space.c 59.1 KB
Newer Older
1
/*******************************************************************************
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
 * This file is part of SWIFT.
 * Copyright (c) 2012 Pedro Gonnet (pedro.gonnet@durham.ac.uk)
 *                    Matthieu Schaller (matthieu.schaller@durham.ac.uk)
 *               2015 Peter W. Draper (p.w.draper@durham.ac.uk)
 *               2016 John A. Regan (john.a.regan@durham.ac.uk)
 *                    Tom Theuns (tom.theuns@durham.ac.uk)
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as published
 * by the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 *
 ******************************************************************************/
Pedro Gonnet's avatar
Pedro Gonnet committed
23
24
25
26
27
28
29
30

/* Config parameters. */
#include "../config.h"

/* Some standard headers. */
#include <float.h>
#include <limits.h>
#include <math.h>
31
#include <stdlib.h>
32
#include <string.h>
Pedro Gonnet's avatar
Pedro Gonnet committed
33

34
35
/* MPI headers. */
#ifdef WITH_MPI
36
#include <mpi.h>
37
38
#endif

39
40
41
/* This object's header. */
#include "space.h"

Pedro Gonnet's avatar
Pedro Gonnet committed
42
/* Local headers. */
43
#include "atomic.h"
44
#include "const.h"
45
#include "cooling.h"
46
#include "engine.h"
47
#include "error.h"
48
49
#include "gravity.h"
#include "hydro.h"
50
#include "kernel_hydro.h"
51
#include "lock.h"
52
#include "memswap.h"
53
#include "minmax.h"
54
#include "runner.h"
55
#include "threadpool.h"
56
#include "tools.h"
Pedro Gonnet's avatar
Pedro Gonnet committed
57
58
59

/* Split size. */
int space_splitsize = space_splitsize_default;
60
int space_subsize = space_subsize_default;
61
int space_maxsize = space_maxsize_default;
62
int space_maxcount = space_maxcount_default;
Pedro Gonnet's avatar
Pedro Gonnet committed
63
64
65

/* Map shift vector to sortlist. */
const int sortlistID[27] = {
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
    /* ( -1 , -1 , -1 ) */ 0,
    /* ( -1 , -1 ,  0 ) */ 1,
    /* ( -1 , -1 ,  1 ) */ 2,
    /* ( -1 ,  0 , -1 ) */ 3,
    /* ( -1 ,  0 ,  0 ) */ 4,
    /* ( -1 ,  0 ,  1 ) */ 5,
    /* ( -1 ,  1 , -1 ) */ 6,
    /* ( -1 ,  1 ,  0 ) */ 7,
    /* ( -1 ,  1 ,  1 ) */ 8,
    /* (  0 , -1 , -1 ) */ 9,
    /* (  0 , -1 ,  0 ) */ 10,
    /* (  0 , -1 ,  1 ) */ 11,
    /* (  0 ,  0 , -1 ) */ 12,
    /* (  0 ,  0 ,  0 ) */ 0,
    /* (  0 ,  0 ,  1 ) */ 12,
    /* (  0 ,  1 , -1 ) */ 11,
    /* (  0 ,  1 ,  0 ) */ 10,
    /* (  0 ,  1 ,  1 ) */ 9,
    /* (  1 , -1 , -1 ) */ 8,
    /* (  1 , -1 ,  0 ) */ 7,
    /* (  1 , -1 ,  1 ) */ 6,
    /* (  1 ,  0 , -1 ) */ 5,
    /* (  1 ,  0 ,  0 ) */ 4,
    /* (  1 ,  0 ,  1 ) */ 3,
    /* (  1 ,  1 , -1 ) */ 2,
    /* (  1 ,  1 ,  0 ) */ 1,
    /* (  1 ,  1 ,  1 ) */ 0};

94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
/**
 * @brief Interval stack necessary for parallel particle sorting.
 */
struct qstack {
  volatile ptrdiff_t i, j;
  volatile int min, max;
  volatile int ready;
};

/**
 * @brief Parallel particle-sorting stack
 */
struct parallel_sort {
  struct part *parts;
  struct gpart *gparts;
  struct xpart *xparts;
  int *ind;
  struct qstack *stack;
  unsigned int stack_size;
  volatile unsigned int first, last, waiting;
};

116
117
118
119
120
121
122
123
124
/**
 * @brief Information required to compute the particle cell indices.
 */
struct index_data {
  struct space *s;
  struct cell *cells;
  int *ind;
};

125
126
127
128
129
130
131
132
133
134
135
/**
 * @brief Get the shift-id of the given pair of cells, swapping them
 *      if need be.
 *
 * @param s The space
 * @param ci Pointer to first #cell.
 * @param cj Pointer second #cell.
 * @param shift Vector from ci to cj.
 *
 * @return The shift ID and set shift, may or may not swap ci and cj.
 */
136
137
138
139
int space_getsid(struct space *s, struct cell **ci, struct cell **cj,
                 double *shift) {

