Actual source code: gr2.c
petsc-3.5.4 2015-05-23
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 = PetscRealPart(xy[2*id+1]);
66: c2 = (int)(PETSC_DRAW_BASIC_COLORS+s*(PetscClipInterval(PetscRealPart(v[k+step*id]),min,max)-min));
67: xmin = PetscMin(xmin,x2);
68: ymin = PetscMin(ymin,y2);
69: xmax = PetscMax(xmax,x2);
70: ymax = PetscMax(ymax,y2);
72: id = i+j*m+1+m;
73: x3 = PetscRealPart(xy[2*id]);
74: y3 = PetscRealPart(xy[2*id+1]);
75: c3 = (int)(PETSC_DRAW_BASIC_COLORS+s*(PetscClipInterval(PetscRealPart(v[k+step*id]),min,max)-min));
76: xmin = PetscMin(xmin,x3);
77: ymin = PetscMin(ymin,y3);
78: xmax = PetscMax(xmax,x3);
79: ymax = PetscMax(ymax,y3);
81: id = i+j*m+m;
82: x4 = PetscRealPart(xy[2*id]);
83: y4 = PetscRealPart(xy[2*id+1]);
84: c4 = (int)(PETSC_DRAW_BASIC_COLORS+s*(PetscClipInterval(PetscRealPart(v[k+step*id]),min,max)-min));
85: xmin = PetscMin(xmin,x4);
86: ymin = PetscMin(ymin,y4);
87: xmax = PetscMax(xmax,x4);
88: ymax = PetscMax(ymax,y4);
90: PetscDrawTriangle(draw,x1,y_1,x2,y2,x3,y3,c1,c2,c3);
91: PetscDrawTriangle(draw,x1,y_1,x3,y3,x4,y4,c1,c3,c4);
92: if (zctx->showgrid) {
93: PetscDrawLine(draw,x1,y_1,x2,y2,PETSC_DRAW_BLACK);
94: PetscDrawLine(draw,x2,y2,x3,y3,PETSC_DRAW_BLACK);
95: PetscDrawLine(draw,x3,y3,x4,y4,PETSC_DRAW_BLACK);
96: PetscDrawLine(draw,x4,y4,x1,y_1,PETSC_DRAW_BLACK);
97: }
98: }
99: }
100: if (zctx->name0) {
101: PetscReal xl,yl,xr,yr,x,y;
102: PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);
103: x = xl + .3*(xr - xl);
104: xl = xl + .01*(xr - xl);
105: y = yr - .3*(yr - yl);
106: yl = yl + .01*(yr - yl);
107: PetscDrawString(draw,x,yl,PETSC_DRAW_BLACK,zctx->name0);
108: PetscDrawStringVertical(draw,xl,y,PETSC_DRAW_BLACK,zctx->name1);
109: }
110: /*
111: Ideally we would use the PetscDrawAxis object to manage displaying the coordinate limits
112: but that may require some refactoring.
113: */
114: MPI_Allreduce(&xmin,&xminf,1,MPIU_REAL,MPIU_MIN,PetscObjectComm((PetscObject)draw));
115: MPI_Allreduce(&xmax,&xmaxf,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)draw));
116: MPI_Allreduce(&ymin,&yminf,1,MPIU_REAL,MPIU_MIN,PetscObjectComm((PetscObject)draw));
117: MPI_Allreduce(&ymax,&ymaxf,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)draw));
118: PetscSNPrintf(value,16,"%f",xminf);
119: PetscDrawString(draw,xminf,yminf - .05*(ymaxf - yminf),PETSC_DRAW_BLACK,value);
120: PetscSNPrintf(value,16,"%f",xmaxf);
121: PetscStrlen(value,&len);
122: PetscDrawStringGetSize(draw,&w,NULL);
123: PetscDrawString(draw,xmaxf - len*w,yminf - .05*(ymaxf - yminf),PETSC_DRAW_BLACK,value);
124: PetscSNPrintf(value,16,"%f",yminf);
125: PetscDrawString(draw,xminf - .05*(xmaxf - xminf),yminf,PETSC_DRAW_BLACK,value);
126: PetscSNPrintf(value,16,"%f",ymaxf);
127: PetscDrawString(draw,xminf - .05*(xmaxf - xminf),ymaxf,PETSC_DRAW_BLACK,value);
128: return(0);
129: }
133: PetscErrorCode VecView_MPI_Draw_DA2d(Vec xin,PetscViewer viewer)
134: {
135: DM da,dac,dag;
136: PetscErrorCode ierr;
137: PetscMPIInt rank;
138: PetscInt N,s,M,w,ncoors = 4;
139: const PetscInt *lx,*ly;
140: PetscReal coors[4],ymin,ymax,xmin,xmax;
141: PetscDraw draw,popup;
142: PetscBool isnull,useports = PETSC_FALSE;
143: MPI_Comm comm;
144: Vec xlocal,xcoor,xcoorl;
145: DMBoundaryType bx,by;
146: DMDAStencilType st;
147: ZoomCtx zctx;
148: PetscDrawViewPorts *ports = NULL;
149: PetscViewerFormat format;
150: PetscInt *displayfields;
151: PetscInt ndisplayfields,i,nbounds;
152: const PetscReal *bounds;
155: zctx.showgrid = PETSC_FALSE;
157: PetscViewerDrawGetDraw(viewer,0,&draw);
158: PetscDrawIsNull(draw,&isnull); if (isnull) return(0);
159: PetscViewerDrawGetBounds(viewer,&nbounds,&bounds);
161: VecGetDM(xin,&da);
162: if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA");
164: PetscObjectGetComm((PetscObject)xin,&comm);
165: MPI_Comm_rank(comm,&rank);
167: DMDAGetInfo(da,0,&M,&N,0,&zctx.m,&zctx.n,0,&w,&s,&bx,&by,0,&st);
168: DMDAGetOwnershipRanges(da,&lx,&ly,NULL);
170: /*
171: Obtain a sequential vector that is going to contain the local values plus ONE layer of
172: ghosted values to draw the graphics from. We also need its corresponding DMDA (dac) that will
173: update the local values pluse ONE layer of ghost values.
