Actual source code: gr2.c
petsc-3.11.0 2019-03-29
2: /*
3: Plots vectors obtained with DMDACreate2d()
4: */
6: #include <petsc/private/dmdaimpl.h>
7: #include <petsc/private/glvisvecimpl.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: 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;
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;
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;
46: /* PetscDraw the contour plot patch */
47: PetscDrawCollectiveBegin(draw);
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);
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);
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);
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);
70: PetscDrawTriangle(draw,x1,y_1,x2,y2,x3,y3,c1,c2,c3);
71: PetscDrawTriangle(draw,x1,y_1,x3,y3,x4,y4,c1,c3,c4);
72: if (zctx->showgrid) {
73: PetscDrawLine(draw,x1,y_1,x2,y2,PETSC_DRAW_BLACK);
74: PetscDrawLine(draw,x2,y2,x3,y3,PETSC_DRAW_BLACK);
75: PetscDrawLine(draw,x3,y3,x4,y4,PETSC_DRAW_BLACK);
76: PetscDrawLine(draw,x4,y4,x1,y_1,PETSC_DRAW_BLACK);
77: }
78: }
79: }
80: if (zctx->showaxis && !zctx->rank) {
81: if (zctx->name0 || zctx->name1) {
82: PetscReal xl,yl,xr,yr,x,y;
83: PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);
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) {PetscDrawString(draw,x,yl,PETSC_DRAW_BLACK,zctx->name0);}
89: if (zctx->name1) {PetscDrawStringVertical(draw,xl,y,PETSC_DRAW_BLACK,zctx->name1);}
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: PetscSNPrintf(value,16,"%0.2e",xmin);
100: PetscDrawString(draw,xmin,ymin - .05*(ymax - ymin),PETSC_DRAW_BLACK,value);
101: PetscSNPrintf(value,16,"%0.2e",xmax);
102: PetscStrlen(value,&len);
103: PetscDrawStringGetSize(draw,&w,NULL);
104: PetscDrawString(draw,xmax - len*w,ymin - .05*(ymax - ymin),PETSC_DRAW_BLACK,value);
105: PetscSNPrintf(value,16,"%0.2e",ymin);
106: PetscDrawString(draw,xmin - .05*(xmax - xmin),ymin,PETSC_DRAW_BLACK,value);
107: PetscSNPrintf(value,16,"%0.2e",ymax);
108: PetscDrawString(draw,xmin - .05*(xmax - xmin),ymax,PETSC_DRAW_BLACK,value);
109: }
110: }
111: PetscDrawCollectiveEnd(draw);
112: return(0);
113: }
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;
136: zctx.showgrid = PETSC_FALSE;
137: zctx.showaxis = PETSC_TRUE;
139: PetscViewerDrawGetDraw(viewer,0,&draw);
140: PetscDrawIsNull(draw,&isnull);
141: if (isnull) return(0);
143: PetscViewerDrawGetBounds(viewer,&nbounds,&bounds);
145: VecGetDM(xin,&da);
146: if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA");
148: PetscObjectGetComm((PetscObject)xin,&comm);
149: MPI_Comm_rank(comm,&zctx.rank);
151: DMDAGetInfo(da,0,&M,&N,0,&zctx.m,&zctx.n,0,&w,&s,&bx,&by,0,&st);
152: DMDAGetOwnershipRanges(da,&lx,&ly,NULL);
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: PetscObjectQuery((PetscObject)da,"GraphicsGhosted",(PetscObject*)&xlocal);
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: DMDACreate2d(comm,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,N,zctx.m,zctx.n,w,1,lx,ly,&dac);
167: DMSetUp(dac);
168: PetscInfo(da,"Creating auxilary DMDA for managing graphics ghost points\n");
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: DMCreateLocalVector(dac,&xlocal);
175: if (dac != da) {
176: /* don't keep any public reference of this DMDA, is is only available through xlocal */
