space.c 57.7 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 "minmax.h"
53
#include "runner.h"
54
#include "threadpool.h"
55
#include "tools.h"
Pedro Gonnet's avatar
Pedro Gonnet committed
56
57
58

/* Split size. */
int space_splitsize = space_splitsize_default;
59
int space_subsize = space_subsize_default;
60
int space_maxsize = space_maxsize_default;
61
int space_maxcount = space_maxcount_default;
Pedro Gonnet's avatar
Pedro Gonnet committed
62
63
64

/* Map shift vector to sortlist. */
const int sortlistID[27] = {
65
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
    /* ( -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};

93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
/**
 * @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;
};

115
116
117
118
119
120
121
122
123
/**
 * @brief Information required to compute the particle cell indices.
 */
struct index_data {
  struct space *s;
  struct cell *cells;
  int *ind;
};

124
125
126
127
128
129
130
131
132
133
134
/**
 * @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.
 */
135
136
137
138
int space_getsid(struct space *s, struct cell **ci, struct cell **cj,
                 double *shift) {

  /* Get the relative distance between the pairs, wrapping. */
139
140
141
  const int periodic = s->periodic;
  double dx[3];
  for (int k = 0; k < 3; k++) {
142
143
144
145
146
147
148
149
150
151
152
    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. */
153
  int sid = 0;
154
  for (int k = 0; k < 3; k++)
155
156
157
158
    sid = 3 * sid + ((dx[k] < 0.0) ? 0 : ((dx[k] > 0.0) ? 2 : 1));

  /* Switch the cells around? */
  if (runner_flip[sid]) {
159
    struct cell *temp = *ci;
160
161
    *ci = *cj;
    *cj = temp;
162
    for (int k = 0; k < 3; k++) shift[k] = -shift[k];
163
164
165
166
167
168
  }
  sid = sortlistID[sid];

  /* Return the sort ID. */
  return sid;
}
169

170
/**
171
 * @brief Recursively dismantle a cell tree.
172
 *
173
174
 * @param s The #space.
 * @param c The #cell to recycle.
175
 */
176
177
178
void space_rebuild_recycle(struct space *s, struct cell *c) {

  if (c->split)
179
    for (int k = 0; k < 8; k++)
180
181
182
183
184
185
186
      if (c->progeny[k] != NULL) {
        space_rebuild_recycle(s, c->progeny[k]);
        space_recycle(s, c->progeny[k]);
        c->progeny[k] = NULL;
      }
}

187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
/**
 * @brief Mapper function to clean out the cell hierarchies for a regrid.
 */
 
void space_clear_cells_mapper(void *map_data, int num_elements, void *extra_data) {
  
  struct cell *cells = (struct cell *)map_data;
  struct space *s = (struct space *)extra_data;
  
  for (int k = 0; k < num_elements; k++) {
    struct cell *c = &cells[k];
      space_rebuild_recycle(s, c);
      c->sorts = NULL;
      c->nr_tasks = 0;
      c->density = NULL;
      c->gradient = NULL;
      c->force = NULL;
      c->grav = NULL;
      c->dx_max = 0.0f;
      c->sorted = 0;
      c->count = 0;
      c->gcount = 0;
      c->init = NULL;
      c->extra_ghost = NULL;
      c->ghost = NULL;
      c->kick = NULL;
      c->cooling = NULL;
      c->sourceterms = NULL;
      c->super = c;
#if WITH_MPI
      c->recv_xv = NULL;
      c->recv_rho = NULL;
      c->recv_gradient = NULL;
      c->recv_ti = NULL;

      c->send_xv = NULL;
      c->send_rho = NULL;
      c->send_gradient = NULL;
      c->send_ti = NULL;
#endif
  }
}

230
/**
231
 * @brief Re-build the top-level cell grid.
232
 *
233
 * @param s The #space.
234
 * @param verbose Print messages to stdout or not.
235
 */
236
void space_regrid(struct space *s, int verbose) {
237

238
  const size_t nr_parts = s->nr_parts;
239
  const ticks tic = getticks();
240
  const int ti_current = (s->e != NULL) ? s->e->ti_current : 0;
241

