Actual source code: pdvec.c
1: /*
2: Code for some of the parallel vector primitives.
3: */
4: #include <../src/vec/vec/impls/mpi/pvecimpl.h>
5: #include <petsc/private/viewerhdf5impl.h>
6: #include <petsc/private/glvisviewerimpl.h>
7: #include <petsc/private/glvisvecimpl.h>
8: #include <petscsf.h>
10: static PetscErrorCode VecResetPreallocationCOO_MPI(Vec v)
11: {
12: Vec_MPI *vmpi = (Vec_MPI *)v->data;
14: PetscFunctionBegin;
15: if (vmpi) {
16: PetscCall(PetscFree(vmpi->jmap1));
17: PetscCall(PetscFree(vmpi->perm1));
18: PetscCall(PetscFree(vmpi->Cperm));
19: PetscCall(PetscFree4(vmpi->imap2, vmpi->jmap2, vmpi->sendbuf, vmpi->recvbuf));
20: PetscCall(PetscFree(vmpi->perm2));
21: PetscCall(PetscSFDestroy(&vmpi->coo_sf));
22: }
23: PetscFunctionReturn(PETSC_SUCCESS);
24: }
26: PetscErrorCode VecDestroy_MPI(Vec v)
27: {
28: Vec_MPI *x = (Vec_MPI *)v->data;
30: PetscFunctionBegin;
31: PetscCall(PetscLogObjectState((PetscObject)v, "Length=%" PetscInt_FMT, v->map->N));
32: if (!x) PetscFunctionReturn(PETSC_SUCCESS);
33: PetscCall(PetscFree(x->array_allocated));
35: /* Destroy local representation of vector if it exists */
36: if (x->localrep) {
37: PetscCall(VecDestroy(&x->localrep));
38: PetscCall(VecScatterDestroy(&x->localupdate));
39: PetscCall(ISDestroy(&x->ghost));
40: }
41: PetscCall(VecAssemblyReset_MPI(v));
43: /* Destroy the stashes: note the order - so that the tags are freed properly */
44: PetscCall(VecStashDestroy_Private(&v->bstash));
45: PetscCall(VecStashDestroy_Private(&v->stash));
47: PetscCall(VecResetPreallocationCOO_MPI(v));
48: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscMatlabEnginePut_C", NULL));
49: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscMatlabEngineGet_C", NULL));
50: PetscCall(PetscFree(v->data));
51: PetscFunctionReturn(PETSC_SUCCESS);
52: }
54: static PetscErrorCode VecView_MPI_ASCII(Vec xin, PetscViewer viewer)
55: {
56: PetscInt i, work = xin->map->n, cnt, len, nLen;
57: PetscMPIInt j, n = 0, size, rank, tag = ((PetscObject)viewer)->tag;
58: MPI_Status status;
59: PetscScalar *values;
60: const PetscScalar *xarray;
61: const char *name;
62: PetscViewerFormat format;
64: PetscFunctionBegin;
65: PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)xin), &size));
66: PetscCall(PetscViewerGetFormat(viewer, &format));
67: if (format == PETSC_VIEWER_LOAD_BALANCE) {
68: PetscInt nmax = 0, nmin = xin->map->n, navg;
69: for (i = 0; i < (PetscInt)size; i++) {
70: nmax = PetscMax(nmax, xin->map->range[i + 1] - xin->map->range[i]);
71: nmin = PetscMin(nmin, xin->map->range[i + 1] - xin->map->range[i]);
72: }
73: navg = xin->map->N / size;
74: PetscCall(PetscViewerASCIIPrintf(viewer, " Load Balance - Local vector size Min %" PetscInt_FMT " avg %" PetscInt_FMT " max %" PetscInt_FMT "\n", nmin, navg, nmax));
75: PetscFunctionReturn(PETSC_SUCCESS);
76: }
78: PetscCall(VecGetArrayRead(xin, &xarray));
79: /* determine maximum message to arrive */
80: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)xin), &rank));
81: PetscCallMPI(MPI_Reduce(&work, &len, 1, MPIU_INT, MPI_MAX, 0, PetscObjectComm((PetscObject)xin)));
82: if (format == PETSC_VIEWER_ASCII_GLVIS) rank = 0, len = 0; /* no parallel distributed write support from GLVis */
83: if (rank == 0) {
84: PetscCall(PetscMalloc1(len, &values));
85: /*
86: MATLAB format and ASCII format are very similar except
87: MATLAB uses %18.16e format while ASCII uses %g
88: */
89: if (format == PETSC_VIEWER_ASCII_MATLAB) {
90: PetscCall(PetscObjectGetName((PetscObject)xin, &name));
91: PetscCall(PetscViewerASCIIPrintf(viewer, "%s = [\n", name));
92: for (i = 0; i < xin->map->n; i++) {
93: #if defined(PETSC_USE_COMPLEX)
94: if (PetscImaginaryPart(xarray[i]) > 0.0) {
95: PetscCall(PetscViewerASCIIPrintf(viewer, "%18.16e + %18.16ei\n", (double)PetscRealPart(xarray[i]), (double)PetscImaginaryPart(xarray[i])));
96: } else if (PetscImaginaryPart(xarray[i]) < 0.0) {
97: PetscCall(PetscViewerASCIIPrintf(viewer, "%18.16e - %18.16ei\n", (double)PetscRealPart(xarray[i]), -(double)PetscImaginaryPart(xarray[i])));
98: } else {
99: PetscCall(PetscViewerASCIIPrintf(viewer, "%18.16e\n", (double)PetscRealPart(xarray[i])));
100: }
101: #else
102: PetscCall(PetscViewerASCIIPrintf(viewer, "%18.16e\n", (double)xarray[i]));
103: #endif
104: }
105: /* receive and print messages */
106: for (j = 1; j < size; j++) {
107: PetscCallMPI(MPI_Recv(values, (PetscMPIInt)len, MPIU_SCALAR, j, tag, PetscObjectComm((PetscObject)xin), &status));
108: PetscCallMPI(MPI_Get_count(&status, MPIU_SCALAR, &n));
109: for (i = 0; i < n; i++) {
110: #if defined(PETSC_USE_COMPLEX)
111: if (PetscImaginaryPart(values[i]) > 0.0) {
112: PetscCall(PetscViewerASCIIPrintf(viewer, "%18.16e + %18.16ei\n", (double)PetscRealPart(values[i]), (double)PetscImaginaryPart(values[i])));
113: } else if (PetscImaginaryPart(values[i]) < 0.0) {
114: PetscCall(PetscViewerASCIIPrintf(viewer, "%18.16e - %18.16ei\n", (double)PetscRealPart(values[i]), -(double)PetscImaginaryPart(values[i])));
115: } else {
116: PetscCall(PetscViewerASCIIPrintf(viewer, "%18.16e\n", (double)PetscRealPart(values[i])));
117: }
118: #else
119: PetscCall(PetscViewerASCIIPrintf(viewer, "%18.16e\n", (double)values[i]));
120: #endif
121: }
122: }
123: PetscCall(PetscViewerASCIIPrintf(viewer, "];\n"));
125: } else if (format == PETSC_VIEWER_ASCII_SYMMODU) {
126: for (i = 0; i < xin->map->n; i++) {
127: #if defined(PETSC_USE_COMPLEX)
128: PetscCall(PetscViewerASCIIPrintf(viewer, "%18.16e %18.16e\n", (double)PetscRealPart(xarray[i]), (double)PetscImaginaryPart(xarray[i])));
129: #else
130: PetscCall(PetscViewerASCIIPrintf(viewer, "%18.16e\n", (double)xarray[i]));
131: #endif
132: }
133: /* receive and print messages */
134: for (j = 1; j < size; j++) {
135: PetscCallMPI(MPI_Recv(values, (PetscMPIInt)len, MPIU_SCALAR, j, tag, PetscObjectComm((PetscObject)xin), &status));
136: PetscCallMPI(MPI_Get_count(&status, MPIU_SCALAR, &n));
137: for (i = 0; i < n; i++) {
138: #if defined(PETSC_USE_COMPLEX)
139: PetscCall(PetscViewerASCIIPrintf(viewer, "%18.16e %18.16e\n", (double)PetscRealPart(values[i]), (double)PetscImaginaryPart(values[i])));
140: #else
141: PetscCall(PetscViewerASCIIPrintf(viewer, "%18.16e\n", (double)values[i]));
142: #endif
143: }
144: }
145: } else if (format == PETSC_VIEWER_ASCII_VTK_DEPRECATED || format == PETSC_VIEWER_ASCII_VTK_CELL_DEPRECATED) {
146: /*
147: state 0: No header has been output
148: state 1: Only POINT_DATA has been output
149: state 2: Only CELL_DATA has been output
150: state 3: Output both, POINT_DATA last
151: state 4: Output both, CELL_DATA last
