Actual source code: gr2.c
petsc-3.4.5 2014-06-29
2: /*
3: Plots vectors obtained with DMDACreate2d()
4: */
6: #include <petsc-private/dmdaimpl.h> /*I "petscdmda.h" I*/
7: #include <petsc-private/vecimpl.h>
8: #include <petscdraw.h>
9: #include <petscviewerhdf5.h>
11: /*
12: The data that is passed into the graphics callback
13: */
14: typedef struct {
15: PetscInt m,n,step,k;
16: PetscReal min,max,scale;
17: PetscScalar *xy,*v;
18: PetscBool showgrid;
19: const char *name0,*name1;
20: } ZoomCtx;
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: */
29: PetscErrorCode VecView_MPI_Draw_DA2d_Zoom(PetscDraw draw,void *ctx)
30: {
31: ZoomCtx *zctx = (ZoomCtx*)ctx;
33: PetscInt m,n,i,j,k,step,id,c1,c2,c3,c4;
34: PetscReal s,min,max,x1,x2,x3,x4,y_1,y2,y3,y4,xmin = PETSC_MAX_REAL,xmax = PETSC_MIN_REAL,ymin = PETSC_MAX_REAL,ymax = PETSC_MIN_REAL;
35: PetscReal xminf,xmaxf,yminf,ymaxf,w;
36: PetscScalar *v,*xy;
37: char value[16];
38: size_t len;
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;
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);
63: id = i+j*m+1;
64: x2 = PetscRealPart(xy[2*id]);
65: y2 = y_1;
66: c2 = (int)(PETSC_DRAW_BASIC_COLORS+s*(PetscClipInterval(PetscRealPart(v[k+step*id]),min,max)-min));
67: xmin = PetscMin(xmin,x2);
68: xmax = PetscMax(xmax,x2);
70: id = i+j*m+1+m;
71: x3 = x2;
72: y3 = PetscRealPart(xy[2*id+1]);
73: c3 = (int)(PETSC_DRAW_BASIC_COLORS+s*(PetscClipInterval(PetscRealPart(v[k+step*id]),min,max)-min));
74: ymin = PetscMin(ymin,y3);
75: ymax = PetscMax(ymax,y3);
77: id = i+j*m+m;
78: x4 = x1;
79: y4 = y3;
80: c4 = (int)(PETSC_DRAW_BASIC_COLORS+s*(PetscClipInterval(PetscRealPart(v[k+step*id]),min,max)-min));
82: PetscDrawTriangle(draw,x1,y_1,x2,y2,x3,y3,c1,c2,c3);
83: PetscDrawTriangle(draw,x1,y_1,x3,y3,x4,y4,c1,c3,c4);
84: if (zctx->showgrid) {
85: PetscDrawLine(draw,x1,y_1,x2,y2,PETSC_DRAW_BLACK);
86: PetscDrawLine(draw,x2,y2,x3,y3,PETSC_DRAW_BLACK);
87: PetscDrawLine(draw,x3,y3,x4,y4,PETSC_DRAW_BLACK);
88: PetscDrawLine(draw,x4,y4,x1,y_1,PETSC_DRAW_BLACK);
89: }
90: }
91: }
92: if (zctx->name0) {
93: PetscReal xl,yl,xr,yr,x,y;
94: PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);
95: x = xl + .3*(xr - xl);
96: xl = xl + .01*(xr - xl);
97: y = yr - .3*(yr - yl);
98: yl = yl + .01*(yr - yl);
99: PetscDrawString(draw,x,yl,PETSC_DRAW_BLACK,zctx->name0);
100: PetscDrawStringVertical(draw,xl,y,PETSC_DRAW_BLACK,zctx->name1);
101: }
102: /*
103: Ideally we would use the PetscDrawAxis object to manage displaying the coordinate limits
104: but that may require some refactoring.