  /* Get the relative distance between the pairs, wrapping. */
140
141
142
  const int periodic = s->periodic;
  double dx[3];
  for (int k = 0; k < 3; k++) {
143
144
145
146
147
148
149
150
151
152
153
    dx[k] = (*cj)->loc[k] - (*ci)->loc[k];
    if (periodic && dx[k] < -s->dim[k] / 2)
      shift[k] = s->dim[k];
    else if (periodic && dx[k] > s->dim[k] / 2)
      shift[k] = -s->dim[k];
    else
      shift[k] = 0.0;
    dx[k] += shift[k];
  }

  /* Get the sorting index. */
154
  int sid = 0;
155
  for (int k = 0; k < 3; k++)
156
157
158
159
    sid = 3 * sid + ((dx[k] < 0.0) ? 0 : ((dx[k] > 0.0) ? 2 : 1));

  /* Switch the cells around? */
  if (runner_flip[sid]) {
160
    struct cell *temp = *ci;
161
162
    *ci = *cj;
    *cj = temp;
163
    for (int k = 0; k < 3; k++) shift[k] = -shift[k];
164
165
166
167
168
169
  }
  sid = sortlistID[sid];

  /* Return the sort ID. */
  return sid;
}
170

171
/**
172
 * @brief Recursively dismantle a cell tree.
173
 *
174
175
 * @param s The #space.
 * @param c The #cell to recycle.
176
 */
177
178
179
void space_rebuild_recycle(struct space *s, struct cell *c) {

  if (c->split)
180
    for (int k = 0; k < 8; k++)
181
182
183
184
185
186
187
      if (c->progeny[k] != NULL) {
        space_rebuild_recycle(s, c->progeny[k]);
        space_recycle(s, c->progeny[k]);
        c->progeny[k] = NULL;
      }
}

188
/**
189
 * @brief Re-build the top-level cell grid.
190
 *
191
 * @param s The #space.
192
 * @param verbose Print messages to stdout or not.
193
 */
194
void space_regrid(struct space *s, int verbose) {
195

196
  const size_t nr_parts = s->nr_parts;
197
  const ticks tic = getticks();
198
  const int ti_current = (s->e != NULL) ? s->e->ti_current : 0;
199

200
  /* Run through the cells and get the current h_max. */
201
  // tic = getticks();
202
  float h_max = s->cell_min / kernel_gamma / space_stretch;
203
  if (nr_parts > 0) {
204
    if (s->cells_top != NULL) {
Tom Theuns's avatar
Tom Theuns committed
205
      for (int k = 0; k < s->nr_cells; k++) {
206
207
208
        if (s->cells_top[k].nodeID == engine_rank &&
            s->cells_top[k].h_max > h_max) {
          h_max = s->cells_top[k].h_max;
209
        }
210
211
      }
    } else {
212
      for (size_t k = 0; k < nr_parts; k++) {
Matthieu Schaller's avatar
Matthieu Schaller committed
213
        if (s->parts[k].h > h_max) h_max = s->parts[k].h;
214
      }
215
216
217
218
219
220
221
222
223
224
    }
  }

/* If we are running in parallel, make sure everybody agrees on
   how large the largest cell should be. */
#ifdef WITH_MPI
  {
    float buff;
    if (MPI_Allreduce(&h_max, &buff, 1, MPI_FLOAT, MPI_MAX, MPI_COMM_WORLD) !=
        MPI_SUCCESS)
225
      error("Failed to aggregate the rebuild flag across nodes.");
226
227
228
    h_max = buff;
  }
#endif
229
  if (verbose) message("h_max is %.3e (cell_min=%.3e).", h_max, s->cell_min);
230
231

  /* Get the new putative cell dimensions. */
232
  const int cdim[3] = {
233
234
235
236
237
238
      floor(s->dim[0] /
            fmax(h_max * kernel_gamma * space_stretch, s->cell_min)),
      floor(s->dim[1] /
            fmax(h_max * kernel_gamma * space_stretch, s->cell_min)),
      floor(s->dim[2] /
            fmax(h_max * kernel_gamma * space_stretch, s->cell_min))};
239
240
241
242
243

  /* Check if we have enough cells for periodicity. */
  if (s->periodic && (cdim[0] < 3 || cdim[1] < 3 || cdim[2] < 3))
    error(
        "Must have at least 3 cells in each spatial dimension when periodicity "
244
245
246
        "is switched on.\nThis error is often caused by any of the "
        "followings:\n"
        " - too few particles to generate a sensible grid,\n"
247
248
        " - the initial value of 'Scheduler:max_top_level_cells' is too "
        "small,\n"
249
        " - the (minimal) time-step is too large leading to particles with "
250
251
252
        "predicted smoothing lengths too large for the box size,\n"
        " - particle with velocities so large that they move by more than two "
        "box sizes per time-step.\n");
253

254
255
256
257
258
259
  /* Check if we have enough cells for gravity. */
  if (s->gravity && (cdim[0] < 8 || cdim[1] < 8 || cdim[2] < 8))
    error(
        "Must have at least 8 cells in each spatial dimension when gravity "
        "is switched on.");

260
261
262
/* In MPI-Land, changing the top-level cell size requires that the
 * global partition is recomputed and the particles redistributed.
 * Be prepared to do that. */
263
#ifdef WITH_MPI
Matthieu Schaller's avatar
Matthieu Schaller committed
264
  double oldwidth[3];
265
266
267
268
269
270
271
272
  double oldcdim[3];
  int *oldnodeIDs = NULL;
  if (cdim[0] < s->cdim[0] || cdim[1] < s->cdim[1] || cdim[2] < s->cdim[2]) {

