Actual source code: gr2.c

petsc-3.3-p7 2013-05-11
  2: /* 
  3:    Plots vectors obtained with DMDACreate2d()
  4: */

  6: #include <petsc-private/daimpl.h>      /*I  "petscdmda.h"   I*/
  7: #include <petsc-private/vecimpl.h> 

  9: /*
 10:         The data that is passed into the graphics callback
 11: */
 12: typedef struct {
 13:   PetscInt     m,n,step,k;
 14:   PetscReal    min,max,scale;
 15:   PetscScalar  *xy,*v;
 16:   PetscBool    showgrid;
 17: } ZoomCtx;

 19: /*
 20:        This does the drawing for one particular field 
 21:     in one particular set of coordinates. It is a callback
 22:     called from PetscDrawZoom()
 23: */
 26: PetscErrorCode VecView_MPI_Draw_DA2d_Zoom(PetscDraw draw,void *ctx)
 27: {
 28:   ZoomCtx        *zctx = (ZoomCtx*)ctx;
 30:   PetscInt       m,n,i,j,k,step,id,c1,c2,c3,c4;
 31:   PetscReal      s,min,x1,x2,x3,x4,y_1,y2,y3,y4;
 32:   PetscScalar   *v,*xy;

 35:   m    = zctx->m;
 36:   n    = zctx->n;
 37:   step = zctx->step;
 38:   k    = zctx->k;
 39:   v    = zctx->v;
 40:   xy   = zctx->xy;
 41:   s    = zctx->scale;
 42:   min  = zctx->min;
 43: 
 44:   /* PetscDraw the contour plot patch */
 45:   for (j=0; j<n-1; j++) {
 46:     for (i=0; i<m-1; i++) {
 47: #if !defined(PETSC_USE_COMPLEX)
 48:       id = i+j*m;    x1 = xy[2*id];y_1 = xy[2*id+1];c1 = (int)(PETSC_DRAW_BASIC_COLORS+s*(v[k+step*id]-min));
 49:       id = i+j*m+1;  x2 = xy[2*id];y2  = y_1;       c2 = (int)(PETSC_DRAW_BASIC_COLORS+s*(v[k+step*id]-min));
 50:       id = i+j*m+1+m;x3 = x2;      y3  = xy[2*id+1];c3 = (int)(PETSC_DRAW_BASIC_COLORS+s*(v[k+step*id]-min));
 51:       id = i+j*m+m;  x4 = x1;      y4  = y3;        c4 = (int)(PETSC_DRAW_BASIC_COLORS+s*(v[k+step*id]-min));
 52: #else
 53:       id = i+j*m;    x1 = PetscRealPart(xy[2*id]);y_1 = PetscRealPart(xy[2*id+1]);c1 = (int)(PETSC_DRAW_BASIC_COLORS+s*(PetscRealPart(v[k+step*id])-min));
 54:       id = i+j*m+1;  x2 = PetscRealPart(xy[2*id]);y2  = y_1;       c2 = (int)(PETSC_DRAW_BASIC_COLORS+s*(PetscRealPart(v[k+step*id])-min));
 55:       id = i+j*m+1+m;x3 = x2;      y3  = PetscRealPart(xy[2*id+1]);c3 = (int)(PETSC_DRAW_BASIC_COLORS+s*(PetscRealPart(v[k+step*id])-min));
 56:       id = i+j*m+m;  x4 = x1;      y4  = y3;        c4 = (int)(PETSC_DRAW_BASIC_COLORS+s*(PetscRealPart(v[k+step*id])-min));
 57: #endif
 58:       PetscDrawTriangle(draw,x1,y_1,x2,y2,x3,y3,c1,c2,c3);
 59:       PetscDrawTriangle(draw,x1,y_1,x3,y3,x4,y4,c1,c3,c4);
 60:       if (zctx->showgrid) {
 61:         PetscDrawLine(draw,x1,y_1,x2,y2,PETSC_DRAW_BLACK);
 62:         PetscDrawLine(draw,x2,y2,x3,y3,PETSC_DRAW_BLACK);
 63:         PetscDrawLine(draw,x3,y3,x4,y4,PETSC_DRAW_BLACK);
 64:         PetscDrawLine(draw,x4,y4,x1,y_1,PETSC_DRAW_BLACK);
 65:       }
 66:     }
 67:   }
 68:   return(0);
 69: }