105: */
106: MPI_Allreduce(&xmin,&xminf,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)draw));
107: MPI_Allreduce(&xmax,&xmaxf,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)draw));
108: MPI_Allreduce(&ymin,&yminf,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)draw));
109: MPI_Allreduce(&ymax,&ymaxf,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)draw));
110: PetscSNPrintf(value,16,"%f",xminf);
111: PetscDrawString(draw,xminf,yminf - .05*(ymaxf - yminf),PETSC_DRAW_BLACK,value);
112: PetscSNPrintf(value,16,"%f",xmaxf);
113: PetscStrlen(value,&len);
114: PetscDrawStringGetSize(draw,&w,NULL);
115: PetscDrawString(draw,xmaxf - len*w,yminf - .05*(ymaxf - yminf),PETSC_DRAW_BLACK,value);
116: PetscSNPrintf(value,16,"%f",yminf);
117: PetscDrawString(draw,xminf - .05*(xmaxf - xminf),yminf,PETSC_DRAW_BLACK,value);
118: PetscSNPrintf(value,16,"%f",ymaxf);
119: PetscDrawString(draw,xminf - .05*(xmaxf - xminf),ymaxf,PETSC_DRAW_BLACK,value);
120: return(0);
121: }
125: PetscErrorCode VecView_MPI_Draw_DA2d(Vec xin,PetscViewer viewer)
126: {
127: DM da,dac,dag;
128: PetscErrorCode ierr;
129: PetscMPIInt rank;
130: PetscInt N,s,M,w,ncoors = 4;
131: const PetscInt *lx,*ly;
132: PetscReal coors[4],ymin,ymax,xmin,xmax;
133: PetscDraw draw,popup;
134: PetscBool isnull,useports = PETSC_FALSE;
135: MPI_Comm comm;
136: Vec xlocal,xcoor,xcoorl;
137: DMDABoundaryType bx,by;
138: DMDAStencilType st;
139: ZoomCtx zctx;
140: PetscDrawViewPorts *ports = NULL;
141: PetscViewerFormat format;
142: PetscInt *displayfields;
143: PetscInt ndisplayfields,i,nbounds;
144: const PetscReal *bounds;
147: zctx.showgrid = PETSC_FALSE;
149: PetscViewerDrawGetDraw(viewer,0,&draw);
150: PetscDrawIsNull(draw,&isnull); if (isnull) return(0);
151: PetscViewerDrawGetBounds(viewer,&nbounds,&bounds);
153: VecGetDM(xin,&da);
154: if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA");
156: PetscObjectGetComm((PetscObject)xin,&comm);
157: MPI_Comm_rank(comm,&rank);
159: DMDAGetInfo(da,0,&M,&N,0,&zctx.m,&zctx.n,0,&w,&s,&bx,&by,0,&st);
160: DMDAGetOwnershipRanges(da,&lx,&ly,NULL);
162: /*
163: Obtain a sequential vector that is going to contain the local values plus ONE layer of
164: ghosted values to draw the graphics from. We also need its corresponding DMDA (dac) that will
165: update the local values pluse ONE layer of ghost values.
166: */
167: PetscObjectQuery((PetscObject)da,"GraphicsGhosted",(PetscObject*)&xlocal);
168: if (!xlocal) {
169: if (bx != DMDA_BOUNDARY_NONE || by != DMDA_BOUNDARY_NONE || s != 1 || st != DMDA_STENCIL_BOX) {
170: /*
171: if original da is not of stencil width one, or periodic or not a box stencil then
172: create a special DMDA to handle one level of ghost points for graphics
173: */
174: DMDACreate2d(comm,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,N,zctx.m,zctx.n,w,1,lx,ly,&dac);
175: PetscInfo(da,"Creating auxilary DMDA for managing graphics ghost points\n");
176: } else {
177: /* otherwise we can use the da we already have */
178: dac = da;
179: }
180: /* create local vector for holding ghosted values used in graphics */
181: DMCreateLocalVector(dac,&xlocal);
182: if (dac != da) {
183: /* don't keep any public reference of this DMDA, is is only available through xlocal */
184: PetscObjectDereference((PetscObject)dac);
185: } else {
186: /* remove association between xlocal and da, because below we compose in the opposite
187: direction and if we left this connect we'd get a loop, so the objects could