    /* Capture state of current space. */
    oldcdim[0] = s->cdim[0];
    oldcdim[1] = s->cdim[1];
    oldcdim[2] = s->cdim[2];
273
274
275
    oldwidth[0] = s->width[0];
    oldwidth[1] = s->width[1];
    oldwidth[2] = s->width[2];
276
277
278
279
280
281
282
283
284

    if ((oldnodeIDs = (int *)malloc(sizeof(int) * s->nr_cells)) == NULL)
      error("Failed to allocate temporary nodeIDs.");

    int cid = 0;
    for (int i = 0; i < s->cdim[0]; i++) {
      for (int j = 0; j < s->cdim[1]; j++) {
        for (int k = 0; k < s->cdim[2]; k++) {
          cid = cell_getid(oldcdim, i, j, k);
285
          oldnodeIDs[cid] = s->cells_top[cid].nodeID;
286
287
288
289
290
        }
      }
    }
  }

291
292
293
294
#endif

  /* Do we need to re-build the upper-level cells? */
  // tic = getticks();
295
  if (s->cells_top == NULL || cdim[0] < s->cdim[0] || cdim[1] < s->cdim[1] ||
296
297
      cdim[2] < s->cdim[2]) {

298
299
300
301
302
303
/* Be verbose about this. */
#ifdef SWIFT_DEBUG_CHECKS
    message("re)griding space cdim=(%d %d %d)", cdim[0], cdim[1], cdim[2]);
    fflush(stdout);
#endif

304
    /* Free the old cells, if they were allocated. */
305
    if (s->cells_top != NULL) {
306
      for (int k = 0; k < s->nr_cells; k++) {
307
308
        space_rebuild_recycle(s, &s->cells_top[k]);
        if (s->cells_top[k].sort != NULL) free(s->cells_top[k].sort);
309
      }
310
      free(s->cells_top);
311
312
313
314
      s->maxdepth = 0;
    }

    /* Set the new cell dimensions only if smaller. */
315
    for (int k = 0; k < 3; k++) {
316
      s->cdim[k] = cdim[k];
317
318
      s->width[k] = s->dim[k] / cdim[k];
      s->iwidth[k] = 1.0 / s->width[k];
319
    }
320
    const float dmin = min(s->width[0], min(s->width[1], s->width[2]));
321
322
323

    /* Allocate the highest level of cells. */
    s->tot_cells = s->nr_cells = cdim[0] * cdim[1] * cdim[2];
324
    if (posix_memalign((void *)&s->cells_top, cell_align,
325
326
                       s->nr_cells * sizeof(struct cell)) != 0)
      error("Failed to allocate cells.");
327
    bzero(s->cells_top, s->nr_cells * sizeof(struct cell));
328
329

    /* Set the cells' locks */
330
    for (int k = 0; k < s->nr_cells; k++)
331
332
      if (lock_init(&s->cells_top[k].lock) != 0)
        error("Failed to init spinlock.");
333
334

    /* Set the cell location and sizes. */
335
336
337
    for (int i = 0; i < cdim[0]; i++)
      for (int j = 0; j < cdim[1]; j++)
        for (int k = 0; k < cdim[2]; k++) {
338
          struct cell *restrict c = &s->cells_top[cell_getid(cdim, i, j, k)];
339
340
341
342
343
344
          c->loc[0] = i * s->width[0];
          c->loc[1] = j * s->width[1];
          c->loc[2] = k * s->width[2];
          c->width[0] = s->width[0];
          c->width[1] = s->width[1];
          c->width[2] = s->width[2];
345
346
347
348
          c->dmin = dmin;
          c->depth = 0;
          c->count = 0;
          c->gcount = 0;
Matthieu Schaller's avatar
Matthieu Schaller committed
349
          // c->super = c;
350
          c->ti_old = ti_current;
351
          lock_init(&c->lock);
Pedro Gonnet's avatar
Pedro Gonnet committed
352
        }
353
354

    /* Be verbose about the change. */
355
356
357
    if (verbose)
      message("set cell dimensions to [ %i %i %i ].", cdim[0], cdim[1],
              cdim[2]);
358

359
#ifdef WITH_MPI
360
361
362
363
364
    if (oldnodeIDs != NULL) {
      /* We have changed the top-level cell dimension, so need to redistribute
       * cells around the nodes. We repartition using the old space node
       * positions as a grid to resample. */
      if (s->e->nodeID == 0)
365
366
367
        message(
            "basic cell dimensions have increased - recalculating the "
            "global partition.");
368

Matthieu Schaller's avatar
Matthieu Schaller committed
369
      if (!partition_space_to_space(oldwidth, oldcdim, oldnodeIDs, s)) {
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387

        /* Failed, try another technique that requires no settings. */
        message("Failed to get a new partition, trying less optimal method");
        struct partition initial_partition;
#ifdef HAVE_METIS
        initial_partition.type = INITPART_METIS_NOWEIGHT;
#else
        initial_partition.type = INITPART_VECTORIZE;
#endif
        partition_initial_partition(&initial_partition, s->e->nodeID,
                                    s->e->nr_nodes, s);
      }