174: */
175: PetscObjectQuery((PetscObject)da,"GraphicsGhosted",(PetscObject*)&xlocal);
176: if (!xlocal) {
177: if (bx != DM_BOUNDARY_NONE || by != DM_BOUNDARY_NONE || s != 1 || st != DMDA_STENCIL_BOX) {
178: /*
179: if original da is not of stencil width one, or periodic or not a box stencil then
180: create a special DMDA to handle one level of ghost points for graphics
181: */
182: DMDACreate2d(comm,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,N,zctx.m,zctx.n,w,1,lx,ly,&dac);
183: PetscInfo(da,"Creating auxilary DMDA for managing graphics ghost points\n");
184: } else {
185: /* otherwise we can use the da we already have */
186: dac = da;
187: }
188: /* create local vector for holding ghosted values used in graphics */
189: DMCreateLocalVector(dac,&xlocal);
190: if (dac != da) {
191: /* don't keep any public reference of this DMDA, is is only available through xlocal */
192: PetscObjectDereference((PetscObject)dac);
193: } else {
194: /* remove association between xlocal and da, because below we compose in the opposite
195: direction and if we left this connect we'd get a loop, so the objects could
196: never be destroyed */
197: PetscObjectRemoveReference((PetscObject)xlocal,"__PETSc_dm");
198: }
199: PetscObjectCompose((PetscObject)da,"GraphicsGhosted",(PetscObject)xlocal);
200: PetscObjectDereference((PetscObject)xlocal);
201: } else {
202: if (bx != DM_BOUNDARY_NONE || by != DM_BOUNDARY_NONE || s != 1 || st != DMDA_STENCIL_BOX) {
203: VecGetDM(xlocal, &dac);
204: } else {
205: dac = da;
206: }
207: }
209: /*
210: Get local (ghosted) values of vector
211: */
212: DMGlobalToLocalBegin(dac,xin,INSERT_VALUES,xlocal);
213: DMGlobalToLocalEnd(dac,xin,INSERT_VALUES,xlocal);
214: VecGetArray(xlocal,&zctx.v);
216: /* get coordinates of nodes */
217: DMGetCoordinates(da,&xcoor);
218: if (!xcoor) {
219: DMDASetUniformCoordinates(da,0.0,1.0,0.0,1.0,0.0,0.0);
220: DMGetCoordinates(da,&xcoor);
221: }
223: /*
224: Determine the min and max coordinates in plot
225: */
226: VecStrideMin(xcoor,0,NULL,&xmin);
227: VecStrideMax(xcoor,0,NULL,&xmax);
228: VecStrideMin(xcoor,1,NULL,&ymin);
229: VecStrideMax(xcoor,1,NULL,&ymax);
230: coors[0] = xmin - .05*(xmax- xmin); coors[2] = xmax + .05*(xmax - xmin);
231: coors[1] = ymin - .05*(ymax- ymin); coors[3] = ymax + .05*(ymax - ymin);
232: 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]);
234: PetscOptionsGetRealArray(NULL,"-draw_coordinates",coors,&ncoors,NULL);
236: /*
237: get local ghosted version of coordinates
238: */
239: PetscObjectQuery((PetscObject)da,"GraphicsCoordinateGhosted",(PetscObject*)&xcoorl);
240: if (!xcoorl) {
241: /* create DMDA to get local version of graphics */
242: DMDACreate2d(comm,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,N,zctx.m,zctx.n,2,1,lx,ly,&dag);
243: PetscInfo(dag,"Creating auxilary DMDA for managing graphics coordinates ghost points\n");
244: DMCreateLocalVector(dag,&xcoorl);
245: PetscObjectCompose((PetscObject)da,"GraphicsCoordinateGhosted",(PetscObject)xcoorl);
246: PetscObjectDereference((PetscObject)dag);
247: PetscObjectDereference((PetscObject)xcoorl);
248: } else {
249: VecGetDM(xcoorl,&dag);
250: }
251: DMGlobalToLocalBegin(dag,xcoor,INSERT_VALUES,xcoorl);
252: DMGlobalToLocalEnd(dag,xcoor,INSERT_VALUES,xcoorl);
253: VecGetArray(xcoorl,&zctx.xy);
255: /*
256: Get information about size of area each processor must do graphics for
257: */
258: DMDAGetInfo(dac,0,&M,&N,0,0,0,0,&zctx.step,0,&bx,&by,0,0);
259: DMDAGetGhostCorners(dac,0,0,0,&zctx.m,&zctx.n,0);