152: */
153: static PetscInt stateId = -1;
154: PetscInt outputState = 0;
155: int doOutput = 0;
156: PetscBool hasState;
157: PetscInt bs, b;
159: if (stateId < 0) PetscCall(PetscObjectComposedDataRegister(&stateId));
160: PetscCall(PetscObjectComposedDataGetInt((PetscObject)viewer, stateId, outputState, hasState));
161: if (!hasState) outputState = 0;
163: PetscCall(PetscObjectGetName((PetscObject)xin, &name));
164: PetscCall(VecGetLocalSize(xin, &nLen));
165: PetscCall(PetscMPIIntCast(nLen, &n));
166: PetscCall(VecGetBlockSize(xin, &bs));
167: if (format == PETSC_VIEWER_ASCII_VTK_DEPRECATED) {
168: if (outputState == 0) {
169: outputState = 1;
170: doOutput = 1;
171: } else if (outputState == 1) doOutput = 0;
172: else if (outputState == 2) {
173: outputState = 3;
174: doOutput = 1;
175: } else if (outputState == 3) doOutput = 0;
176: else PetscCheck(outputState != 4, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Tried to output POINT_DATA again after intervening CELL_DATA");
178: if (doOutput) PetscCall(PetscViewerASCIIPrintf(viewer, "POINT_DATA %" PetscInt_FMT "\n", xin->map->N / bs));
179: } else {
180: if (outputState == 0) {
181: outputState = 2;
182: doOutput = 1;
183: } else if (outputState == 1) {
184: outputState = 4;
185: doOutput = 1;
186: } else if (outputState == 2) {
187: doOutput = 0;
188: } else {
189: PetscCheck(outputState != 3, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Tried to output CELL_DATA again after intervening POINT_DATA");
190: if (outputState == 4) doOutput = 0;
191: }
193: if (doOutput) PetscCall(PetscViewerASCIIPrintf(viewer, "CELL_DATA %" PetscInt_FMT "\n", xin->map->N / bs));
194: }
195: PetscCall(PetscObjectComposedDataSetInt((PetscObject)viewer, stateId, outputState));
196: if (name) {
197: if (bs == 3) {
198: PetscCall(PetscViewerASCIIPrintf(viewer, "VECTORS %s double\n", name));
199: } else {
200: PetscCall(PetscViewerASCIIPrintf(viewer, "SCALARS %s double %" PetscInt_FMT "\n", name, bs));
201: }
202: } else {
203: PetscCall(PetscViewerASCIIPrintf(viewer, "SCALARS scalars double %" PetscInt_FMT "\n", bs));
204: }
205: if (bs != 3) PetscCall(PetscViewerASCIIPrintf(viewer, "LOOKUP_TABLE default\n"));
206: for (i = 0; i < n / bs; i++) {
207: for (b = 0; b < bs; b++) {
208: if (b > 0) PetscCall(PetscViewerASCIIPrintf(viewer, " "));
209: PetscCall(PetscViewerASCIIPrintf(viewer, "%g", (double)PetscRealPart(xarray[i * bs + b])));
210: }
211: PetscCall(PetscViewerASCIIPrintf(viewer, "\n"));
212: }
213: for (j = 1; j < size; j++) {
214: PetscCallMPI(MPI_Recv(values, (PetscMPIInt)len, MPIU_SCALAR, j, tag, PetscObjectComm((PetscObject)xin), &status));
215: PetscCallMPI(MPI_Get_count(&status, MPIU_SCALAR, &n));
216: for (i = 0; i < n / bs; i++) {
217: for (b = 0; b < bs; b++) {
218: if (b > 0) PetscCall(PetscViewerASCIIPrintf(viewer, " "));
219: PetscCall(PetscViewerASCIIPrintf(viewer, "%g", (double)PetscRealPart(values[i * bs + b])));
220: }
221: PetscCall(PetscViewerASCIIPrintf(viewer, "\n"));
222: }
223: }
224: } else if (format == PETSC_VIEWER_ASCII_VTK_COORDS_DEPRECATED) {
225: PetscInt bs, b;
227: PetscCall(VecGetLocalSize(xin, &nLen));
228: PetscCall(PetscMPIIntCast(nLen, &n));
229: PetscCall(VecGetBlockSize(xin, &bs));
230: PetscCheck(bs >= 1 && bs <= 3, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "VTK can only handle 3D objects, but vector dimension is %" PetscInt_FMT, bs);
232: for (i = 0; i < n / bs; i++) {
233: for (b = 0; b < bs; b++) {
234: if (b > 0) PetscCall(PetscViewerASCIIPrintf(viewer, " "));
235: PetscCall(PetscViewerASCIIPrintf(viewer, "%g", (double)PetscRealPart(xarray[i * bs + b])));
236: }
237: for (b = bs; b < 3; b++) PetscCall(PetscViewerASCIIPrintf(viewer, " 0.0"));
238: PetscCall(PetscViewerASCIIPrintf(viewer, "\n"));
239: }
240: for (j = 1; j < size; j++) {
241: PetscCallMPI(MPI_Recv(values, (PetscMPIInt)len, MPIU_SCALAR, j, tag, PetscObjectComm((PetscObject)xin), &status));
242: PetscCallMPI(MPI_Get_count(&status, MPIU_SCALAR, &n));
243: for (i = 0; i < n / bs; i++) {
244: for (b = 0; b < bs; b++) {
245: if (b > 0) PetscCall(PetscViewerASCIIPrintf(viewer, " "));
246: PetscCall(PetscViewerASCIIPrintf(viewer, "%g", (double)PetscRealPart(values[i * bs + b])));
247: }
248: for (b = bs; b < 3; b++) PetscCall(PetscViewerASCIIPrintf(viewer, " 0.0"));
249: PetscCall(PetscViewerASCIIPrintf(viewer, "\n"));
250: }
251: }
252: } else if (format == PETSC_VIEWER_ASCII_PCICE) {
253: PetscInt bs, b, vertexCount = 1;
255: PetscCall(VecGetLocalSize(xin, &nLen));
256: PetscCall(PetscMPIIntCast(nLen, &n));
257: PetscCall(VecGetBlockSize(xin, &bs));
258: PetscCheck(bs >= 1 && bs <= 3, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "PCICE can only handle up to 3D objects, but vector dimension is %" PetscInt_FMT, bs);
260: PetscCall(PetscViewerASCIIPrintf(viewer, "%" PetscInt_FMT "\n", xin->map->N / bs));
261: for (i = 0; i < n / bs; i++) {
262: PetscCall(PetscViewerASCIIPrintf(viewer, "%7" PetscInt_FMT " ", vertexCount++));
263: for (b = 0; b < bs; b++) {
264: if (b > 0) PetscCall(PetscViewerASCIIPrintf(viewer, " "));
265: #if !defined(PETSC_USE_COMPLEX)
266: PetscCall(PetscViewerASCIIPrintf(viewer, "% 12.5E", (double)xarray[i * bs + b]));
267: #endif
268: }
269: PetscCall(PetscViewerASCIIPrintf(viewer, "\n"));
270: }
271: for (j = 1; j < size; j++) {
272: PetscCallMPI(MPI_Recv(values, (PetscMPIInt)len, MPIU_SCALAR, j, tag, PetscObjectComm((PetscObject)xin), &status));
273: PetscCallMPI(MPI_Get_count(&status, MPIU_SCALAR, &n));
274: for (i = 0; i < n / bs; i++) {
275: PetscCall(PetscViewerASCIIPrintf(viewer, "%7" PetscInt_FMT " ", vertexCount++));
276: for (b = 0; b < bs; b++) {
277: if (b > 0) PetscCall(PetscViewerASCIIPrintf(viewer, " "));
278: #if !defined(PETSC_USE_COMPLEX)
279: PetscCall(PetscViewerASCIIPrintf(viewer, "% 12.5E", (double)values[i * bs + b]));
280: #endif
281: }
282: PetscCall(PetscViewerASCIIPrintf(viewer, "\n"));
283: }
284: }
285: } else if (format == PETSC_VIEWER_ASCII_GLVIS) {
286: /* GLVis ASCII visualization/dump: this function mimics mfem::GridFunction::Save() */
287: const PetscScalar *array;
288: PetscInt i, n, vdim, ordering = 1; /* mfem::FiniteElementSpace::Ordering::byVDIM */
289: PetscContainer glvis_container;
290: PetscViewerGLVisVecInfo glvis_vec_info;
291: PetscViewerGLVisInfo glvis_info;
293: /* mfem::FiniteElementSpace::Save() */
294: PetscCall(VecGetBlockSize(xin, &vdim));
295: PetscCall(PetscViewerASCIIPrintf(viewer, "FiniteElementSpace\n"));
296: PetscCall(PetscObjectQuery((PetscObject)xin, "_glvis_info_container", (PetscObject *)&glvis_container));