177: PetscObjectDereference((PetscObject)dac);
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: PetscObjectRemoveReference((PetscObject)xlocal,"__PETSc_dm");
183: }
184: PetscObjectCompose((PetscObject)da,"GraphicsGhosted",(PetscObject)xlocal);
185: PetscObjectDereference((PetscObject)xlocal);
186: } else {
187: if (bx != DM_BOUNDARY_NONE || by != DM_BOUNDARY_NONE || s != 1 || st != DMDA_STENCIL_BOX) {
188: VecGetDM(xlocal, &dac);
189: } else {
190: dac = da;
191: }
192: }
194: /*
195: Get local (ghosted) values of vector
196: */
197: DMGlobalToLocalBegin(dac,xin,INSERT_VALUES,xlocal);
198: DMGlobalToLocalEnd(dac,xin,INSERT_VALUES,xlocal);
199: VecGetArrayRead(xlocal,&zctx.v);
201: /*
202: Get coordinates of nodes
203: */
204: DMGetCoordinates(da,&xcoor);
205: if (!xcoor) {
206: DMDASetUniformCoordinates(da,0.0,1.0,0.0,1.0,0.0,0.0);
207: DMGetCoordinates(da,&xcoor);
208: }
210: /*
211: Determine the min and max coordinates in plot
212: */
213: VecStrideMin(xcoor,0,NULL,&zctx.xmin);
214: VecStrideMax(xcoor,0,NULL,&zctx.xmax);
215: VecStrideMin(xcoor,1,NULL,&zctx.ymin);
216: VecStrideMax(xcoor,1,NULL,&zctx.ymax);
217: PetscOptionsGetBool(NULL,NULL,"-draw_contour_axis",&zctx.showaxis,NULL);
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: PetscOptionsGetRealArray(NULL,NULL,"-draw_coordinates",coors,&ncoors,NULL);
225: 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]);
227: /*
228: Get local ghosted version of coordinates
229: */
230: PetscObjectQuery((PetscObject)da,"GraphicsCoordinateGhosted",(PetscObject*)&xcoorl);
231: if (!xcoorl) {
232: /* create DMDA to get local version of graphics */
233: DMDACreate2d(comm,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_BOX,M,N,zctx.m,zctx.n,2,1,lx,ly,&dag);
234: DMSetUp(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: VecGetArrayRead(xcoorl,&zctx.xy);
246: DMDAGetCoordinateName(da,0,&zctx.name0);
247: DMDAGetCoordinateName(da,1,&zctx.name1);
249: /*
250: Get information about size of area each processor must do graphics for
251: */
252: DMDAGetInfo(dac,NULL,&M,&N,NULL,NULL,NULL,NULL,&zctx.dof,NULL,&bx,&by,NULL,NULL);
253: DMDAGetGhostCorners(dac,NULL,NULL,NULL,&zctx.m,&zctx.n,NULL);
254: PetscOptionsGetBool(NULL,NULL,"-draw_contour_grid",&zctx.showgrid,NULL);
256: DMDASelectFields(da,&ndisplayfields,&displayfields);
257: PetscViewerGetFormat(viewer,&format);
258: PetscOptionsGetBool(NULL,NULL,"-draw_ports",&useports,NULL);
259: if (format == PETSC_VIEWER_DRAW_PORTS) useports = PETSC_TRUE;
260: if (useports) {
261: PetscViewerDrawGetDraw(viewer,0,&draw);
262: PetscDrawCheckResizedWindow(draw);
263: PetscDrawClear(draw);
264: PetscDrawViewPortsCreate(draw,ndisplayfields,&ports);
265: }
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];
273: /* determine the min and max value in plot */
274: VecStrideMin(xin,zctx.k,NULL,&zctx.min);
275: VecStrideMax(xin,zctx.k,NULL,&zctx.max);
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: PetscInfo2(da,"DMDA 2d contour plot min %g max %g\n",(double)zctx.min,(double)zctx.max);
286: if (useports) {
287: PetscDrawViewPortsSet(ports,i);
288: } else {
289: const char *title;
290: PetscViewerDrawGetDraw(viewer,i,&draw);
291: DMDAGetFieldName(da,zctx.k,&title);
292: if (title) {PetscDrawSetTitle(draw,title);}
293: }
295: PetscDrawGetPopup(draw,&popup);
