained with DMDACreate2d() 4 */ 5 6 #include <petsc/private/dmdaimpl.h> /*I "petscdmda.h" I*/ 7 #include <petsc/private/glvisvecimpl.h> 8 #include <petscdraw.h> 9 #include <petscviewerhdf5.h> 10 11 /* 12 The data that is passed into the graphics callback 13 */ 14 typedef struct { 15 PetscMPIInt rank; 16 PetscInt m,n,dof,k; 17 PetscReal xmin,xmax,ymin,ymax,min,max; 18 const PetscScalar *xy,*v; 19 PetscBool showaxis,showgrid; 20 const char *name0,*name1; 21 } ZoomCtx; 22 23 /* 24 This does the drawing for one particular field 25 in one particular set of coordinates. It is a callback 26 called from PetscDrawZoom() 27 */ 28 PetscErrorCode VecView_MPI_Draw_DA2d_Zoom(PetscDraw draw,void *ctx) 29 { 30 ZoomCtx *zctx = (ZoomCtx*)ctx; 31 PetscErrorCode ierr; 32 PetscInt m,n,i,j,k,dof,id,c1,c2,c3,c4; 33 PetscReal min,max,x1,x2,x3,x4,y_1,y2,y3,y4; 34 const PetscScalar *xy,*v; 35 36 PetscFunctionBegin; 37 m = zctx->m; 38 n = zctx->n; 39 dof = zctx->dof; 40 k = zctx->k; 41 xy = zctx->xy; 42 v = zctx->v; 43 min = zctx->min; 44 max = zctx->max; 45 46 /* PetscDraw the contour plot patch */ 47 ierr = PetscDrawCollectiveBegin(draw);CHKERRQ(ierr); 48 for (j=0; j<n-1; j++) { 49 for (i=0; i<m-1; i++) { 50 id = i+j*m; 51 x1 = PetscRealPart(xy[2*id]); 52 y_1 = PetscRealPart(xy[2*id+1]); 53 c1 = PetscDrawRealToColor(PetscRealPart(v[k+dof*id]),min,max); 54 55 id = i+j*m+1; 56 x2 = PetscRealPart(xy[2*id]); 57 y2 = PetscRealPart(xy[2*id+1]); 58 c2 = PetscDrawRealToColor(PetscRealPart(v[k+dof*id]),min,max); 59 60 id = i+j*m+1+m; 61 x3 = PetscRealPart(xy[2*id]); 62 y3 = PetscRealPart(xy[2*id+1]); 63 c3 = PetscDrawRealToColor(PetscRealPart(v[k+dof*id]),min,max); 64 65 id = i+j*m+m; 66 x4 = PetscRealPart(xy[2*id]); 67 y4 = PetscRealPart(xy[2*id+1]); 68 c4 = PetscDrawRealToColor(PetscRealPart(v[k+dof*id]),min,max); 69 70 ierr = PetscDrawTriangle(draw,x1,y_1,x2,y2,x3,y3,c1,c2,c3);CHKERRQ(ierr); 71 ierr = PetscDrawTriangle(draw,x1,y_1,x3,y3,x4,y4,c1,c3,c4);CHKERRQ(ierr); 72 if (zctx->showgrid) { 73 ierr = PetscDrawLine(draw,x1,y_1,x2,y2,PETSC_DRAW_BLACK);CHKERRQ(ierr); 74 ierr = PetscDrawLine(draw,x2,y2,x3,y3,PETSC_DRAW_BLACK);CHKERRQ(ierr); 75 ierr = PetscDrawLine(draw,x3,y3,x4,y4,PETSC_DRAW_BLACK);CHKERRQ(ierr); 76 ierr = PetscDrawLine(draw,x4,y4,x1,y_1,PETSC_DRAW_BLACK);CHKERRQ(ierr); 77 } 78 } 79 } 80 if (zctx->showaxis && !zctx->rank) { 81 if (zctx->name0 || zctx->name1) { 82 PetscReal xl,yl,xr,yr,x,y; 83 ierr = PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);CHKERRQ(ierr); 84 x = xl + .30*(xr - xl); 85 xl = xl + .01*(xr - xl); 86 y = yr - .30*(yr - yl); 87 yl = yl + .01*(yr - yl); 88 if (zctx->name0) {ierr = PetscDrawString(draw,x,yl,PETSC_DRAW_BLACK,zctx->name0);CHKERRQ(ierr);} 89 if (zctx->name1) {ierr = PetscDrawStringVertical(draw,xl,y,PETSC_DRAW_BLACK,zctx->name1);CHKERRQ(ierr);} 90 } 91 /* 92 Ideally we would use the PetscDrawAxis object to manage displaying the coordinate limits 93 but that may require some refactoring. 94 */ 95 { 96 double xmin = (double)zctx->xmin, ymin = (double)zctx->ymin; 97 double xmax = (double)zctx->xmax, ymax = (double)zctx->ymax; 98 char value[16]; size_t len; PetscReal w; 99 ierr = PetscSNPrintf(value,16,"%0.2e",xmin);CHKERRQ(ierr); 100 ierr = PetscDrawString(draw,xmin,ymin - .05*(ymax - ymin),PETSC_DRAW_BLACK,value);CHKERRQ(ierr); 101 ierr = PetscSNPrintf(value,16,"%0.2e",xmax);CHKERRQ(ierr); 102 ierr = PetscStrlen(value,&len);CHKERRQ(ierr); 103 ierr = PetscDrawStringGetSize(draw,&w,NULL);CHKERRQ(ierr); 104 ierr = PetscDrawString(draw,xmax - len*w,ymin - .05*(ymax - ymin),PETSC_DRAW_BLACK,value);CHKERRQ(ierr); 105 ierr = PetscSNPrintf(value,16,"%0.2e",ymin);CHKERRQ(ierr); 106 ierr = PetscDrawString(draw,xmin - .05*(xmax - xmin),ymin,PETSC_DRAW_BLACK,value);CHKERRQ(ierr); 107 ierr = PetscSNPrintf(value,16,"%0.2e",ymax);CHKERRQ(ierr); 108 ierr = PetscDrawString(draw,xmin - .05*(xmax - xmin),ymax,PETSC_DRAW_BLACK,value);CHKERRQ(ierr); 109 } 110 } 111 ierr = PetscDrawCollectiveEnd(draw);CHKERRQ(ierr); 112 PetscFunctionReturn(0); 113 } 114 115 PetscErrorCode VecView_MPI_Draw_DA2d(Vec xin,PetscViewer viewer) 116 { 117 DM da,dac,dag; 118 PetscErrorCode ierr; 119 PetscInt N,s,M,w,ncoors = 4; 120 const PetscInt *lx,*ly; 121 PetscReal coors[4]; 122 PetscDraw draw,popup; 123 PetscBool isnull,useports = PETSC_FALSE; 124 MPI_Comm comm; 125 Vec xlocal,xcoor,xcoorl; 126 DMBoundaryType bx,by; 127 DMDAStencilType st; 128 ZoomCtx zctx; 129 PetscDrawViewPorts *ports = NULL; 130 PetscViewerFormat format; 131 PetscInt *displayfields; 132 PetscInt ndisplayfields,i,nbounds; 133 const PetscReal *bounds; 134 135 PetscFunctionBegin; 136 zctx.showgrid = PETSC_FALSE; 137 zctx.showaxis = PETSC_TRUE; 138 139 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 140 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); 141 if (isnull) PetscFunctionReturn(0); 142 143 ierr = PetscViewerDrawGetBounds(viewer,&nbounds,&bounds);CHKERRQ(ierr); 144 145 ierr = VecGetDM(xin,&da);CHKERRQ(ierr); 146 if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA"); 147 148 ierr = PetscObjectGetComm((PetscObject)xin,&comm);CHKERRQ(ierr); 149 ierr = MPI_Comm_rank(comm,&zctx.rank);CHKERRQ(ierr); 150 151 ierr = DMDAGetInfo(da,0,&M,&N,0,&zctx.m,&zctx.n,0,&w,&s,&bx,&by,0,&st);CHKERRQ(ierr); 152 ierr = DMDAGetOwnershipRanges(da,&lx,&ly,NULL);CHKERRQ(ierr); 153 154 /* 155 Obtain a sequential vector that is going to contain the local values plus ONE layer of 156 ghosted values to draw the graphics from. We also need its corresponding DMDA (dac) that will 157 update the local values pluse ONE layer of ghost values. 