297: PetscCheck(glvis_container, PetscObjectComm((PetscObject)xin), PETSC_ERR_PLIB, "Missing GLVis container");
298: PetscCall(PetscContainerGetPointer(glvis_container, (void **)&glvis_vec_info));
299: PetscCall(PetscViewerASCIIPrintf(viewer, "%s\n", glvis_vec_info->fec_type));
300: PetscCall(PetscViewerASCIIPrintf(viewer, "VDim: %" PetscInt_FMT "\n", vdim));
301: PetscCall(PetscViewerASCIIPrintf(viewer, "Ordering: %" PetscInt_FMT "\n", ordering));
302: PetscCall(PetscViewerASCIIPrintf(viewer, "\n"));
303: /* mfem::Vector::Print() */
304: PetscCall(PetscObjectQuery((PetscObject)viewer, "_glvis_info_container", (PetscObject *)&glvis_container));
305: PetscCheck(glvis_container, PetscObjectComm((PetscObject)viewer), PETSC_ERR_PLIB, "Missing GLVis container");
306: PetscCall(PetscContainerGetPointer(glvis_container, (void **)&glvis_info));
307: if (glvis_info->enabled) {
308: PetscCall(VecGetLocalSize(xin, &n));
309: PetscCall(VecGetArrayRead(xin, &array));
310: for (i = 0; i < n; i++) {
311: PetscCall(PetscViewerASCIIPrintf(viewer, glvis_info->fmt, (double)PetscRealPart(array[i])));
312: PetscCall(PetscViewerASCIIPrintf(viewer, "\n"));
313: }
314: PetscCall(VecRestoreArrayRead(xin, &array));
315: }
316: } else if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) {
317: /* No info */
318: } else {
319: if (format != PETSC_VIEWER_ASCII_COMMON) PetscCall(PetscViewerASCIIPrintf(viewer, "Process [%d]\n", rank));
320: cnt = 0;
321: for (i = 0; i < xin->map->n; i++) {
322: if (format == PETSC_VIEWER_ASCII_INDEX) PetscCall(PetscViewerASCIIPrintf(viewer, "%" PetscInt_FMT ": ", cnt++));
323: #if defined(PETSC_USE_COMPLEX)
324: if (PetscImaginaryPart(xarray[i]) > 0.0) {
325: PetscCall(PetscViewerASCIIPrintf(viewer, "%g + %g i\n", (double)PetscRealPart(xarray[i]), (double)PetscImaginaryPart(xarray[i])));
326: } else if (PetscImaginaryPart(xarray[i]) < 0.0) {
327: PetscCall(PetscViewerASCIIPrintf(viewer, "%g - %g i\n", (double)PetscRealPart(xarray[i]), -(double)PetscImaginaryPart(xarray[i])));
328: } else {
329: PetscCall(PetscViewerASCIIPrintf(viewer, "%g\n", (double)PetscRealPart(xarray[i])));
330: }
331: #else
332: PetscCall(PetscViewerASCIIPrintf(viewer, "%g\n", (double)xarray[i]));
333: #endif
334: }
335: /* receive and print messages */
336: for (j = 1; j < size; j++) {
337: PetscCallMPI(MPI_Recv(values, (PetscMPIInt)len, MPIU_SCALAR, j, tag, PetscObjectComm((PetscObject)xin), &status));
338: PetscCallMPI(MPI_Get_count(&status, MPIU_SCALAR, &n));
339: if (format != PETSC_VIEWER_ASCII_COMMON) PetscCall(PetscViewerASCIIPrintf(viewer, "Process [%d]\n", j));
340: for (i = 0; i < n; i++) {
341: if (format == PETSC_VIEWER_ASCII_INDEX) PetscCall(PetscViewerASCIIPrintf(viewer, "%" PetscInt_FMT ": ", cnt++));
342: #if defined(PETSC_USE_COMPLEX)
343: if (PetscImaginaryPart(values[i]) > 0.0) {
344: PetscCall(PetscViewerASCIIPrintf(viewer, "%g + %g i\n", (double)PetscRealPart(values[i]), (double)PetscImaginaryPart(values[i])));
345: } else if (PetscImaginaryPart(values[i]) < 0.0) {
346: PetscCall(PetscViewerASCIIPrintf(viewer, "%g - %g i\n", (double)PetscRealPart(values[i]), -(double)PetscImaginaryPart(values[i])));
347: } else {
348: PetscCall(PetscViewerASCIIPrintf(viewer, "%g\n", (double)PetscRealPart(values[i])));
349: }
350: #else
351: PetscCall(PetscViewerASCIIPrintf(viewer, "%g\n", (double)values[i]));
352: #endif
353: }
354: }
355: }
356: PetscCall(PetscFree(values));
357: } else {
358: if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) {
359: /* Rank 0 is not trying to receive anything, so don't send anything */
360: } else {
361: if (format == PETSC_VIEWER_ASCII_MATLAB || format == PETSC_VIEWER_ASCII_VTK_DEPRECATED || format == PETSC_VIEWER_ASCII_VTK_CELL_DEPRECATED) {
362: /* this may be a collective operation so make sure everyone calls it */
363: PetscCall(PetscObjectGetName((PetscObject)xin, &name));
364: }
365: PetscCallMPI(MPIU_Send((void *)xarray, xin->map->n, MPIU_SCALAR, 0, tag, PetscObjectComm((PetscObject)xin)));
366: }
367: }
368: PetscCall(PetscViewerFlush(viewer));
369: PetscCall(VecRestoreArrayRead(xin, &xarray));
370: PetscFunctionReturn(PETSC_SUCCESS);
371: }
373: PetscErrorCode VecView_MPI_Binary(Vec xin, PetscViewer viewer)
374: {
375: return VecView_Binary(xin, viewer);
376: }
378: #include <petscdraw.h>
379: PetscErrorCode VecView_MPI_Draw_LG(Vec xin, PetscViewer viewer)
380: {
381: PetscDraw draw;
382: PetscBool isnull;
383: PetscDrawLG lg;
384: PetscMPIInt i, size, rank, n, N, *lens = NULL, *disp = NULL;
385: PetscReal *values, *xx = NULL, *yy = NULL;
386: const PetscScalar *xarray;
387: int colors[] = {PETSC_DRAW_RED};
389: PetscFunctionBegin;
390: PetscCall(PetscViewerDrawGetDraw(viewer, 0, &draw));
391: PetscCall(PetscDrawIsNull(draw, &isnull));
392: if (isnull) PetscFunctionReturn(PETSC_SUCCESS);
393: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)xin), &rank));
394: PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)xin), &size));
395: PetscCall(PetscMPIIntCast(xin->map->n, &n));
396: PetscCall(PetscMPIIntCast(xin->map->N, &N));
398: PetscCall(VecGetArrayRead(xin, &xarray));
399: #if defined(PETSC_USE_COMPLEX)
400: PetscCall(PetscMalloc1(n + 1, &values));
401: for (i = 0; i < n; i++) values[i] = PetscRealPart(xarray[i]);
402: #else
403: values = (PetscReal *)xarray;
404: #endif
405: if (rank == 0) {
406: PetscCall(PetscMalloc2(N, &xx, N, &yy));
407: for (i = 0; i < N; i++) xx[i] = (PetscReal)i;
408: PetscCall(PetscMalloc2(size, &lens, size, &disp));
409: for (i = 0; i < size; i++) lens[i] = (PetscMPIInt)xin->map->range[i + 1] - (PetscMPIInt)xin->map->range[i];
410: for (i = 0; i < size; i++) disp[i] = (PetscMPIInt)xin->map->range[i];
411: }
412: PetscCallMPI(MPI_Gatherv(values, n, MPIU_REAL, yy, lens, disp, MPIU_REAL, 0, PetscObjectComm((PetscObject)xin)));
413: PetscCall(PetscFree2(lens, disp));
414: #if defined(PETSC_USE_COMPLEX)
415: PetscCall(PetscFree(values));
416: #endif
417: PetscCall(VecRestoreArrayRead(xin, &xarray));
419: PetscCall(PetscViewerDrawGetDrawLG(viewer, 0, &lg));
420: PetscCall(PetscDrawLGReset(lg));
421: PetscCall(PetscDrawLGSetDimension(lg, 1));
422: PetscCall(PetscDrawLGSetColors(lg, colors));
423: if (rank == 0) {
424: PetscCall(PetscDrawLGAddPoints(lg, N, &xx, &yy));
425: PetscCall(PetscFree2(xx, yy));
426: }
427: PetscCall(PetscDrawLGDraw(lg));
428: PetscCall(PetscDrawLGSave(lg));
429: PetscFunctionReturn(PETSC_SUCCESS);
430: }
432: PETSC_INTERN PetscErrorCode VecView_MPI_Draw(Vec xin, PetscViewer viewer)
433: {
434: PetscMPIInt rank, size, tag = ((PetscObject)viewer)->tag;