296: PetscDrawScalePopup(popup,zctx.min,zctx.max);
297: PetscDrawSetCoordinates(draw,coors[0],coors[1],coors[2],coors[3]);
298: PetscDrawZoom(draw,VecView_MPI_Draw_DA2d_Zoom,&zctx);
299: if (!useports) {PetscDrawSave(draw);}
300: }
301: if (useports) {
302: PetscViewerDrawGetDraw(viewer,0,&draw);
303: PetscDrawSave(draw);
304: }
306: PetscDrawViewPortsDestroy(ports);
307: PetscFree(displayfields);
308: VecRestoreArrayRead(xcoorl,&zctx.xy);
309: VecRestoreArrayRead(xlocal,&zctx.v);
310: return(0);
311: }
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;
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;
326: MPI_Comm_size(PetscObjectComm((PetscObject)xin), &comm_size);
327: avg_local_vec_size = (hsize_t) ceil(vec_size*1.0/comm_size); /* we will attempt to use this as the chunk size */
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);
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: }
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: return(0);
409: }
410: #endif
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;
436: PetscViewerHDF5OpenGroup(viewer, &file_id, &group);
437: PetscViewerHDF5GetTimestep(viewer, ×tep);
438: PetscViewerHDF5GetBaseDimension2(viewer,&dim2);
439: PetscViewerHDF5GetSPOutput(viewer,&spoutput);
441: VecGetDM(xin,&dm);
442: if (!dm) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA");
443: da = (DM_DA*)dm->data;
444: DMGetDimension(dm, &dimension);
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: PetscHDF5IntCast(da->P,dims+dim);
466: maxDims[dim] = dims[dim];
467: chunkDims[dim] = dims[dim];
468: ++dim;
469: }
470: if (dimension > 1) {
471: PetscHDF5IntCast(da->N,dims+dim);
472: maxDims[dim] = dims[dim];
473: chunkDims[dim] = dims[dim];
474: ++dim;
475: }
476: PetscHDF5IntCast(da->M,dims+dim);
477: maxDims[dim] = dims[dim];
478: chunkDims[dim] = dims[dim];
479: ++dim;
480: if (da->w > 1 || dim2) {
481: PetscHDF5IntCast(da->w,dims+dim);
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
493: VecGetHDF5ChunkSize(da, xin, dimension, timestep, chunkDims);
495: PetscStackCallHDF5Return(filespace,H5Screate_simple,(dim, dims, maxDims));
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
510: /* Create the dataset with default properties and close filespace */
511: PetscObjectGetName((PetscObject)xin,&vecname);
512: if (!H5Lexists(group, vecname, H5P_DEFAULT)) {
513: /* Create chunk */
514: PetscStackCallHDF5Return(chunkspace,H5Pcreate,(H5P_DATASET_CREATE));
515: PetscStackCallHDF5(H5Pset_chunk,(chunkspace, dim, chunkDims));
517: PetscStackCallHDF5Return(dset_id,H5Dcreate2,(group, vecname, filescalartype, filespace, H5P_DEFAULT, chunkspace, H5P_DEFAULT));
518: } else {
519: PetscStackCallHDF5Return(dset_id,H5Dopen2,(group, vecname, H5P_DEFAULT));
520: PetscStackCallHDF5(H5Dset_extent,(dset_id, dims));
521: }
522: PetscStackCallHDF5(H5Sclose,(filespace));
524: /* Each process defines a dataset and writes it to the hyperslab in the file */
525: dim = 0;
526: if (timestep >= 0) {
527: offset[dim] = timestep;
528: ++dim;
529: }
530: if (dimension == 3) {PetscHDF5IntCast(da->zs,offset + dim++);}
531: if (dimension > 1) {PetscHDF5IntCast(da->ys,offset + dim++);}
532: PetscHDF5IntCast(da->xs/da->w,offset + dim++);
533: if (da->w > 1 || dim2) offset[dim++] = 0;
534: #if defined(PETSC_USE_COMPLEX)
535: offset[dim++] = 0;