158 */ 159 ierr = PetscObjectQuery((PetscObject)da,"GraphicsGhosted",(PetscObject*)&xlocal);CHKERRQ(ierr); 160 if (!xlocal) { 161 if (bx != DM_BOUNDARY_NONE || by != DM_BOUNDARY_NONE || s != 1 || st != DMDA_STENCIL_BOX) { 162 /* 163 if original da is not of stencil width one, or periodic or not a box stencil then 164 create a special DMDA to handle one level of ghost points for graphics 165 */ 166 ierr = DMDACreate2d(comm,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,N,zctx.m,zctx.n,w,1,lx,ly,&dac);CHKERRQ(ierr); 167 ierr = DMSetUp(dac);CHKERRQ(ierr); 168 ierr = PetscInfo(da,"Creating auxilary DMDA for managing graphics ghost points\n");CHKERRQ(ierr); 169 } else { 170 /* otherwise we can use the da we already have */ 171 dac = da; 172 } 173 /* create local vector for holding ghosted values used in graphics */ 174 ierr = DMCreateLocalVector(dac,&xlocal);CHKERRQ(ierr); 175 if (dac != da) { 176 /* don't keep any public reference of this DMDA, is is only available through xlocal */ 177 ierr = PetscObjectDereference((PetscObject)dac);CHKERRQ(ierr); 178 } else { 179 /* remove association between xlocal and da, because below we compose in the opposite 180 direction and if we left this connect we'd get a loop, so the objects could 181 never be destroyed */ 182 ierr = PetscObjectRemoveReference((PetscObject)xlocal,"__PETSc_dm");CHKERRQ(ierr); 183 } 184 ierr = PetscObjectCompose((PetscObject)da,"GraphicsGhosted",(PetscObject)xlocal);CHKERRQ(ierr); 185 ierr = PetscObjectDereference((PetscObject)xlocal);CHKERRQ(ierr); 186 } else { 187 if (bx != DM_BOUNDARY_NONE || by != DM_BOUNDARY_NONE || s != 1 || st != DMDA_STENCIL_BOX) { 188 ierr = VecGetDM(xlocal, &dac);CHKERRQ(ierr); 189 } else { 190 dac = da; 191 } 192 } 193 194 /* 195 Get local (ghosted) values of vector 196 */ 197 ierr = DMGlobalToLocalBegin(dac,xin,INSERT_VALUES,xlocal);CHKERRQ(ierr); 198 ierr = DMGlobalToLocalEnd(dac,xin,INSERT_VALUES,xlocal);CHKERRQ(ierr); 199 ierr = VecGetArrayRead(xlocal,&zctx.v);CHKERRQ(ierr); 200 201 /* 202 Get coordinates of nodes 203 */ 204 ierr = DMGetCoordinates(da,&xcoor);CHKERRQ(ierr); 205 if (!xcoor) { 206 ierr = DMDASetUniformCoordinates(da,0.0,1.0,0.0,1.0,0.0,0.0);CHKERRQ(ierr); 207 ierr = DMGetCoordinates(da,&xcoor);CHKERRQ(ierr); 208 } 209 210 /* 211 Determine the min and max coordinates in plot 212 */ 213 ierr = VecStrideMin(xcoor,0,NULL,&zctx.xmin);CHKERRQ(ierr); 214 ierr = VecStrideMax(xcoor,0,NULL,&zctx.xmax);CHKERRQ(ierr); 215 ierr = VecStrideMin(xcoor,1,NULL,&zctx.ymin);CHKERRQ(ierr); 216 ierr = VecStrideMax(xcoor,1,NULL,&zctx.ymax);CHKERRQ(ierr); 217 ierr = PetscOptionsGetBool(NULL,NULL,"-draw_contour_axis",&zctx.showaxis,NULL);CHKERRQ(ierr); 218 if (zctx.showaxis) { 219 coors[0] = zctx.xmin - .05*(zctx.xmax - zctx.xmin); coors[1] = zctx.ymin - .05*(zctx.ymax - zctx.ymin); 220 coors[2] = zctx.xmax + .05*(zctx.xmax - zctx.xmin); coors[3] = zctx.ymax + .05*(zctx.ymax - zctx.ymin); 221 } else { 222 coors[0] = zctx.xmin; coors[1] = zctx.ymin; coors[2] = zctx.xmax; coors[3] = zctx.ymax; 223 } 224 ierr = PetscOptionsGetRealArray(NULL,NULL,"-draw_coordinates",coors,&ncoors,NULL);CHKERRQ(ierr); 225 ierr = PetscInfo4(da,"Preparing DMDA 2d contour plot coordinates %g %g %g %g\n",(double)coors[0],(double)coors[1],(double)coors[2],(double)coors[3]);CHKERRQ(ierr); 226 227 /* 228 Get local ghosted version of coordinates 229 */ 230 ierr = PetscObjectQuery((PetscObject)da,"GraphicsCoordinateGhosted",(PetscObject*)&xcoorl);CHKERRQ(ierr); 231 if (!xcoorl) { 232 /* create DMDA to get local version of graphics */ 233 ierr = DMDACreate2d(comm,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,N,zctx.m,zctx.n,2,1,lx,ly,&dag);CHKERRQ(ierr); 234 ierr = DMSetUp(dag);CHKERRQ(ierr); 235 ierr = PetscInfo(dag,"Creating auxilary DMDA for managing graphics coordinates ghost points\n");CHKERRQ(ierr); 236 ierr = DMCreateLocalVector(dag,&xcoorl);CHKERRQ(ierr); 237 ierr = PetscObjectCompose((PetscObject)da,"GraphicsCoordinateGhosted",(PetscObject)xcoorl);CHKERRQ(ierr); 238 ierr = PetscObjectDereference((PetscObject)dag);CHKERRQ(ierr); 239 ierr = PetscObjectDereference((PetscObject)xcoorl);CHKERRQ(ierr); 240 } else { 241 ierr = VecGetDM(xcoorl,&dag);CHKERRQ(ierr); 242 } 243 ierr = DMGlobalToLocalBegin(dag,xcoor,INSERT_VALUES,xcoorl);CHKERRQ(ierr); 244 ierr = DMGlobalToLocalEnd(dag,xcoor,INSERT_VALUES,xcoorl);CHKERRQ(ierr); 245 ierr = VecGetArrayRead(xcoorl,&zctx.xy);CHKERRQ(ierr); 246 ierr = DMDAGetCoordinateName(da,0,&zctx.name0);CHKERRQ(ierr); 247 ierr = DMDAGetCoordinateName(da,1,&zctx.name1);CHKERRQ(ierr); 248 249 /* 250 Get information about size of area each processor must do graphics for 251 */ 252 ierr = DMDAGetInfo(dac,NULL,&M,&N,NULL,NULL,NULL,NULL,&zctx.dof,NULL,&bx,&by,NULL,NULL);CHKERRQ(ierr); 253 ierr = DMDAGetGhostCorners(dac,NULL,NULL,NULL,&zctx.m,&zctx.n,NULL);CHKERRQ(ierr); 254 ierr = PetscOptionsGetBool(NULL,NULL,"-draw_contour_grid",&zctx.showgrid,NULL);CHKERRQ(ierr); 255 256 ierr = DMDASelectFields(da,&ndisplayfields,&displayfields);CHKERRQ(ierr); 257 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 258 ierr = PetscOptionsGetBool(NULL,NULL,"-draw_ports",&useports,NULL);CHKERRQ(ierr); 259 if (format == PETSC_VIEWER_DRAW_PORTS) useports = PETSC_TRUE; 260 if (useports) { 261 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 262 ierr = PetscDrawCheckResizedWindow(draw);CHKERRQ(ierr); 263 ierr = PetscDrawClear(draw);CHKERRQ(ierr); 264 ierr = PetscDrawViewPortsCreate(draw,ndisplayfields,&ports);CHKERRQ(ierr); 265 } 266 267 /* 268 Loop over each field; drawing each in a different window 269 */ 270 for (i=0; i<ndisplayfields; i++) { 271 zctx.k = displayfields[i]; 272 273 /* determine the min and max value in plot */ 274 ierr = VecStrideMin(xin,zctx.k,NULL,&zctx.min);CHKERRQ(ierr); 275 ierr = VecStrideMax(xin,zctx.k,NULL,&zctx.max);CHKERRQ(ierr); 276 if (zctx.k < nbounds) { 277 zctx.min = bounds[2*zctx.k]; 278 zctx.max = bounds[2*zctx.k+1]; 279 } 280 if (zctx.min == zctx.max) { 281 zctx.min -= 1.e-12; 282 zctx.max += 1.e-12; 283 } 284 ierr = PetscInfo2(da,"DMDA 2d contour plot min %g max %g\n",(double)zctx.min,(double)zctx.max);CHKERRQ(ierr); 285 286 if (useports) { 287 ierr = PetscDrawViewPortsSet(ports,i);CHKERRQ(ierr); 288 } else { 289 const char *title; 290 ierr = PetscViewerDrawGetDraw(viewer,i,&draw);CHKERRQ(ierr); 291 ierr = DMDAGetFieldName(da,zctx.k,&title);CHKERRQ(ierr); 292 if (title) {ierr = PetscDrawSetTitle(draw,title);CHKERRQ(ierr);} 293 } 294 295 ierr = PetscDrawGetPopup(draw,&popup);CHKERRQ(ierr); 296 ierr = PetscDrawScalePopup(popup,zctx.min,zctx.max);CHKERRQ(ierr); 297 ierr = PetscDrawSetCoordinates(draw,coors[0],coors[1],coors[2],coors[3]);CHKERRQ(ierr); 298 ierr = PetscDrawZoom(draw,VecView_MPI_Draw_DA2d_Zoom,&zctx);CHKERRQ(ierr); 299 if (!useports) {ierr = PetscDrawSave(draw);CHKERRQ(ierr);} 300 } 301 if (useports) { 302 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 303 ierr = PetscDrawSave(draw);CHKERRQ(ierr); 304 } 305 306 ierr = PetscDrawViewPortsDestroy(ports);CHKERRQ(ierr); 307 ierr = PetscFree(displayfields);CHKERRQ(ierr); 308 ierr = VecRestoreArrayRead(xcoorl,&zctx.xy);CHKERRQ(ierr); 309 ierr = VecRestoreArrayRead(xlocal,&zctx.v);CHKERRQ(ierr); 310 PetscFunctionReturn(0); 311 } 312 313 #if defined(PETSC_HAVE_HDF5) 314 static PetscErrorCode VecGetHDF5ChunkSize(DM_DA *da, Vec xin, PetscInt dimension, PetscInt timestep, hsize_t *chunkDims) 315 { 316 PetscMPIInt comm_size; 317 PetscErrorCode ierr; 318 hsize_t chunk_size, target_size, dim; 319 hsize_t vec_size = sizeof(PetscScalar)*da->M*da->N*da->P*da->w; 320 hsize_t avg_local_vec_size,KiB = 1024,MiB = KiB*KiB,GiB = MiB*KiB,min_size = MiB; 321 hsize_t max_chunks = 64*KiB; /* HDF5 internal limitation */ 322 hsize_t max_chunk_size = 4*GiB; /* HDF5 internal limitation */ 323 PetscInt zslices=da->p, yslices=da->n, xslices=da->m; 324 325 PetscFunctionBegin; 326 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)xin), &comm_size);CHKERRQ(ierr); 327 avg_local_vec_size = (hsize_t) ceil(vec_size*1.0/comm_size); /* we will attempt to use this as the chunk size */ 328 329 target_size = (hsize_t) ceil(PetscMin(vec_size,PetscMin(max_chunk_size,PetscMax(avg_local_vec_size,PetscMax(ceil(vec_size*1.0/max_chunks),min_size))))); 330 /* following line uses sizeof(PetscReal) instead of sizeof(PetscScalar) because the last dimension of chunkDims[] captures the 2* when complex numbers are being used */ 331 chunk_size = (hsize_t) PetscMax(1,chunkDims[0])*PetscMax(1,chunkDims[1])*PetscMax(1,chunkDims[2])*PetscMax(1,chunkDims[3])*PetscMax(1,chunkDims[4])*PetscMax(1,chunkDims[5])*sizeof(PetscReal); 332 333 /* 334 if size/rank > max_chunk_size, we need radical measures: even going down to 335 avg_local_vec_size is not enough, so we simply use chunk size of 4 GiB no matter 336 what, composed in the most efficient way possible. 337 N.B. this minimises the number of chunks, which may or may not be the optimal 338 solution. In a BG, for example, the optimal solution is probably to make # chunks = # 339 IO nodes involved, but this author has no access to a BG to figure out how to 340 reliably find the right number. And even then it may or may not be enough. 