      /* Re-distribute the particles to their new nodes. */
      engine_redistribute(s->e);

      /* Make the proxies. */
      engine_makeproxies(s->e);
388

389
390
      /* Finished with these. */
      free(oldnodeIDs);
391
    }
Pedro Gonnet's avatar
Pedro Gonnet committed
392
#endif /* WITH_MPI */
393
394
395
396

    // message( "rebuilding upper-level cells took %.3f %s." ,
    // clocks_from_ticks(double)(getticks() - tic), clocks_getunit());

397
398
  } /* re-build upper-level cells? */

399
  else { /* Otherwise, just clean up the cells. */
400
401

    /* Free the old cells, if they were allocated. */
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
    for (int k = 0; k < s->nr_cells; k++) {
      space_rebuild_recycle(s, &s->cells_top[k]);
      s->cells_top[k].sorts = NULL;
      s->cells_top[k].nr_tasks = 0;
      s->cells_top[k].density = NULL;
      s->cells_top[k].gradient = NULL;
      s->cells_top[k].force = NULL;
      s->cells_top[k].grav = NULL;
      s->cells_top[k].dx_max = 0.0f;
      s->cells_top[k].sorted = 0;
      s->cells_top[k].count = 0;
      s->cells_top[k].gcount = 0;
      s->cells_top[k].init = NULL;
      s->cells_top[k].extra_ghost = NULL;
      s->cells_top[k].ghost = NULL;
      s->cells_top[k].kick = NULL;
418
      s->cells_top[k].drift = NULL;
419
420
421
      s->cells_top[k].cooling = NULL;
      s->cells_top[k].sourceterms = NULL;
      s->cells_top[k].super = &s->cells_top[k];
Matthieu Schaller's avatar
Matthieu Schaller committed
422
      s->cells_top[k].ti_old = 0;
423
424
425
426
427
428
429
430
431
432
433
434
#if WITH_MPI
      s->cells_top[k].recv_xv = NULL;
      s->cells_top[k].recv_rho = NULL;
      s->cells_top[k].recv_gradient = NULL;
      s->cells_top[k].recv_ti = NULL;

      s->cells_top[k].send_xv = NULL;
      s->cells_top[k].send_rho = NULL;
      s->cells_top[k].send_gradient = NULL;
      s->cells_top[k].send_ti = NULL;
#endif
    }
435
436
    s->maxdepth = 0;
  }
437
438
439
440

  if (verbose)
    message("took %.3f %s.", clocks_from_ticks(getticks() - tic),
            clocks_getunit());
441
}
442
443
444
445
446

/**
 * @brief Re-build the cells as well as the tasks.
 *
 * @param s The #space in which to update the cells.
447
 * @param verbose Print messages to stdout or not
448
449
 *
 */
450
void space_rebuild(struct space *s, int verbose) {
451

Matthieu Schaller's avatar
Matthieu Schaller committed
452
  const ticks tic = getticks();
453

454
455
456
457
458
/* Be verbose about this. */
#ifdef SWIFT_DEBUG_CHECKS
  message("re)building space");
  fflush(stdout);
#endif
459
460

  /* Re-grid if necessary, or just re-set the cell data. */
461
  space_regrid(s, verbose);
462

Pedro Gonnet's avatar
Pedro Gonnet committed
463
464
  size_t nr_parts = s->nr_parts;
  size_t nr_gparts = s->nr_gparts;
465
  struct cell *restrict cells_top = s->cells_top;
466
  const int ti_current = (s->e != NULL) ? s->e->ti_current : 0;
467

Pedro Gonnet's avatar
Pedro Gonnet committed
468
469
470
  /* Run through the particles and get their cell index. Allocates
     an index that is larger than the number of particles to avoid
     re-allocating after shuffling. */
471
  const size_t ind_size = s->size_parts + 100;
472
473
  int *ind;
  if ((ind = (int *)malloc(sizeof(int) * ind_size)) == NULL)
474
    error("Failed to allocate temporary particle indices.");
475
  if (s->size_parts > 0) space_parts_get_cell_index(s, ind, cells_top, verbose);
476

477
  /* Run through the gravity particles and get their cell index. */
478
  const size_t gind_size = s->size_gparts + 100;
479
480
481
  int *gind;
  if ((gind = (int *)malloc(sizeof(int) * gind_size)) == NULL)
    error("Failed to allocate temporary g-particle indices.");
Pedro Gonnet's avatar
Pedro Gonnet committed
482
483
  if (s->size_gparts > 0)
    space_gparts_get_cell_index(s, gind, cells_top, verbose);
484
485