 73: PetscErrorCode VecView_MPI_Draw_DA2d(Vec xin,PetscViewer viewer)
 74: {
 75:   DM                 da,dac,dag;
 76:   PetscErrorCode     ierr;
 77:   PetscMPIInt        rank;
 78:   PetscInt           N,s,M,w;
 79:   const PetscInt     *lx,*ly;
 80:   PetscReal          coors[4],ymin,ymax,xmin,xmax;
 81:   PetscDraw          draw,popup;
 82:   PetscBool          isnull,useports = PETSC_FALSE;
 83:   MPI_Comm           comm;
 84:   Vec                xlocal,xcoor,xcoorl;
 85:   DMDABoundaryType   bx,by;
 86:   DMDAStencilType    st;
 87:   ZoomCtx            zctx;
 88:   PetscDrawViewPorts *ports = PETSC_NULL;
 89:   PetscViewerFormat  format;
 90:   PetscInt           *displayfields;
 91:   PetscInt           ndisplayfields,i,nbounds;
 92:   PetscBool          flg;
 93:   const PetscReal    *bounds;

 96:   zctx.showgrid = PETSC_FALSE;
 97:   PetscViewerDrawGetDraw(viewer,0,&draw);
 98:   PetscDrawIsNull(draw,&isnull); if (isnull) return(0);
 99:   PetscViewerDrawGetBounds(viewer,&nbounds,&bounds);

101:   PetscObjectQuery((PetscObject)xin,"DM",(PetscObject*)&da);
102:   if (!da) SETERRQ(((PetscObject)xin)->comm,PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA");

104:   PetscObjectGetComm((PetscObject)xin,&comm);
105:   MPI_Comm_rank(comm,&rank);

107:   DMDAGetInfo(da,0,&M,&N,0,&zctx.m,&zctx.n,0,&w,&s,&bx,&by,0,&st);
108:   DMDAGetOwnershipRanges(da,&lx,&ly,PETSC_NULL);

110:   /* 
111:         Obtain a sequential vector that is going to contain the local values plus ONE layer of 
112:      ghosted values to draw the graphics from. We also need its corresponding DMDA (dac) that will
113:      update the local values pluse ONE layer of ghost values. 
114:   */
115:   PetscObjectQuery((PetscObject)da,"GraphicsGhosted",(PetscObject*)&xlocal);
116:   if (!xlocal) {
117:     if (bx !=  DMDA_BOUNDARY_NONE || by !=  DMDA_BOUNDARY_NONE || s != 1 || st != DMDA_STENCIL_BOX) {
118:       /* 
119:          if original da is not of stencil width one, or periodic or not a box stencil then
120:          create a special DMDA to handle one level of ghost points for graphics
121:       */
122:       DMDACreate2d(comm,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,N,zctx.m,zctx.n,w,1,lx,ly,&dac);
123:       PetscInfo(da,"Creating auxilary DMDA for managing graphics ghost points\n");
124:     } else {
125:       /* otherwise we can use the da we already have */
126:       dac = da;
127:     }
128:     /* create local vector for holding ghosted values used in graphics */
129:     DMCreateLocalVector(dac,&xlocal);
130:     if (dac != da) {
131:       /* don't keep any public reference of this DMDA, is is only available through xlocal */
132:       PetscObjectDereference((PetscObject)dac);
133:     } else {
134:       /* remove association between xlocal and da, because below we compose in the opposite
135:          direction and if we left this connect we'd get a loop, so the objects could 
136:          never be destroyed */
137:       PetscObjectRemoveReference((PetscObject)xlocal,"DM");
138:     }
139:     PetscObjectCompose((PetscObject)da,"GraphicsGhosted",(PetscObject)xlocal);
140:     PetscObjectDereference((PetscObject)xlocal);
141:   } else {
142:     if (bx !=  DMDA_BOUNDARY_NONE || by !=  DMDA_BOUNDARY_NONE || s != 1 || st != DMDA_STENCIL_BOX) {
143:       PetscObjectQuery((PetscObject)xlocal,"DM",(PetscObject*)&dac);
144:     } else {
145:       dac = da;
146:     }
147:   }

149:   /*
150:       Get local (ghosted) values of vector
151:   */
152:   DMGlobalToLocalBegin(dac,xin,INSERT_VALUES,xlocal);
153:   DMGlobalToLocalEnd(dac,xin,INSERT_VALUES,xlocal);
154:   VecGetArray(xlocal,&zctx.v);

156:   /* get coordinates of nodes */
157:   DMDAGetCoordinates(da,&xcoor);
158:   if (!xcoor) {
159:     DMDASetUniformCoordinates(da,0.0,1.0,0.0,1.0,0.0,0.0);
160:     DMDAGetCoordinates(da,&xcoor);
161:   }