242
  /* Run through the cells and get the current h_max. */
243
  // tic = getticks();
244
  float h_max = s->cell_min / kernel_gamma / space_stretch;
245
  if (nr_parts > 0) {
246
    if (s->cells_top != NULL) {
Tom Theuns's avatar
Tom Theuns committed
247
      for (int k = 0; k < s->nr_cells; k++) {
248
249
250
        if (s->cells_top[k].nodeID == engine_rank &&
            s->cells_top[k].h_max > h_max) {
          h_max = s->cells_top[k].h_max;
251
        }
252
253
      }
    } else {
254
      for (size_t k = 0; k < nr_parts; k++) {
Matthieu Schaller's avatar
Matthieu Schaller committed
255
        if (s->parts[k].h > h_max) h_max = s->parts[k].h;
256
      }
257
258
259
260
261
262
263
264
265
266
    }
  }

/* 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)
267
      error("Failed to aggregate the rebuild flag across nodes.");
268
269
270
    h_max = buff;
  }
#endif
271
  if (verbose) message("h_max is %.3e (cell_min=%.3e).", h_max, s->cell_min);
272
273

  /* Get the new putative cell dimensions. */
274
  const int cdim[3] = {
275
276
277
278
279
280
      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))};
281
282
283
284
285

  /* 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 "
286
287
288
        "is switched on.\nThis error is often caused by any of the "
        "followings:\n"
        " - too few particles to generate a sensible grid,\n"
289
290
        " - the initial value of 'Scheduler:max_top_level_cells' is too "
        "small,\n"
291
        " - the (minimal) time-step is too large leading to particles with "
292
293
294
        "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");
295

296
297
298
299
300
301
  /* 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.");

302
303
304
/* 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. */
305
#ifdef WITH_MPI
Matthieu Schaller's avatar
Matthieu Schaller committed
306
  double oldwidth[3];
307
308
309
310
311
312
313
314
  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];
315
316
317
    oldwidth[0] = s->width[0];
    oldwidth[1] = s->width[1];
    oldwidth[2] = s->width[2];
318
319
320
321
322
323
324
325
326

    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);
327
          oldnodeIDs[cid] = s->cells_top[cid].nodeID;
328
329
330
331
332
        }
      }
    }
  }

333
334
335
336
#endif

  /* Do we need to re-build the upper-level cells? */
  // tic = getticks();
337
  if (s->cells_top == NULL || cdim[0] < s->cdim[0] || cdim[1] < s->cdim[1] ||
338
339
340
      cdim[2] < s->cdim[2]) {

    /* Free the old cells, if they were allocated. */
341
    if (s->cells_top != NULL) {
342
      for (int k = 0; k < s->nr_cells; k++) {
343
344
        space_rebuild_recycle(s, &s->cells_top[k]);
        if (s->cells_top[k].sort != NULL) free(s->cells_top[k].sort);
345
      }
346
      free(s->cells_top);
347
348
349
350
      s->maxdepth = 0;
    }

    /* Set the new cell dimensions only if smaller. */
351
    for (int k = 0; k < 3; k++) {
352
      s->cdim[k] = cdim[k];
353
354
      s->width[k] = s->dim[k] / cdim[k];
      s->iwidth[k] = 1.0 / s->width[k];
355
    }
356
    const float dmin = min(s->width[0], min(s->width[1], s->width[2]));
357
358
359

    /* Allocate the highest level of cells. */
    s->tot_cells = s->nr_cells = cdim[0] * cdim[1] * cdim[2];
360
    if (posix_memalign((void *)&s->cells_top, cell_align,
361
362
                       s->nr_cells * sizeof(struct cell)) != 0)
      error("Failed to allocate cells.");
363
    bzero(s->cells_top, s->nr_cells * sizeof(struct cell));
364
    for (int k = 0; k < s->nr_cells; k++)
365
366
      if (lock_init(&s->cells_top[k].lock) != 0)
        error("Failed to init spinlock.");
367
368