188: never be destroyed */
189: PetscObjectRemoveReference((PetscObject)xlocal,"__PETSc_dm");
190: }
191: PetscObjectCompose((PetscObject)da,"GraphicsGhosted",(PetscObject)xlocal);
192: PetscObjectDereference((PetscObject)xlocal);
193: } else {
194: if (bx != DMDA_BOUNDARY_NONE || by != DMDA_BOUNDARY_NONE || s != 1 || st != DMDA_STENCIL_BOX) {
195: VecGetDM(xlocal, &dac);
196: } else {
197: dac = da;
198: }
199: }
201: /*
202: Get local (ghosted) values of vector
203: */
204: DMGlobalToLocalBegin(dac,xin,INSERT_VALUES,xlocal);
205: DMGlobalToLocalEnd(dac,xin,INSERT_VALUES,xlocal);
206: VecGetArray(xlocal,&zctx.v);
208: /* get coordinates of nodes */
209: DMGetCoordinates(da,&xcoor);
210: if (!xcoor) {
211: DMDASetUniformCoordinates(da,0.0,1.0,0.0,1.0,0.0,0.0);
212: DMGetCoordinates(da,&xcoor);
213: }
215: /*
216: Determine the min and max coordinates in plot
217: */
218: VecStrideMin(xcoor,0,NULL,&xmin);
219: VecStrideMax(xcoor,0,NULL,&xmax);
220: VecStrideMin(xcoor,1,NULL,&ymin);
221: VecStrideMax(xcoor,1,NULL,&ymax);
222: coors[0] = xmin - .05*(xmax- xmin); coors[2] = xmax + .05*(xmax - xmin);
223: coors[1] = ymin - .05*(ymax- ymin); coors[3] = ymax + .05*(ymax - ymin);
224: PetscInfo4(da,"Preparing DMDA 2d contour plot coordinates %G %G %G %G\n",coors[0],coors[1],coors[2],coors[3]);
226: PetscOptionsGetRealArray(NULL,"-draw_coordinates",coors,&ncoors,NULL);
228: /*
229: get local ghosted version of coordinates
230: */
231: PetscObjectQuery((PetscObject)da,"GraphicsCoordinateGhosted",(PetscObject*)&xcoorl);
232: if (!xcoorl) {
233: /* create DMDA to get local version of graphics */
234: DMDACreate2d(comm,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,N,zctx.m,zctx.n,2,1,lx,ly,&dag);
235: PetscInfo(dag,"Creating auxilary DMDA for managing graphics coordinates ghost points\n");
236: DMCreateLocalVector(dag,&xcoorl);
237: PetscObjectCompose((PetscObject)da,"GraphicsCoordinateGhosted",(PetscObject)xcoorl);
238: PetscObjectDereference((PetscObject)dag);
239: PetscObjectDereference((PetscObject)xcoorl);
240: } else {
241: VecGetDM(xcoorl,&dag);
242: }
243: DMGlobalToLocalBegin(dag,xcoor,INSERT_VALUES,xcoorl);
244: DMGlobalToLocalEnd(dag,xcoor,INSERT_VALUES,xcoorl);
245: VecGetArray(xcoorl,&zctx.xy);
247: /*
248: Get information about size of area each processor must do graphics for
249: */
250: DMDAGetInfo(dac,0,&M,&N,0,0,0,0,&zctx.step,0,&bx,&by,0,0);
251: DMDAGetGhostCorners(dac,0,0,0,&zctx.m,&zctx.n,0);
253: PetscOptionsGetBool(NULL,"-draw_contour_grid",&zctx.showgrid,NULL);
255: DMDASelectFields(da,&ndisplayfields,&displayfields);
257: PetscViewerGetFormat(viewer,&format);
258: PetscOptionsGetBool(NULL,"-draw_ports",&useports,NULL);
259: if (useports || format == PETSC_VIEWER_DRAW_PORTS) {
260: PetscDrawSynchronizedClear(draw);
261: PetscDrawViewPortsCreate(draw,ndisplayfields,&ports);
262: zctx.name0 = 0;
263: zctx.name1 = 0;
264: } else {
265: DMDAGetCoordinateName(da,0,&zctx.name0);
266: DMDAGetCoordinateName(da,1,&zctx.name1);
267: }
269: /*
270: Loop over each field; drawing each in a different window
271: */
272: for (i=0; i<ndisplayfields; i++) {
273: zctx.k = displayfields[i];
274: if (useports) {
275: PetscDrawViewPortsSet(ports,i);
276: } else {
277: PetscViewerDrawGetDraw(viewer,i,&draw);
278: }
280: /*
281: Determine the min and max color in plot
282: */
283: VecStrideMin(xin,zctx.k,NULL,&zctx.min);
284: VecStrideMax(xin,zctx.k,NULL,&zctx.max);
