Actual source code: chaco.c
2: #include src/mat/impls/adj/mpi/mpiadj.h
4: #ifdef PETSC_HAVE_UNISTD_H
5: #include <unistd.h>
6: #endif
8: #ifdef PETSC_HAVE_STDLIB_H
9: #include <stdlib.h>
10: #endif
12: #include "petscfix.h"
14: EXTERN_C_BEGIN
15: /* Chaco does not have an include file */
16: extern int interface(int nvtxs, int *start, int *adjacency, int *vwgts,
17: float *ewgts, float *x, float *y, float *z, char *outassignname,
18: char *outfilename, short *assignment, int architecture, int ndims_tot,
19: int mesh_dims[3], double *goal, int global_method, int local_method,
20: int rqi_flag, int vmax, int ndims, double eigtol, long seed);
22: extern int FREE_GRAPH;
24: /*
25: int nvtxs; number of vertices in full graph
26: int *start; start of edge list for each vertex
27: int *adjacency; edge list data
28: int *vwgts; weights for all vertices
29: float *ewgts; weights for all edges
30: float *x, *y, *z; coordinates for inertial method
31: char *outassignname; name of assignment output file
32: char *outfilename; output file name
33: short *assignment; set number of each vtx (length n)
34: int architecture; 0 => hypercube, d => d-dimensional mesh
35: int ndims_tot; total number of cube dimensions to divide
36: int mesh_dims[3]; dimensions of mesh of processors
37: double *goal; desired set sizes for each set
38: int global_method; global partitioning algorithm
39: int local_method; local partitioning algorithm
40: int rqi_flag; should I use RQI/Symmlq eigensolver?
41: int vmax; how many vertices to coarsen down to?
42: int ndims; number of eigenvectors (2^d sets)
43: double eigtol; tolerance on eigenvectors
44: long seed; for random graph mutations
45: */
47: EXTERN_C_END
49: typedef struct {
50: int architecture;
51: int ndims_tot;
52: int mesh_dims[3];
53: int rqi_flag;
54: int numbereigen;
55: double eigtol;
56: int global_method; /* global method */
57: int local_method; /* local method */
58: int nbvtxcoarsed; /* number of vertices for the coarse graph */
59: char *mesg_log;
60: } MatPartitioning_Chaco;
62: #define SIZE_LOG 10000 /* size of buffer for msg_log */
66: static int MatPartitioningApply_Chaco(MatPartitioning part, IS *partitioning)
67: {
68: int ierr, *parttab, *locals, i, size, rank;
69: Mat mat = part->adj, matMPI, matSeq;
70: int nb_locals;
71: Mat_MPIAdj *adj;
72: MatPartitioning_Chaco *chaco = (MatPartitioning_Chaco *) part->data;
73: PetscTruth flg;
74: #ifdef PETSC_HAVE_UNISTD_H
75: int fd_stdout, fd_pipe[2], count;
76: #endif
80: FREE_GRAPH = 0; /* otherwise Chaco will attempt to free memory for adjacency graph */
81:
82: MPI_Comm_size(mat->comm, &size);
84: PetscTypeCompare((PetscObject) mat, MATMPIADJ, &flg);
86: /* check if the matrix is sequential, use MatGetSubMatrices if necessary */
87: if (size > 1) {
88: int M, N;
89: IS isrow, iscol;
90: Mat *A;
92: if (flg) {
93: SETERRQ(0, "Distributed matrix format MPIAdj is not supported for sequential partitioners");
94: }
95: PetscPrintf(part->comm, "Converting distributed matrix to sequential: this could be a performance loss\n");
97: MatGetSize(mat, &M, &N);
98: ISCreateStride(PETSC_COMM_SELF, M, 0, 1, &isrow);
99: ISCreateStride(PETSC_COMM_SELF, N, 0, 1, &iscol);
100: MatGetSubMatrices(mat, 1, &isrow, &iscol, MAT_INITIAL_MATRIX, &A);
101: ISDestroy(isrow);
102: ISDestroy(iscol);
103: matSeq = *A;
104: } else
105: matSeq = mat;
107: /* check for the input format that is supported only for a MPIADJ type
108: and set it to matMPI */
109: if (!flg) {
110: MatConvert(matSeq, MATMPIADJ, &matMPI);
111: } else
112: matMPI = matSeq;
114: adj = (Mat_MPIAdj *) matMPI->data; /* finaly adj contains adjacency graph */
116: {
117: /* arguments for Chaco library */
118: int nvtxs = mat->M; /* number of vertices in full graph */
119: int *start = adj->i; /* start of edge list for each vertex */
120: int *adjacency; /* = adj -> j; edge list data */