536: #endif
537: dim = 0;
538: if (timestep >= 0) {
539: count[dim] = 1;
540: ++dim;
541: }
542: if (dimension == 3) {PetscHDF5IntCast(da->ze - da->zs,count + dim++);}
543: if (dimension > 1) {PetscHDF5IntCast(da->ye - da->ys,count + dim++);}
544: PetscHDF5IntCast((da->xe - da->xs)/da->w,count + dim++);
545: if (da->w > 1 || dim2) {PetscHDF5IntCast(da->w,count + dim++);}
546: #if defined(PETSC_USE_COMPLEX)
547: count[dim++] = 2;
548: #endif
549: PetscStackCallHDF5Return(memspace,H5Screate_simple,(dim, count, NULL));
550: PetscStackCallHDF5Return(filespace,H5Dget_space,(dset_id));
551: PetscStackCallHDF5(H5Sselect_hyperslab,(filespace, H5S_SELECT_SET, offset, NULL, count, NULL));
553: /* Create property list for collective dataset write */
554: PetscStackCallHDF5Return(plist_id,H5Pcreate,(H5P_DATASET_XFER));
555: #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
556: PetscStackCallHDF5(H5Pset_dxpl_mpio,(plist_id, H5FD_MPIO_COLLECTIVE));
557: #endif
558: /* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */
560: VecGetArrayRead(xin, &x);
561: PetscStackCallHDF5(H5Dwrite,(dset_id, memscalartype, memspace, filespace, plist_id, x));
562: PetscStackCallHDF5(H5Fflush,(file_id, H5F_SCOPE_GLOBAL));
563: VecRestoreArrayRead(xin, &x);
565: /* Close/release resources */
566: if (group != file_id) {
567: PetscStackCallHDF5(H5Gclose,(group));
568: }
569: PetscStackCallHDF5(H5Pclose,(plist_id));
570: PetscStackCallHDF5(H5Sclose,(filespace));
571: PetscStackCallHDF5(H5Sclose,(memspace));
572: PetscStackCallHDF5(H5Dclose,(dset_id));
573: PetscInfo1(xin,"Wrote Vec object with name %s\n",vecname);
574: return(0);
575: }
576: #endif
578: extern PetscErrorCode VecView_MPI_Draw_DA1d(Vec,PetscViewer);
580: #if defined(PETSC_HAVE_MPIIO)
581: static PetscErrorCode DMDAArrayMPIIO(DM da,PetscViewer viewer,Vec xin,PetscBool write)
582: {
583: PetscErrorCode ierr;
584: MPI_File mfdes;
585: PetscMPIInt gsizes[4],lsizes[4],lstarts[4],asiz,dof;
586: MPI_Datatype view;
587: const PetscScalar *array;
588: MPI_Offset off;
589: MPI_Aint ub,ul;
590: PetscInt type,rows,vecrows,tr[2];
591: DM_DA *dd = (DM_DA*)da->data;
592: PetscBool skipheader;
595: VecGetSize(xin,&vecrows);
596: PetscViewerBinaryGetSkipHeader(viewer,&skipheader);
597: if (!write) {
598: /* Read vector header. */
599: if (!skipheader) {
600: PetscViewerBinaryRead(viewer,tr,2,NULL,PETSC_INT);
601: type = tr[0];
602: rows = tr[1];
603: if (type != VEC_FILE_CLASSID) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_WRONG,"Not vector next in file");
604: if (rows != vecrows) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_SIZ,"Vector in file not same size as DMDA vector");
605: }
606: } else {
607: tr[0] = VEC_FILE_CLASSID;
608: tr[1] = vecrows;
609: if (!skipheader) {
610: PetscViewerBinaryWrite(viewer,tr,2,PETSC_INT,PETSC_TRUE);
611: }
612: }
614: PetscMPIIntCast(dd->w,&dof);
615: gsizes[0] = dof;
616: PetscMPIIntCast(dd->M,gsizes+1);
617: PetscMPIIntCast(dd->N,gsizes+2);
618: PetscMPIIntCast(dd->P,gsizes+3);
619: lsizes[0] = dof;
620: PetscMPIIntCast((dd->xe-dd->xs)/dof,lsizes+1);
621: PetscMPIIntCast(dd->ye-dd->ys,lsizes+2);
622: PetscMPIIntCast(dd->ze-dd->zs,lsizes+3);
623: lstarts[0] = 0;
624: PetscMPIIntCast(dd->xs/dof,lstarts+1);
625: PetscMPIIntCast(dd->ys,lstarts+2);
626: PetscMPIIntCast(dd->zs,lstarts+3);