261: PetscOptionsGetBool(NULL,"-draw_contour_grid",&zctx.showgrid,NULL);
263: DMDASelectFields(da,&ndisplayfields,&displayfields);
265: PetscViewerGetFormat(viewer,&format);
266: PetscOptionsGetBool(NULL,"-draw_ports",&useports,NULL);
267: if (useports || format == PETSC_VIEWER_DRAW_PORTS) {
268: PetscDrawSynchronizedClear(draw);
269: PetscDrawViewPortsCreate(draw,ndisplayfields,&ports);
270: zctx.name0 = 0;
271: zctx.name1 = 0;
272: } else {
273: DMDAGetCoordinateName(da,0,&zctx.name0);
274: DMDAGetCoordinateName(da,1,&zctx.name1);
275: }
277: /*
278: Loop over each field; drawing each in a different window
279: */
280: for (i=0; i<ndisplayfields; i++) {
281: zctx.k = displayfields[i];
282: if (useports) {
283: PetscDrawViewPortsSet(ports,i);
284: } else {
285: PetscViewerDrawGetDraw(viewer,i,&draw);
286: }
288: /*
289: Determine the min and max color in plot
290: */
291: VecStrideMin(xin,zctx.k,NULL,&zctx.min);
292: VecStrideMax(xin,zctx.k,NULL,&zctx.max);
293: if (zctx.k < nbounds) {
294: zctx.min = bounds[2*zctx.k];
295: zctx.max = bounds[2*zctx.k+1];
296: }
297: if (zctx.min == zctx.max) {
298: zctx.min -= 1.e-12;
299: zctx.max += 1.e-12;
300: }
302: if (!rank) {
303: const char *title;
305: DMDAGetFieldName(da,zctx.k,&title);
306: if (title) {
307: PetscDrawSetTitle(draw,title);
308: }
309: }
310: PetscDrawSetCoordinates(draw,coors[0],coors[1],coors[2],coors[3]);
311: PetscInfo2(da,"DMDA 2d contour plot min %g max %g\n",(double)zctx.min,(double)zctx.max);
313: PetscDrawGetPopup(draw,&popup);
314: if (popup) {PetscDrawScalePopup(popup,zctx.min,zctx.max);}
316: zctx.scale = (245.0 - PETSC_DRAW_BASIC_COLORS)/(zctx.max - zctx.min);
318: PetscDrawZoom(draw,VecView_MPI_Draw_DA2d_Zoom,&zctx);
319: }
320: PetscFree(displayfields);
321: PetscDrawViewPortsDestroy(ports);
323: VecRestoreArray(xcoorl,&zctx.xy);
324: VecRestoreArray(xlocal,&zctx.v);
325: return(0);
326: }
328: #if defined(PETSC_HAVE_HDF5)
331: static PetscErrorCode VecGetHDF5ChunkSize(DM_DA *da, Vec xin, PetscInt timestep, hsize_t *chunkDims)
332: {
333: PetscMPIInt comm_size;
335: hsize_t chunk_size, target_size, dim;
336: hsize_t vec_size = sizeof(PetscScalar)*da->M*da->N*da->P*da->w;
337: hsize_t avg_local_vec_size,KiB = 1024,MiB = KiB*KiB,GiB = MiB*KiB,min_size = MiB;
338: hsize_t max_chunks = 64*KiB; /* HDF5 internal limitation */
339: hsize_t max_chunk_size = 4*GiB; /* HDF5 internal limitation */
340: PetscInt zslices=da->p, yslices=da->n, xslices=da->m;
343: MPI_Comm_size(PetscObjectComm((PetscObject)xin), &comm_size);
344: avg_local_vec_size = (hsize_t) ceil(vec_size*1.0/comm_size); /* we will attempt to use this as the chunk size */
346: target_size = (hsize_t) ceil(PetscMin(vec_size,
347: PetscMin(max_chunk_size,
348: PetscMax(avg_local_vec_size,
349: PetscMax(ceil(vec_size*1.0/max_chunks),
350: min_size)))));
351: 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(PetscScalar);
353: /*
354: if size/rank > max_chunk_size, we need radical measures: even going down to
355: avg_local_vec_size is not enough, so we simply use chunk size of 4 GiB no matter
356: what, composed in the most efficient way possible.
357: N.B. this minimises the number of chunks, which may or may not be the optimal
358: solution. In a BG, for example, the optimal solution is probably to make # chunks = #
359: IO nodes involved, but this author has no access to a BG to figure out how to
360: reliably find the right number. And even then it may or may not be enough.