285: if (zctx.k < nbounds) {
286: zctx.min = bounds[2*zctx.k];
287: zctx.max = bounds[2*zctx.k+1];
288: }
289: if (zctx.min == zctx.max) {
290: zctx.min -= 1.e-12;
291: zctx.max += 1.e-12;
292: }
294: if (!rank) {
295: const char *title;
297: DMDAGetFieldName(da,zctx.k,&title);
298: if (title) {
299: PetscDrawSetTitle(draw,title);
300: }
301: }
302: PetscDrawSetCoordinates(draw,coors[0],coors[1],coors[2],coors[3]);
303: PetscInfo2(da,"DMDA 2d contour plot min %G max %G\n",zctx.min,zctx.max);
305: PetscDrawGetPopup(draw,&popup);
306: if (popup) {PetscDrawScalePopup(popup,zctx.min,zctx.max);}
308: zctx.scale = (245.0 - PETSC_DRAW_BASIC_COLORS)/(zctx.max - zctx.min);
310: PetscDrawZoom(draw,VecView_MPI_Draw_DA2d_Zoom,&zctx);
311: }
312: PetscFree(displayfields);
313: PetscDrawViewPortsDestroy(ports);
315: VecRestoreArray(xcoorl,&zctx.xy);
316: VecRestoreArray(xlocal,&zctx.v);
317: return(0);
318: }
321: #if defined(PETSC_HAVE_HDF5)
324: PetscErrorCode VecView_MPI_HDF5_DA(Vec xin,PetscViewer viewer)
325: {
326: DM dm;
327: DM_DA *da;
328: hid_t filespace; /* file dataspace identifier */
329: hid_t chunkspace; /* chunk dataset property identifier */
330: hid_t plist_id; /* property list identifier */
331: hid_t dset_id; /* dataset identifier */
332: hid_t memspace; /* memory dataspace identifier */
333: hid_t file_id;
334: hid_t group;
335: hid_t scalartype; /* scalar type (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */
336: herr_t status;
337: hsize_t dim;
338: hsize_t maxDims[6], dims[6], chunkDims[6], count[6], offset[6];
339: PetscInt timestep;
340: PetscScalar *x;
341: const char *vecname;
345: PetscViewerHDF5OpenGroup(viewer, &file_id, &group);
346: PetscViewerHDF5GetTimestep(viewer, ×tep);
348: VecGetDM(xin,&dm);
349: if (!dm) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA");
350: da = (DM_DA*)dm->data;
352: /* Create the dataspace for the dataset.
353: *
354: * dims - holds the current dimensions of the dataset
355: *
356: * maxDims - holds the maximum dimensions of the dataset (unlimited
357: * for the number of time steps with the current dimensions for the
358: * other dimensions; so only additional time steps can be added).
359: *
360: * chunkDims - holds the size of a single time step (required to
361: * permit extending dataset).
362: */
363: dim = 0;
364: if (timestep >= 0) {
365: dims[dim] = timestep+1;
366: maxDims[dim] = H5S_UNLIMITED;
367: chunkDims[dim] = 1;
368: ++dim;
369: }
370: if (da->dim == 3) {
371: PetscHDF5IntCast(da->P,dims+dim);
372: maxDims[dim] = dims[dim];
373: chunkDims[dim] = dims[dim];
374: ++dim;
375: }
376: if (da->dim > 1) {
377: PetscHDF5IntCast(da->N,dims+dim);
378: maxDims[dim] = dims[dim];
379: chunkDims[dim] = dims[dim];
380: ++dim;
381: }
382: PetscHDF5IntCast(da->M,dims+dim);
383: maxDims[dim] = dims[dim];
384: chunkDims[dim] = dims[dim];
385: ++dim;
386: if (da->w > 1) {
387: PetscHDF5IntCast(da->w,dims+dim);
388: maxDims[dim] = dims[dim];
389: chunkDims[dim] = dims[dim];
390: ++dim;
391: }
392: #if defined(PETSC_USE_COMPLEX)
393: dims[dim] = 2;
394: maxDims[dim] = dims[dim];
395: chunkDims[dim] = dims[dim];
396: ++dim;
397: #endif
398: filespace = H5Screate_simple(dim, dims, maxDims);
399: if (filespace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Screate_simple()");
401: #if defined(PETSC_USE_REAL_SINGLE)
402: scalartype = H5T_NATIVE_FLOAT;
403: #elif defined(PETSC_USE_REAL___FLOAT128)
404: #error "HDF5 output with 128 bit floats not supported."