341 */ 342 if (avg_local_vec_size > max_chunk_size) { 343 /* check if we can just split local z-axis: is that enough? */ 344 zslices = (PetscInt)ceil(vec_size*1.0/(da->p*max_chunk_size))*zslices; 345 if (zslices > da->P) { 346 /* lattice is too large in xy-directions, splitting z only is not enough */ 347 zslices = da->P; 348 yslices= (PetscInt)ceil(vec_size*1.0/(zslices*da->n*max_chunk_size))*yslices; 349 if (yslices > da->N) { 350 /* lattice is too large in x-direction, splitting along z, y is not enough */ 351 yslices = da->N; 352 xslices= (PetscInt)ceil(vec_size*1.0/(zslices*yslices*da->m*max_chunk_size))*xslices; 353 } 354 } 355 dim = 0; 356 if (timestep >= 0) { 357 ++dim; 358 } 359 /* prefer to split z-axis, even down to planar slices */ 360 if (dimension == 3) { 361 chunkDims[dim++] = (hsize_t) da->P/zslices; 362 chunkDims[dim++] = (hsize_t) da->N/yslices; 363 chunkDims[dim++] = (hsize_t) da->M/xslices; 364 } else { 365 /* This is a 2D world exceeding 4GiB in size; yes, I've seen them, even used myself */ 366 chunkDims[dim++] = (hsize_t) da->N/yslices; 367 chunkDims[dim++] = (hsize_t) da->M/xslices; 368 } 369 chunk_size = (hsize_t) PetscMax(1,chunkDims[0])*PetscMax(1,chunkDims[1])*PetscMax(1,chunkDims[2])*PetscMax(1,chunkDims[3])*PetscMax(1,chunkDims[4])*PetscMax(1,chunkDims[5])*sizeof(double); 370 } else { 371 if (target_size < chunk_size) { 372 /* only change the defaults if target_size < chunk_size */ 373 dim = 0; 374 if (timestep >= 0) { 375 ++dim; 376 } 377 /* prefer to split z-axis, even down to planar slices */ 378 if (dimension == 3) { 379 /* try splitting the z-axis to core-size bits, i.e. divide chunk size by # comm_size in z-direction */ 380 if (target_size >= chunk_size/da->p) { 381 /* just make chunks the size of <local_z>x<whole_world_y>x<whole_world_x>x<dof> */ 382 chunkDims[dim] = (hsize_t) ceil(da->P*1.0/da->p); 383 } else { 384 /* oops, just splitting the z-axis is NOT ENOUGH, need to split more; let's be 385 radical and let everyone write all they've got */ 386 chunkDims[dim++] = (hsize_t) ceil(da->P*1.0/da->p); 387 chunkDims[dim++] = (hsize_t) ceil(da->N*1.0/da->n); 388 chunkDims[dim++] = (hsize_t) ceil(da->M*1.0/da->m); 389 } 390 } else { 391 /* This is a 2D world exceeding 4GiB in size; yes, I've seen them, even used myself */ 392 if (target_size >= chunk_size/da->n) { 393 /* just make chunks the size of <local_z>x<whole_world_y>x<whole_world_x>x<dof> */ 394 chunkDims[dim] = (hsize_t) ceil(da->N*1.0/da->n); 395 } else { 396 /* oops, just splitting the z-axis is NOT ENOUGH, need to split more; let's be 397 radical and let everyone write all they've got */ 398 chunkDims[dim++] = (hsize_t) ceil(da->N*1.0/da->n); 399 chunkDims[dim++] = (hsize_t) ceil(da->M*1.0/da->m); 400 } 401 402 } 403 chunk_size = (hsize_t) PetscMax(1,chunkDims[0])*PetscMax(1,chunkDims[1])*PetscMax(1,chunkDims[2])*PetscMax(1,chunkDims[3])*PetscMax(1,chunkDims[4])*PetscMax(1,chunkDims[5])*sizeof(double); 404 } else { 405 /* precomputed chunks are fine, we don't need to do anything */ 406 } 407 } 408 PetscFunctionReturn(0); 409 } 410 #endif 411 412 #if defined(PETSC_HAVE_HDF5) 413 PetscErrorCode VecView_MPI_HDF5_DA(Vec xin,PetscViewer viewer) 414 { 415 DM dm; 416 DM_DA *da; 417 hid_t filespace; /* file dataspace identifier */ 418 hid_t chunkspace; /* chunk dataset property identifier */ 419 hid_t plist_id; /* property list identifier */ 420 hid_t dset_id; /* dataset identifier */ 421 hid_t memspace; /* memory dataspace identifier */ 422 hid_t file_id; 423 hid_t group; 424 hid_t memscalartype; /* scalar type for mem (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */ 425 hid_t filescalartype; /* scalar type for file (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */ 426 hsize_t dim; 427 hsize_t maxDims[6]={0}, dims[6]={0}, chunkDims[6]={0}, count[6]={0}, offset[6]={0}; /* we depend on these being sane later on */ 428 PetscInt timestep, dimension; 429 const PetscScalar *x; 430 const char *vecname; 431 PetscErrorCode ierr; 432 PetscBool dim2; 433 PetscBool spoutput; 434 435 PetscFunctionBegin; 436 ierr = PetscViewerHDF5OpenGroup(viewer, &file_id, &group);CHKERRQ(ierr); 437 ierr = PetscViewerHDF5GetTimestep(viewer, ×tep);CHKERRQ(ierr); 438 ierr = PetscViewerHDF5GetBaseDimension2(viewer,&dim2);CHKERRQ(ierr); 439 ierr = PetscViewerHDF5GetSPOutput(viewer,&spoutput);CHKERRQ(ierr); 440 441 ierr = VecGetDM(xin,&dm);CHKERRQ(ierr); 442 if (!dm) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA"); 443 da = (DM_DA*)dm->data; 444 ierr = DMGetDimension(dm, &dimension);CHKERRQ(ierr); 445 446 /* Create the dataspace for the dataset. 447 * 448 * dims - holds the current dimensions of the dataset 449 * 450 * maxDims - holds the maximum dimensions of the dataset (unlimited 451 * for the number of time steps with the current dimensions for the 452 * other dimensions; so only additional time steps can be added). 453 * 454 * chunkDims - holds the size of a single time step (required to 455 * permit extending dataset). 