361: */
362: if (avg_local_vec_size > max_chunk_size) {
363: /* check if we can just split local z-axis: is that enough? */
364: zslices = (PetscInt)ceil(vec_size*1.0/(da->p*max_chunk_size))*zslices;
365: if (zslices > da->P) {
366: /* lattice is too large in xy-directions, splitting z only is not enough */
367: zslices = da->P;
368: yslices= (PetscInt)ceil(vec_size*1.0/(zslices*da->n*max_chunk_size))*yslices;
369: if (yslices > da->N) {
370: /* lattice is too large in x-direction, splitting along z, y is not enough */
371: yslices = da->N;
372: xslices= (PetscInt)ceil(vec_size*1.0/(zslices*yslices*da->m*max_chunk_size))*xslices;
373: }
374: }
375: dim = 0;
376: if (timestep >= 0) {
377: ++dim;
378: }
379: /* prefer to split z-axis, even down to planar slices */
380: if (da->dim == 3) {
381: chunkDims[dim++] = (hsize_t) da->P/zslices;
382: chunkDims[dim++] = (hsize_t) da->N/yslices;
383: chunkDims[dim++] = (hsize_t) da->M/xslices;
384: } else {
385: /* This is a 2D world exceeding 4GiB in size; yes, I've seen them, even used myself */
386: chunkDims[dim++] = (hsize_t) da->N/yslices;
387: chunkDims[dim++] = (hsize_t) da->M/xslices;
388: }
389: 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);
390: } else {
391: if (target_size < chunk_size) {
392: /* only change the defaults if target_size < chunk_size */
393: dim = 0;
394: if (timestep >= 0) {
395: ++dim;
396: }
397: /* prefer to split z-axis, even down to planar slices */
398: if (da->dim == 3) {
399: /* try splitting the z-axis to core-size bits, i.e. divide chunk size by # comm_size in z-direction */
400: if (target_size >= chunk_size/da->p) {
401: /* just make chunks the size of <local_z>x<whole_world_y>x<whole_world_x>x<dof> */
402: chunkDims[dim] = (hsize_t) ceil(da->P*1.0/da->p);
403: } else {
404: /* oops, just splitting the z-axis is NOT ENOUGH, need to split more; let's be
405: radical and let everyone write all they've got */
406: chunkDims[dim++] = (hsize_t) ceil(da->P*1.0/da->p);
407: chunkDims[dim++] = (hsize_t) ceil(da->N*1.0/da->n);
408: chunkDims[dim++] = (hsize_t) ceil(da->M*1.0/da->m);
409: }
410: } else {
411: /* This is a 2D world exceeding 4GiB in size; yes, I've seen them, even used myself */
412: if (target_size >= chunk_size/da->n) {
413: /* just make chunks the size of <local_z>x<whole_world_y>x<whole_world_x>x<dof> */
414: chunkDims[dim] = (hsize_t) ceil(da->N*1.0/da->n);
415: } else {
416: /* oops, just splitting the z-axis is NOT ENOUGH, need to split more; let's be
417: radical and let everyone write all they've got */
418: chunkDims[dim++] = (hsize_t) ceil(da->N*1.0/da->n);
419: chunkDims[dim++] = (hsize_t) ceil(da->M*1.0/da->m);
420: }
422: }
423: 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);
424: } else {
425: /* precomputed chunks are fine, we don't need to do anything */
426: }
427: }
428: return(0);
429: }
430: #endif
432: #if defined(PETSC_HAVE_HDF5)
435: PetscErrorCode VecView_MPI_HDF5_DA(Vec xin,PetscViewer viewer)
436: {
437: DM dm;
438: DM_DA *da;
439: hid_t filespace; /* file dataspace identifier */
440: hid_t chunkspace; /* chunk dataset property identifier */
441: hid_t plist_id; /* property list identifier */
442: hid_t dset_id; /* dataset identifier */
443: hid_t memspace; /* memory dataspace identifier */
444: hid_t file_id;
445: hid_t group;
446: hid_t scalartype; /* scalar type (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */
447: herr_t status;
448: hsize_t dim;
449: hsize_t maxDims[6]={0}, dims[6]={0}, chunkDims[6]={0}, count[6]={0}, offset[6]={0}; /* we depend on these being sane later on */
450: PetscInt timestep;
451: PetscScalar *x;
452: const char *vecname;
456: PetscViewerHDF5OpenGroup(viewer, &file_id, &group);
457: PetscViewerHDF5GetTimestep(viewer, ×tep);
459: VecGetDM(xin,&dm);
460: if (!dm) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA");
461: da = (DM_DA*)dm->data;
463: /* Create the dataspace for the dataset.
464: *
465: * dims - holds the current dimensions of the dataset
466: *
467: * maxDims - holds the maximum dimensions of the dataset (unlimited
468: * for the number of time steps with the current dimensions for the
469: * other dimensions; so only additional time steps can be added).
470: *
471: * chunkDims - holds the size of a single time step (required to
472: * permit extending dataset).