627: MPI_Type_create_subarray(da->dim+1,gsizes,lsizes,lstarts,MPI_ORDER_FORTRAN,MPIU_SCALAR,&view);
628: MPI_Type_commit(&view);
630: PetscViewerBinaryGetMPIIODescriptor(viewer,&mfdes);
631: PetscViewerBinaryGetMPIIOOffset(viewer,&off);
632: MPI_File_set_view(mfdes,off,MPIU_SCALAR,view,(char*)"native",MPI_INFO_NULL);
633: VecGetArrayRead(xin,&array);
634: asiz = lsizes[1]*(lsizes[2] > 0 ? lsizes[2] : 1)*(lsizes[3] > 0 ? lsizes[3] : 1)*dof;
635: if (write) {
636: MPIU_File_write_all(mfdes,(PetscScalar*)array,asiz,MPIU_SCALAR,MPI_STATUS_IGNORE);
637: } else {
638: MPIU_File_read_all(mfdes,(PetscScalar*)array,asiz,MPIU_SCALAR,MPI_STATUS_IGNORE);
639: }
640: MPI_Type_get_extent(view,&ul,&ub);
641: PetscViewerBinaryAddMPIIOOffset(viewer,ub);
642: VecRestoreArrayRead(xin,&array);
643: MPI_Type_free(&view);
644: return(0);
645: }
646: #endif
648: PetscErrorCode VecView_MPI_DA(Vec xin,PetscViewer viewer)
649: {
650: DM da;
651: PetscErrorCode ierr;
652: PetscInt dim;
653: Vec natural;
654: PetscBool isdraw,isvtk,isglvis;
655: #if defined(PETSC_HAVE_HDF5)
656: PetscBool ishdf5;
657: #endif
658: const char *prefix,*name;
659: PetscViewerFormat format;
662: VecGetDM(xin,&da);
663: if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA");
664: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);
665: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERVTK,&isvtk);
666: #if defined(PETSC_HAVE_HDF5)
667: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);
668: #endif
669: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERGLVIS,&isglvis);
670: if (isdraw) {
671: DMDAGetInfo(da,&dim,0,0,0,0,0,0,0,0,0,0,0,0);
672: if (dim == 1) {
673: VecView_MPI_Draw_DA1d(xin,viewer);
674: } else if (dim == 2) {
675: VecView_MPI_Draw_DA2d(xin,viewer);
676: } else SETERRQ1(PetscObjectComm((PetscObject)da),PETSC_ERR_SUP,"Cannot graphically view vector associated with this dimensional DMDA %D",dim);
677: } else if (isvtk) { /* Duplicate the Vec */
678: Vec Y;
679: VecDuplicate(xin,&Y);
680: if (((PetscObject)xin)->name) {
681: /* If xin was named, copy the name over to Y. The duplicate names are safe because nobody else will ever see Y. */
682: PetscObjectSetName((PetscObject)Y,((PetscObject)xin)->name);
683: }
684: VecCopy(xin,Y);
685: {
686: PetscObject dmvtk;
687: PetscBool compatible,compatibleSet;
688: PetscViewerVTKGetDM(viewer,&dmvtk);
689: if (dmvtk) {
691: DMGetCompatibility(da,(DM)dmvtk,&compatible,&compatibleSet);
692: if (!compatibleSet || !compatible) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_INCOMP,"Cannot confirm compatibility of DMs associated with Vecs viewed in the same VTK file. Check that grids are the same.");
693: }
694: PetscViewerVTKAddField(viewer,(PetscObject)da,DMDAVTKWriteAll,PETSC_VTK_POINT_FIELD,PETSC_FALSE,(PetscObject)Y);
695: }
696: #if defined(PETSC_HAVE_HDF5)
697: } else if (ishdf5) {
698: VecView_MPI_HDF5_DA(xin,viewer);
699: #endif
700: } else if (isglvis) {
701: VecView_GLVis(xin,viewer);
702: } else {
703: #if defined(PETSC_HAVE_MPIIO)
704: PetscBool isbinary,isMPIIO;
706: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);
707: if (isbinary) {
708: PetscViewerBinaryGetUseMPIIO(viewer,&isMPIIO);
709: if (isMPIIO) {
710: DMDAArrayMPIIO(da,viewer,xin,PETSC_TRUE);
711: return(0);
712: }
713: }
714: #endif
716: /* call viewer on natural ordering */