163:   /*
164:       Determine the min and max  coordinates in plot 
165:   */
166:   VecStrideMin(xcoor,0,PETSC_NULL,&xmin);
167:   VecStrideMax(xcoor,0,PETSC_NULL,&xmax);
168:   VecStrideMin(xcoor,1,PETSC_NULL,&ymin);
169:   VecStrideMax(xcoor,1,PETSC_NULL,&ymax);
170:   coors[0] = xmin - .05*(xmax- xmin); coors[2] = xmax + .05*(xmax - xmin);
171:   coors[1] = ymin - .05*(ymax- ymin); coors[3] = ymax + .05*(ymax - ymin);
172:   PetscInfo4(da,"Preparing DMDA 2d contour plot coordinates %G %G %G %G\n",coors[0],coors[1],coors[2],coors[3]);

174:   /*
175:        get local ghosted version of coordinates 
176:   */
177:   PetscObjectQuery((PetscObject)da,"GraphicsCoordinateGhosted",(PetscObject*)&xcoorl);
178:   if (!xcoorl) {
179:     /* create DMDA to get local version of graphics */
180:     DMDACreate2d(comm,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,N,zctx.m,zctx.n,2,1,lx,ly,&dag);
181:     PetscInfo(dag,"Creating auxilary DMDA for managing graphics coordinates ghost points\n");
182:     DMCreateLocalVector(dag,&xcoorl);
183:     PetscObjectCompose((PetscObject)da,"GraphicsCoordinateGhosted",(PetscObject)xcoorl);
184:     PetscObjectDereference((PetscObject)dag);
185:     PetscObjectDereference((PetscObject)xcoorl);
186:   } else {
187:     PetscObjectQuery((PetscObject)xcoorl,"DM",(PetscObject*)&dag);
188:   }
189:   DMGlobalToLocalBegin(dag,xcoor,INSERT_VALUES,xcoorl);
190:   DMGlobalToLocalEnd(dag,xcoor,INSERT_VALUES,xcoorl);
191:   VecGetArray(xcoorl,&zctx.xy);
192: 
193:   /*
194:         Get information about size of area each processor must do graphics for
195:   */
196:   DMDAGetInfo(dac,0,&M,&N,0,0,0,0,&zctx.step,0,&bx,&by,0,0);
197:   DMDAGetGhostCorners(dac,0,0,0,&zctx.m,&zctx.n,0);

199:   PetscOptionsGetBool(PETSC_NULL,"-draw_contour_grid",&zctx.showgrid,PETSC_NULL);
200:   PetscMalloc(zctx.step*sizeof(PetscInt),&displayfields);
201:   for (i=0; i<zctx.step; i++) displayfields[i] = i;
202:   ndisplayfields = zctx.step;
203:   PetscOptionsGetIntArray(PETSC_NULL,"-draw_fields",displayfields,&ndisplayfields,&flg);
204:   if (!flg) ndisplayfields = zctx.step;

206:   PetscViewerGetFormat(viewer,&format);
207:   PetscOptionsGetBool(PETSC_NULL,"-draw_ports",&useports,PETSC_NULL);
208:   if (useports || format == PETSC_VIEWER_DRAW_PORTS){
209:     PetscDrawSynchronizedClear(draw);
210:     PetscDrawViewPortsCreate(draw,ndisplayfields,&ports);
211:   }

213:   /*
214:      Loop over each field; drawing each in a different window
215:   */
216:   for (i=0; i<ndisplayfields; i++) {
217:     zctx.k = displayfields[i];
218:     if (useports) {
219:       PetscDrawViewPortsSet(ports,i);
220:     } else {
221:       PetscViewerDrawGetDraw(viewer,i,&draw);
222:       PetscDrawSynchronizedClear(draw);
223:     }

225:     /*
226:         Determine the min and max color in plot 
227:     */
228:     VecStrideMin(xin,zctx.k,PETSC_NULL,&zctx.min);
229:     VecStrideMax(xin,zctx.k,PETSC_NULL,&zctx.max);
230:     if (zctx.k < nbounds) {
231:       zctx.min = PetscMin(zctx.min,bounds[2*zctx.k]);
232:       zctx.max = PetscMax(zctx.max,bounds[2*zctx.k+1]);
233:     }
234:     if (zctx.min == zctx.max) {
235:       zctx.min -= 1.e-12;
236:       zctx.max += 1.e-12;
237:     }