#ifdef WITH_MPI
486

487
  /* Move non-local parts to the end of the list. */
488
  const int local_nodeID = s->e->nodeID;
489
  for (size_t k = 0; k < nr_parts;) {
490
    if (cells_top[ind[k]].nodeID != local_nodeID) {
491
      nr_parts -= 1;
Matthieu Schaller's avatar
Bug fix    
Matthieu Schaller committed
492
      const struct part tp = s->parts[k];
493
494
      s->parts[k] = s->parts[nr_parts];
      s->parts[nr_parts] = tp;
495
      if (s->parts[k].gpart != NULL) {
496
        s->parts[k].gpart->id_or_neg_offset = -k;
497
498
      }
      if (s->parts[nr_parts].gpart != NULL) {
499
        s->parts[nr_parts].gpart->id_or_neg_offset = -nr_parts;
500
      }
Matthieu Schaller's avatar
Bug fix    
Matthieu Schaller committed
501
      const struct xpart txp = s->xparts[k];
502
503
      s->xparts[k] = s->xparts[nr_parts];
      s->xparts[nr_parts] = txp;
Matthieu Schaller's avatar
Bug fix    
Matthieu Schaller committed
504
      const int t = ind[k];
505
506
      ind[k] = ind[nr_parts];
      ind[nr_parts] = t;
Matthieu Schaller's avatar
Matthieu Schaller committed
507
    } else {
508
509
510
511
      /* Increment when not exchanging otherwise we need to retest "k".*/
      k++;
    }
  }
512

513
#ifdef SWIFT_DEBUG_CHECKS
Peter W. Draper's avatar
Peter W. Draper committed
514
  /* Check that all parts are in the correct places. */
515
  for (size_t k = 0; k < nr_parts; k++) {
516
    if (cells_top[ind[k]].nodeID != local_nodeID) {
517
518
519
520
      error("Failed to move all non-local parts to send list");
    }
  }
  for (size_t k = nr_parts; k < s->nr_parts; k++) {
521
    if (cells_top[ind[k]].nodeID == local_nodeID) {
522
      error("Failed to remove local parts from send list");
523
    }
524
525
  }
#endif
526

527
  /* Move non-local gparts to the end of the list. */
528
  for (size_t k = 0; k < nr_gparts;) {
529
    if (cells_top[gind[k]].nodeID != local_nodeID) {
530
      nr_gparts -= 1;
Matthieu Schaller's avatar
Bug fix    
Matthieu Schaller committed
531
      const struct gpart tp = s->gparts[k];
532
533
      s->gparts[k] = s->gparts[nr_gparts];
      s->gparts[nr_gparts] = tp;
534
535
      if (s->gparts[k].id_or_neg_offset <= 0) {
        s->parts[-s->gparts[k].id_or_neg_offset].gpart = &s->gparts[k];
536
      }
537
538
539
      if (s->gparts[nr_gparts].id_or_neg_offset <= 0) {
        s->parts[-s->gparts[nr_gparts].id_or_neg_offset].gpart =
            &s->gparts[nr_gparts];
540
      }
Matthieu Schaller's avatar
Bug fix    
Matthieu Schaller committed
541
542
543
      const int t = gind[k];
      gind[k] = gind[nr_gparts];
      gind[nr_gparts] = t;
Matthieu Schaller's avatar
Matthieu Schaller committed
544
    } else {
545
546
547
548
      /* Increment when not exchanging otherwise we need to retest "k".*/
      k++;
    }
  }
549

550
#ifdef SWIFT_DEBUG_CHECKS
551
552
  /* Check that all gparts are in the correct place (untested). */
  for (size_t k = 0; k < nr_gparts; k++) {
553
    if (cells_top[gind[k]].nodeID != local_nodeID) {
554
555
556
557
      error("Failed to move all non-local gparts to send list");
    }
  }
  for (size_t k = nr_gparts; k < s->nr_gparts; k++) {
558
    if (cells_top[gind[k]].nodeID == local_nodeID) {
559
      error("Failed to remove local gparts from send list");
560
    }
561
562
  }
#endif
563

564
565
  /* Exchange the strays, note that this potentially re-allocates
     the parts arrays. */
566
  size_t nr_parts_exchanged = s->nr_parts - nr_parts;
567
  size_t nr_gparts_exchanged = s->nr_gparts - nr_gparts;
Pedro Gonnet's avatar
Pedro Gonnet committed
568
569
570
571
  engine_exchange_strays(s->e, nr_parts, &ind[nr_parts], &nr_parts_exchanged,
                         nr_gparts, &gind[nr_gparts], &nr_gparts_exchanged);

  /* Set the new particle counts. */
572
  s->nr_parts = nr_parts + nr_parts_exchanged;
573
  s->nr_gparts = nr_gparts + nr_gparts_exchanged;
574
575

  /* Re-allocate the index array if needed.. */
576
  if (s->nr_parts + 1 > ind_size) {
577
    int *ind_new;
578
    if ((ind_new = (int *)malloc(sizeof(int) * (s->nr_parts + 1))) == NULL)
579
      error("Failed to allocate temporary particle indices.");
580
    memcpy(ind_new, ind, sizeof(int) * nr_parts);
581
582
    free(ind);
    ind = ind_new;
583
584
  }

585
586
587
  const int cdim[3] = {s->cdim[0], s->cdim[1], s->cdim[2]};
  const double ih[3] = {s->iwidth[0], s->iwidth[1], s->iwidth[2]};