    /* Set the cell location and sizes. */
369
370
371
    for (int i = 0; i < cdim[0]; i++)
      for (int j = 0; j < cdim[1]; j++)
        for (int k = 0; k < cdim[2]; k++) {
372
          struct cell *restrict c = &s->cells_top[cell_getid(cdim, i, j, k)];
373
374
375
376
377
378
          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];
379
380
381
382
383
          c->dmin = dmin;
          c->depth = 0;
          c->count = 0;
          c->gcount = 0;
          c->super = c;
384
          c->ti_old = ti_current;
385
          lock_init(&c->lock);
Pedro Gonnet's avatar
Pedro Gonnet committed
386
        }
387
388

    /* Be verbose about the change. */
389
390
391
    if (verbose)
      message("set cell dimensions to [ %i %i %i ].", cdim[0], cdim[1],
              cdim[2]);
392
393
    fflush(stdout);

394
#ifdef WITH_MPI
395
396
397
398
399
    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)
400
401
402
        message(
            "basic cell dimensions have increased - recalculating the "
            "global partition.");
403

Matthieu Schaller's avatar
Matthieu Schaller committed
404
      if (!partition_space_to_space(oldwidth, oldcdim, oldnodeIDs, s)) {
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422

        /* 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);
423

424
425
      /* Finished with these. */
      free(oldnodeIDs);
426
    }
427
#endif  /* WITH_MPI */
428
429
430
431

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

432
433
  } /* re-build upper-level cells? */

434
  else { /* Otherwise, just clean up the cells. */
435
436

    /* Free the old cells, if they were allocated. */
437
438
439
    threadpool_map(&s->e->threadpool, space_clear_cells_mapper,
                    s->cells_top, s->nr_cells, sizeof(struct cell), 100, s);
    // space_clear_cells_mapper(s->cells_top, s->nr_cells, s);
440
441
    s->maxdepth = 0;
  }
442
443
444
445

  if (verbose)
    message("took %.3f %s.", clocks_from_ticks(getticks() - tic),
            clocks_getunit());
446
}
447
448
449
450
451

/**
 * @brief Re-build the cells as well as the tasks.
 *
 * @param s The #space in which to update the cells.
452
 * @param verbose Print messages to stdout or not
453
454
 *
 */
455
void space_rebuild(struct space *s, int verbose) {
456

Matthieu Schaller's avatar
Matthieu Schaller committed
457
  const ticks tic = getticks();
458
459

  /* Be verbose about this. */
460
  // message("re)building space..."); fflush(stdout);
461
462

  /* Re-grid if necessary, or just re-set the cell data. */
463
  space_regrid(s, verbose);
464

Pedro Gonnet's avatar
Pedro Gonnet committed
465
466
  size_t nr_parts = s->nr_parts;
  size_t nr_gparts = s->nr_gparts;
467
  struct cell *restrict cells_top = s->cells_top;
468
  const int ti_current = (s->e != NULL) ? s->e->ti_current : 0;
469
470

  /* Run through the particles and get their cell index. */
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.");
482
  if (s->size_gparts > 0) space_gparts_get_cell_index(s, gind, cells_top, verbose);
483
484

#ifdef WITH_MPI
485

486
  /* Move non-local parts to the end of the list. */
487
  const int local_nodeID = s->e->nodeID;
488
  for (size_t k = 0; k < nr_parts;) {
489
    if (cells_top[ind[k]].nodeID != local_nodeID) {
490
      nr_parts -= 1;
Matthieu Schaller's avatar
Bug fix    
Matthieu Schaller committed
491
      const struct part tp = s->parts[k];
492
493
      s->parts[k] = s->parts[nr_parts];
      s->parts[nr_parts] = tp;
494
      if (s->parts[k].gpart != NULL) {
495
        s->parts[k].gpart->id_or_neg_offset = -k;
496
497
      }
      if (s->parts[nr_parts].gpart != NULL) {
498
        s->parts[nr_parts].gpart->id_or_neg_offset = -nr_parts;
499
      }
Matthieu Schaller's avatar
Bug fix    
Matthieu Schaller committed
500
      const struct xpart txp = s->xparts[k];
501
502
      s->xparts[k] = s->xparts[nr_parts];
      s->xparts[nr_parts] = txp;
Matthieu Schaller's avatar
Bug fix    
Matthieu Schaller committed
503
      const int t = ind[k];
504
505
      ind[k] = ind[nr_parts];
      ind[nr_parts] = t;
Matthieu Schaller's avatar
Matthieu Schaller committed
506
    } else {
507
508
509
510
      /* Increment when not exchanging otherwise we need to retest "k".*/
      k++;
    }
  }
511