121: int *vwgts = NULL; /* weights for all vertices */
122: float *ewgts = NULL; /* weights for all edges */
123: float *x = NULL, *y = NULL, *z = NULL; /* coordinates for inertial method */
124: char *outassignname = NULL; /* name of assignment output file */
125: char *outfilename = NULL; /* output file name */
126: short *assignment; /* set number of each vtx (length n) */
127: int architecture = chaco->architecture; /* 0 => hypercube, d => d-dimensional mesh */
128: int ndims_tot = chaco->ndims_tot; /* total number of cube dimensions to divide */
129: int *mesh_dims = chaco->mesh_dims; /* dimensions of mesh of processors */
130: double *goal = NULL; /* desired set sizes for each set */
131: int global_method = chaco->global_method; /* global partitioning algorithm */
132: int local_method = chaco->local_method; /* local partitioning algorithm */
133: int rqi_flag = chaco->rqi_flag; /* should I use RQI/Symmlq eigensolver? */
134: int vmax = chaco->nbvtxcoarsed; /* how many vertices to coarsen down to? */
135: int ndims = chaco->numbereigen; /* number of eigenvectors (2^d sets) */
136: double eigtol = chaco->eigtol; /* tolerance on eigenvectors */
137: long seed = 123636512; /* for random graph mutations */
139: /* return value of Chaco */
140: PetscMalloc((mat->M) * sizeof(short), &assignment);
141:
142: /* index change for libraries that have fortran implementation */
143: PetscMalloc(sizeof(int) * start[nvtxs], &adjacency);
144: for (i = 0; i < start[nvtxs]; i++)
145: adjacency[i] = (adj->j)[i] + 1;
147: /* redirect output to buffer: chaco -> mesg_log */
148: #ifdef PETSC_HAVE_UNISTD_H
149: fd_stdout = dup(1);
150: pipe(fd_pipe);
151: close(1);
152: dup2(fd_pipe[1], 1);
153: PetscMalloc(SIZE_LOG * sizeof(char), &(chaco->mesg_log));
154: #endif
156: /* library call */
157: interface(nvtxs, start, adjacency, vwgts, ewgts, x, y, z,
158: outassignname, outfilename, assignment, architecture, ndims_tot,
159: mesh_dims, goal, global_method, local_method, rqi_flag, vmax, ndims,
160: eigtol, seed);
162: #ifdef PETSC_HAVE_UNISTD_H
163: fflush(stdout);
164: count = read(fd_pipe[0], chaco->mesg_log, (SIZE_LOG - 1) * sizeof(char));
165: if (count < 0)
166: count = 0;
167: chaco->mesg_log[count] = 0;
168: close(1);
169: dup2(fd_stdout, 1);
170: close(fd_stdout);
171: close(fd_pipe[0]);
172: close(fd_pipe[1]);
173: #endif
175: if (ierr) { SETERRQ(1, chaco->mesg_log); }
177: PetscFree(adjacency);
179: PetscMalloc((mat->M) * sizeof(int), &parttab);
180: for (i = 0; i < nvtxs; i++) {
181: parttab[i] = assignment[i];
182: }
183: PetscFree(assignment);
184: }
186: /* Creation of the index set */
187: MPI_Comm_rank(part->comm, &rank);
188: MPI_Comm_size(part->comm, &size);
189: nb_locals = mat->M / size;
190: locals = parttab + rank * nb_locals;
191: if (rank < mat->M % size) {
192: nb_locals++;
193: locals += rank;
194: } else
195: locals += mat->M % size;
196: ISCreateGeneral(part->comm, nb_locals, locals, partitioning);
198: /* destroy temporary objects */
199: PetscFree(parttab);
200: if (matSeq != mat) {
201: MatDestroy(matSeq);
202: }
203: if (matMPI != mat) {
204: MatDestroy(matMPI);
205: }
207: return(0);
208: }
213: int MatPartitioningView_Chaco(MatPartitioning part, PetscViewer viewer)
214: {
216: MatPartitioning_Chaco *chaco = (MatPartitioning_Chaco *) part->data;
217: int ierr, rank;
218: PetscTruth isascii;
222: MPI_Comm_rank(part->comm, &rank);
223: PetscTypeCompare((PetscObject) viewer, PETSC_VIEWER_ASCII, &isascii);
224: if (isascii) {
225: if (!rank && chaco->mesg_log) {
226: PetscViewerASCIIPrintf(viewer, "%s\n", chaco->mesg_log);
227: }
228: } else {
229: SETERRQ1(1, "Viewer type %s not supported for this Chaco partitioner",
230: ((PetscObject) viewer)->type_name);
231: }
233: return(0);
234: }
238: /*@
239: MatPartitioningChacoSetGlobal - Set method for global partitioning.