473: */
474: dim = 0;
475: if (timestep >= 0) {
476: dims[dim] = timestep+1;
477: maxDims[dim] = H5S_UNLIMITED;
478: chunkDims[dim] = 1;
479: ++dim;
480: }
481: if (da->dim == 3) {
482: PetscHDF5IntCast(da->P,dims+dim);
483: maxDims[dim] = dims[dim];
484: chunkDims[dim] = dims[dim];
485: ++dim;
486: }
487: if (da->dim > 1) {
488: PetscHDF5IntCast(da->N,dims+dim);
489: maxDims[dim] = dims[dim];
490: chunkDims[dim] = dims[dim];
491: ++dim;
492: }
493: PetscHDF5IntCast(da->M,dims+dim);
494: maxDims[dim] = dims[dim];
495: chunkDims[dim] = dims[dim];
496: ++dim;
497: if (da->w > 1) {
498: PetscHDF5IntCast(da->w,dims+dim);
499: maxDims[dim] = dims[dim];
500: chunkDims[dim] = dims[dim];
501: ++dim;
502: }
503: #if defined(PETSC_USE_COMPLEX)
504: dims[dim] = 2;
505: maxDims[dim] = dims[dim];
506: chunkDims[dim] = dims[dim];
507: ++dim;
508: #endif
510: VecGetHDF5ChunkSize(da, xin, timestep, chunkDims);
512: filespace = H5Screate_simple(dim, dims, maxDims);
513: if (filespace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Screate_simple()");
515: #if defined(PETSC_USE_REAL_SINGLE)
516: scalartype = H5T_NATIVE_FLOAT;
517: #elif defined(PETSC_USE_REAL___FLOAT128)
518: #error "HDF5 output with 128 bit floats not supported."
519: #else
520: scalartype = H5T_NATIVE_DOUBLE;
521: #endif
523: /* Create the dataset with default properties and close filespace */
524: PetscObjectGetName((PetscObject)xin,&vecname);
525: if (!H5Lexists(group, vecname, H5P_DEFAULT)) {
526: /* Create chunk */
527: chunkspace = H5Pcreate(H5P_DATASET_CREATE);
528: if (chunkspace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Pcreate()");
529: status = H5Pset_chunk(chunkspace, dim, chunkDims);CHKERRQ(status);
531: #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
532: dset_id = H5Dcreate2(group, vecname, scalartype, filespace, H5P_DEFAULT, chunkspace, H5P_DEFAULT);
533: #else
534: dset_id = H5Dcreate(group, vecname, scalartype, filespace, H5P_DEFAULT);
535: #endif
536: if (dset_id == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Dcreate2()");
537: } else {
538: dset_id = H5Dopen2(group, vecname, H5P_DEFAULT);
539: status = H5Dset_extent(dset_id, dims);CHKERRQ(status);
540: }
541: status = H5Sclose(filespace);CHKERRQ(status);
543: /* Each process defines a dataset and writes it to the hyperslab in the file */
544: dim = 0;
545: if (timestep >= 0) {
546: offset[dim] = timestep;
547: ++dim;
548: }
549: if (da->dim == 3) {PetscHDF5IntCast(da->zs,offset + dim++);}
550: if (da->dim > 1) {PetscHDF5IntCast(da->ys,offset + dim++);}
551: PetscHDF5IntCast(da->xs/da->w,offset + dim++);
552: if (da->w > 1) offset[dim++] = 0;
553: #if defined(PETSC_USE_COMPLEX)
554: offset[dim++] = 0;
555: #endif
556: dim = 0;
557: if (timestep >= 0) {
558: count[dim] = 1;
559: ++dim;
560: }
561: if (da->dim == 3) {PetscHDF5IntCast(da->ze - da->zs,count + dim++);}
562: if (da->dim > 1) {PetscHDF5IntCast(da->ye - da->ys,count + dim++);}
563: PetscHDF5IntCast((da->xe - da->xs)/da->w,count + dim++);
564: if (da->w > 1) {PetscHDF5IntCast(da->w,count + dim++);}
565: #if defined(PETSC_USE_COMPLEX)
566: count[dim++] = 2;
567: #endif
568: memspace = H5Screate_simple(dim, count, NULL);
569: if (memspace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Screate_simple()");
571: filespace = H5Dget_space(dset_id);
572: if (filespace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Dget_space()");
573: status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, count, NULL);CHKERRQ(status);
575: /* Create property list for collective dataset write */
576: plist_id = H5Pcreate(H5P_DATASET_XFER);
577: if (plist_id == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Pcreate()");
578: #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
579: status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);CHKERRQ(status);
580: #endif
581: /* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */
583: VecGetArray(xin, &x);
584: status = H5Dwrite(dset_id, scalartype, memspace, filespace, plist_id, x);CHKERRQ(status);