435: PetscInt i, start, end;
436: MPI_Status status;
437: PetscReal min, max, tmp = 0.0;
438: PetscDraw draw;
439: PetscBool isnull;
440: PetscDrawAxis axis;
441: const PetscScalar *xarray;
443: PetscFunctionBegin;
444: PetscCall(PetscViewerDrawGetDraw(viewer, 0, &draw));
445: PetscCall(PetscDrawIsNull(draw, &isnull));
446: if (isnull) PetscFunctionReturn(PETSC_SUCCESS);
447: PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)xin), &size));
448: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)xin), &rank));
450: PetscCall(VecMin(xin, NULL, &min));
451: PetscCall(VecMax(xin, NULL, &max));
452: if (min == max) {
453: min -= 1.e-5;
454: max += 1.e-5;
455: }
457: PetscCall(PetscDrawCheckResizedWindow(draw));
458: PetscCall(PetscDrawClear(draw));
460: PetscCall(PetscDrawAxisCreate(draw, &axis));
461: PetscCall(PetscDrawAxisSetLimits(axis, 0.0, (PetscReal)xin->map->N, min, max));
462: PetscCall(PetscDrawAxisDraw(axis));
463: PetscCall(PetscDrawAxisDestroy(&axis));
465: /* draw local part of vector */
466: PetscCall(VecGetArrayRead(xin, &xarray));
467: PetscCall(VecGetOwnershipRange(xin, &start, &end));
468: if (rank < size - 1) { /* send value to right */
469: PetscCallMPI(MPI_Send((void *)&xarray[xin->map->n - 1], 1, MPIU_REAL, rank + 1, tag, PetscObjectComm((PetscObject)xin)));
470: }
471: if (rank) { /* receive value from right */
472: PetscCallMPI(MPI_Recv(&tmp, 1, MPIU_REAL, rank - 1, tag, PetscObjectComm((PetscObject)xin), &status));
473: }
474: PetscDrawCollectiveBegin(draw);
475: if (rank) PetscCall(PetscDrawLine(draw, (PetscReal)start - 1, tmp, (PetscReal)start, PetscRealPart(xarray[0]), PETSC_DRAW_RED));
476: for (i = 1; i < xin->map->n; i++) PetscCall(PetscDrawLine(draw, (PetscReal)(i - 1 + start), PetscRealPart(xarray[i - 1]), (PetscReal)(i + start), PetscRealPart(xarray[i]), PETSC_DRAW_RED));
477: PetscDrawCollectiveEnd(draw);
478: PetscCall(VecRestoreArrayRead(xin, &xarray));
480: PetscCall(PetscDrawFlush(draw));
481: PetscCall(PetscDrawPause(draw));
482: PetscCall(PetscDrawSave(draw));
483: PetscFunctionReturn(PETSC_SUCCESS);
484: }
486: #if defined(PETSC_HAVE_MATLAB)
487: PetscErrorCode VecView_MPI_Matlab(Vec xin, PetscViewer viewer)
488: {
489: PetscMPIInt rank, size, *lens;
490: PetscInt i, N = xin->map->N;
491: const PetscScalar *xarray;
492: PetscScalar *xx;
494: PetscFunctionBegin;
495: PetscCall(VecGetArrayRead(xin, &xarray));
496: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)xin), &rank));
497: PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)xin), &size));
498: if (rank == 0) {
499: PetscCall(PetscMalloc1(N, &xx));
500: PetscCall(PetscMalloc1(size, &lens));
501: for (i = 0; i < size; i++) lens[i] = xin->map->range[i + 1] - xin->map->range[i];
503: PetscCallMPI(MPI_Gatherv((void *)xarray, xin->map->n, MPIU_SCALAR, xx, lens, xin->map->range, MPIU_SCALAR, 0, PetscObjectComm((PetscObject)xin)));
504: PetscCall(PetscFree(lens));
506: PetscCall(PetscObjectName((PetscObject)xin));
507: PetscCall(PetscViewerMatlabPutArray(viewer, N, 1, xx, ((PetscObject)xin)->name));
509: PetscCall(PetscFree(xx));
510: } else {
511: PetscCallMPI(MPI_Gatherv((void *)xarray, xin->map->n, MPIU_SCALAR, 0, 0, 0, MPIU_SCALAR, 0, PetscObjectComm((PetscObject)xin)));
512: }
513: PetscCall(VecRestoreArrayRead(xin, &xarray));
514: PetscFunctionReturn(PETSC_SUCCESS);
515: }
516: #endif
518: #if defined(PETSC_HAVE_ADIOS)
519: #include <adios.h>
520: #include <adios_read.h>
521: #include <petsc/private/vieweradiosimpl.h>
522: #include <petsc/private/viewerimpl.h>
524: PetscErrorCode VecView_MPI_ADIOS(Vec xin, PetscViewer viewer)
525: {
526: PetscViewer_ADIOS *adios = (PetscViewer_ADIOS *)viewer->data;
527: const char *vecname;
528: int64_t id;
529: PetscInt n, N, rstart;
530: const PetscScalar *array;
531: char nglobalname[16], nlocalname[16], coffset[16];
533: PetscFunctionBegin;
534: PetscCall(PetscObjectGetName((PetscObject)xin, &vecname));
536: PetscCall(VecGetLocalSize(xin, &n));
537: PetscCall(VecGetSize(xin, &N));
538: PetscCall(VecGetOwnershipRange(xin, &rstart, NULL));
540: PetscCall(PetscSNPrintf(nlocalname, PETSC_STATIC_ARRAY_LENGTH(nlocalname), "%" PetscInt_FMT, n));
541: PetscCall(PetscSNPrintf(nglobalname, PETSC_STATIC_ARRAY_LENGTH(nglobalname), "%" PetscInt_FMT, N));
542: PetscCall(PetscSNPrintf(coffset, PETSC_STATIC_ARRAY_LENGTH(coffset), "%" PetscInt_FMT, rstart));
543: id = adios_define_var(Petsc_adios_group, vecname, "", adios_double, nlocalname, nglobalname, coffset);
544: PetscCall(VecGetArrayRead(xin, &array));
545: PetscCallExternal(adios_write_byid, adios->adios_handle, id, array);
546: PetscCall(VecRestoreArrayRead(xin, &array));
547: PetscFunctionReturn(PETSC_SUCCESS);
548: }
549: #endif
551: #if defined(PETSC_HAVE_HDF5)
552: PetscErrorCode VecView_MPI_HDF5(Vec xin, PetscViewer viewer)
553: {
554: PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
555: /* TODO: It looks like we can remove the H5Sclose(filespace) and H5Dget_space(dset_id). Why do we do this? */
556: hid_t filespace; /* file dataspace identifier */
557: hid_t chunkspace; /* chunk dataset property identifier */
558: hid_t dset_id; /* dataset identifier */
559: hid_t memspace; /* memory dataspace identifier */
560: hid_t file_id;
561: hid_t group;
562: hid_t memscalartype; /* scalar type for mem (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */
563: hid_t filescalartype; /* scalar type for file (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */
564: PetscInt bs = PetscAbs(xin->map->bs);
565: hsize_t dim;
566: hsize_t maxDims[4], dims[4], chunkDims[4], count[4], offset[4];
567: PetscBool timestepping, dim2, spoutput;
568: PetscInt timestep = PETSC_INT_MIN, low;
569: hsize_t chunksize;
570: const PetscScalar *x;
571: const char *vecname;
572: size_t len;
574: PetscFunctionBegin;
575: PetscCall(PetscViewerHDF5OpenGroup(viewer, NULL, &file_id, &group));
576: PetscCall(PetscViewerHDF5IsTimestepping(viewer, ×tepping));
577: if (timestepping) PetscCall(PetscViewerHDF5GetTimestep(viewer, ×tep));
578: PetscCall(PetscViewerHDF5GetBaseDimension2(viewer, &dim2));
579: PetscCall(PetscViewerHDF5GetSPOutput(viewer, &spoutput));
581: /* Create the dataspace for the dataset.
582: *
583: * dims - holds the current dimensions of the dataset
584: *
585: * maxDims - holds the maximum dimensions of the dataset (unlimited
586: * for the number of time steps with the current dimensions for the
587: * other dimensions; so only additional time steps can be added).
588: *
589: * chunkDims - holds the size of a single time step (required to
590: * permit extending dataset).