405: #else
406: scalartype = H5T_NATIVE_DOUBLE;
407: #endif
409: /* Create the dataset with default properties and close filespace */
410: PetscObjectGetName((PetscObject)xin,&vecname);
411: if (!H5Lexists(group, vecname, H5P_DEFAULT)) {
412: /* Create chunk */
413: chunkspace = H5Pcreate(H5P_DATASET_CREATE);
414: if (chunkspace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Pcreate()");
415: status = H5Pset_chunk(chunkspace, dim, chunkDims);CHKERRQ(status);
417: #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
418: dset_id = H5Dcreate2(group, vecname, scalartype, filespace, H5P_DEFAULT, chunkspace, H5P_DEFAULT);
419: #else
420: dset_id = H5Dcreate(group, vecname, scalartype, filespace, H5P_DEFAULT);
421: #endif
422: if (dset_id == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Dcreate2()");
423: } else {
424: dset_id = H5Dopen2(group, vecname, H5P_DEFAULT);
425: status = H5Dset_extent(dset_id, dims);CHKERRQ(status);
426: }
427: status = H5Sclose(filespace);CHKERRQ(status);
429: /* Each process defines a dataset and writes it to the hyperslab in the file */
430: dim = 0;
431: if (timestep >= 0) {
432: offset[dim] = timestep;
433: ++dim;
434: }
435: if (da->dim == 3) {PetscHDF5IntCast(da->zs,offset + dim++);}
436: if (da->dim > 1) {PetscHDF5IntCast(da->ys,offset + dim++);}
437: PetscHDF5IntCast(da->xs/da->w,offset + dim++);
438: if (da->w > 1) offset[dim++] = 0;
439: #if defined(PETSC_USE_COMPLEX)
440: offset[dim++] = 0;
441: #endif
442: dim = 0;
443: if (timestep >= 0) {
444: count[dim] = 1;
445: ++dim;
446: }
447: if (da->dim == 3) {PetscHDF5IntCast(da->ze - da->zs,count + dim++);}
448: if (da->dim > 1) {PetscHDF5IntCast(da->ye - da->ys,count + dim++);}
449: PetscHDF5IntCast((da->xe - da->xs)/da->w,count + dim++);
450: if (da->w > 1) {PetscHDF5IntCast(da->w,count + dim++);}
451: #if defined(PETSC_USE_COMPLEX)
452: count[dim++] = 2;
453: #endif
454: memspace = H5Screate_simple(dim, count, NULL);
455: if (memspace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Screate_simple()");
457: filespace = H5Dget_space(dset_id);
458: if (filespace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Dget_space()");
459: status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, count, NULL);CHKERRQ(status);
461: /* Create property list for collective dataset write */
462: plist_id = H5Pcreate(H5P_DATASET_XFER);
463: if (plist_id == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Pcreate()");
464: #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
465: status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);CHKERRQ(status);
466: #endif
467: /* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */
469: VecGetArray(xin, &x);
470: status = H5Dwrite(dset_id, scalartype, memspace, filespace, plist_id, x);CHKERRQ(status);
471: status = H5Fflush(file_id, H5F_SCOPE_GLOBAL);CHKERRQ(status);
472: VecRestoreArray(xin, &x);
474: /* Close/release resources */
475: if (group != file_id) {
476: status = H5Gclose(group);CHKERRQ(status);
477: }
478: status = H5Pclose(plist_id);CHKERRQ(status);
479: status = H5Sclose(filespace);CHKERRQ(status);
480: status = H5Sclose(memspace);CHKERRQ(status);
481: status = H5Dclose(dset_id);CHKERRQ(status);
482: PetscInfo1(xin,"Wrote Vec object with name %s\n",vecname);
483: return(0);
484: }
485: #endif
487: extern PetscErrorCode VecView_MPI_Draw_DA1d(Vec,PetscViewer);
489: #if defined(PETSC_HAVE_MPIIO)
492: static PetscErrorCode DMDAArrayMPIIO(DM da,PetscViewer viewer,Vec xin,PetscBool write)
493: {
494: PetscErrorCode ierr;
495: MPI_File mfdes;
496: PetscMPIInt gsizes[4],lsizes[4],lstarts[4],asiz,dof;
497: MPI_Datatype view;
498: const PetscScalar *array;
499: MPI_Offset off;
500: MPI_Aint ub,ul;
501: PetscInt type,rows,vecrows,tr[2];