588
  /* Assign each particle to its cell. */
Pedro Gonnet's avatar
Pedro Gonnet committed
589
  for (size_t k = nr_parts; k < s->nr_parts; k++) {
Matthieu Schaller's avatar
Matthieu Schaller committed
590
    const struct part *const p = &s->parts[k];
591
    ind[k] =
592
        cell_getid(cdim, p->x[0] * ih[0], p->x[1] * ih[1], p->x[2] * ih[2]);
593
#ifdef SWIFT_DEBUG_CHECKS
594
    if (cells_top[ind[k]].nodeID != local_nodeID)
595
      error("Received part that does not belong to me (nodeID=%i).",
596
            cells_top[ind[k]].nodeID);
597
#endif
598
  }
599
  nr_parts = s->nr_parts;
600
601

#endif /* WITH_MPI */
602
603

  /* Sort the parts according to their cells. */
604
605
  if (nr_parts > 0)
    space_parts_sort(s, ind, nr_parts, 0, s->nr_cells - 1, verbose);
606
607

  /* Re-link the gparts. */
608
  if (nr_parts > 0 && nr_gparts > 0) part_relink_gparts(s->parts, nr_parts, 0);
609

610
#ifdef SWIFT_DEBUG_CHECKS
611
  /* Verify space_sort_struct. */
612
613
614
  for (size_t k = 1; k < nr_parts; k++) {
    if (ind[k - 1] > ind[k]) {
      error("Sort failed!");
615
    } else if (ind[k] != cell_getid(s->cdim, s->parts[k].x[0] * s->iwidth[0],
616
617
                                    s->parts[k].x[1] * s->iwidth[1],
                                    s->parts[k].x[2] * s->iwidth[2])) {
618
619
620
621
      error("Incorrect indices!");
    }
  }
#endif
622

623
624
625
626
627
628
629
630
631
632
  /* Extract the cell counts from the sorted indices. */
  size_t last_index = 0;
  ind[nr_parts] = s->nr_cells;  // sentinel.
  for (size_t k = 0; k < nr_parts; k++) {
    if (ind[k] < ind[k + 1]) {
      cells_top[ind[k]].count = k - last_index + 1;
      last_index = k + 1;
    }
  }

633
  /* We no longer need the indices as of here. */
634
  free(ind);
635

636
637
638
#ifdef WITH_MPI

  /* Re-allocate the index array if needed.. */
639
  if (s->nr_gparts + 1 > gind_size) {
640
    int *gind_new;
641
    if ((gind_new = (int *)malloc(sizeof(int) * (s->nr_gparts + 1))) == NULL)
642
      error("Failed to allocate temporary g-particle indices.");
643
    memcpy(gind_new, gind, sizeof(int) * nr_gparts);
644
645
646
647
648
    free(gind);
    gind = gind_new;
  }

  /* Assign each particle to its cell. */
649
  for (size_t k = nr_gparts; k < s->nr_gparts; k++) {
Matthieu Schaller's avatar
Matthieu Schaller committed
650
    const struct gpart *const p = &s->gparts[k];
651
652
    gind[k] =
        cell_getid(cdim, p->x[0] * ih[0], p->x[1] * ih[1], p->x[2] * ih[2]);
653
654

#ifdef SWIFT_DEBUG_CHECKS
655
    if (cells_top[gind[k]].nodeID != s->e->nodeID)
656
      error("Received part that does not belong to me (nodeID=%i).",
657
            cells_top[gind[k]].nodeID);
658
#endif
659
660
661
662
  }
  nr_gparts = s->nr_gparts;

#endif
663

664
  /* Sort the gparts according to their cells. */
665
666
  if (nr_gparts > 0)
    space_gparts_sort(s, gind, nr_gparts, 0, s->nr_cells - 1, verbose);
667
668

  /* Re-link the parts. */
669
670
  if (nr_parts > 0 && nr_gparts > 0)
    part_relink_parts(s->gparts, nr_gparts, s->parts);
671

672
673
  /* Extract the cell counts from the sorted indices. */
  size_t last_gindex = 0;
674
  gind[nr_gparts] = s->nr_cells;
675
676
  for (size_t k = 0; k < nr_gparts; k++) {
    if (gind[k] < gind[k + 1]) {
677
      cells_top[gind[k]].gcount = k - last_gindex + 1;
678
679
680
681
      last_gindex = k + 1;
    }
  }

682
  /* We no longer need the indices as of here. */
683
  free(gind);
684

685
#ifdef SWIFT_DEBUG_CHECKS
686
687
688
  /* Verify that the links are correct */
  for (size_t k = 0; k < nr_gparts; ++k) {

689
    if (s->gparts[k].id_or_neg_offset < 0) {
690

691
      const struct part *part = &s->parts[-s->gparts[k].id_or_neg_offset];
692

693
694
695
696
      if (part->gpart != &s->gparts[k]) error("Linking problem !");

      if (s->gparts[k].x[0] != part->x[0] || s->gparts[k].x[1] != part->x[1] ||
          s->gparts[k].x[2] != part->x[2])
697
698
699
700
701
        error("Linked particles are not at the same position !");
    }
  }
  for (size_t k = 0; k < nr_parts; ++k) {

702
    if (s->parts[k].gpart != NULL &&
703
        s->parts[k].gpart->id_or_neg_offset != -(ptrdiff_t)k) {
704
      error("Linking problem !");
705
706
    }
  }
707
#endif
708