585: status = H5Fflush(file_id, H5F_SCOPE_GLOBAL);CHKERRQ(status);
586: VecRestoreArray(xin, &x);
588: /* Close/release resources */
589: if (group != file_id) {
590: status = H5Gclose(group);CHKERRQ(status);
591: }
592: status = H5Pclose(plist_id);CHKERRQ(status);
593: status = H5Sclose(filespace);CHKERRQ(status);
594: status = H5Sclose(memspace);CHKERRQ(status);
595: status = H5Dclose(dset_id);CHKERRQ(status);
596: PetscInfo1(xin,"Wrote Vec object with name %s\n",vecname);
597: return(0);
598: }
599: #endif
601: extern PetscErrorCode VecView_MPI_Draw_DA1d(Vec,PetscViewer);
603: #if defined(PETSC_HAVE_MPIIO)
606: static PetscErrorCode DMDAArrayMPIIO(DM da,PetscViewer viewer,Vec xin,PetscBool write)
607: {
608: PetscErrorCode ierr;
609: MPI_File mfdes;
610: PetscMPIInt gsizes[4],lsizes[4],lstarts[4],asiz,dof;
611: MPI_Datatype view;
612: const PetscScalar *array;
613: MPI_Offset off;
614: MPI_Aint ub,ul;
615: PetscInt type,rows,vecrows,tr[2];
616: DM_DA *dd = (DM_DA*)da->data;
617: PetscBool skipheader;
620: VecGetSize(xin,&vecrows);
621: PetscViewerBinaryGetSkipHeader(viewer,&skipheader);
622: if (!write) {
623: /* Read vector header. */
624: if (!skipheader) {
625: PetscViewerBinaryRead(viewer,tr,2,PETSC_INT);
626: type = tr[0];
627: rows = tr[1];
628: if (type != VEC_FILE_CLASSID) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_WRONG,"Not vector next in file");
629: if (rows != vecrows) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_SIZ,"Vector in file not same size as DMDA vector");
630: }
631: } else {
632: tr[0] = VEC_FILE_CLASSID;
633: tr[1] = vecrows;
634: if (!skipheader) {
635: PetscViewerBinaryWrite(viewer,tr,2,PETSC_INT,PETSC_TRUE);
636: }
637: }
639: PetscMPIIntCast(dd->w,&dof);
640: gsizes[0] = dof;
641: PetscMPIIntCast(dd->M,gsizes+1);
642: PetscMPIIntCast(dd->N,gsizes+2);
643: PetscMPIIntCast(dd->P,gsizes+3);
644: lsizes[0] = dof;
645: PetscMPIIntCast((dd->xe-dd->xs)/dof,lsizes+1);
646: PetscMPIIntCast(dd->ye-dd->ys,lsizes+2);
647: PetscMPIIntCast(dd->ze-dd->zs,lsizes+3);
648: lstarts[0] = 0;
649: PetscMPIIntCast(dd->xs/dof,lstarts+1);
650: PetscMPIIntCast(dd->ys,lstarts+2);
651: PetscMPIIntCast(dd->zs,lstarts+3);
652: MPI_Type_create_subarray(dd->dim+1,gsizes,lsizes,lstarts,MPI_ORDER_FORTRAN,MPIU_SCALAR,&view);
653: MPI_Type_commit(&view);
655: PetscViewerBinaryGetMPIIODescriptor(viewer,&mfdes);
656: PetscViewerBinaryGetMPIIOOffset(viewer,&off);
657: MPI_File_set_view(mfdes,off,MPIU_SCALAR,view,(char*)"native",MPI_INFO_NULL);
658: VecGetArrayRead(xin,&array);
659: asiz = lsizes[1]*(lsizes[2] > 0 ? lsizes[2] : 1)*(lsizes[3] > 0 ? lsizes[3] : 1)*dof;
660: if (write) {
661: MPIU_File_write_all(mfdes,(PetscScalar*)array,asiz,MPIU_SCALAR,MPI_STATUS_IGNORE);
662: } else {
663: MPIU_File_read_all(mfdes,(PetscScalar*)array,asiz,MPIU_SCALAR,MPI_STATUS_IGNORE);
664: }
665: MPI_Type_get_extent(view,&ul,&ub);
666: PetscViewerBinaryAddMPIIOOffset(viewer,ub);
667: VecRestoreArrayRead(xin,&array);
668: MPI_Type_free(&view);
669: return(0);
670: }
671: #endif
675: PetscErrorCode VecView_MPI_DA(Vec xin,PetscViewer viewer)
676: {
677: DM da;
678: PetscErrorCode ierr;
679: PetscInt dim;
680: Vec natural;
681: PetscBool isdraw,isvtk;
682: #if defined(PETSC_HAVE_HDF5)
683: PetscBool ishdf5;
684: #endif
685: const char *prefix,*name;
686: PetscViewerFormat format;
689: VecGetDM(xin,&da);
690: if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA");
691: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);
692: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERVTK,&isvtk);
693: #if defined(PETSC_HAVE_HDF5)
694: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);
695: #endif
696: if (isdraw) {
697: DMDAGetInfo(da,&dim,0,0,0,0,0,0,0,0,0,0,0,0);
698: if (dim == 1) {
699: VecView_MPI_Draw_DA1d(xin,viewer);
700: } else if (dim == 2) {
701: VecView_MPI_Draw_DA2d(xin,viewer);
702: } else SETERRQ1(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Cannot graphically view vector associated with this dimensional DMDA %D",dim);
703: } else if (isvtk) { /* Duplicate the Vec and hold a reference to the DM */