456 */ 457 dim = 0; 458 if (timestep >= 0) { 459 dims[dim] = timestep+1; 460 maxDims[dim] = H5S_UNLIMITED; 461 chunkDims[dim] = 1; 462 ++dim; 463 } 464 if (dimension == 3) { 465 ierr = PetscHDF5IntCast(da->P,dims+dim);CHKERRQ(ierr); 466 maxDims[dim] = dims[dim]; 467 chunkDims[dim] = dims[dim]; 468 ++dim; 469 } 470 if (dimension > 1) { 471 ierr = PetscHDF5IntCast(da->N,dims+dim);CHKERRQ(ierr); 472 maxDims[dim] = dims[dim]; 473 chunkDims[dim] = dims[dim]; 474 ++dim; 475 } 476 ierr = PetscHDF5IntCast(da->M,dims+dim);CHKERRQ(ierr); 477 maxDims[dim] = dims[dim]; 478 chunkDims[dim] = dims[dim]; 479 ++dim; 480 if (da->w > 1 || dim2) { 481 ierr = PetscHDF5IntCast(da->w,dims+dim);CHKERRQ(ierr); 482 maxDims[dim] = dims[dim]; 483 chunkDims[dim] = dims[dim]; 484 ++dim; 485 } 486 #if defined(PETSC_USE_COMPLEX) 487 dims[dim] = 2; 488 maxDims[dim] = dims[dim]; 489 chunkDims[dim] = dims[dim]; 490 ++dim; 491 #endif 492 493 ierr = VecGetHDF5ChunkSize(da, xin, dimension, timestep, chunkDims); CHKERRQ(ierr); 494 495 PetscStackCallHDF5Return(filespace,H5Screate_simple,(dim, dims, maxDims)); 496 497 #if defined(PETSC_USE_REAL_SINGLE) 498 memscalartype = H5T_NATIVE_FLOAT; 499 filescalartype = H5T_NATIVE_FLOAT; 500 #elif defined(PETSC_USE_REAL___FLOAT128) 501 #error "HDF5 output with 128 bit floats not supported." 502 #elif defined(PETSC_USE_REAL___FP16) 503 #error "HDF5 output with 16 bit floats not supported." 504 #else 505 memscalartype = H5T_NATIVE_DOUBLE; 506 if (spoutput == PETSC_TRUE) filescalartype = H5T_NATIVE_FLOAT; 507 else filescalartype = H5T_NATIVE_DOUBLE; 508 #endif 509 510 /* Create the dataset with default properties and close filespace */ 511 ierr = PetscObjectGetName((PetscObject)xin,&vecname);CHKERRQ(ierr); 512 if (!H5Lexists(group, vecname, H5P_DEFAULT)) { 513 /* Create chunk */ 514 PetscStackCallHDF5Return(chunkspace,H5Pcreate,(H5P_DATASET_CREATE)); 515 PetscStackCallHDF5(H5Pset_chunk,(chunkspace, dim, chunkDims)); 516 517 #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800) 518 PetscStackCallHDF5Return(dset_id,H5Dcreate2,(group, vecname, filescalartype, filespace, H5P_DEFAULT, chunkspace, H5P_DEFAULT)); 519 #else 520 PetscStackCallHDF5Return(dset_id,H5Dcreate,(group, vecname, filescalartype, filespace, H5P_DEFAULT)); 521 #endif 522 } else { 523 PetscStackCallHDF5Return(dset_id,H5Dopen2,(group, vecname, H5P_DEFAULT)); 524 PetscStackCallHDF5(H5Dset_extent,(dset_id, dims)); 525 } 526 PetscStackCallHDF5(H5Sclose,(filespace)); 527 528 /* Each process defines a dataset and writes it to the hyperslab in the file */ 529 dim = 0; 530 if (timestep >= 0) { 531 offset[dim] = timestep; 532 ++dim; 533 } 534 if (dimension == 3) {ierr = PetscHDF5IntCast(da->zs,offset + dim++);CHKERRQ(ierr);} 535 if (dimension > 1) {ierr = PetscHDF5IntCast(da->ys,offset + dim++);CHKERRQ(ierr);} 536 ierr = PetscHDF5IntCast(da->xs/da->w,offset + dim++);CHKERRQ(ierr); 537 if (da->w > 1 || dim2) offset[dim++] = 0; 538 #if defined(PETSC_USE_COMPLEX) 539 offset[dim++] = 0; 540 #endif 541 dim = 0; 542 if (timestep >= 0) { 543 count[dim] = 1; 544 ++dim; 545 } 546 if (dimension == 3) {ierr = PetscHDF5IntCast(da->ze - da->zs,count + dim++);CHKERRQ(ierr);} 547 if (dimension > 1) {ierr = PetscHDF5IntCast(da->ye - da->ys,count + dim++);CHKERRQ(ierr);} 548 ierr = PetscHDF5IntCast((da->xe - da->xs)/da->w,count + dim++);CHKERRQ(ierr); 549 if (da->w > 1 || dim2) {ierr = PetscHDF5IntCast(da->w,count + dim++);CHKERRQ(ierr);} 550 #if defined(PETSC_USE_COMPLEX) 551 count[dim++] = 2; 552 #endif 553 PetscStackCallHDF5Return(memspace,H5Screate_simple,(dim, count, NULL)); 554 PetscStackCallHDF5Return(filespace,H5Dget_space,(dset_id)); 555 PetscStackCallHDF5(H5Sselect_hyperslab,(filespace, H5S_SELECT_SET, offset, NULL, count, NULL)); 556 557 /* Create property list for collective dataset write */ 558 PetscStackCallHDF5Return(plist_id,H5Pcreate,(H5P_DATASET_XFER)); 559 #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO) 560 PetscStackCallHDF5(H5Pset_dxpl_mpio,(plist_id, H5FD_MPIO_COLLECTIVE)); 561 #endif 562 /* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */ 563 564 ierr = VecGetArrayRead(xin, &x);CHKERRQ(ierr); 565 PetscStackCallHDF5(H5Dwrite,(dset_id, memscalartype, memspace, filespace, plist_id, x)); 566 PetscStackCallHDF5(H5Fflush,(file_id, H5F_SCOPE_GLOBAL)); 567 ierr = VecRestoreArrayRead(xin, &x);CHKERRQ(ierr); 568 569 /* Close/release resources */ 570 if (group != file_id) { 571 PetscStackCallHDF5(H5Gclose,(group)); 572 } 573 PetscStackCallHDF5(H5Pclose,(plist_id)); 574 PetscStackCallHDF5(H5Sclose,(filespace)); 575 PetscStackCallHDF5(H5Sclose,(memspace)); 576 PetscStackCallHDF5(H5Dclose,(dset_id)); 577 ierr = PetscInfo1(xin,"Wrote Vec object with name %s\n",vecname);CHKERRQ(ierr); 578 PetscFunctionReturn(0); 579 } 580 #endif 581 582 extern PetscErrorCode VecView_MPI_Draw_DA1d(Vec,PetscViewer); 583 584 #if defined(PETSC_HAVE_MPIIO) 585 static PetscErrorCode DMDAArrayMPIIO(DM da,PetscViewer viewer,Vec xin,PetscBool write) 586 { 587 PetscErrorCode ierr; 588 MPI_File mfdes; 589 PetscMPIInt gsizes[4],lsizes[4],lstarts[4],asiz,dof; 590 MPI_Datatype view; 591 const PetscScalar *array; 592 MPI_Offset off; 593 MPI_Aint ub,ul; 594 PetscInt type,rows,vecrows,tr[2]; 595 DM_DA *dd = (DM_DA*)da->data; 596 PetscBool skipheader; 597 598 PetscFunctionBegin; 599 ierr = VecGetSize(xin,&vecrows);CHKERRQ(ierr); 600 ierr = PetscViewerBinaryGetSkipHeader(viewer,&skipheader);CHKERRQ(ierr); 601 if (!write) { 602 /* Read vector header. */ 603 if (!skipheader) { 