241: Input Parameter:
242: . part - the partitioning context
243: . method - MP_CHACO_MULTILEVEL_KL, MP_CHACO_SPECTRAL, MP_CHACO_LINEAR,
244: MP_CHACO_RANDOM or MP_CHACO_SCATTERED
246: Level: advanced
248: @*/
249: int MatPartitioningChacoSetGlobal(MatPartitioning part, MPChacoGlobalType method)
250: {
251: MatPartitioning_Chaco *chaco = (MatPartitioning_Chaco *) part->data;
255: switch (method) {
256: case MP_CHACO_MULTILEVEL_KL:
257: chaco->global_method = 1;
258: break;
259: case MP_CHACO_SPECTRAL:
260: chaco->global_method = 2;
261: break;
262: case MP_CHACO_LINEAR:
263: chaco->global_method = 4;
264: break;
265: case MP_CHACO_RANDOM:
266: chaco->global_method = 5;
267: break;
268: case MP_CHACO_SCATTERED:
269: chaco->global_method = 6;
270: break;
271: default:
272: SETERRQ(PETSC_ERR_SUP, "Chaco: Unknown or unsupported option");
273: }
274: return(0);
275: }
279: /*@
280: MatPartitioningChacoSetLocal - Set method for local partitioning.
282: Input Parameter:
283: . part - the partitioning context
284: . method - MP_CHACO_KERNIGHAN_LIN or MP_CHACO_NONE
286: Level: advanced
288: @*/
289: int MatPartitioningChacoSetLocal(MatPartitioning part, MPChacoLocalType method)
290: {
291: MatPartitioning_Chaco *chaco = (MatPartitioning_Chaco *) part->data;
295: switch (method) {
296: case MP_CHACO_KERNIGHAN_LIN:
297: chaco->local_method = 1;
298: break;
299: case MP_CHACO_NONE:
300: chaco->local_method = 2;
301: break;
302: default:
303: SETERRQ(PETSC_ERR_ARG_CORRUPT, "Chaco: Unknown or unsupported option");
304: }
306: return(0);
307: }
311: /*@
312: MatPartitioningChacoSetCoarseLevel - Set the coarse level
313:
314: Input Parameter:
315: . part - the partitioning context
316: . level - the coarse level in range [0.0,1.0]
318: Level: advanced
320: @*/
321: int MatPartitioningChacoSetCoarseLevel(MatPartitioning part, PetscReal level)
322: {
323: MatPartitioning_Chaco *chaco = (MatPartitioning_Chaco *) part->data;
327: if (level < 0 || level > 1.0) {
328: SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,
329: "Chaco: level of coarsening out of range [0.01-1.0]");
330: } else
331: chaco->nbvtxcoarsed = part->adj->N * level;
333: if (chaco->nbvtxcoarsed < 20)
334: chaco->nbvtxcoarsed = 20;
336: return(0);
337: }
341: /*@
342: MatPartitioningChacoSetEigenSolver - Set method for eigensolver.
344: Input Parameter:
345: . method - MP_CHACO_LANCZOS or MP_CHACO_RQI_SYMMLQ
347: Level: advanced
349: @*/
350: int MatPartitioningChacoSetEigenSolver(MatPartitioning part,
351: MPChacoEigenType method)
352: {
353: MatPartitioning_Chaco *chaco = (MatPartitioning_Chaco *) part->data;
357: switch (method) {
358: case MP_CHACO_LANCZOS:
359: chaco->rqi_flag = 0;
360: break;
361: case MP_CHACO_RQI_SYMMLQ:
362: chaco->rqi_flag = 1;
363: break;
364: default:
365: SETERRQ(PETSC_ERR_ARG_CORRUPT, "Chaco: Unknown or unsupported option");
366: }
368: return(0);
369: }
373: /*@
374: MatPartitioningChacoSetEigenTol - Set tolerance for eigensolver.
376: Input Parameter:
377: . tol - Tolerance requested.
379: Level: advanced
381: @*/
382: int MatPartitioningChacoSetEigenTol(MatPartitioning part, PetscReal tol)
383: {
384: MatPartitioning_Chaco *chaco = (MatPartitioning_Chaco *) part->data;
388: if (tol <= 0.0) {
389: SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,
390: "Chaco: Eigensolver tolerance out of range");
391: } else
392: chaco->eigtol = tol;
394: return(0);
395: }
399: /*@
400: MatPartitioningChacoSetEigenNumber - Set number of eigenvectors for partitioning.