709
710
  /* Hook the cells up to the parts. */
  // tic = getticks();
711
712
713
  struct part *finger = s->parts;
  struct xpart *xfinger = s->xparts;
  struct gpart *gfinger = s->gparts;
714
  for (int k = 0; k < s->nr_cells; k++) {
715
    struct cell *restrict c = &cells_top[k];
716
    c->ti_old = ti_current;
717
718
719
720
721
722
723
    c->parts = finger;
    c->xparts = xfinger;
    c->gparts = gfinger;
    finger = &finger[c->count];
    xfinger = &xfinger[c->count];
    gfinger = &gfinger[c->gcount];
  }
724
  // message( "hooking up cells took %.3f %s." ,
Matthieu Schaller's avatar
Matthieu Schaller committed
725
  // clocks_from_ticks(getticks() - tic), clocks_getunit());
726
727
728

  /* At this point, we have the upper-level cells, old or new. Now make
     sure that the parts in each cell are ok. */
729
  space_split(s, cells_top, s->nr_cells, verbose);
730
731
732
733
734
735
736
737
738

  if (verbose)
    message("took %.3f %s.", clocks_from_ticks(getticks() - tic),
            clocks_getunit());
}

/**
 * @brief Split particles between cells of a hierarchy
 *
739
740
 * This is done in parallel using threads in the #threadpool.
 *
741
 * @param s The #space.
742
743
 * @param cells The cell hierarchy.
 * @param nr_cells The number of cells.
744
745
 * @param verbose Are we talkative ?
 */
746
747
void space_split(struct space *s, struct cell *cells, int nr_cells,
                 int verbose) {
748

Matthieu Schaller's avatar
Matthieu Schaller committed
749
  const ticks tic = getticks();
750

751
  threadpool_map(&s->e->threadpool, space_split_mapper, cells, nr_cells,
752
                 sizeof(struct cell), 1, s);
753

754
755
756
  if (verbose)
    message("took %.3f %s.", clocks_from_ticks(getticks() - tic),
            clocks_getunit());
757
}
758

759
760
761
762
763
764
765
766
/**
 * @brief Runs through the top-level cells and checks whether tasks associated
 * with them can be split. If not, try to sanitize the cells.
 *
 * @param s The #space to act upon.
 */
void space_sanitize(struct space *s) {

767
768
  s->sanitized = 1;

769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
  for (int k = 0; k < s->nr_cells; k++) {

    struct cell *c = &s->cells_top[k];
    const double min_width = c->dmin;

    /* Do we have a problem ? */
    if (c->h_max * kernel_gamma * space_stretch > min_width * 0.5 &&
        c->count > space_maxcount) {

      /* Ok, clean-up the mess */
      cell_sanitize(c);
    }
  }
}

784
/**
785
 * @brief #threadpool mapper function to compute the particle cell indices.
786
 *
787
 * @param map_data Pointer towards the particles.
788
 * @param nr_parts The number of particles to treat.
789
 * @param extra_data Pointers to the space and index list
790
 */
791
792
void space_parts_get_cell_index_mapper(void *map_data, int nr_parts,
                                       void *extra_data) {
793

794
795
796
797
  /* Unpack the data */
  struct part *restrict parts = (struct part *)map_data;
  struct index_data *data = (struct index_data *)extra_data;
  struct space *s = data->s;
798
  int *const ind = data->ind + (ptrdiff_t)(parts - s->parts);
799
800

  /* Get some constants */
801
802
803
  const double dim_x = s->dim[0];
  const double dim_y = s->dim[1];
  const double dim_z = s->dim[2];
Matthieu Schaller's avatar
Matthieu Schaller committed
804
  const int cdim[3] = {s->cdim[0], s->cdim[1], s->cdim[2]};
805
806
807
  const double ih_x = s->iwidth[0];
  const double ih_y = s->iwidth[1];
  const double ih_z = s->iwidth[2];
808

809
  for (int k = 0; k < nr_parts; k++) {
810
811
812
813

    /* Get the particle */
    struct part *restrict p = &parts[k];

814
815
816
817
    const double old_pos_x = p->x[0];
    const double old_pos_y = p->x[1];
    const double old_pos_z = p->x[2];

818
    /* Put it back into the simulation volume */
819
820
821
    const double pos_x = box_wrap(old_pos_x, 0.0, dim_x);
    const double pos_y = box_wrap(old_pos_y, 0.0, dim_y);
    const double pos_z = box_wrap(old_pos_z, 0.0, dim_z);
822
823

    /* Get its cell index */
Matthieu Schaller's avatar
Matthieu Schaller committed
824
825
    const int index =
        cell_getid(cdim, pos_x * ih_x, pos_y * ih_y, pos_z * ih_z);
826
    ind[k] = index;
827

828
829
830
831
    /* Update the position */
    p->x[0] = pos_x;
    p->x[1] = pos_y;
    p->x[2] = pos_z;
832
833
834
835
  }
}

/**
836
 * @brief #threadpool mapper function to compute the g-particle cell indices.
837
 *
838
 * @param map_data Pointer towards the g-particles.
839
 * @param nr_gparts The number of g-particles to treat.
840
 * @param extra_data Pointers to the space and index list
841
 */
842
843
void space_gparts_get_cell_index_mapper(void *map_data, int nr_gparts,
                                        void *extra_data) {
844