512
#ifdef SWIFT_DEBUG_CHECKS
Peter W. Draper's avatar
Peter W. Draper committed
513
  /* Check that all parts are in the correct places. */
514
  for (size_t k = 0; k < nr_parts; k++) {
515
    if (cells_top[ind[k]].nodeID != local_nodeID) {
516
517
518
519
      error("Failed to move all non-local parts to send list");
    }
  }
  for (size_t k = nr_parts; k < s->nr_parts; k++) {
520
    if (cells_top[ind[k]].nodeID == local_nodeID) {
521
      error("Failed to remove local parts from send list");
522
    }
523
524
  }
#endif
525

526
  /* Move non-local gparts to the end of the list. */
527
  for (size_t k = 0; k < nr_gparts;) {
528
    if (cells_top[gind[k]].nodeID != local_nodeID) {
529
      nr_gparts -= 1;
Matthieu Schaller's avatar
Bug fix    
Matthieu Schaller committed
530
      const struct gpart tp = s->gparts[k];
531
532
      s->gparts[k] = s->gparts[nr_gparts];
      s->gparts[nr_gparts] = tp;
533
534
      if (s->gparts[k].id_or_neg_offset <= 0) {
        s->parts[-s->gparts[k].id_or_neg_offset].gpart = &s->gparts[k];
535
      }
536
537
538
      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];
539
      }
Matthieu Schaller's avatar
Bug fix    
Matthieu Schaller committed
540
541
542
      const int t = gind[k];
      gind[k] = gind[nr_gparts];
      gind[nr_gparts] = t;
Matthieu Schaller's avatar
Matthieu Schaller committed
543
    } else {
544
545
546
547
      /* Increment when not exchanging otherwise we need to retest "k".*/
      k++;
    }
  }
548

549
#ifdef SWIFT_DEBUG_CHECKS
550
551
  /* Check that all gparts are in the correct place (untested). */
  for (size_t k = 0; k < nr_gparts; k++) {
552
    if (cells_top[gind[k]].nodeID != local_nodeID) {
553
554
555
556
      error("Failed to move all non-local gparts to send list");
    }
  }
  for (size_t k = nr_gparts; k < s->nr_gparts; k++) {
557
    if (cells_top[gind[k]].nodeID == local_nodeID) {
558
      error("Failed to remove local gparts from send list");
559
    }
560
561
  }
#endif
562

563
564
  /* Exchange the strays, note that this potentially re-allocates
     the parts arrays. */
565
  size_t nr_parts_exchanged = s->nr_parts - nr_parts;
566
  size_t nr_gparts_exchanged = s->nr_gparts - nr_gparts;
Pedro Gonnet's avatar
Pedro Gonnet committed
567
568
569
570
  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. */
571
  s->nr_parts = nr_parts + nr_parts_exchanged;
572
  s->nr_gparts = nr_gparts + nr_gparts_exchanged;
573
574

  /* Re-allocate the index array if needed.. */
575
  if (s->nr_parts + 1 > ind_size) {
576
    int *ind_new;
577
    if ((ind_new = (int *)malloc(sizeof(int) * (s->nr_parts + 1))) == NULL)
578
      error("Failed to allocate temporary particle indices.");
579
    memcpy(ind_new, ind, sizeof(int) * nr_parts);
580
581
    free(ind);
    ind = ind_new;
582
583
  }

584
585
586
  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]};