502: DM_DA *dd = (DM_DA*)da->data;
505: VecGetSize(xin,&vecrows);
506: if (!write) {
507: /* Read vector header. */
508: PetscViewerBinaryRead(viewer,tr,2,PETSC_INT);
509: type = tr[0];
510: rows = tr[1];
511: if (type != VEC_FILE_CLASSID) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_WRONG,"Not vector next in file");
512: if (rows != vecrows) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_SIZ,"Vector in file not same size as DMDA vector");
513: } else {
514: tr[0] = VEC_FILE_CLASSID;
515: tr[1] = vecrows;
516: PetscViewerBinaryWrite(viewer,tr,2,PETSC_INT,PETSC_TRUE);
517: }
519: PetscMPIIntCast(dd->w,&dof);
520: gsizes[0] = dof;
521: PetscMPIIntCast(dd->M,gsizes+1);
522: PetscMPIIntCast(dd->N,gsizes+2);
523: PetscMPIIntCast(dd->P,gsizes+3);
524: lsizes[0] = dof;
525: PetscMPIIntCast((dd->xe-dd->xs)/dof,lsizes+1);
526: PetscMPIIntCast(dd->ye-dd->ys,lsizes+2);
527: PetscMPIIntCast(dd->ze-dd->zs,lsizes+3);
528: lstarts[0] = 0;
529: PetscMPIIntCast(dd->xs/dof,lstarts+1);
530: PetscMPIIntCast(dd->ys,lstarts+2);
531: PetscMPIIntCast(dd->zs,lstarts+3);
532: MPI_Type_create_subarray(dd->dim+1,gsizes,lsizes,lstarts,MPI_ORDER_FORTRAN,MPIU_SCALAR,&view);
533: MPI_Type_commit(&view);
535: PetscViewerBinaryGetMPIIODescriptor(viewer,&mfdes);
536: PetscViewerBinaryGetMPIIOOffset(viewer,&off);
537: MPI_File_set_view(mfdes,off,MPIU_SCALAR,view,(char*)"native",MPI_INFO_NULL);
538: VecGetArrayRead(xin,&array);
539: asiz = lsizes[1]*(lsizes[2] > 0 ? lsizes[2] : 1)*(lsizes[3] > 0 ? lsizes[3] : 1)*dof;
540: if (write) {
541: MPIU_File_write_all(mfdes,(PetscScalar*)array,asiz,MPIU_SCALAR,MPI_STATUS_IGNORE);
542: } else {
543: MPIU_File_read_all(mfdes,(PetscScalar*)array,asiz,MPIU_SCALAR,MPI_STATUS_IGNORE);
544: }
545: MPI_Type_get_extent(view,&ul,&ub);
546: PetscViewerBinaryAddMPIIOOffset(viewer,ub);
547: VecRestoreArrayRead(xin,&array);
548: MPI_Type_free(&view);
549: return(0);
550: }
551: #endif
555: PetscErrorCode VecView_MPI_DA(Vec xin,PetscViewer viewer)
556: {
557: DM da;
558: PetscErrorCode ierr;
559: PetscInt dim;
560: Vec natural;
561: PetscBool isdraw,isvtk;
562: #if defined(PETSC_HAVE_HDF5)
563: PetscBool ishdf5;
564: #endif
565: const char *prefix,*name;
566: PetscViewerFormat format;
569: VecGetDM(xin,&da);
570: if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA");
571: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);
572: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERVTK,&isvtk);
573: #if defined(PETSC_HAVE_HDF5)
574: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);
575: #endif
576: if (isdraw) {
577: DMDAGetInfo(da,&dim,0,0,0,0,0,0,0,0,0,0,0,0);
578: if (dim == 1) {
579: VecView_MPI_Draw_DA1d(xin,viewer);
580: } else if (dim == 2) {
581: VecView_MPI_Draw_DA2d(xin,viewer);
582: } else SETERRQ1(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Cannot graphically view vector associated with this dimensional DMDA %D",dim);
583: } else if (isvtk) { /* Duplicate the Vec and hold a reference to the DM */
584: Vec Y;
585: PetscObjectReference((PetscObject)da);
586: VecDuplicate(xin,&Y);
587: if (((PetscObject)xin)->name) {
588: /* If xin was named, copy the name over to Y. The duplicate names are safe because nobody else will ever see Y. */
589: PetscObjectSetName((PetscObject)Y,((PetscObject)xin)->name);
590: }
591: VecCopy(xin,Y);
592: PetscViewerVTKAddField(viewer,(PetscObject)da,DMDAVTKWriteAll,PETSC_VTK_POINT_FIELD,(PetscObject)Y);
593: #if defined(PETSC_HAVE_HDF5)
594: } else if (ishdf5) {
595: VecView_MPI_HDF5_DA(xin,viewer);
596: #endif
597: } else {
598: #if defined(PETSC_HAVE_MPIIO)
599: PetscBool isbinary,isMPIIO;
601: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);
602: if (isbinary) {
603: PetscViewerBinaryGetMPIIO(viewer,&isMPIIO);
604: if (isMPIIO) {