704: Vec Y;
705: PetscObjectReference((PetscObject)da);
706: VecDuplicate(xin,&Y);
707: if (((PetscObject)xin)->name) {
708: /* If xin was named, copy the name over to Y. The duplicate names are safe because nobody else will ever see Y. */
709: PetscObjectSetName((PetscObject)Y,((PetscObject)xin)->name);
710: }
711: VecCopy(xin,Y);
712: PetscViewerVTKAddField(viewer,(PetscObject)da,DMDAVTKWriteAll,PETSC_VTK_POINT_FIELD,(PetscObject)Y);
713: #if defined(PETSC_HAVE_HDF5)
714: } else if (ishdf5) {
715: VecView_MPI_HDF5_DA(xin,viewer);
716: #endif
717: } else {
718: #if defined(PETSC_HAVE_MPIIO)
719: PetscBool isbinary,isMPIIO;
721: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);
722: if (isbinary) {
723: PetscViewerBinaryGetMPIIO(viewer,&isMPIIO);
724: if (isMPIIO) {
725: DMDAArrayMPIIO(da,viewer,xin,PETSC_TRUE);
726: return(0);
727: }
728: }
729: #endif
731: /* call viewer on natural ordering */
732: PetscObjectGetOptionsPrefix((PetscObject)xin,&prefix);
733: DMDACreateNaturalVector(da,&natural);
734: PetscObjectSetOptionsPrefix((PetscObject)natural,prefix);
735: DMDAGlobalToNaturalBegin(da,xin,INSERT_VALUES,natural);
736: DMDAGlobalToNaturalEnd(da,xin,INSERT_VALUES,natural);
737: PetscObjectGetName((PetscObject)xin,&name);
738: PetscObjectSetName((PetscObject)natural,name);
740: PetscViewerGetFormat(viewer,&format);
741: if (format == PETSC_VIEWER_BINARY_MATLAB) {
742: /* temporarily remove viewer format so it won't trigger in the VecView() */
743: PetscViewerSetFormat(viewer,PETSC_VIEWER_DEFAULT);
744: }
746: VecView(natural,viewer);
748: if (format == PETSC_VIEWER_BINARY_MATLAB) {
749: MPI_Comm comm;
750: FILE *info;
751: const char *fieldname;
752: char fieldbuf[256];
753: PetscInt dim,ni,nj,nk,pi,pj,pk,dof,n;
755: /* set the viewer format back into the viewer */
756: PetscViewerSetFormat(viewer,format);
757: PetscObjectGetComm((PetscObject)viewer,&comm);
758: PetscViewerBinaryGetInfoPointer(viewer,&info);
759: DMDAGetInfo(da,&dim,&ni,&nj,&nk,&pi,&pj,&pk,&dof,0,0,0,0,0);
760: PetscFPrintf(comm,info,"#--- begin code written by PetscViewerBinary for MATLAB format ---#\n");
761: PetscFPrintf(comm,info,"#$$ tmp = PetscBinaryRead(fd); \n");
762: if (dim == 1) { PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d);\n",dof,ni); }
763: if (dim == 2) { PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d,%d);\n",dof,ni,nj); }
764: if (dim == 3) { PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d,%d,%d);\n",dof,ni,nj,nk); }
766: for (n=0; n<dof; n++) {
767: DMDAGetFieldName(da,n,&fieldname);
768: if (!fieldname || !fieldname[0]) {
769: PetscSNPrintf(fieldbuf,sizeof fieldbuf,"field%D",n);
770: fieldname = fieldbuf;
771: }
772: if (dim == 1) { PetscFPrintf(comm,info,"#$$ Set.%s.%s = squeeze(tmp(%d,:))';\n",name,fieldname,n+1); }
773: if (dim == 2) { PetscFPrintf(comm,info,"#$$ Set.%s.%s = squeeze(tmp(%d,:,:))';\n",name,fieldname,n+1); }
774: if (dim == 3) { PetscFPrintf(comm,info,"#$$ Set.%s.%s = permute(squeeze(tmp(%d,:,:,:)),[2 1 3]);\n",name,fieldname,n+1);}
775: }
776: PetscFPrintf(comm,info,"#$$ clear tmp; \n");
777: PetscFPrintf(comm,info,"#--- end code written by PetscViewerBinary for MATLAB format ---#\n\n");
778: }
780: VecDestroy(&natural);
781: }
782: return(0);
783: }
785: #if defined(PETSC_HAVE_HDF5)
788: PetscErrorCode VecLoad_HDF5_DA(Vec xin, PetscViewer viewer)
789: {
790: DM da;
792: hsize_t dim;
793: hsize_t count[5];
794: hsize_t offset[5];
795: PetscInt cnt = 0;
796: PetscScalar *x;
797: const char *vecname;
798: hid_t filespace; /* file dataspace identifier */
799: hid_t plist_id; /* property list identifier */
800: hid_t dset_id; /* dataset identifier */
801: hid_t memspace; /* memory dataspace identifier */
802: hid_t file_id,group;
803: hid_t scalartype; /* scalar type (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */
804: herr_t status;
805: DM_DA *dd;
808: #if defined(PETSC_USE_REAL_SINGLE)
809: scalartype = H5T_NATIVE_FLOAT;
810: #elif defined(PETSC_USE_REAL___FLOAT128)
811: #error "HDF5 output with 128 bit floats not supported."