591: */
592: dim = 0;
593: chunksize = 1;
594: if (timestep >= 0) {
595: dims[dim] = timestep + 1;
596: maxDims[dim] = H5S_UNLIMITED;
597: chunkDims[dim] = 1;
598: ++dim;
599: }
600: PetscCall(PetscHDF5IntCast(xin->map->N / bs, dims + dim));
602: maxDims[dim] = dims[dim];
603: chunkDims[dim] = PetscMax(1, dims[dim]);
604: chunksize *= chunkDims[dim];
605: ++dim;
606: if (bs > 1 || dim2) {
607: dims[dim] = bs;
608: maxDims[dim] = dims[dim];
609: chunkDims[dim] = PetscMax(1, dims[dim]);
610: chunksize *= chunkDims[dim];
611: ++dim;
612: }
613: #if defined(PETSC_USE_COMPLEX)
614: dims[dim] = 2;
615: maxDims[dim] = dims[dim];
616: chunkDims[dim] = PetscMax(1, dims[dim]);
617: chunksize *= chunkDims[dim];
618: /* hdf5 chunks must be less than 4GB */
619: if (chunksize > PETSC_HDF5_MAX_CHUNKSIZE / 64) {
620: if (bs > 1 || dim2) {
621: if (chunkDims[dim - 2] > (hsize_t)PetscSqrtReal((PetscReal)(PETSC_HDF5_MAX_CHUNKSIZE / 128))) chunkDims[dim - 2] = (hsize_t)PetscSqrtReal((PetscReal)(PETSC_HDF5_MAX_CHUNKSIZE / 128));
622: if (chunkDims[dim - 1] > (hsize_t)PetscSqrtReal((PetscReal)(PETSC_HDF5_MAX_CHUNKSIZE / 128))) chunkDims[dim - 1] = (hsize_t)PetscSqrtReal((PetscReal)(PETSC_HDF5_MAX_CHUNKSIZE / 128));
623: } else {
624: chunkDims[dim - 1] = PETSC_HDF5_MAX_CHUNKSIZE / 128;
625: }
626: }
627: ++dim;
628: #else
629: /* hdf5 chunks must be less than 4GB */
630: if (chunksize > PETSC_HDF5_MAX_CHUNKSIZE / 64) {
631: if (bs > 1 || dim2) {
632: if (chunkDims[dim - 2] > (hsize_t)PetscSqrtReal((PetscReal)(PETSC_HDF5_MAX_CHUNKSIZE / 64))) chunkDims[dim - 2] = (hsize_t)PetscSqrtReal((PetscReal)(PETSC_HDF5_MAX_CHUNKSIZE / 64));
633: if (chunkDims[dim - 1] > (hsize_t)PetscSqrtReal((PetscReal)(PETSC_HDF5_MAX_CHUNKSIZE / 64))) chunkDims[dim - 1] = (hsize_t)PetscSqrtReal((PetscReal)(PETSC_HDF5_MAX_CHUNKSIZE / 64));
634: } else {
635: chunkDims[dim - 1] = PETSC_HDF5_MAX_CHUNKSIZE / 64;
636: }
637: }
638: #endif
640: PetscCallHDF5Return(filespace, H5Screate_simple, ((int)dim, dims, maxDims));
642: #if defined(PETSC_USE_REAL_SINGLE)
643: memscalartype = H5T_NATIVE_FLOAT;
644: filescalartype = H5T_NATIVE_FLOAT;
645: #elif defined(PETSC_USE_REAL___FLOAT128)
646: #error "HDF5 output with 128 bit floats not supported."
647: #elif defined(PETSC_USE_REAL___FP16)
648: #error "HDF5 output with 16 bit floats not supported."
649: #else
650: memscalartype = H5T_NATIVE_DOUBLE;
651: if (spoutput == PETSC_TRUE) filescalartype = H5T_NATIVE_FLOAT;
652: else filescalartype = H5T_NATIVE_DOUBLE;
653: #endif
655: /* Create the dataset with default properties and close filespace */
656: PetscCall(PetscObjectGetName((PetscObject)xin, &vecname));
657: PetscCall(PetscStrlen(vecname, &len));
658: PetscCheck(len, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONG, "Object must be named");
659: if (H5Lexists(group, vecname, H5P_DEFAULT) < 1) {
660: /* Create chunk */
661: PetscCallHDF5Return(chunkspace, H5Pcreate, (H5P_DATASET_CREATE));
662: PetscCallHDF5(H5Pset_chunk, (chunkspace, (int)dim, chunkDims));
664: PetscCallHDF5Return(dset_id, H5Dcreate2, (group, vecname, filescalartype, filespace, H5P_DEFAULT, chunkspace, H5P_DEFAULT));
665: PetscCallHDF5(H5Pclose, (chunkspace));
666: } else {
667: PetscCallHDF5Return(dset_id, H5Dopen2, (group, vecname, H5P_DEFAULT));
668: PetscCallHDF5(H5Dset_extent, (dset_id, dims));
669: }
670: PetscCallHDF5(H5Sclose, (filespace));
672: /* Each process defines a dataset and writes it to the hyperslab in the file */
673: dim = 0;
674: if (timestep >= 0) {
675: count[dim] = 1;
676: ++dim;
677: }
678: PetscCall(PetscHDF5IntCast(xin->map->n / bs, count + dim));
679: ++dim;
680: if (bs > 1 || dim2) {
681: count[dim] = bs;
682: ++dim;
683: }
684: #if defined(PETSC_USE_COMPLEX)
685: count[dim] = 2;
686: ++dim;
687: #endif
688: if (xin->map->n > 0 || H5_VERSION_GE(1, 10, 0)) {
689: PetscCallHDF5Return(memspace, H5Screate_simple, ((int)dim, count, NULL));
690: } else {
691: /* Can't create dataspace with zero for any dimension, so create null dataspace. */
692: PetscCallHDF5Return(memspace, H5Screate, (H5S_NULL));
693: }
695: /* Select hyperslab in the file */
696: PetscCall(VecGetOwnershipRange(xin, &low, NULL));
697: dim = 0;
698: if (timestep >= 0) {
699: offset[dim] = timestep;
700: ++dim;
701: }
702: PetscCall(PetscHDF5IntCast(low / bs, offset + dim));
703: ++dim;
704: if (bs > 1 || dim2) {
705: offset[dim] = 0;
706: ++dim;
707: }
708: #if defined(PETSC_USE_COMPLEX)
709: offset[dim] = 0;
710: ++dim;
711: #endif
712: if (xin->map->n > 0 || H5_VERSION_GE(1, 10, 0)) {
713: PetscCallHDF5Return(filespace, H5Dget_space, (dset_id));
714: PetscCallHDF5(H5Sselect_hyperslab, (filespace, H5S_SELECT_SET, offset, NULL, count, NULL));
715: } else {
716: /* Create null filespace to match null memspace. */
717: PetscCallHDF5Return(filespace, H5Screate, (H5S_NULL));
718: }
720: PetscCall(VecGetArrayRead(xin, &x));
721: PetscCallHDF5(H5Dwrite, (dset_id, memscalartype, memspace, filespace, hdf5->dxpl_id, x));
722: PetscCallHDF5(H5Fflush, (file_id, H5F_SCOPE_GLOBAL));
723: PetscCall(VecRestoreArrayRead(xin, &x));
725: /* Close/release resources */
726: PetscCallHDF5(H5Gclose, (group));
727: PetscCallHDF5(H5Sclose, (filespace));
728: PetscCallHDF5(H5Sclose, (memspace));
729: PetscCallHDF5(H5Dclose, (dset_id));
731: #if defined(PETSC_USE_COMPLEX)
732: {
733: PetscBool tru = PETSC_TRUE;
734: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)xin, "complex", PETSC_BOOL, &tru));
735: }
736: #endif
737: if (timestepping) PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)xin, "timestepping", PETSC_BOOL, ×tepping));
738: PetscCall(PetscInfo(xin, "Wrote Vec object with name %s\n", vecname));
739: PetscFunctionReturn(PETSC_SUCCESS);
740: }
741: #endif
743: PETSC_EXTERN PetscErrorCode VecView_MPI(Vec xin, PetscViewer viewer)
744: {
745: PetscBool iascii, isbinary, isdraw;
746: #if defined(PETSC_HAVE_MATHEMATICA)
747: PetscBool ismathematica;
748: #endif
749: #if defined(PETSC_HAVE_HDF5)
750: PetscBool ishdf5;
751: #endif
752: #if defined(PETSC_HAVE_MATLAB)
753: PetscBool ismatlab;
754: #endif
755: #if defined(PETSC_HAVE_ADIOS)
756: PetscBool isadios;
757: #endif
758: PetscBool isglvis;
760: PetscFunctionBegin;
761: PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERASCII, &iascii));
762: PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERBINARY, &isbinary));
763: PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERDRAW, &isdraw));