605: DMDAArrayMPIIO(da,viewer,xin,PETSC_TRUE);
606: return(0);
607: }
608: }
609: #endif
611: /* call viewer on natural ordering */
612: PetscObjectGetOptionsPrefix((PetscObject)xin,&prefix);
613: DMDACreateNaturalVector(da,&natural);
614: PetscObjectSetOptionsPrefix((PetscObject)natural,prefix);
615: DMDAGlobalToNaturalBegin(da,xin,INSERT_VALUES,natural);
616: DMDAGlobalToNaturalEnd(da,xin,INSERT_VALUES,natural);
617: PetscObjectGetName((PetscObject)xin,&name);
618: PetscObjectSetName((PetscObject)natural,name);
620: PetscViewerGetFormat(viewer,&format);
621: if (format == PETSC_VIEWER_BINARY_MATLAB) {
622: /* temporarily remove viewer format so it won't trigger in the VecView() */
623: PetscViewerSetFormat(viewer,PETSC_VIEWER_DEFAULT);
624: }
626: VecView(natural,viewer);
628: if (format == PETSC_VIEWER_BINARY_MATLAB) {
629: MPI_Comm comm;
630: FILE *info;
631: const char *fieldname;
632: char fieldbuf[256];
633: PetscInt dim,ni,nj,nk,pi,pj,pk,dof,n;
635: /* set the viewer format back into the viewer */
636: PetscViewerSetFormat(viewer,format);
637: PetscObjectGetComm((PetscObject)viewer,&comm);
638: PetscViewerBinaryGetInfoPointer(viewer,&info);
639: DMDAGetInfo(da,&dim,&ni,&nj,&nk,&pi,&pj,&pk,&dof,0,0,0,0,0);
640: PetscFPrintf(comm,info,"#--- begin code written by PetscViewerBinary for MATLAB format ---#\n");
641: PetscFPrintf(comm,info,"#$$ tmp = PetscBinaryRead(fd); \n");
642: if (dim == 1) { PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d);\n",dof,ni); }
643: if (dim == 2) { PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d,%d);\n",dof,ni,nj); }
644: if (dim == 3) { PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d,%d,%d);\n",dof,ni,nj,nk); }
646: for (n=0; n<dof; n++) {
647: DMDAGetFieldName(da,n,&fieldname);
648: if (!fieldname || !fieldname[0]) {
649: PetscSNPrintf(fieldbuf,sizeof fieldbuf,"field%D",n);
650: fieldname = fieldbuf;
651: }
652: if (dim == 1) { PetscFPrintf(comm,info,"#$$ Set.%s.%s = squeeze(tmp(%d,:))';\n",name,fieldname,n+1); }
653: if (dim == 2) { PetscFPrintf(comm,info,"#$$ Set.%s.%s = squeeze(tmp(%d,:,:))';\n",name,fieldname,n+1); }
654: if (dim == 3) { PetscFPrintf(comm,info,"#$$ Set.%s.%s = permute(squeeze(tmp(%d,:,:,:)),[2 1 3]);\n",name,fieldname,n+1);}
655: }
656: PetscFPrintf(comm,info,"#$$ clear tmp; \n");
657: PetscFPrintf(comm,info,"#--- end code written by PetscViewerBinary for MATLAB format ---#\n\n");
658: }
660: VecDestroy(&natural);
661: }
662: return(0);
663: }
665: #if defined(PETSC_HAVE_HDF5)
668: PetscErrorCode VecLoad_HDF5_DA(Vec xin, PetscViewer viewer)
669: {
670: DM da;
672: hsize_t dim;
673: hsize_t count[5];
674: hsize_t offset[5];
675: PetscInt cnt = 0;
676: PetscScalar *x;
677: const char *vecname;
678: hid_t filespace; /* file dataspace identifier */
679: hid_t plist_id; /* property list identifier */
680: hid_t dset_id; /* dataset identifier */
681: hid_t memspace; /* memory dataspace identifier */
682: hid_t file_id;
683: herr_t status;
684: DM_DA *dd;
687: PetscViewerHDF5GetFileId(viewer, &file_id);
688: VecGetDM(xin,&da);
689: dd = (DM_DA*)da->data;
691: /* Create the dataspace for the dataset */
692: PetscHDF5IntCast(dd->dim + ((dd->w == 1) ? 0 : 1),&dim);
693: #if defined(PETSC_USE_COMPLEX)
694: dim++;
695: #endif
697: /* Create the dataset with default properties and close filespace */
698: PetscObjectGetName((PetscObject)xin,&vecname);
699: #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
700: dset_id = H5Dopen2(file_id, vecname, H5P_DEFAULT);
701: #else
702: dset_id = H5Dopen(file_id, vecname);
703: #endif
704: if (dset_id == -1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Dopen2() with Vec named %s",vecname);
705: filespace = H5Dget_space(dset_id);
707: /* Each process defines a dataset and reads it from the hyperslab in the file */