604 ierr = PetscViewerBinaryRead(viewer,tr,2,NULL,PETSC_INT);CHKERRQ(ierr); 605 type = tr[0]; 606 rows = tr[1]; 607 if (type != VEC_FILE_CLASSID) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_WRONG,"Not vector next in file"); 608 if (rows != vecrows) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_SIZ,"Vector in file not same size as DMDA vector"); 609 } 610 } else { 611 tr[0] = VEC_FILE_CLASSID; 612 tr[1] = vecrows; 613 if (!skipheader) { 614 ierr = PetscViewerBinaryWrite(viewer,tr,2,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 615 } 616 } 617 618 ierr = PetscMPIIntCast(dd->w,&dof);CHKERRQ(ierr); 619 gsizes[0] = dof; 620 ierr = PetscMPIIntCast(dd->M,gsizes+1);CHKERRQ(ierr); 621 ierr = PetscMPIIntCast(dd->N,gsizes+2);CHKERRQ(ierr); 622 ierr = PetscMPIIntCast(dd->P,gsizes+3);CHKERRQ(ierr); 623 lsizes[0] = dof; 624 ierr = PetscMPIIntCast((dd->xe-dd->xs)/dof,lsizes+1);CHKERRQ(ierr); 625 ierr = PetscMPIIntCast(dd->ye-dd->ys,lsizes+2);CHKERRQ(ierr); 626 ierr = PetscMPIIntCast(dd->ze-dd->zs,lsizes+3);CHKERRQ(ierr); 627 lstarts[0] = 0; 628 ierr = PetscMPIIntCast(dd->xs/dof,lstarts+1);CHKERRQ(ierr); 629 ierr = PetscMPIIntCast(dd->ys,lstarts+2);CHKERRQ(ierr); 630 ierr = PetscMPIIntCast(dd->zs,lstarts+3);CHKERRQ(ierr); 631 ierr = MPI_Type_create_subarray(da->dim+1,gsizes,lsizes,lstarts,MPI_ORDER_FORTRAN,MPIU_SCALAR,&view);CHKERRQ(ierr); 632 ierr = MPI_Type_commit(&view);CHKERRQ(ierr); 633 634 ierr = PetscViewerBinaryGetMPIIODescriptor(viewer,&mfdes);CHKERRQ(ierr); 635 ierr = PetscViewerBinaryGetMPIIOOffset(viewer,&off);CHKERRQ(ierr); 636 ierr = MPI_File_set_view(mfdes,off,MPIU_SCALAR,view,(char*)"native",MPI_INFO_NULL);CHKERRQ(ierr); 637 ierr = VecGetArrayRead(xin,&array);CHKERRQ(ierr); 638 asiz = lsizes[1]*(lsizes[2] > 0 ? lsizes[2] : 1)*(lsizes[3] > 0 ? lsizes[3] : 1)*dof; 639 if (write) { 640 ierr = MPIU_File_write_all(mfdes,(PetscScalar*)array,asiz,MPIU_SCALAR,MPI_STATUS_IGNORE);CHKERRQ(ierr); 641 } else { 642 ierr = MPIU_File_read_all(mfdes,(PetscScalar*)array,asiz,MPIU_SCALAR,MPI_STATUS_IGNORE);CHKERRQ(ierr); 643 } 644 ierr = MPI_Type_get_extent(view,&ul,&ub);CHKERRQ(ierr); 645 ierr = PetscViewerBinaryAddMPIIOOffset(viewer,ub);CHKERRQ(ierr); 646 ierr = VecRestoreArrayRead(xin,&array);CHKERRQ(ierr); 647 ierr = MPI_Type_free(&view);CHKERRQ(ierr); 648 PetscFunctionReturn(0); 649 } 650 #endif 651 652 PetscErrorCode VecView_MPI_DA(Vec xin,PetscViewer viewer) 653 { 654 DM da; 655 PetscErrorCode ierr; 656 PetscInt dim; 657 Vec natural; 658 PetscBool isdraw,isvtk,isglvis; 659 #if defined(PETSC_HAVE_HDF5) 660 PetscBool ishdf5; 661 #endif 662 const char *prefix,*name; 663 PetscViewerFormat format; 664 665 PetscFunctionBegin; 666 ierr = VecGetDM(xin,&da);CHKERRQ(ierr); 667 if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA"); 668 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 669 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERVTK,&isvtk);CHKERRQ(ierr); 670 #if defined(PETSC_HAVE_HDF5) 671 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);CHKERRQ(ierr); 672 #endif 673 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERGLVIS,&isglvis);CHKERRQ(ierr); 674 if (isdraw) { 675 ierr = DMDAGetInfo(da,&dim,0,0,0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr); 676 if (dim == 1) { 677 ierr = VecView_MPI_Draw_DA1d(xin,viewer);CHKERRQ(ierr); 678 } else if (dim == 2) { 679 ierr = VecView_MPI_Draw_DA2d(xin,viewer);CHKERRQ(ierr); 680 } else SETERRQ1(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Cannot graphically view vector associated with this dimensional DMDA %D",dim); 681 } else if (isvtk) { /* Duplicate the Vec */ 682 Vec Y; 683 ierr = VecDuplicate(xin,&Y);CHKERRQ(ierr); 684 if (((PetscObject)xin)->name) { 685 /* If xin was named, copy the name over to Y. The duplicate names are safe because nobody else will ever see Y. */ 686 ierr = PetscObjectSetName((PetscObject)Y,((PetscObject)xin)->name);CHKERRQ(ierr); 687 } 688 ierr = VecCopy(xin,Y);CHKERRQ(ierr); 689 ierr = PetscViewerVTKAddField(viewer,(PetscObject)da,DMDAVTKWriteAll,PETSC_VTK_POINT_FIELD,(PetscObject)Y);CHKERRQ(ierr); 690 #if defined(PETSC_HAVE_HDF5) 691 } else if (ishdf5) { 692 ierr = VecView_MPI_HDF5_DA(xin,viewer);CHKERRQ(ierr); 693 #endif 694 } else if (isglvis) { 695 ierr = VecView_GLVis(xin,viewer);CHKERRQ(ierr); 696 } else { 697 #if defined(PETSC_HAVE_MPIIO) 698 PetscBool isbinary,isMPIIO; 699 700 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 701 if (isbinary) { 702 ierr = PetscViewerBinaryGetUseMPIIO(viewer,&isMPIIO);CHKERRQ(ierr); 703 if (isMPIIO) { 704 ierr = DMDAArrayMPIIO(da,viewer,xin,PETSC_TRUE);CHKERRQ(ierr); 705 PetscFunctionReturn(0); 706 } 707 } 708 #endif 709 710 /* call viewer on natural ordering */ 711 ierr = PetscObjectGetOptionsPrefix((PetscObject)xin,&prefix);CHKERRQ(ierr); 712 ierr = DMDACreateNaturalVector(da,&natural);CHKERRQ(ierr); 713 ierr = PetscObjectSetOptionsPrefix((PetscObject)natural,prefix);CHKERRQ(ierr); 714 ierr = DMDAGlobalToNaturalBegin(da,xin,INSERT_VALUES,natural);CHKERRQ(ierr); 715 ierr = DMDAGlobalToNaturalEnd(da,xin,INSERT_VALUES,natural);CHKERRQ(ierr); 716 ierr = PetscObjectGetName((PetscObject)xin,&name);CHKERRQ(ierr); 717 ierr = PetscObjectSetName((PetscObject)natural,name);CHKERRQ(ierr); 718 719 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 720 if (format == PETSC_VIEWER_BINARY_MATLAB) { 721 /* temporarily remove viewer format so it won't trigger in the VecView() */ 722 ierr = PetscViewerPushFormat(viewer,PETSC_VIEWER_DEFAULT);CHKERRQ(ierr); 723 } 724 725 ((PetscObject)natural)->donotPetscObjectPrintClassNamePrefixType = PETSC_TRUE; 726 ierr = VecView(natural,viewer);CHKERRQ(ierr); 727 ((PetscObject)natural)->donotPetscObjectPrintClassNamePrefixType = PETSC_FALSE; 728 729 if (format == PETSC_VIEWER_BINARY_MATLAB) { 730 MPI_Comm comm; 731 FILE *info; 732 const char *fieldname; 733 char fieldbuf[256]; 734 PetscInt dim,ni,nj,nk,pi,pj,pk,dof,n; 735 736 /* set the viewer format back into the viewer */ 737 ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr); 738 ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr); 739 ierr = PetscViewerBinaryGetInfoPointer(viewer,&info);CHKERRQ(ierr); 740 ierr = DMDAGetInfo(da,&dim,&ni,&nj,&nk,&pi,&pj,&pk,&dof,0,0,0,0,0);CHKERRQ(ierr); 741 ierr = PetscFPrintf(comm,info,"#--- begin code written by PetscViewerBinary for MATLAB format ---#\n");CHKERRQ(ierr); 742 ierr = PetscFPrintf(comm,info,"#$$ tmp = PetscBinaryRead(fd); \n");CHKERRQ(ierr); 743 if (dim == 1) { ierr = PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d);\n",dof,ni);CHKERRQ(ierr); } 744 if (dim == 2) { ierr = PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d,%d);\n",dof,ni,nj);CHKERRQ(ierr); } 745 if (dim == 3) { ierr = PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d,%d,%d);\n",dof,ni,nj,nk);CHKERRQ(ierr); } 746 747 for (n=0; n<dof; n++) { 748 ierr = DMDAGetFieldName(da,n,&fieldname);CHKERRQ(ierr); 749 if (!fieldname || !fieldname[0]) { 750 ierr = PetscSNPrintf(fieldbuf,sizeof fieldbuf,"field%D",n);CHKERRQ(ierr); 751 fieldname = fieldbuf; 752 } 753 if (dim == 1) { ierr = PetscFPrintf(comm,info,"#$$ Set.%s.%s = squeeze(tmp(%d,:))';\n",name,fieldname,n+1);CHKERRQ(ierr); } 754 if (dim == 2) { ierr = PetscFPrintf(comm,info,"#$$ Set.%s.%s = squeeze(tmp(%d,:,:))';\n",name,fieldname,n+1);CHKERRQ(ierr); } 755 if (dim == 3) { ierr = PetscFPrintf(comm,info,"#$$ Set.%s.%s = permute(squeeze(tmp(%d,:,:,:)),[2 1 3]);\n",name,fieldname,n+1);CHKERRQ(ierr);} 756 } 757 ierr = PetscFPrintf(comm,info,"#$$ clear tmp; \n");CHKERRQ(ierr); 758 ierr = PetscFPrintf(comm,info,"#--- end code written by PetscViewerBinary for MATLAB format ---#\n\n");CHKERRQ(ierr); 759 } 760 761 ierr = VecDestroy(&natural);CHKERRQ(ierr); 762 } 763 PetscFunctionReturn(0); 764 } 765 766 #if defined(PETSC_HAVE_HDF5) 767 PetscErrorCode VecLoad_HDF5_DA(Vec xin, PetscViewer viewer) 768 { 769 DM da; 770 PetscErrorCode ierr; 771 hsize_t dim,rdim; 772 hsize_t dims[6]={0},count[6]={0},offset[6]={0}; 773 PetscInt dimension,timestep,dofInd; 774 PetscScalar *x; 775 const char *vecname; 776 hid_t filespace; /* file dataspace identifier */ 777 hid_t plist_id; /* property list identifier */ 778 hid_t dset_id; /* dataset identifier */ 779 hid_t memspace; /* memory dataspace identifier */ 780 hid_t file_id,group; 781 hid_t scalartype; /* scalar type (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */ 782 DM_DA *dd; 783 PetscBool dim2 = PETSC_FALSE; 784 785 PetscFunctionBegin; 786 #if defined(PETSC_USE_REAL_SINGLE) 787 scalartype = H5T_NATIVE_FLOAT; 788 #elif defined(PETSC_USE_REAL___FLOAT128) 789 #error "HDF5 output with 128 bit floats not supported." 790 #elif defined(PETSC_USE_REAL___FP16) 791 #error "HDF5 output with 16 bit floats not supported." 792 #else 793 scalartype = H5T_NATIVE_DOUBLE; 794 #endif 795 796 ierr = PetscViewerHDF5OpenGroup(viewer, &file_id, &group);CHKERRQ(ierr); 797 ierr = PetscViewerHDF5GetTimestep(viewer, ×tep);CHKERRQ(ierr); 798 ierr = PetscObjectGetName((PetscObject)xin,&vecname);CHKERRQ(ierr); 799 ierr = VecGetDM(xin,&da);CHKERRQ(ierr); 800 dd = (DM_DA*)da->data; 801 ierr = DMGetDimension(da, &dimension);CHKERRQ(ierr); 802 803 /* Open dataset */ 804 #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800) 805 PetscStackCallHDF5Return(dset_id,H5Dopen2,(group, vecname, H5P_DEFAULT)); 806 #else 807 PetscStackCallHDF5Return(dset_id,H5Dopen,(group, vecname)); 808 #endif 809 810 /* Retrieve the dataspace for the dataset */ 811 PetscStackCallHDF5Return(filespace,H5Dget_space,(dset_id)); 812 PetscStackCallHDF5Return(rdim,H5Sget_simple_extent_dims,(filespace, dims, NULL)); 813 814 /* Expected dimension for holding the dof's */ 815 #if defined(PETSC_USE_COMPLEX) 816 dofInd = rdim-2; 817 #else 818 dofInd = rdim-1; 819 #endif 820 821 /* The expected number of dimensions, assuming basedimension2 = false */ 822 dim = dimension; 823 if (dd->w > 1) ++dim; 824 if (timestep >= 0) ++dim; 825 #if defined(PETSC_USE_COMPLEX) 826 ++dim; 827 #endif 828 829 /* In this case the input dataset have one extra, unexpected dimension. */ 830 if (rdim == dim+1) { 831 /* In this case