764: #if defined(PETSC_HAVE_MATHEMATICA)
765: PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERMATHEMATICA, &ismathematica));
766: #endif
767: #if defined(PETSC_HAVE_HDF5)
768: PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5));
769: #endif
770: #if defined(PETSC_HAVE_MATLAB)
771: PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERMATLAB, &ismatlab));
772: #endif
773: PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERGLVIS, &isglvis));
774: #if defined(PETSC_HAVE_ADIOS)
775: PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERADIOS, &isadios));
776: #endif
777: if (iascii) {
778: PetscCall(VecView_MPI_ASCII(xin, viewer));
779: } else if (isbinary) {
780: PetscCall(VecView_MPI_Binary(xin, viewer));
781: } else if (isdraw) {
782: PetscViewerFormat format;
783: PetscCall(PetscViewerGetFormat(viewer, &format));
784: if (format == PETSC_VIEWER_DRAW_LG) {
785: PetscCall(VecView_MPI_Draw_LG(xin, viewer));
786: } else {
787: PetscCall(VecView_MPI_Draw(xin, viewer));
788: }
789: #if defined(PETSC_HAVE_MATHEMATICA)
790: } else if (ismathematica) {
791: PetscCall(PetscViewerMathematicaPutVector(viewer, xin));
792: #endif
793: #if defined(PETSC_HAVE_HDF5)
794: } else if (ishdf5) {
795: PetscCall(VecView_MPI_HDF5(xin, viewer));
796: #endif
797: #if defined(PETSC_HAVE_ADIOS)
798: } else if (isadios) {
799: PetscCall(VecView_MPI_ADIOS(xin, viewer));
800: #endif
801: #if defined(PETSC_HAVE_MATLAB)
802: } else if (ismatlab) {
803: PetscCall(VecView_MPI_Matlab(xin, viewer));
804: #endif
805: } else if (isglvis) PetscCall(VecView_GLVis(xin, viewer));
806: PetscFunctionReturn(PETSC_SUCCESS);
807: }
809: PetscErrorCode VecGetSize_MPI(Vec xin, PetscInt *N)
810: {
811: PetscFunctionBegin;
812: *N = xin->map->N;
813: PetscFunctionReturn(PETSC_SUCCESS);
814: }
816: PetscErrorCode VecGetValues_MPI(Vec xin, PetscInt ni, const PetscInt ix[], PetscScalar y[])
817: {
818: const PetscScalar *xx;
819: const PetscInt start = xin->map->range[xin->stash.rank];
821: PetscFunctionBegin;
822: PetscCall(VecGetArrayRead(xin, &xx));
823: for (PetscInt i = 0; i < ni; i++) {
824: if (xin->stash.ignorenegidx && ix[i] < 0) continue;
825: const PetscInt tmp = ix[i] - start;
827: PetscCheck(tmp >= 0 && tmp < xin->map->n, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Can only get local values, trying %" PetscInt_FMT, ix[i]);
828: y[i] = xx[tmp];
829: }
830: PetscCall(VecRestoreArrayRead(xin, &xx));
831: PetscFunctionReturn(PETSC_SUCCESS);
832: }
834: PetscErrorCode VecSetValues_MPI(Vec xin, PetscInt ni, const PetscInt ix[], const PetscScalar y[], InsertMode addv)
835: {
836: const PetscBool ignorenegidx = xin->stash.ignorenegidx;
837: const PetscBool donotstash = xin->stash.donotstash;
838: const PetscMPIInt rank = xin->stash.rank;
839: const PetscInt *owners = xin->map->range;
840: const PetscInt start = owners[rank], end = owners[rank + 1];
841: PetscScalar *xx;
843: PetscFunctionBegin;
844: if (PetscDefined(USE_DEBUG)) {
845: PetscCheck(xin->stash.insertmode != INSERT_VALUES || addv != ADD_VALUES, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "You have already inserted values; you cannot now add");
846: PetscCheck(xin->stash.insertmode != ADD_VALUES || addv != INSERT_VALUES, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "You have already added values; you cannot now insert");
847: }
848: PetscCall(VecGetArray(xin, &xx));
849: xin->stash.insertmode = addv;
850: for (PetscInt i = 0; i < ni; ++i) {
851: PetscInt row;
853: if (ignorenegidx && ix[i] < 0) continue;
854: PetscCheck(ix[i] >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Out of range index value %" PetscInt_FMT " cannot be negative", ix[i]);
855: if ((row = ix[i]) >= start && row < end) {
856: if (addv == INSERT_VALUES) {
857: xx[row - start] = y[i];
858: } else {
859: xx[row - start] += y[i];
860: }
861: } else if (!donotstash) {
862: PetscCheck(ix[i] < xin->map->N, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Out of range index value %" PetscInt_FMT ", should be less than %" PetscInt_FMT, ix[i], xin->map->N);
863: PetscCall(VecStashValue_Private(&xin->stash, row, y[i]));
864: }
865: }
866: PetscCall(VecRestoreArray(xin, &xx));
867: PetscFunctionReturn(PETSC_SUCCESS);
868: }
870: PetscErrorCode VecSetValuesBlocked_MPI(Vec xin, PetscInt ni, const PetscInt ix[], const PetscScalar yin[], InsertMode addv)
871: {
872: PetscMPIInt rank = xin->stash.rank;
873: PetscInt *owners = xin->map->range, start = owners[rank];
874: PetscInt end = owners[rank + 1], i, row, bs = PetscAbs(xin->map->bs), j;
875: PetscScalar *xx, *y = (PetscScalar *)yin;
877: PetscFunctionBegin;
878: PetscCall(VecGetArray(xin, &xx));
879: if (PetscDefined(USE_DEBUG)) {
880: PetscCheck(xin->stash.insertmode != INSERT_VALUES || addv != ADD_VALUES, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "You have already inserted values; you cannot now add");
881: PetscCheck(xin->stash.insertmode != ADD_VALUES || addv != INSERT_VALUES, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "You have already added values; you cannot now insert");
882: }
883: xin->stash.insertmode = addv;
885: if (addv == INSERT_VALUES) {
886: for (i = 0; i < ni; i++) {
887: if ((row = bs * ix[i]) >= start && row < end) {
888: for (j = 0; j < bs; j++) xx[row - start + j] = y[j];
889: } else if (!xin->stash.donotstash) {
890: if (ix[i] < 0) {
891: y += bs;
892: continue;
893: }
894: PetscCheck(ix[i] < xin->map->N, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Out of range index value %" PetscInt_FMT ", should be less than %" PetscInt_FMT, ix[i], xin->map->N);
895: PetscCall(VecStashValuesBlocked_Private(&xin->bstash, ix[i], y));
896: }
897: y += bs;
898: }
899: } else {
900: for (i = 0; i < ni; i++) {
901: if ((row = bs * ix[i]) >= start && row < end) {
902: for (j = 0; j < bs; j++) xx[row - start + j] += y[j];
903: } else if (!xin->stash.donotstash) {
904: if (ix[i] < 0) {
905: y += bs;
906: continue;
907: }
908: PetscCheck(ix[i] <= xin->map->N, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Out of range index value %" PetscInt_FMT ", should be less than %" PetscInt_FMT, ix[i], xin->map->N);
909: PetscCall(VecStashValuesBlocked_Private(&xin->bstash, ix[i], y));
910: }
911: y += bs;
912: }
913: }
914: PetscCall(VecRestoreArray(xin, &xx));
915: PetscFunctionReturn(PETSC_SUCCESS);
916: }
918: /*
919: Since nsends or nreceives may be zero we add 1 in certain mallocs
920: to make sure we never malloc an empty one.