587
  /* Assign each particle to its cell. */
Pedro Gonnet's avatar
Pedro Gonnet committed
588
  for (size_t k = nr_parts; k < s->nr_parts; k++) {
Matthieu Schaller's avatar
Matthieu Schaller committed
589
    const struct part *const p = &s->parts[k];
590
    ind[k] =
591
        cell_getid(cdim, p->x[0] * ih[0], p->x[1] * ih[1], p->x[2] * ih[2]);
592
#ifdef SWIFT_DEBUG_CHECKS
593
    if (cells_top[ind[k]].nodeID != local_nodeID)
594
      error("Received part that does not belong to me (nodeID=%i).",
595
            cells_top[ind[k]].nodeID);
596
#endif
597
  }
598
  nr_parts = s->nr_parts;
599
600

#endif /* WITH_MPI */
601
602

  /* Sort the parts according to their cells. */
603
  space_parts_sort(s, ind, nr_parts, 0, s->nr_cells - 1, verbose);
604
605

  /* Re-link the gparts. */
606
  if (nr_parts > 0 && nr_gparts > 0) part_relink_gparts(s->parts, nr_parts, 0);
607

608
#ifdef SWIFT_DEBUG_CHECKS
609
  /* Verify space_sort_struct. */
610
611
612
  for (size_t k = 1; k < nr_parts; k++) {
    if (ind[k - 1] > ind[k]) {
      error("Sort failed!");
613
    } else if (ind[k] != cell_getid(s->cdim, s->parts[k].x[0] * s->iwidth[0],
614
615
                                    s->parts[k].x[1] * s->iwidth[1],
                                    s->parts[k].x[2] * s->iwidth[2])) {
616
617
618
619
      error("Incorrect indices!");
    }
  }
#endif
620

621
622
623
624
625
626
627
628
629
630
  /* 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;
    }
  }

631
  /* We no longer need the indices as of here. */
632
  free(ind);
633

634
635
636
#ifdef WITH_MPI

  /* Re-allocate the index array if needed.. */
637
  if (s->nr_gparts + 1 > gind_size) {
638
    int *gind_new;
639
    if ((gind_new = (int *)malloc(sizeof(int) * (s->nr_gparts + 1))) == NULL)
640
      error("Failed to allocate temporary g-particle indices.");
641
    memcpy(gind_new, gind, sizeof(int) * nr_gparts);
642
643
644
645
646
    free(gind);
    gind = gind_new;
  }

  /* Assign each particle to its cell. */
647
  for (size_t k = nr_gparts; k < s->nr_gparts; k++) {
Matthieu Schaller's avatar
Matthieu Schaller committed
648
    const struct gpart *const p = &s->gparts[k];
649
650
    gind[k] =
        cell_getid(cdim, p->x[0] * ih[0], p->x[1] * ih[1], p->x[2] * ih[2]);
651
652
653
654
655
656

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

#endif
661

662
  /* Sort the gparts according to their cells. */
Matthieu Schaller's avatar
Matthieu Schaller committed
663
  space_gparts_sort(s, gind, nr_gparts, 0, s->nr_cells - 1, verbose);
664
665

  /* Re-link the parts. */
666
667
  if (nr_parts > 0 && nr_gparts > 0)
    part_relink_parts(s->gparts, nr_gparts, s->parts);
668

669
670
671
672
673
674
675
676
677
678
  /* Extract the cell counts from the sorted indices. */
  size_t last_gindex = 0;
  gind[nr_parts] = s->nr_cells;
  for (size_t k = 0; k < nr_gparts; k++) {
    if (gind[k] < gind[k + 1]) {
      cells_top[ind[k]].gcount = k - last_gindex + 1;
      last_gindex = k + 1;
    }
  }

679
  /* We no longer need the indices as of here. */
680
  free(gind);
681

682
#ifdef SWIFT_DEBUG_CHECKS
683
684
685
  /* Verify that the links are correct */
  for (size_t k = 0; k < nr_gparts; ++k) {

686
    if (s->gparts[k].id_or_neg_offset < 0) {
687

688
      const struct part *part = &s->parts[-s->gparts[k].id_or_neg_offset];
689

690
691
692
693
      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])
694
695
696
697
698
        error("Linked particles are not at the same position !");
    }
  }
  for (size_t k = 0; k < nr_parts; ++k) {