the block size unity */ 832 if (dd->w == 1 && dims[dofInd] == 1) dim2 = PETSC_TRUE; 833 834 /* Special error message for the case where dof does not match the input file */ 835 else if (dd->w != (PetscInt) dims[dofInd]) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Number of dofs in file is %D, not %D as expected",(PetscInt)dims[dofInd],dd->w); 836 837 /* Other cases where rdim != dim cannot be handled currently */ 838 } else if (rdim != dim) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Dimension of array in file is %d, not %d as expected with dof = %D",rdim,dim,dd->w); 839 840 /* Set up the hyperslab size */ 841 dim = 0; 842 if (timestep >= 0) { 843 offset[dim] = timestep; 844 count[dim] = 1; 845 ++dim; 846 } 847 if (dimension == 3) { 848 ierr = PetscHDF5IntCast(dd->zs,offset + dim);CHKERRQ(ierr); 849 ierr = PetscHDF5IntCast(dd->ze - dd->zs,count + dim);CHKERRQ(ierr); 850 ++dim; 851 } 852 if (dimension > 1) { 853 ierr = PetscHDF5IntCast(dd->ys,offset + dim);CHKERRQ(ierr); 854 ierr = PetscHDF5IntCast(dd->ye - dd->ys,count + dim);CHKERRQ(ierr); 855 ++dim; 856 } 857 ierr = PetscHDF5IntCast(dd->xs/dd->w,offset + dim);CHKERRQ(ierr); 858 ierr = PetscHDF5IntCast((dd->xe - dd->xs)/dd->w,count + dim);CHKERRQ(ierr); 859 ++dim; 860 if (dd->w > 1 || dim2) { 861 offset[dim] = 0; 862 ierr = PetscHDF5IntCast(dd->w,count + dim);CHKERRQ(ierr); 863 ++dim; 864 } 865 #if defined(PETSC_USE_COMPLEX) 866 offset[dim] = 0; 867 count[dim] = 2; 868 ++dim; 869 #endif 870 871 /* Create the memory and filespace */ 872 PetscStackCallHDF5Return(memspace,H5Screate_simple,(dim, count, NULL)); 873 PetscStackCallHDF5(H5Sselect_hyperslab,(filespace, H5S_SELECT_SET, offset, NULL, count, NULL)); 874 875 /* Create property list for collective dataset write */ 876 PetscStackCallHDF5Return(plist_id,H5Pcreate,(H5P_DATASET_XFER)); 877 #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO) 878 PetscStackCallHDF5(H5Pset_dxpl_mpio,(plist_id, H5FD_MPIO_COLLECTIVE)); 879 #endif 880 /* To read dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */ 881 882 ierr = VecGetArray(xin, &x);CHKERRQ(ierr); 883 PetscStackCallHDF5(H5Dread,(dset_id, scalartype, memspace, filespace, plist_id, x)); 884 ierr = VecRestoreArray(xin, &x);CHKERRQ(ierr); 885 886 /* Close/release resources */ 887 if (group != file_id) { 888 PetscStackCallHDF5(H5Gclose,(group)); 889 } 890 PetscStackCallHDF5(H5Pclose,(plist_id)); 891 PetscStackCallHDF5(H5Sclose,(filespace)); 892 PetscStackCallHDF5(H5Sclose,(memspace)); 893 PetscStackCallHDF5(H5Dclose,(dset_id)); 894 PetscFunctionReturn(0); 895 } 896 #endif 897 898 PetscErrorCode VecLoad_Binary_DA(Vec xin, PetscViewer viewer) 899 { 900 DM da; 901 PetscErrorCode ierr; 902 Vec natural; 903 const char *prefix; 904 PetscInt bs; 905 PetscBool flag; 906 DM_DA *dd; 907 #if defined(PETSC_HAVE_MPIIO) 908 PetscBool isMPIIO; 909 #endif 910 911 PetscFunctionBegin; 912 ierr = VecGetDM(xin,&da);CHKERRQ(ierr); 913 dd = (DM_DA*)da->data; 914 #if defined(PETSC_HAVE_MPIIO) 915 ierr = PetscViewerBinaryGetUseMPIIO(viewer,&isMPIIO);CHKERRQ(ierr); 916 if (isMPIIO) { 917 ierr = DMDAArrayMPIIO(da,viewer,xin,PETSC_FALSE);CHKERRQ(ierr); 918 PetscFunctionReturn(0); 919 } 920 #endif 921 922 ierr = PetscObjectGetOptionsPrefix((PetscObject)xin,&prefix);CHKERRQ(ierr); 923 ierr = DMDACreateNaturalVector(da,&natural);CHKERRQ(ierr); 924 ierr = PetscObjectSetName((PetscObject)natural,((PetscObject)xin)->name);CHKERRQ(ierr); 925 ierr = PetscObjectSetOptionsPrefix((PetscObject)natural,prefix);CHKERRQ(ierr); 926 ierr = VecLoad(natural,viewer);CHKERRQ(ierr); 927 ierr = DMDANaturalToGlobalBegin(da,natural,INSERT_VALUES,xin);CHKERRQ(ierr); 928 ierr = DMDANaturalToGlobalEnd(da,natural,INSERT_VALUES,xin);CHKERRQ(ierr); 929 ierr = VecDestroy(&natural);CHKERRQ(ierr); 930 ierr = PetscInfo(xin,"Loading vector from natural ordering into DMDA\n");CHKERRQ(ierr); 931 ierr = PetscOptionsGetInt(NULL,((PetscObject)xin)->prefix,"-vecload_block_size",&bs,&flag);CHKERRQ(ierr); 932 if (flag && bs != dd->w) { 933 ierr = PetscInfo2(xin,"Block size in file %D not equal to DMDA's dof %D\n",bs,dd->w);CHKERRQ(ierr); 934 } 935 PetscFunctionReturn(0); 936 } 937 938 PetscErrorCode VecLoad_Default_DA(Vec xin, PetscViewer viewer) 939 { 940 PetscErrorCode ierr; 941 DM da; 942 PetscBool isbinary; 943 #if defined(PETSC_HAVE_HDF5) 944 PetscBool ishdf5; 945 #endif 946 947 PetscFunctionBegin; 948 ierr = VecGetDM(xin,&da);CHKERRQ(ierr); 949 if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA"); 950 951 #if defined(PETSC_HAVE_HDF5) 952 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);CHKERRQ(ierr); 953 #endif 954 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 955 956 if (isbinary) { 957 ierr = VecLoad_Binary_DA(xin,viewer);CHKERRQ(ierr); 958 #if defined(PETSC_HAVE_HDF5) 959 } else if (ishdf5) { 960 ierr = VecLoad_HDF5_DA(xin,viewer);CHKERRQ(ierr); 961 #endif 962 } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Viewer type %s not supported for vector loading", ((PetscObject)viewer)->type_name); 963 PetscFunctionReturn(0); 964 } 965