402: Input Parameter:
403: . num - This argument should have a value of 1, 2 or 3 indicating
404: partitioning by bisection, quadrisection, or octosection.
406: Level: advanced
408: @*/
409: int MatPartitioningChacoSetEigenNumber(MatPartitioning part, int num)
410: {
411: MatPartitioning_Chaco *chaco = (MatPartitioning_Chaco *) part->data;
415: if (num > 3 || num < 1) {
416: SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,
417: "Chaco: number of eigenvectors out of range");
418: } else
419: chaco->numbereigen = num;
421: return(0);
422: }
426: int MatPartitioningSetFromOptions_Chaco(MatPartitioning part)
427: {
428: int ierr, i;
429: PetscReal r;
430: PetscTruth flag;
431: const char *global[] =
432: { "multilevel-kl", "spectral", "linear", "random", "scattered" };
433: const char *local[] = { "kernighan-lin", "none" };
434: const char *eigen[] = { "lanczos", "rqi_symmlq" };
437: PetscOptionsHead("Set Chaco partitioning options");
439: PetscOptionsEList("-mat_partitioning_chaco_global",
440: "Global method to use", "MatPartitioningChacoSetGlobal", global, 5,
441: global[0], &i, &flag);
442: if (flag)
443: MatPartitioningChacoSetGlobal(part, i);
445: PetscOptionsEList("-mat_partitioning_chaco_local",
446: "Local method to use", "MatPartitioningChacoSetLocal", local, 2,
447: local[0], &i, &flag);
448: if (flag)
449: MatPartitioningChacoSetLocal(part, i);
451: PetscOptionsReal("-mat_partitioning_chaco_coarse_level",
452: "Coarse level", "MatPartitioningChacoSetCoarseLevel", 0, &r,
453: &flag);
454: if (flag)
455: MatPartitioningChacoSetCoarseLevel(part, r);
457: PetscOptionsEList("-mat_partitioning_chaco_eigen_solver",
458: "Eigensolver to use in spectral method", "MatPartitioningChacoSetEigenSolver",
459: eigen, 2, eigen[0], &i, &flag);
460: if (flag)
461: MatPartitioningChacoSetEigenSolver(part, i);
463: PetscOptionsReal("-mat_partitioning_chaco_eigen_tol",
464: "Tolerance for eigensolver", "MatPartitioningChacoSetEigenTol", 0.001,
465: &r, &flag);
466: if (flag)
467: MatPartitioningChacoSetEigenTol(part, r);
469: PetscOptionsInt("-mat_partitioning_chaco_eigen_number",
470: "Number of eigenvectors: 1, 2, or 3 (bi-, quadri-, or octosection)",
471: "MatPartitioningChacoSetEigenNumber", 1, &i, &flag);
472: if (flag)
473: MatPartitioningChacoSetEigenNumber(part, i);
475: PetscOptionsTail();
476: return(0);
477: }
482: int MatPartitioningDestroy_Chaco(MatPartitioning part)
483: {
484: MatPartitioning_Chaco *chaco = (MatPartitioning_Chaco *) part->data;
489: if (chaco->mesg_log) {
490: PetscFree(chaco->mesg_log);
491: }
493: PetscFree(chaco);
495: return(0);
496: }
498: EXTERN_C_BEGIN
501: int MatPartitioningCreate_Chaco(MatPartitioning part)
502: {
504: MatPartitioning_Chaco *chaco;
507: PetscNew(MatPartitioning_Chaco, &chaco);
509: chaco->architecture = 1;
510: chaco->ndims_tot = 0;
511: chaco->mesh_dims[0] = part->n;
512: chaco->global_method = 1;
513: chaco->local_method = 1;
514: chaco->rqi_flag = 0;
515: chaco->nbvtxcoarsed = 200;
516: chaco->numbereigen = 1;
517: chaco->eigtol = 0.001;
518: chaco->mesg_log = NULL;
520: part->ops->apply = MatPartitioningApply_Chaco;
521: part->ops->view = MatPartitioningView_Chaco;
522: part->ops->destroy = MatPartitioningDestroy_Chaco;
523: part->ops->setfromoptions = MatPartitioningSetFromOptions_Chaco;
524: part->data = (void *) chaco;
526: return(0);
527: }
529: EXTERN_C_END