717: PetscObjectGetOptionsPrefix((PetscObject)xin,&prefix);
718: DMDACreateNaturalVector(da,&natural);
719: PetscObjectSetOptionsPrefix((PetscObject)natural,prefix);
720: DMDAGlobalToNaturalBegin(da,xin,INSERT_VALUES,natural);
721: DMDAGlobalToNaturalEnd(da,xin,INSERT_VALUES,natural);
722: PetscObjectGetName((PetscObject)xin,&name);
723: PetscObjectSetName((PetscObject)natural,name);
725: PetscViewerGetFormat(viewer,&format);
726: if (format == PETSC_VIEWER_BINARY_MATLAB) {
727: /* temporarily remove viewer format so it won't trigger in the VecView() */
728: PetscViewerPushFormat(viewer,PETSC_VIEWER_DEFAULT);
729: }
731: ((PetscObject)natural)->donotPetscObjectPrintClassNamePrefixType = PETSC_TRUE;
732: VecView(natural,viewer);
733: ((PetscObject)natural)->donotPetscObjectPrintClassNamePrefixType = PETSC_FALSE;
735: if (format == PETSC_VIEWER_BINARY_MATLAB) {
736: MPI_Comm comm;
737: FILE *info;
738: const char *fieldname;
739: char fieldbuf[256];
740: PetscInt dim,ni,nj,nk,pi,pj,pk,dof,n;
742: /* set the viewer format back into the viewer */
743: PetscViewerPopFormat(viewer);
744: PetscObjectGetComm((PetscObject)viewer,&comm);
745: PetscViewerBinaryGetInfoPointer(viewer,&info);
746: DMDAGetInfo(da,&dim,&ni,&nj,&nk,&pi,&pj,&pk,&dof,0,0,0,0,0);
747: PetscFPrintf(comm,info,"#--- begin code written by PetscViewerBinary for MATLAB format ---#\n");
748: PetscFPrintf(comm,info,"#$$ tmp = PetscBinaryRead(fd); \n");
749: if (dim == 1) { PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d);\n",dof,ni); }
750: if (dim == 2) { PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d,%d);\n",dof,ni,nj); }
751: if (dim == 3) { PetscFPrintf(comm,info,"#$$ tmp = reshape(tmp,%d,%d,%d,%d);\n",dof,ni,nj,nk); }
753: for (n=0; n<dof; n++) {
754: DMDAGetFieldName(da,n,&fieldname);
755: if (!fieldname || !fieldname[0]) {
756: PetscSNPrintf(fieldbuf,sizeof fieldbuf,"field%D",n);
757: fieldname = fieldbuf;
758: }
759: if (dim == 1) { PetscFPrintf(comm,info,"#$$ Set.%s.%s = squeeze(tmp(%d,:))';\n",name,fieldname,n+1); }
760: if (dim == 2) { PetscFPrintf(comm,info,"#$$ Set.%s.%s = squeeze(tmp(%d,:,:))';\n",name,fieldname,n+1); }
761: if (dim == 3) { PetscFPrintf(comm,info,"#$$ Set.%s.%s = permute(squeeze(tmp(%d,:,:,:)),[2 1 3]);\n",name,fieldname,n+1);}
762: }
763: PetscFPrintf(comm,info,"#$$ clear tmp; \n");
764: PetscFPrintf(comm,info,"#--- end code written by PetscViewerBinary for MATLAB format ---#\n\n");
765: }
767: VecDestroy(&natural);
768: }
769: return(0);
770: }
772: #if defined(PETSC_HAVE_HDF5)
773: PetscErrorCode VecLoad_HDF5_DA(Vec xin, PetscViewer viewer)
774: {
775: DM da;
777: int dim,rdim;
778: hsize_t dims[6]={0},count[6]={0},offset[6]={0};
779: PetscInt dimension,timestep,dofInd;
780: PetscScalar *x;
781: const char *vecname;
782: hid_t filespace; /* file dataspace identifier */
783: hid_t plist_id; /* property list identifier */
784: hid_t dset_id; /* dataset identifier */
785: hid_t memspace; /* memory dataspace identifier */
786: hid_t file_id,group;
787: hid_t scalartype; /* scalar type (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */
788: DM_DA *dd;
789: PetscBool dim2 = PETSC_FALSE;
792: #if defined(PETSC_USE_REAL_SINGLE)
793: scalartype = H5T_NATIVE_FLOAT;
794: #elif defined(PETSC_USE_REAL___FLOAT128)
795: #error "HDF5 output with 128 bit floats not supported."