239:     if (!rank) {
240:       const char *title;

242:       DMDAGetFieldName(da,zctx.k,&title);
243:       if (title) {
244:         PetscDrawSetTitle(draw,title);
245:       }
246:     }
247:     PetscDrawSetCoordinates(draw,coors[0],coors[1],coors[2],coors[3]);
248:     PetscInfo2(da,"DMDA 2d contour plot min %G max %G\n",zctx.min,zctx.max);

250:     PetscDrawGetPopup(draw,&popup);
251:     if (popup) {PetscDrawScalePopup(popup,zctx.min,zctx.max);}

253:     zctx.scale = (245.0 - PETSC_DRAW_BASIC_COLORS)/(zctx.max - zctx.min);

255:     PetscDrawZoom(draw,VecView_MPI_Draw_DA2d_Zoom,&zctx);
256:   }
257:   PetscFree(displayfields);
258:   PetscDrawViewPortsDestroy(ports);

260:   VecRestoreArray(xcoorl,&zctx.xy);
261:   VecRestoreArray(xlocal,&zctx.v);
262:   return(0);
263: }


266: #if defined(PETSC_HAVE_HDF5)
269: PetscErrorCode VecView_MPI_HDF5_DA(Vec xin,PetscViewer viewer)
270: {
271:   DM             dm;
272:   DM_DA          *da;
273:   hid_t          filespace;  /* file dataspace identifier */
274:   hid_t          chunkspace; /* chunk dataset property identifier */
275:   hid_t                 plist_id;   /* property list identifier */
276:   hid_t          dset_id;    /* dataset identifier */
277:   hid_t          memspace;   /* memory dataspace identifier */
278:   hid_t          file_id;
279:   hid_t          group;
280:   hid_t          scalartype; /* scalar type (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */
281:   herr_t         status;
282:   hsize_t        dim;
283:   hsize_t        maxDims[6], dims[6], chunkDims[6], count[6], offset[6];
284:   PetscInt       timestep;
285:   PetscScalar    *x;
286:   const char     *vecname;

290:   PetscViewerHDF5OpenGroup(viewer, &file_id, &group);
291:   PetscViewerHDF5GetTimestep(viewer, &timestep);

293:   PetscObjectQuery((PetscObject)xin,"DM",(PetscObject*)&dm);
294:   if (!dm) SETERRQ(((PetscObject)xin)->comm,PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA");
295:   da = (DM_DA*)dm->data;

297:   /* Create the dataspace for the dataset.
298:    *
299:    * dims - holds the current dimensions of the dataset
300:    *
301:    * maxDims - holds the maximum dimensions of the dataset (unlimited
302:    * for the number of time steps with the current dimensions for the
303:    * other dimensions; so only additional time steps can be added).
304:    *
305:    * chunkDims - holds the size of a single time step (required to
306:    * permit extending dataset).
307:    */
308:   dim = 0;
309:   if (timestep >= 0) {
310:     dims[dim]      = timestep+1;
311:     maxDims[dim]   = H5S_UNLIMITED;
312:     chunkDims[dim] = 1;
313:     ++dim;
314:   }
315:   if (da->dim == 3) {
316:     dims[dim]      = PetscHDF5IntCast(da->P);
317:     maxDims[dim]   = dims[dim];
318:     chunkDims[dim] = dims[dim];
319:     ++dim;
320:   }
321:   if (da->dim > 1) {
322:     dims[dim]      = PetscHDF5IntCast(da->N);
323:     maxDims[dim]   = dims[dim];
324:     chunkDims[dim] = dims[dim];
325:     ++dim;
326:   }
327:   dims[dim]    = PetscHDF5IntCast(da->M);
328:   maxDims[dim]   = dims[dim];
329:   chunkDims[dim] = dims[dim];
330:   ++dim;
331:   if (da->w > 1) {
332:     dims[dim]      = PetscHDF5IntCast(da->w);
333:     maxDims[dim]   = dims[dim];
334:     chunkDims[dim] = dims[dim];
335:     ++dim;
336:   }
337: #if defined(PETSC_USE_COMPLEX)
338:     dims[dim]      = 2;
339:     maxDims[dim]   = dims[dim];
340:     chunkDims[dim] = dims[dim];
341:     ++dim;
342: #endif
343:   filespace = H5Screate_simple(dim, dims, maxDims);
344:   if (filespace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Screate_simple()");