812: #else
813: scalartype = H5T_NATIVE_DOUBLE;
814: #endif
815:
816: PetscViewerHDF5OpenGroup(viewer, &file_id, &group);
817: VecGetDM(xin,&da);
818: dd = (DM_DA*)da->data;
820: /* Create the dataspace for the dataset */
821: PetscHDF5IntCast(dd->dim + ((dd->w == 1) ? 0 : 1),&dim);
822: #if defined(PETSC_USE_COMPLEX)
823: dim++;
824: #endif
826: /* Create the dataset with default properties and close filespace */
827: PetscObjectGetName((PetscObject)xin,&vecname);
828: #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
829: dset_id = H5Dopen2(group, vecname, H5P_DEFAULT);
830: #else
831: dset_id = H5Dopen(group, vecname);
832: #endif
833: if (dset_id == -1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Dopen2() with Vec named %s",vecname);
834: filespace = H5Dget_space(dset_id);
836: /* Each process defines a dataset and reads it from the hyperslab in the file */
837: cnt = 0;
838: if (dd->dim == 3) {PetscHDF5IntCast(dd->zs,offset + cnt++);}
839: if (dd->dim > 1) {PetscHDF5IntCast(dd->ys,offset + cnt++);}
840: PetscHDF5IntCast(dd->xs/dd->w,offset + cnt++);
841: if (dd->w > 1) offset[cnt++] = 0;
842: #if defined(PETSC_USE_COMPLEX)
843: offset[cnt++] = 0;
844: #endif
845: cnt = 0;
846: if (dd->dim == 3) {PetscHDF5IntCast(dd->ze - dd->zs,count + cnt++);}
847: if (dd->dim > 1) {PetscHDF5IntCast(dd->ye - dd->ys,count + cnt++);}
848: PetscHDF5IntCast((dd->xe - dd->xs)/dd->w,count + cnt++);
849: if (dd->w > 1) {PetscHDF5IntCast(dd->w,count + cnt++);}
850: #if defined(PETSC_USE_COMPLEX)
851: count[cnt++] = 2;
852: #endif
853: memspace = H5Screate_simple(dim, count, NULL);
854: if (memspace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Screate_simple()");
856: status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, count, NULL);CHKERRQ(status);
858: /* Create property list for collective dataset write */
859: plist_id = H5Pcreate(H5P_DATASET_XFER);
860: if (plist_id == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Pcreate()");
861: #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
862: status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);CHKERRQ(status);
863: #endif
864: /* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */
866: VecGetArray(xin, &x);
867: status = H5Dread(dset_id, scalartype, memspace, filespace, plist_id, x);CHKERRQ(status);
868: VecRestoreArray(xin, &x);
870: /* Close/release resources */
871: if (group != file_id) {
872: status = H5Gclose(group);CHKERRQ(status);
873: }
874: status = H5Pclose(plist_id);CHKERRQ(status);
875: status = H5Sclose(filespace);CHKERRQ(status);
876: status = H5Sclose(memspace);CHKERRQ(status);
877: status = H5Dclose(dset_id);CHKERRQ(status);
878: return(0);
879: }
880: #endif
884: PetscErrorCode VecLoad_Binary_DA(Vec xin, PetscViewer viewer)
885: {
886: DM da;
888: Vec natural;
889: const char *prefix;
890: PetscInt bs;
891: PetscBool flag;
892: DM_DA *dd;
893: #if defined(PETSC_HAVE_MPIIO)
894: PetscBool isMPIIO;
895: #endif
898: VecGetDM(xin,&da);
899: dd = (DM_DA*)da->data;
900: #if defined(PETSC_HAVE_MPIIO)
901: PetscViewerBinaryGetMPIIO(viewer,&isMPIIO);
902: if (isMPIIO) {
903: DMDAArrayMPIIO(da,viewer,xin,PETSC_FALSE);
904: return(0);
905: }
906: #endif
908: PetscObjectGetOptionsPrefix((PetscObject)xin,&prefix);
909: DMDACreateNaturalVector(da,&natural);
910: PetscObjectSetName((PetscObject)natural,((PetscObject)xin)->name);
911: PetscObjectSetOptionsPrefix((PetscObject)natural,prefix);
912: VecLoad(natural,viewer);
913: DMDANaturalToGlobalBegin(da,natural,INSERT_VALUES,xin);
914: DMDANaturalToGlobalEnd(da,natural,INSERT_VALUES,xin);
915: VecDestroy(&natural);
916: PetscInfo(xin,"Loading vector from natural ordering into DMDA\n");
917: PetscOptionsGetInt(((PetscObject)xin)->prefix,"-vecload_block_size",&bs,&flag);
918: if (flag && bs != dd->w) {
919: PetscInfo2(xin,"Block size in file %D not equal to DMDA's dof %D\n",bs,dd->w);
920: }
921: return(0);
922: }
926: PetscErrorCode VecLoad_Default_DA(Vec xin, PetscViewer viewer)
927: {
929: DM da;
930: PetscBool isbinary;
931: #if defined(PETSC_HAVE_HDF5)
932: PetscBool ishdf5;
933: #endif
936: VecGetDM(xin,&da);
937: if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA");
939: #if defined(PETSC_HAVE_HDF5)
940: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);
941: #endif
942: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);
944: if (isbinary) {
945: VecLoad_Binary_DA(xin,viewer);
946: #if defined(PETSC_HAVE_HDF5)
947: } else if (ishdf5) {
948: VecLoad_HDF5_DA(xin,viewer);
949: #endif
950: } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Viewer type %s not supported for vector loading", ((PetscObject)viewer)->type_name);
951: return(0);
952: }