845
846
847
848
  /* Unpack the data */
  struct gpart *restrict gparts = (struct gpart *)map_data;
  struct index_data *data = (struct index_data *)extra_data;
  struct space *s = data->s;
849
  int *const ind = data->ind + (ptrdiff_t)(gparts - s->gparts);
850
851

  /* Get some constants */
Matthieu Schaller's avatar
Matthieu Schaller committed
852
853
854
  const double dim_x = s->dim[0];
  const double dim_y = s->dim[1];
  const double dim_z = s->dim[2];
855
  const int cdim[3] = {s->cdim[0], s->cdim[1], s->cdim[2]};
Matthieu Schaller's avatar
Matthieu Schaller committed
856
857
858
  const double ih_x = s->iwidth[0];
  const double ih_y = s->iwidth[1];
  const double ih_z = s->iwidth[2];
859

860
  for (int k = 0; k < nr_gparts; k++) {
861
862
863
864

    /* Get the particle */
    struct gpart *restrict gp = &gparts[k];

Matthieu Schaller's avatar
Matthieu Schaller committed
865
866
867
868
    const double old_pos_x = gp->x[0];
    const double old_pos_y = gp->x[1];
    const double old_pos_z = gp->x[2];

869
    /* Put it back into the simulation volume */
Matthieu Schaller's avatar
Matthieu Schaller committed
870
871
872
    const double pos_x = box_wrap(old_pos_x, 0.0, dim_x);
    const double pos_y = box_wrap(old_pos_y, 0.0, dim_y);
    const double pos_z = box_wrap(old_pos_z, 0.0, dim_z);
873
874
875

    /* Get its cell index */
    const int index =
Matthieu Schaller's avatar
Matthieu Schaller committed
876
        cell_getid(cdim, pos_x * ih_x, pos_y * ih_y, pos_z * ih_z);
877
    ind[k] = index;
Matthieu Schaller's avatar
Matthieu Schaller committed
878
879
880
881
882

    /* Update the position */
    gp->x[0] = pos_x;
    gp->x[1] = pos_y;
    gp->x[2] = pos_z;
883
884
885
  }
}

886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
/**
 * @brief Computes the cell index of all the particles and update the cell
 * count.
 *
 * @param s The #space.
 * @param ind The array of indices to fill.
 * @param cells The array of #cell to update.
 * @param verbose Are we talkative ?
 */
void space_parts_get_cell_index(struct space *s, int *ind, struct cell *cells,
                                int verbose) {

  const ticks tic = getticks();

  /* Pack the extra information */
  struct index_data data;
  data.s = s;
  data.cells = cells;
  data.ind = ind;

  threadpool_map(&s->e->threadpool, space_parts_get_cell_index_mapper, s->parts,
                 s->nr_parts, sizeof(struct part), 1000, &data);

  if (verbose)
    message("took %.3f %s.", clocks_from_ticks(getticks() - tic),
            clocks_getunit());
}

/**
 * @brief Computes the cell index of all the g-particles and update the cell
 * gcount.
 *
 * @param s The #space.
 * @param gind The array of indices to fill.
 * @param cells The array of #cell to update.
 * @param verbose Are we talkative ?
 */
void space_gparts_get_cell_index(struct space *s, int *gind, struct cell *cells,
                                 int verbose) {

  const ticks tic = getticks();

  /* Pack the extra information */
  struct index_data data;
  data.s = s;
  data.cells = cells;
  data.ind = gind;

  threadpool_map(&s->e->threadpool, space_gparts_get_cell_index_mapper,
                 s->gparts, s->nr_gparts, sizeof(struct gpart), 1000, &data);

  if (verbose)
    message("took %.3f %s.", clocks_from_ticks(getticks() - tic),
            clocks_getunit());
}

942
/**
943
 * @brief Sort the particles and condensed particles according to the given
944
 * indices.
945
 *
Matthieu Schaller's avatar
Matthieu Schaller committed
946
 * @param s The #space.
947
948
949
950
 * @param ind The indices with respect to which the parts are sorted.
 * @param N The number of parts
 * @param min Lowest index.
 * @param max highest index.
951
 * @param verbose Are we talkative ?
952
 */
953
void space_parts_sort(struct space *s, int *ind, size_t N, int min, int max,
954
955
                      int verbose) {

Matthieu Schaller's avatar
Matthieu Schaller committed
956
  const ticks tic = getticks();
957

958
959
960
961
962
963
  /* Populate a parallel_sort structure with the input data */
  struct parallel_sort sort_struct;
  sort_struct.parts = s->parts;
  sort_struct.xparts = s->xparts;
  sort_struct.ind = ind;
  sort_struct.stack_size = 2 * (max - min + 1) + 10 + s->e->nr_threads;
964
965
  if ((sort_struct.stack =
           malloc(sizeof(struct qstack) * sort_struct.stack_size)) == NULL)
966
    error("Failed to allocate sorting stack.");
Matthieu Schaller's avatar
Matthieu Schaller committed
967
  for (unsigned int i = 0; i < sort_struct.stack_size; i++)
968
    sort_struct.stack[i].ready = 0;
969