796: #elif defined(PETSC_USE_REAL___FP16)
797: #error "HDF5 output with 16 bit floats not supported."
798: #else
799: scalartype = H5T_NATIVE_DOUBLE;
800: #endif
802: PetscViewerHDF5OpenGroup(viewer, &file_id, &group);
803: PetscViewerHDF5GetTimestep(viewer, ×tep);
804: PetscObjectGetName((PetscObject)xin,&vecname);
805: VecGetDM(xin,&da);
806: dd = (DM_DA*)da->data;
807: DMGetDimension(da, &dimension);
809: /* Open dataset */
810: PetscStackCallHDF5Return(dset_id,H5Dopen2,(group, vecname, H5P_DEFAULT));
812: /* Retrieve the dataspace for the dataset */
813: PetscStackCallHDF5Return(filespace,H5Dget_space,(dset_id));
814: PetscStackCallHDF5Return(rdim,H5Sget_simple_extent_dims,(filespace, dims, NULL));
816: /* Expected dimension for holding the dof's */
817: #if defined(PETSC_USE_COMPLEX)
818: dofInd = rdim-2;
819: #else
820: dofInd = rdim-1;
821: #endif
823: /* The expected number of dimensions, assuming basedimension2 = false */
824: dim = dimension;
825: if (dd->w > 1) ++dim;
826: if (timestep >= 0) ++dim;
827: #if defined(PETSC_USE_COMPLEX)
828: ++dim;
829: #endif
831: /* In this case the input dataset have one extra, unexpected dimension. */
832: if (rdim == dim+1) {
833: /* In this case the block size unity */
834: if (dd->w == 1 && dims[dofInd] == 1) dim2 = PETSC_TRUE;
836: /* Special error message for the case where dof does not match the input file */
837: 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);
839: /* Other cases where rdim != dim cannot be handled currently */
840: } 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);
842: /* Set up the hyperslab size */
843: dim = 0;
844: if (timestep >= 0) {
845: offset[dim] = timestep;
846: count[dim] = 1;
847: ++dim;
848: }
849: if (dimension == 3) {
850: PetscHDF5IntCast(dd->zs,offset + dim);
851: PetscHDF5IntCast(dd->ze - dd->zs,count + dim);
852: ++dim;
853: }
854: if (dimension > 1) {
855: PetscHDF5IntCast(dd->ys,offset + dim);
856: PetscHDF5IntCast(dd->ye - dd->ys,count + dim);
857: ++dim;
858: }
859: PetscHDF5IntCast(dd->xs/dd->w,offset + dim);
860: PetscHDF5IntCast((dd->xe - dd->xs)/dd->w,count + dim);
861: ++dim;
862: if (dd->w > 1 || dim2) {
863: offset[dim] = 0;
864: PetscHDF5IntCast(dd->w,count + dim);
865: ++dim;
866: }
867: #if defined(PETSC_USE_COMPLEX)
868: offset[dim] = 0;
869: count[dim] = 2;
870: ++dim;
871: #endif
873: /* Create the memory and filespace */
874: PetscStackCallHDF5Return(memspace,H5Screate_simple,(dim, count, NULL));
875: PetscStackCallHDF5(H5Sselect_hyperslab,(filespace, H5S_SELECT_SET, offset, NULL, count, NULL));
877: /* Create property list for collective dataset write */
878: PetscStackCallHDF5Return(plist_id,H5Pcreate,(H5P_DATASET_XFER));