699
    if (s->parts[k].gpart != NULL &&
700
        s->parts[k].gpart->id_or_neg_offset != -(ptrdiff_t)k) {
701
      error("Linking problem !");
702
703
    }
  }
704
#endif
705

706
707
  /* Hook the cells up to the parts. */
  // tic = getticks();
708
709
710
  struct part *finger = s->parts;
  struct xpart *xfinger = s->xparts;
  struct gpart *gfinger = s->gparts;
711
  for (int k = 0; k < s->nr_cells; k++) {
712
    struct cell *restrict c = &cells_top[k];
713
    c->ti_old = ti_current;
714
715
716
717
718
719
720
    c->parts = finger;
    c->xparts = xfinger;
    c->gparts = gfinger;
    finger = &finger[c->count];
    xfinger = &xfinger[c->count];
    gfinger = &gfinger[c->gcount];
  }
721
  // message( "hooking up cells took %.3f %s." ,
Matthieu Schaller's avatar
Matthieu Schaller committed
722
  // clocks_from_ticks(getticks() - tic), clocks_getunit());
723
724
725

  /* At this point, we have the upper-level cells, old or new. Now make
     sure that the parts in each cell are ok. */
726
  space_split(s, cells_top, s->nr_cells, verbose);
727
728
729
730
731
732
733
734
735

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

/**
 * @brief Split particles between cells of a hierarchy
 *
736
737
 * This is done in parallel using threads in the #threadpool.
 *
738
 * @param s The #space.
739
740
 * @param cells The cell hierarchy.
 * @param nr_cells The number of cells.
741
742
 * @param verbose Are we talkative ?
 */
743
744
void space_split(struct space *s, struct cell *cells, int nr_cells,
                 int verbose) {
745

Matthieu Schaller's avatar
Matthieu Schaller committed
746
  const ticks tic = getticks();
747

748
  threadpool_map(&s->e->threadpool, space_split_mapper, cells, nr_cells,
749
                 sizeof(struct cell), 1, s);
750

751
752
753
  if (verbose)
    message("took %.3f %s.", clocks_from_ticks(getticks() - tic),
            clocks_getunit());
754
}
755

756
757
758
759
760
761
762
763
/**
 * @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) {

764
765
  s->sanitized = 1;

766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
  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);
    }
  }
}

781
/**
782
 * @brief #threadpool mapper function to compute the particle cell indices.
783
 *
784
 * @param map_data Pointer towards the particles.
785
 * @param nr_parts The number of particles to treat.
786
 * @param extra_data Pointers to the space and index list
787
 */
788
789
void space_parts_get_cell_index_mapper(void *map_data, int nr_parts,
                                       void *extra_data) {
790

791
792
793
794
  /* 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;
795
  int *const ind = data->ind + (ptrdiff_t)(parts - s->parts);
796
797

  /* Get some constants */
798
799
800
  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
801
  const int cdim[3] = {s->cdim[0], s->cdim[1], s->cdim[2]};
802
803
804
  const double ih_x = s->iwidth[0];
  const double ih_y = s->iwidth[1];
  const double ih_z = s->iwidth[2];
805

806
  for (int k = 0; k < nr_parts; k++) {
807
808
809
810

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

811
812
813
814
    const double old_pos_x = p->x[0];
    const double old_pos_y = p->x[1];
    const double old_pos_z = p->x[2];

815
    /* Put it back into the simulation volume */
816
817
818
    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);
819
820

    /* Get its cell index */
Matthieu Schaller's avatar
Matthieu Schaller committed
821
822
    const int index =
        cell_getid(cdim, pos_x * ih_x, pos_y * ih_y, pos_z * ih_z);
823
    ind[k] = index;
824

825
826
827
828
    /* Update the position */
    p->x[0] = pos_x;
    p->x[1] = pos_y;
    p->x[2] = pos_z;
829
830
831
832
  }
}