708: cnt = 0;
709: if (dd->dim == 3) {PetscHDF5IntCast(dd->zs,offset + cnt++);}
710: if (dd->dim > 1) {PetscHDF5IntCast(dd->ys,offset + cnt++);}
711: PetscHDF5IntCast(dd->xs/dd->w,offset + cnt++);
712: if (dd->w > 1) offset[cnt++] = 0;
713: #if defined(PETSC_USE_COMPLEX)
714: offset[cnt++] = 0;
715: #endif
716: cnt = 0;
717: if (dd->dim == 3) {PetscHDF5IntCast(dd->ze - dd->zs,count + cnt++);}
718: if (dd->dim > 1) {PetscHDF5IntCast(dd->ye - dd->ys,count + cnt++);}
719: PetscHDF5IntCast((dd->xe - dd->xs)/dd->w,count + cnt++);
720: if (dd->w > 1) {PetscHDF5IntCast(dd->w,count + cnt++);}
721: #if defined(PETSC_USE_COMPLEX)
722: count[cnt++] = 2;
723: #endif
724: memspace = H5Screate_simple(dim, count, NULL);
725: if (memspace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Screate_simple()");
727: status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, count, NULL);CHKERRQ(status);
729: /* Create property list for collective dataset write */
730: plist_id = H5Pcreate(H5P_DATASET_XFER);
731: if (plist_id == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Pcreate()");
732: #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
733: status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);CHKERRQ(status);
734: #endif
735: /* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */
737: VecGetArray(xin, &x);
738: status = H5Dread(dset_id, H5T_NATIVE_DOUBLE, memspace, filespace, plist_id, x);CHKERRQ(status);
739: VecRestoreArray(xin, &x);
741: /* Close/release resources */
742: status = H5Pclose(plist_id);CHKERRQ(status);
743: status = H5Sclose(filespace);CHKERRQ(status);
744: status = H5Sclose(memspace);CHKERRQ(status);
745: status = H5Dclose(dset_id);CHKERRQ(status);
746: return(0);
747: }
748: #endif
752: PetscErrorCode VecLoad_Binary_DA(Vec xin, PetscViewer viewer)
753: {
754: DM da;
756: Vec natural;
757: const char *prefix;
758: PetscInt bs;
759: PetscBool flag;
760: DM_DA *dd;
761: #if defined(PETSC_HAVE_MPIIO)
762: PetscBool isMPIIO;
763: #endif
766: VecGetDM(xin,&da);
767: dd = (DM_DA*)da->data;
768: #if defined(PETSC_HAVE_MPIIO)
769: PetscViewerBinaryGetMPIIO(viewer,&isMPIIO);
770: if (isMPIIO) {
771: DMDAArrayMPIIO(da,viewer,xin,PETSC_FALSE);
772: return(0);
773: }
774: #endif
776: PetscObjectGetOptionsPrefix((PetscObject)xin,&prefix);
777: DMDACreateNaturalVector(da,&natural);
778: PetscObjectSetName((PetscObject)natural,((PetscObject)xin)->name);
779: PetscObjectSetOptionsPrefix((PetscObject)natural,prefix);
780: VecLoad(natural,viewer);
781: DMDANaturalToGlobalBegin(da,natural,INSERT_VALUES,xin);
782: DMDANaturalToGlobalEnd(da,natural,INSERT_VALUES,xin);
783: VecDestroy(&natural);
784: PetscInfo(xin,"Loading vector from natural ordering into DMDA\n");
785: PetscOptionsGetInt(((PetscObject)xin)->prefix,"-vecload_block_size",&bs,&flag);
786: if (flag && bs != dd->w) {
787: PetscInfo2(xin,"Block size in file %D not equal to DMDA's dof %D\n",bs,dd->w);
788: }
789: return(0);
790: }
794: PetscErrorCode VecLoad_Default_DA(Vec xin, PetscViewer viewer)
795: {
797: DM da;
798: PetscBool isbinary;
799: #if defined(PETSC_HAVE_HDF5)
800: PetscBool ishdf5;
801: #endif
804: VecGetDM(xin,&da);
805: if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA");
807: #if defined(PETSC_HAVE_HDF5)
808: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);
809: #endif
810: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);
812: if (isbinary) {
813: VecLoad_Binary_DA(xin,viewer);
814: #if defined(PETSC_HAVE_HDF5)
815: } else if (ishdf5) {
816: VecLoad_HDF5_DA(xin,viewer);
817: #endif
818: } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Viewer type %s not supported for vector loading", ((PetscObject)viewer)->type_name);
819: return(0);
820: }