879: #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
880: PetscStackCallHDF5(H5Pset_dxpl_mpio,(plist_id, H5FD_MPIO_COLLECTIVE));
881: #endif
882: /* To read dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */
884: VecGetArray(xin, &x);
885: PetscStackCallHDF5(H5Dread,(dset_id, scalartype, memspace, filespace, plist_id, x));
886: VecRestoreArray(xin, &x);
888: /* Close/release resources */
889: if (group != file_id) {
890: PetscStackCallHDF5(H5Gclose,(group));
891: }
892: PetscStackCallHDF5(H5Pclose,(plist_id));
893: PetscStackCallHDF5(H5Sclose,(filespace));
894: PetscStackCallHDF5(H5Sclose,(memspace));
895: PetscStackCallHDF5(H5Dclose,(dset_id));
896: return(0);
897: }
898: #endif
900: PetscErrorCode VecLoad_Binary_DA(Vec xin, PetscViewer viewer)
901: {
902: DM da;
904: Vec natural;
905: const char *prefix;
906: PetscInt bs;
907: PetscBool flag;
908: DM_DA *dd;
909: #if defined(PETSC_HAVE_MPIIO)
910: PetscBool isMPIIO;
911: #endif
914: VecGetDM(xin,&da);
915: dd = (DM_DA*)da->data;
916: #if defined(PETSC_HAVE_MPIIO)
917: PetscViewerBinaryGetUseMPIIO(viewer,&isMPIIO);
918: if (isMPIIO) {
919: DMDAArrayMPIIO(da,viewer,xin,PETSC_FALSE);
920: return(0);
921: }
922: #endif
924: PetscObjectGetOptionsPrefix((PetscObject)xin,&prefix);
925: DMDACreateNaturalVector(da,&natural);
926: PetscObjectSetName((PetscObject)natural,((PetscObject)xin)->name);
927: PetscObjectSetOptionsPrefix((PetscObject)natural,prefix);
928: VecLoad(natural,viewer);
929: DMDANaturalToGlobalBegin(da,natural,INSERT_VALUES,xin);
930: DMDANaturalToGlobalEnd(da,natural,INSERT_VALUES,xin);
931: VecDestroy(&natural);
932: PetscInfo(xin,"Loading vector from natural ordering into DMDA\n");
933: PetscOptionsGetInt(NULL,((PetscObject)xin)->prefix,"-vecload_block_size",&bs,&flag);
934: if (flag && bs != dd->w) {
935: PetscInfo2(xin,"Block size in file %D not equal to DMDA's dof %D\n",bs,dd->w);
936: }
937: return(0);
938: }
940: PetscErrorCode VecLoad_Default_DA(Vec xin, PetscViewer viewer)
941: {
943: DM da;
944: PetscBool isbinary;
945: #if defined(PETSC_HAVE_HDF5)
946: PetscBool ishdf5;
947: #endif
950: VecGetDM(xin,&da);
951: if (!da) SETERRQ(PetscObjectComm((PetscObject)xin),PETSC_ERR_ARG_WRONG,"Vector not generated from a DMDA");
953: #if defined(PETSC_HAVE_HDF5)
954: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);
955: #endif
956: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);
958: if (isbinary) {
959: VecLoad_Binary_DA(xin,viewer);
960: #if defined(PETSC_HAVE_HDF5)
961: } else if (ishdf5) {
962: VecLoad_HDF5_DA(xin,viewer);
963: #endif
964: } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Viewer type %s not supported for vector loading", ((PetscObject)viewer)->type_name);
965: return(0);
966: }