921: */
922: PetscErrorCode VecAssemblyBegin_MPI(Vec xin)
923: {
924: PetscInt *owners = xin->map->range, *bowners, i, bs, nstash, reallocs;
925: PetscMPIInt size;
926: InsertMode addv;
927: MPI_Comm comm;
929: PetscFunctionBegin;
930: PetscCall(PetscObjectGetComm((PetscObject)xin, &comm));
931: if (xin->stash.donotstash) PetscFunctionReturn(PETSC_SUCCESS);
933: PetscCallMPI(MPIU_Allreduce((PetscEnum *)&xin->stash.insertmode, (PetscEnum *)&addv, 1, MPIU_ENUM, MPI_BOR, comm));
934: PetscCheck(addv != (ADD_VALUES | INSERT_VALUES), comm, PETSC_ERR_ARG_NOTSAMETYPE, "Some processors inserted values while others added");
935: xin->stash.insertmode = addv; /* in case this processor had no cache */
936: xin->bstash.insertmode = addv; /* Block stash implicitly tracks InsertMode of scalar stash */
938: PetscCall(VecGetBlockSize(xin, &bs));
939: PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)xin), &size));
940: if (!xin->bstash.bowners && xin->map->bs != -1) {
941: PetscCall(PetscMalloc1(size + 1, &bowners));
942: for (i = 0; i < size + 1; i++) bowners[i] = owners[i] / bs;
943: xin->bstash.bowners = bowners;
944: } else bowners = xin->bstash.bowners;
946: PetscCall(VecStashScatterBegin_Private(&xin->stash, owners));
947: PetscCall(VecStashScatterBegin_Private(&xin->bstash, bowners));
948: PetscCall(VecStashGetInfo_Private(&xin->stash, &nstash, &reallocs));
949: PetscCall(PetscInfo(xin, "Stash has %" PetscInt_FMT " entries, uses %" PetscInt_FMT " mallocs.\n", nstash, reallocs));
950: PetscCall(VecStashGetInfo_Private(&xin->bstash, &nstash, &reallocs));
951: PetscCall(PetscInfo(xin, "Block-Stash has %" PetscInt_FMT " entries, uses %" PetscInt_FMT " mallocs.\n", nstash, reallocs));
952: PetscFunctionReturn(PETSC_SUCCESS);
953: }
955: PetscErrorCode VecAssemblyEnd_MPI(Vec vec)
956: {
957: PetscInt base, i, j, *row, flg, bs;
958: PetscMPIInt n;
959: PetscScalar *val, *vv, *array, *xarray;
961: PetscFunctionBegin;
962: if (!vec->stash.donotstash) {
963: PetscCall(VecGetArray(vec, &xarray));
964: PetscCall(VecGetBlockSize(vec, &bs));
965: base = vec->map->range[vec->stash.rank];
967: /* Process the stash */
968: while (1) {
969: PetscCall(VecStashScatterGetMesg_Private(&vec->stash, &n, &row, &val, &flg));
970: if (!flg) break;
971: if (vec->stash.insertmode == ADD_VALUES) {
972: for (i = 0; i < n; i++) xarray[row[i] - base] += val[i];
973: } else if (vec->stash.insertmode == INSERT_VALUES) {
974: for (i = 0; i < n; i++) xarray[row[i] - base] = val[i];
975: } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_CORRUPT, "Insert mode is not set correctly; corrupted vector");
976: }
977: PetscCall(VecStashScatterEnd_Private(&vec->stash));
979: /* now process the block-stash */
980: while (1) {
981: PetscCall(VecStashScatterGetMesg_Private(&vec->bstash, &n, &row, &val, &flg));
982: if (!flg) break;
983: for (i = 0; i < n; i++) {
984: array = xarray + row[i] * bs - base;
985: vv = val + i * bs;
986: if (vec->stash.insertmode == ADD_VALUES) {
987: for (j = 0; j < bs; j++) array[j] += vv[j];
988: } else if (vec->stash.insertmode == INSERT_VALUES) {
989: for (j = 0; j < bs; j++) array[j] = vv[j];
990: } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_CORRUPT, "Insert mode is not set correctly; corrupted vector");
991: }
992: }
993: PetscCall(VecStashScatterEnd_Private(&vec->bstash));
994: PetscCall(VecRestoreArray(vec, &xarray));
995: }
996: vec->stash.insertmode = NOT_SET_VALUES;
997: PetscFunctionReturn(PETSC_SUCCESS);
998: }
1000: PetscErrorCode VecSetPreallocationCOO_MPI(Vec x, PetscCount coo_n, const PetscInt coo_i[])
1001: {
1002: PetscInt m, M, rstart, rend;
1003: Vec_MPI *vmpi = (Vec_MPI *)x->data;
1004: PetscCount k, p, q, rem; /* Loop variables over coo arrays */
1005: PetscMPIInt size;
1006: MPI_Comm comm;
1008: PetscFunctionBegin;
1009: PetscCall(PetscObjectGetComm((PetscObject)x, &comm));
1010: PetscCallMPI(MPI_Comm_size(comm, &size));
1011: PetscCall(VecResetPreallocationCOO_MPI(x));
1013: PetscCall(PetscLayoutSetUp(x->map));
1014: PetscCall(VecGetOwnershipRange(x, &rstart, &rend));
1015: PetscCall(VecGetLocalSize(x, &m));
1016: PetscCall(VecGetSize(x, &M));
1018: /* ---------------------------------------------------------------------------*/
1019: /* Sort COOs along with a permutation array, so that negative indices come */
1020: /* first, then local ones, then remote ones. */
1021: /* ---------------------------------------------------------------------------*/
1022: PetscCount n1 = coo_n, nneg, *perm;
1023: PetscInt *i1; /* Copy of input COOs along with a permutation array */
1024: PetscCall(PetscMalloc1(n1, &i1));
1025: PetscCall(PetscMalloc1(n1, &perm));
1026: PetscCall(PetscArraycpy(i1, coo_i, n1)); /* Make a copy since we'll modify it */
1027: for (k = 0; k < n1; k++) perm[k] = k;
1029: /* Manipulate i1[] so that entries with negative indices will have the smallest
1030: index, local entries will have greater but negative indices, and remote entries
1031: will have positive indices.
1032: */
1033: for (k = 0; k < n1; k++) {
1034: if (i1[k] < 0) {
1035: if (x->stash.ignorenegidx) i1[k] = PETSC_INT_MIN; /* e.g., -2^31, minimal to move them ahead */
1036: else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Found a negative index in VecSetPreallocateCOO() but VEC_IGNORE_NEGATIVE_INDICES was not set");
1037: } else if (i1[k] >= rstart && i1[k] < rend) {
1038: i1[k] -= PETSC_INT_MAX; /* e.g., minus 2^31-1 to shift local rows to range of [-PETSC_INT_MAX, -1] */
1039: } else {
1040: PetscCheck(i1[k] < M, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Found index %" PetscInt_FMT " in VecSetPreallocateCOO() larger than the global size %" PetscInt_FMT, i1[k], M);
1041: if (x->stash.donotstash) i1[k] = PETSC_INT_MIN; /* Ignore off-proc indices as if they were negative */
1042: }
1043: }
1045: /* Sort the indices, after that, [0,nneg) have ignored entries, [nneg,rem) have local entries and [rem,n1) have remote entries */
1046: PetscCall(PetscSortIntWithCountArray(n1, i1, perm));
1047: for (k = 0; k < n1; k++) {
1048: if (i1[k] > PETSC_INT_MIN) break;
1049: } /* Advance k to the first entry we need to take care of */
1050: nneg = k;
1051: PetscCall(PetscSortedIntUpperBound(i1, nneg, n1, rend - 1 - PETSC_INT_MAX, &rem)); /* rem is upper bound of the last local row */
1052: for (k = nneg; k < rem; k++) i1[k] += PETSC_INT_MAX; /* Revert indices of local entries */
1054: /* ---------------------------------------------------------------------------*/
1055: /* Build stuff for local entries */
1056: /* ---------------------------------------------------------------------------*/
1057: PetscCount tot1, *jmap1, *perm1;
1058: PetscCall(PetscCalloc1(m + 1, &jmap1));
1059: for (k = nneg; k < rem; k++) jmap1[i1[k] - rstart + 1]++; /* Count repeats of each local entry */
1060: for (k = 0; k < m; k++) jmap1[k + 1] += jmap1[k]; /* Transform jmap1[] to CSR-like data structure */
1061: tot1 = jmap1[m];
1062: PetscAssert(tot1 == rem - nneg, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Unexpected errors in VecSetPreallocationCOO_MPI");
1063: PetscCall(PetscMalloc1(tot1, &perm1));
1064: PetscCall(PetscArraycpy(perm1, perm + nneg, tot1));
1066: /* ---------------------------------------------------------------------------*/
1067: /* Record the permutation array for filling the send buffer */
1068: /* ---------------------------------------------------------------------------*/
1069: PetscCount *Cperm;
1070: PetscCall(PetscMalloc1(n1 - rem, &Cperm));
1071: PetscCall(PetscArraycpy(Cperm, perm + rem, n1 - rem));
1072: PetscCall(PetscFree(perm));
1074: /* ---------------------------------------------------------------------------*/
1075: /* Send remote entries to their owner */
1076: /* ---------------------------------------------------------------------------*/