/**
833
 * @brief #threadpool mapper function to compute the g-particle cell indices.
834
 *
835
 * @param map_data Pointer towards the g-particles.
836
 * @param nr_gparts The number of g-particles to treat.
837
 * @param extra_data Pointers to the space and index list
838
 */
839
840
void space_gparts_get_cell_index_mapper(void *map_data, int nr_gparts,
                                        void *extra_data) {
841

842
843
844
845
  /* 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;
846
  int *const ind = data->ind + (ptrdiff_t)(gparts - s->gparts);
847
848

  /* Get some constants */
Matthieu Schaller's avatar
Matthieu Schaller committed
849
850
851
  const double dim_x = s->dim[0];
  const double dim_y = s->dim[1];
  const double dim_z = s->dim[2];
852
  const int cdim[3] = {s->cdim[0], s->cdim[1], s->cdim[2]};
Matthieu Schaller's avatar
Matthieu Schaller committed
853
854
855
  const double ih_x = s->iwidth[0];
  const double ih_y = s->iwidth[1];
  const double ih_z = s->iwidth[2];
856

857
  for (int k = 0; k < nr_gparts; k++) {
858
859
860
861

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

Matthieu Schaller's avatar
Matthieu Schaller committed
862
863
864
865
    const double old_pos_x = gp->x[0];
    const double old_pos_y = gp->x[1];
    const double old_pos_z = gp->x[2];

866
    /* Put it back into the simulation volume */
Matthieu Schaller's avatar
Matthieu Schaller committed
867
868
869
    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);
870
871
872

    /* Get its cell index */
    const int index =
Matthieu Schaller's avatar
Matthieu Schaller committed
873
        cell_getid(cdim, pos_x * ih_x, pos_y * ih_y, pos_z * ih_z);
874
    ind[k] = index;
Matthieu Schaller's avatar
Matthieu Schaller committed
875
876
877
878
879

    /* Update the position */
    gp->x[0] = pos_x;
    gp->x[1] = pos_y;
    gp->x[2] = pos_z;
880
881
882
  }
}

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
/**
 * @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());
}

939
/**
940
 * @brief Sort the particles and condensed particles according to the given
941
 * indices.
942
 *
Matthieu Schaller's avatar
Matthieu Schaller committed
943
 * @param s The #space.
944
945
946
947
 * @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.
948
 * @param verbose Are we talkative ?
949
 */
950
void space_parts_sort(struct space *s, int *ind, size_t N, int min, int max,
951
952
                      int verbose) {

Matthieu Schaller's avatar
Matthieu Schaller committed
953
  const ticks tic = getticks();
954

955
956
957
958
959
960
  /* 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;
961
962
  if ((sort_struct.stack =
           malloc(sizeof(struct qstack) * sort_struct.stack_size)) == NULL)
963
    error("Failed to allocate sorting stack.");
Matthieu Schaller's avatar
Matthieu Schaller committed
964
  for (unsigned int i = 0; i < sort_struct.stack_size; i++)
965
    sort_struct.stack[i].ready = 0;
966

967
  /* Add the first interval. */
968
969
970
971
972
973
974
975
976
977
978
  sort_struct.stack[0].i = 0;
  sort_struct.stack[0].j = N - 1;
  sort_struct.stack[0].min = min;
  sort_struct.stack[0].max = max;
  sort_struct.stack[0].ready = 1;
  sort_struct.first = 0;
  sort_struct.last = 1;
  sort_struct.waiting = 1;

  /* Launch the sorting tasks with a stride of zero such that the same
     map data is passed to each thread. */
979
980
  threadpool_map(&s->e->threadpool, space_parts_sort_mapper, &sort_struct,
                 s->e->threadpool.num_threads, 0, 1, NULL);
981

982
#ifdef SWIFT_DEBUG_CHECKS
983
  /* Verify space_sort_struct. */
984
  for (size_t i = 1; i < N; i++)
985
    if (ind[i - 1] > ind[i])
986
      error("Sorting failed (ind[%zu]=%i,ind[%zu]=%i), min=%i, max=%i.", i - 1,
987
988
989
            ind[i - 1], i, ind[i], min, max);
  message("Sorting succeeded.");
#endif
990