346: #if defined(PETSC_USE_REAL_SINGLE)
347:   scalartype = H5T_NATIVE_FLOAT;
348: #elif defined(PETSC_USE_REAL___FLOAT128)
349: #error "HDF5 output with 128 bit floats not supported."
350: #else
351:   scalartype = H5T_NATIVE_DOUBLE;
352: #endif

354:   /* Create the dataset with default properties and close filespace */
355:   PetscObjectGetName((PetscObject)xin,&vecname);
356:   if (!H5Lexists(group, vecname, H5P_DEFAULT)) {
357:     /* Create chunk */
358:     chunkspace = H5Pcreate(H5P_DATASET_CREATE);
359:     if (chunkspace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Pcreate()");
360:     status = H5Pset_chunk(chunkspace, dim, chunkDims); CHKERRQ(status);
361: 
362: #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
363:     dset_id = H5Dcreate2(group, vecname, scalartype, filespace, H5P_DEFAULT, chunkspace, H5P_DEFAULT);
364: #else
365:     dset_id = H5Dcreate(group, vecname, scalartype, filespace, H5P_DEFAULT);
366: #endif
367:     if (dset_id == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Dcreate2()");
368:   } else {
369:     dset_id = H5Dopen2(group, vecname, H5P_DEFAULT);
370:     status = H5Dset_extent(dset_id, dims);CHKERRQ(status);
371:   }
372:   status = H5Sclose(filespace);CHKERRQ(status);

374:   /* Each process defines a dataset and writes it to the hyperslab in the file */
375:   dim = 0;
376:   if (timestep >= 0) {
377:     offset[dim] = timestep;
378:     ++dim;
379:   }
380:   if (da->dim == 3) offset[dim++] = PetscHDF5IntCast(da->zs);
381:   if (da->dim > 1)  offset[dim++] = PetscHDF5IntCast(da->ys);
382:   offset[dim++] = PetscHDF5IntCast(da->xs/da->w);
383:   if (da->w > 1) offset[dim++] = 0;
384: #if defined(PETSC_USE_COMPLEX)
385:   offset[dim++] = 0;
386: #endif
387:   dim = 0;
388:   if (timestep >= 0) {
389:     count[dim] = 1;
390:     ++dim;
391:   }
392:   if (da->dim == 3) count[dim++] = PetscHDF5IntCast(da->ze - da->zs);
393:   if (da->dim > 1)  count[dim++] = PetscHDF5IntCast(da->ye - da->ys);
394:   count[dim++] = PetscHDF5IntCast((da->xe - da->xs)/da->w);
395:   if (da->w > 1) count[dim++] = PetscHDF5IntCast(da->w);
396: #if defined(PETSC_USE_COMPLEX)
397:   count[dim++] = 2;
398: #endif
399:   memspace = H5Screate_simple(dim, count, NULL);
400:   if (memspace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Screate_simple()");

402:   filespace = H5Dget_space(dset_id);
403:   if (filespace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Dget_space()");
404:   status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, count, NULL);CHKERRQ(status);

406:   /* Create property list for collective dataset write */
407:   plist_id = H5Pcreate(H5P_DATASET_XFER);
408:   if (plist_id == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Pcreate()");
409: #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
410:   status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);CHKERRQ(status);
411: #endif
412:   /* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */

414:   VecGetArray(xin, &x);
415:   status = H5Dwrite(dset_id, scalartype, memspace, filespace, plist_id, x);CHKERRQ(status);
416:   status = H5Fflush(file_id, H5F_SCOPE_GLOBAL);CHKERRQ(status);
417:   VecRestoreArray(xin, &x);

419:   /* Close/release resources */
420:   if (group != file_id) {
421:     status = H5Gclose(group);CHKERRQ(status);
422:   }
423:   status = H5Pclose(plist_id);CHKERRQ(status);
424:   status = H5Sclose(filespace);CHKERRQ(status);
425:   status = H5Sclose(memspace);CHKERRQ(status);
426:   status = H5Dclose(dset_id);CHKERRQ(status);
427:   PetscInfo1(xin,"Wrote Vec object with name %s\n",vecname);
428:   return(0);
429: }
430: #endif

432: extern PetscErrorCode VecView_MPI_Draw_DA1d(Vec,PetscViewer);

434: #if defined(PETSC_HAVE_MPIIO)
437: static PetscErrorCode DMDAArrayMPIIO(DM da,PetscViewer viewer,Vec xin,PetscBool  write)
438: {
439:   PetscErrorCode    ierr;
440:   MPI_File          mfdes;
441:   PetscMPIInt       gsizes[4],lsizes[4],lstarts[4],asiz,dof;
442:   MPI_Datatype      view;
443:   const PetscScalar *array;
444:   MPI_Offset        off;
445:   MPI_Aint          ub,ul;
446:   PetscInt          type,rows,vecrows,tr[2];
447:   DM_DA             *dd = (DM_DA*)da->data;