1077: /* Find which entries should be sent to which remote ranks*/
1078: PetscInt nsend = 0; /* Number of MPI ranks to send data to */
1079: PetscMPIInt *sendto; /* [nsend], storing remote ranks */
1080: PetscInt *nentries; /* [nsend], storing number of entries sent to remote ranks; Assume PetscInt is big enough for this count, and error if not */
1081: const PetscInt *ranges;
1082: PetscInt maxNsend = size >= 128 ? 128 : size; /* Assume max 128 neighbors; realloc when needed */
1084: PetscCall(PetscLayoutGetRanges(x->map, &ranges));
1085: PetscCall(PetscMalloc2(maxNsend, &sendto, maxNsend, &nentries));
1086: for (k = rem; k < n1;) {
1087: PetscMPIInt owner;
1088: PetscInt firstRow, lastRow;
1090: /* Locate a row range */
1091: firstRow = i1[k]; /* first row of this owner */
1092: PetscCall(PetscLayoutFindOwner(x->map, firstRow, &owner));
1093: lastRow = ranges[owner + 1] - 1; /* last row of this owner */
1095: /* Find the first index 'p' in [k,n) with i[p] belonging to next owner */
1096: PetscCall(PetscSortedIntUpperBound(i1, k, n1, lastRow, &p));
1098: /* All entries in [k,p) belong to this remote owner */
1099: if (nsend >= maxNsend) { /* Double the remote ranks arrays if not long enough */
1100: PetscMPIInt *sendto2;
1101: PetscInt *nentries2;
1102: PetscInt maxNsend2 = (maxNsend <= size / 2) ? maxNsend * 2 : size;
1104: PetscCall(PetscMalloc2(maxNsend2, &sendto2, maxNsend2, &nentries2));
1105: PetscCall(PetscArraycpy(sendto2, sendto, maxNsend));
1106: PetscCall(PetscArraycpy(nentries2, nentries2, maxNsend + 1));
1107: PetscCall(PetscFree2(sendto, nentries2));
1108: sendto = sendto2;
1109: nentries = nentries2;
1110: maxNsend = maxNsend2;
1111: }
1112: sendto[nsend] = owner;
1113: PetscCall(PetscIntCast(p - k, &nentries[nsend]));
1114: nsend++;
1115: k = p;
1116: }
1118: /* Build 1st SF to know offsets on remote to send data */
1119: PetscSF sf1;
1120: PetscInt nroots = 1, nroots2 = 0;
1121: PetscInt nleaves = nsend, nleaves2 = 0;
1122: PetscInt *offsets;
1123: PetscSFNode *iremote;
1125: PetscCall(PetscSFCreate(comm, &sf1));
1126: PetscCall(PetscMalloc1(nsend, &iremote));
1127: PetscCall(PetscMalloc1(nsend, &offsets));
1128: for (k = 0; k < nsend; k++) {
1129: iremote[k].rank = sendto[k];
1130: iremote[k].index = 0;
1131: nleaves2 += nentries[k];
1132: PetscCheck(nleaves2 >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of SF leaves is too large for PetscInt");
1133: }
1134: PetscCall(PetscSFSetGraph(sf1, nroots, nleaves, NULL, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER));
1135: PetscCall(PetscSFFetchAndOpWithMemTypeBegin(sf1, MPIU_INT, PETSC_MEMTYPE_HOST, &nroots2 /*rootdata*/, PETSC_MEMTYPE_HOST, nentries /*leafdata*/, PETSC_MEMTYPE_HOST, offsets /*leafupdate*/, MPI_SUM));
1136: PetscCall(PetscSFFetchAndOpEnd(sf1, MPIU_INT, &nroots2, nentries, offsets, MPI_SUM)); /* Would nroots2 overflow, we check offsets[] below */
1137: PetscCall(PetscSFDestroy(&sf1));
1138: PetscAssert(nleaves2 == n1 - rem, PETSC_COMM_SELF, PETSC_ERR_PLIB, "nleaves2 %" PetscInt_FMT " != number of remote entries %" PetscCount_FMT, nleaves2, n1 - rem);
1140: /* Build 2nd SF to send remote COOs to their owner */
1141: PetscSF sf2;
1142: nroots = nroots2;
1143: nleaves = nleaves2;
1144: PetscCall(PetscSFCreate(comm, &sf2));
1145: PetscCall(PetscSFSetFromOptions(sf2));
1146: PetscCall(PetscMalloc1(nleaves, &iremote));
1147: p = 0;
1148: for (k = 0; k < nsend; k++) {
1149: PetscCheck(offsets[k] >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of SF roots is too large for PetscInt");
1150: for (q = 0; q < nentries[k]; q++, p++) {
1151: iremote[p].rank = sendto[k];
1152: PetscCall(PetscIntCast(offsets[k] + q, &iremote[p].index));
1153: }
1154: }
1155: PetscCall(PetscSFSetGraph(sf2, nroots, nleaves, NULL, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER));
1157: /* Send the remote COOs to their owner */
1158: PetscInt n2 = nroots, *i2; /* Buffers for received COOs from other ranks, along with a permutation array */
1159: PetscCount *perm2;
1160: PetscCall(PetscMalloc1(n2, &i2));
1161: PetscCall(PetscMalloc1(n2, &perm2));
1162: PetscCall(PetscSFReduceWithMemTypeBegin(sf2, MPIU_INT, PETSC_MEMTYPE_HOST, i1 + rem, PETSC_MEMTYPE_HOST, i2, MPI_REPLACE));
1163: PetscCall(PetscSFReduceEnd(sf2, MPIU_INT, i1 + rem, i2, MPI_REPLACE));
1165: PetscCall(PetscFree(i1));
1166: PetscCall(PetscFree(offsets));
1167: PetscCall(PetscFree2(sendto, nentries));
1169: /* ---------------------------------------------------------------*/
1170: /* Sort received COOs along with a permutation array */
1171: /* ---------------------------------------------------------------*/
1172: PetscCount *imap2;
1173: PetscCount *jmap2, nnz2;
1174: PetscScalar *sendbuf, *recvbuf;
1175: PetscInt old;
1176: PetscCount sendlen = n1 - rem, recvlen = n2;
1178: for (k = 0; k < n2; k++) perm2[k] = k;
1179: PetscCall(PetscSortIntWithCountArray(n2, i2, perm2));
1181: /* nnz2 will be # of unique entries in the recvbuf */
1182: nnz2 = n2;
1183: for (k = 1; k < n2; k++) {
1184: if (i2[k] == i2[k - 1]) nnz2--;
1185: }
1187: /* Build imap2[] and jmap2[] for each unique entry */
1188: PetscCall(PetscMalloc4(nnz2, &imap2, nnz2 + 1, &jmap2, sendlen, &sendbuf, recvlen, &recvbuf));
1189: p = -1;
1190: old = -1;
1191: jmap2[0] = 0;
1192: jmap2++;
1193: for (k = 0; k < n2; k++) {
1194: if (i2[k] != old) { /* Meet a new entry */
1195: p++;
1196: imap2[p] = i2[k] - rstart;
1197: jmap2[p] = 1;
1198: old = i2[k];
1199: } else {
1200: jmap2[p]++;
1201: }
1202: }
1203: jmap2--;
1204: for (k = 0; k < nnz2; k++) jmap2[k + 1] += jmap2[k];
1206: PetscCall(PetscFree(i2));
1208: vmpi->coo_n = coo_n;
1209: vmpi->tot1 = tot1;
1210: vmpi->jmap1 = jmap1;
1211: vmpi->perm1 = perm1;
1212: vmpi->nnz2 = nnz2;
1213: vmpi->imap2 = imap2;
1214: vmpi->jmap2 = jmap2;
1215: vmpi->perm2 = perm2;
1217: vmpi->Cperm = Cperm;
1218: vmpi->sendbuf = sendbuf;
1219: vmpi->recvbuf = recvbuf;
1220: vmpi->sendlen = sendlen;
1221: vmpi->recvlen = recvlen;
1222: vmpi->coo_sf = sf2;
1223: PetscFunctionReturn(PETSC_SUCCESS);
1224: }
1226: PetscErrorCode VecSetValuesCOO_MPI(Vec x, const PetscScalar v[], InsertMode imode)
1227: {
1228: Vec_MPI *vmpi = (Vec_MPI *)x->data;
1229: PetscInt m;
1230: PetscScalar *a, *sendbuf = vmpi->sendbuf, *recvbuf = vmpi->recvbuf;
1231: const PetscCount *jmap1 = vmpi->jmap1;
1232: const PetscCount *perm1 = vmpi->perm1;
1233: const PetscCount *imap2 = vmpi->imap2;
1234: const PetscCount *jmap2 = vmpi->jmap2;
1235: const PetscCount *perm2 = vmpi->perm2;
1236: const PetscCount *Cperm = vmpi->Cperm;
1237: const PetscCount nnz2 = vmpi->nnz2;
1239: PetscFunctionBegin;
1240: PetscCall(VecGetLocalSize(x, &m));
1241: PetscCall(VecGetArray(x, &a));
1243: /* Pack entries to be sent to remote */
1244: for (PetscInt i = 0; i < vmpi->sendlen; i++) sendbuf[i] = v[Cperm[i]];
1246: /* Send remote entries to their owner and overlap the communication with local computation */
1247: PetscCall(PetscSFReduceWithMemTypeBegin(vmpi->coo_sf, MPIU_SCALAR, PETSC_MEMTYPE_HOST, sendbuf, PETSC_MEMTYPE_HOST, recvbuf, MPI_REPLACE));
1248: /* Add local entries to A and B */
1249: for (PetscInt i = 0; i < m; i++) { /* All entries in a[] are either zero'ed or added with a value (i.e., initialized) */
1250: PetscScalar sum = 0.0; /* Do partial summation first to improve numerical stability */
1251: for (PetscCount k = jmap1[i]; k < jmap1[i + 1]; k++) sum += v[perm1[k]];
1252: a[i] = (imode == INSERT_VALUES ? 0.0 : a[i]) + sum;
1253: }
1254: PetscCall(PetscSFReduceEnd(vmpi->coo_sf, MPIU_SCALAR, sendbuf, recvbuf, MPI_REPLACE));
1256: /* Add received remote entries to A and B */
1257: for (PetscInt i = 0; i < nnz2; i++) {
1258: for (PetscCount k = jmap2[i]; k < jmap2[i + 1]; k++) a[imap2[i]] += recvbuf[perm2[k]];
1259: }
1261: PetscCall(VecRestoreArray(x, &a));
1262: PetscFunctionReturn(PETSC_SUCCESS);
1263: }