450:   VecGetSize(xin,&vecrows);
451:   if (!write) {
452:     /* Read vector header. */
453:     PetscViewerBinaryRead(viewer,tr,2,PETSC_INT);
454:     type = tr[0];
455:     rows = tr[1];
456:     if (type != VEC_FILE_CLASSID) SETERRQ(((PetscObject)da)->comm,PETSC_ERR_ARG_WRONG,"Not vector next in file");
457:     if (rows != vecrows) SETERRQ(((PetscObject)da)->comm,PETSC_ERR_ARG_SIZ,"Vector in file not same size as DMDA vector");
458:   } else {
459:     tr[0] = VEC_FILE_CLASSID;
460:     tr[1] = vecrows;
461:     PetscViewerBinaryWrite(viewer,tr,2,PETSC_INT,PETSC_TRUE);
462:   }

464:   dof = PetscMPIIntCast(dd->w);
465:   gsizes[0]  = dof; gsizes[1] = PetscMPIIntCast(dd->M); gsizes[2] = PetscMPIIntCast(dd->N); gsizes[3] = PetscMPIIntCast(dd->P);
466:   lsizes[0]  = dof;lsizes[1] = PetscMPIIntCast((dd->xe-dd->xs)/dof); lsizes[2] = PetscMPIIntCast(dd->ye-dd->ys); lsizes[3] = PetscMPIIntCast(dd->ze-dd->zs);
467:   lstarts[0] = 0;  lstarts[1] = PetscMPIIntCast(dd->xs/dof); lstarts[2] = PetscMPIIntCast(dd->ys); lstarts[3] = PetscMPIIntCast(dd->zs);
468:   MPI_Type_create_subarray(dd->dim+1,gsizes,lsizes,lstarts,MPI_ORDER_FORTRAN,MPIU_SCALAR,&view);
469:   MPI_Type_commit(&view);
470: 
471:   PetscViewerBinaryGetMPIIODescriptor(viewer,&mfdes);
472:   PetscViewerBinaryGetMPIIOOffset(viewer,&off);
473:   MPI_File_set_view(mfdes,off,MPIU_SCALAR,view,(char *)"native",MPI_INFO_NULL);
474:   VecGetArrayRead(xin,&array);
475:   asiz = lsizes[1]*(lsizes[2] > 0 ? lsizes[2] : 1)*(lsizes[3] > 0 ? lsizes[3] : 1)*dof;
476:   if (write) {
477:     MPIU_File_write_all(mfdes,(PetscScalar*)array,asiz,MPIU_SCALAR,MPI_STATUS_IGNORE);
478:   } else {
479:     MPIU_File_read_all(mfdes,(PetscScalar*)array,asiz,MPIU_SCALAR,MPI_STATUS_IGNORE);
480:   }
481:   MPI_Type_get_extent(view,&ul,&ub);
482:   PetscViewerBinaryAddMPIIOOffset(viewer,ub);
483:   VecRestoreArrayRead(xin,&array);
484:   MPI_Type_free(&view);
485:   return(0);
486: }
487: #endif

489: EXTERN_C_BEGIN
492: PetscErrorCode  VecView_MPI_DA(Vec xin,PetscViewer viewer)
493: {
494:   DM             da;
496:   PetscInt       dim;
497:   Vec            natural;
498:   PetscBool      isdraw,isvtk;
499: #if defined(PETSC_HAVE_HDF5)
500:   PetscBool      ishdf5;
501: #endif
502:   const char     *prefix,*name;

505:   PetscObjectQuery((PetscObject)xin,"DM",(PetscObject*)&da);
506:   if (!da) SETERRQ(((PetscObject)xin)->comm,PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA");
507:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);
508:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERVTK,&isvtk);
509: #if defined(PETSC_HAVE_HDF5)
510:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);
511: #endif
512:   if (isdraw) {
513:     DMDAGetInfo(da,&dim,0,0,0,0,0,0,0,0,0,0,0,0);
514:     if (dim == 1) {
515:       VecView_MPI_Draw_DA1d(xin,viewer);
516:     } else if (dim == 2) {
517:       VecView_MPI_Draw_DA2d(xin,viewer);
518:     } else {
519:       SETERRQ1(((PetscObject)da)->comm,PETSC_ERR_SUP,"Cannot graphically view vector associated with this dimensional DMDA %D",dim);
520:     }
521:   } else if (isvtk) {           /* Duplicate the Vec and hold a reference to the DM */
522:     Vec Y;
523:     PetscObjectReference((PetscObject)da);
524:     VecDuplicate(xin,&Y);
525:     if (((PetscObject)xin)->name) {
526:       /* If xin was named, copy the name over to Y. The duplicate names are safe because nobody else will ever see Y. */
527:       PetscObjectSetName((PetscObject)Y,((PetscObject)xin)->name);
528:     }
529:     VecCopy(xin,Y);
530:     PetscViewerVTKAddField(viewer,(PetscObject)da,DMDAVTKWriteAll,PETSC_VTK_POINT_FIELD,(PetscObject)Y);
531: #if defined(PETSC_HAVE_HDF5)
532:   } else if (ishdf5) {
533:     VecView_MPI_HDF5_DA(xin,viewer);
534: #endif
535:   } else {
536: #if defined(PETSC_HAVE_MPIIO)
537:     PetscBool  isbinary,isMPIIO;

539:     PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);
540:     if (isbinary) {
541:       PetscViewerBinaryGetMPIIO(viewer,&isMPIIO);
542:       if (isMPIIO) {
543:        DMDAArrayMPIIO(da,viewer,xin,PETSC_TRUE);
544:        return(0);
545:       }
546:     }
547: #endif
548: 
549:     /* call viewer on natural ordering */
550:     PetscObjectGetOptionsPrefix((PetscObject)xin,&prefix);
551:     DMDACreateNaturalVector(da,&natural);
552:     PetscObjectSetOptionsPrefix((PetscObject)natural,prefix);
553:     DMDAGlobalToNaturalBegin(da,xin,INSERT_VALUES,natural);
554:     DMDAGlobalToNaturalEnd(da,xin,INSERT_VALUES,natural);
555:     PetscObjectGetName((PetscObject)xin,&name);
556:     PetscObjectSetName((PetscObject)natural,name);
557:     VecView(natural,viewer);
558:     VecDestroy(&natural);
559:   }
560:   return(0);
561: }
562: EXTERN_C_END

564: #if defined(PETSC_HAVE_HDF5)
567: PetscErrorCode VecLoad_HDF5_DA(Vec xin, PetscViewer viewer)
568: {
569:   DM             da;
571:   hsize_t        dim;
572:   hsize_t        count[5];
573:   hsize_t        offset[5];
574:   PetscInt       cnt = 0;
575:   PetscScalar    *x;
576:   const char     *vecname;
577:   hid_t          filespace; /* file dataspace identifier */
578:   hid_t                 plist_id;  /* property list identifier */
579:   hid_t          dset_id;   /* dataset identifier */
580:   hid_t          memspace;  /* memory dataspace identifier */
581:   hid_t          file_id;
582:   herr_t         status;
583:   DM_DA          *dd;

586:   PetscViewerHDF5GetFileId(viewer, &file_id);
587:   PetscObjectQuery((PetscObject)xin,"DM",(PetscObject*)&da);
588:   dd = (DM_DA*)da->data;

590:   /* Create the dataspace for the dataset */
591:   dim       = PetscHDF5IntCast(dd->dim + ((dd->w == 1) ? 0 : 1));
592: #if defined(PETSC_USE_COMPLEX)
593:   dim++;
594: #endif

596:   /* Create the dataset with default properties and close filespace */
597:   PetscObjectGetName((PetscObject)xin,&vecname);
598: #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
599:   dset_id = H5Dopen2(file_id, vecname, H5P_DEFAULT);
600: #else
601:   dset_id = H5Dopen(file_id, vecname);
602: #endif
603:   if (dset_id == -1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Dopen2() with Vec named %s",vecname);
604:   filespace = H5Dget_space(dset_id);

606:   /* Each process defines a dataset and reads it from the hyperslab in the file */
607:   cnt = 0;
608:   if (dd->dim == 3) offset[cnt++] = PetscHDF5IntCast(dd->zs);
609:   if (dd->dim > 1)  offset[cnt++] = PetscHDF5IntCast(dd->ys);
610:   offset[cnt++] = PetscHDF5IntCast(dd->xs/dd->w);
611:   if (dd->w > 1) offset[cnt++] = 0;
612: #if defined(PETSC_USE_COMPLEX)
613:   offset[cnt++] = 0;
614: #endif
615:   cnt = 0;
616:   if (dd->dim == 3) count[cnt++] = PetscHDF5IntCast(dd->ze - dd->zs);
617:   if (dd->dim > 1)  count[cnt++] = PetscHDF5IntCast(dd->ye - dd->ys);
618:   count[cnt++] = PetscHDF5IntCast((dd->xe - dd->xs)/dd->w);
619:   if (dd->w > 1) count[cnt++] = PetscHDF5IntCast(dd->w);
620: #if defined(PETSC_USE_COMPLEX)
621:   count[cnt++] = 2;
622: #endif
623:   memspace = H5Screate_simple(dim, count, NULL);
624:   if (memspace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Screate_simple()");

626:   status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, count, NULL);CHKERRQ(status);

628:   /* Create property list for collective dataset write */
629:   plist_id = H5Pcreate(H5P_DATASET_XFER);
630:   if (plist_id == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Pcreate()");
631: #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
632:   status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);CHKERRQ(status);
633: #endif
634:   /* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */

636:   VecGetArray(xin, &x);
637:   status = H5Dread(dset_id, H5T_NATIVE_DOUBLE, memspace, filespace, plist_id, x);CHKERRQ(status);
638:   VecRestoreArray(xin, &x);

640:   /* Close/release resources */
641:   status = H5Pclose(plist_id);CHKERRQ(status);
642:   status = H5Sclose(filespace);CHKERRQ(status);
643:   status = H5Sclose(memspace);CHKERRQ(status);
644:   status = H5Dclose(dset_id);CHKERRQ(status);
645:   return(0);
646: }
647: #endif

651: PetscErrorCode VecLoad_Binary_DA(Vec xin, PetscViewer viewer)
652: {
653:   DM             da;
655:   Vec            natural;
656:   const char     *prefix;
657:   PetscInt       bs;
658:   PetscBool      flag;
659:   DM_DA          *dd;
660: #if defined(PETSC_HAVE_MPIIO)
661:   PetscBool      isMPIIO;
662: #endif

665:   PetscObjectQuery((PetscObject)xin,"DM",(PetscObject*)&da);
666:   dd   = (DM_DA*)da->data;
667: #if defined(PETSC_HAVE_MPIIO)
668:   PetscViewerBinaryGetMPIIO(viewer,&isMPIIO);
669:   if (isMPIIO) {
670:     DMDAArrayMPIIO(da,viewer,xin,PETSC_FALSE);
671:     return(0);
672:   }
673: #endif

675:   PetscObjectGetOptionsPrefix((PetscObject)xin,&prefix);
676:   DMDACreateNaturalVector(da,&natural);
677:   PetscObjectSetName((PetscObject)natural,((PetscObject)xin)->name);
678:   PetscObjectSetOptionsPrefix((PetscObject)natural,prefix);
679:   VecLoad_Binary(natural,viewer);
680:   DMDANaturalToGlobalBegin(da,natural,INSERT_VALUES,xin);
681:   DMDANaturalToGlobalEnd(da,natural,INSERT_VALUES,xin);
682:   VecDestroy(&natural);
683:   PetscInfo(xin,"Loading vector from natural ordering into DMDA\n");
684:   PetscOptionsGetInt(((PetscObject)xin)->prefix,"-vecload_block_size",&bs,&flag);
685:   if (flag && bs != dd->w) {
686:     PetscInfo2(xin,"Block size in file %D not equal to DMDA's dof %D\n",bs,dd->w);
687:   }
688:   return(0);
689: }

691: EXTERN_C_BEGIN
694: PetscErrorCode  VecLoad_Default_DA(Vec xin, PetscViewer viewer)
695: {
697:   DM             da;
698:   PetscBool      isbinary;
699: #if defined(PETSC_HAVE_HDF5)
700:   PetscBool      ishdf5;
701: #endif

704:   PetscObjectQuery((PetscObject)xin,"DM",(PetscObject*)&da);
705:   if (!da) SETERRQ(((PetscObject)xin)->comm,PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA");

707: #if defined(PETSC_HAVE_HDF5)
708:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);
709: #endif
710:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);

712:   if (isbinary) {
713:     VecLoad_Binary_DA(xin,viewer);
714: #if defined(PETSC_HAVE_HDF5)
715:   } else if (ishdf5) {
716:     VecLoad_HDF5_DA(xin,viewer);
717: #endif
718:   } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Viewer type %s not supported for vector loading", ((PetscObject)viewer)->type_name);
719:   return(0);
720: }
721: EXTERN_C_END