space.c 151 KB
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/*******************************************************************************
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 * 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/>.
 *
 ******************************************************************************/
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/* Config parameters. */
#include "../config.h"

/* Some standard headers. */
#include <float.h>
#include <limits.h>
#include <math.h>
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#include <stdlib.h>
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#include <string.h>
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/* MPI headers. */
#ifdef WITH_MPI
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#include <mpi.h>
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#endif

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

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/* Local headers. */
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#include "atomic.h"
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#include "chemistry.h"
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#include "const.h"
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#include "cooling.h"
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#include "debug.h"
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#include "engine.h"
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#include "error.h"
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#include "gravity.h"
#include "hydro.h"
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#include "kernel_hydro.h"
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#include "lock.h"
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#include "memswap.h"
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#include "minmax.h"
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#include "multipole.h"
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#include "restart.h"
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#include "sort_part.h"
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#include "stars.h"
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#include "threadpool.h"
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#include "tools.h"
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#include "tracers.h"
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/* Split size. */
int space_splitsize = space_splitsize_default;
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int space_subsize_pair_hydro = space_subsize_pair_hydro_default;
int space_subsize_self_hydro = space_subsize_self_hydro_default;
int space_subsize_pair_grav = space_subsize_pair_grav_default;
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int space_subsize_self_grav = space_subsize_self_grav_default;
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int space_subsize_pair_stars = space_subsize_pair_stars_default;
int space_subsize_self_stars = space_subsize_self_stars_default;
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int space_subdepth_diff_grav = space_subdepth_diff_grav_default;
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int space_maxsize = space_maxsize_default;
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/*! Number of extra #part we allocate memory for per top-level cell */
int space_extra_parts = space_extra_parts_default;

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/*! Number of extra #spart we allocate memory for per top-level cell */
int space_extra_sparts = space_extra_sparts_default;

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/*! Number of extra #gpart we allocate memory for per top-level cell */
int space_extra_gparts = space_extra_gparts_default;

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/*! Expected maximal number of strays received at a rebuild */
int space_expected_max_nr_strays = space_expected_max_nr_strays_default;
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#ifdef SWIFT_DEBUG_CHECKS
int last_cell_id;
#endif
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/**
 * @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;
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  struct spart *sparts;
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  int *ind;
  struct qstack *stack;
  unsigned int stack_size;
  volatile unsigned int first, last, waiting;
};

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/**
 * @brief Information required to compute the particle cell indices.
 */
struct index_data {
  struct space *s;
  int *ind;
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  int *cell_counts;
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  size_t count_inhibited_part;
  size_t count_inhibited_gpart;
  size_t count_inhibited_spart;
  size_t count_extra_part;
  size_t count_extra_gpart;
  size_t count_extra_spart;
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};

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/**
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 * @brief Recursively dismantle a cell tree.
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 *
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 * @param s The #space.
 * @param c The #cell to recycle.
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 * @param cell_rec_begin Pointer to the start of the list of cells to recycle.
 * @param cell_rec_end Pointer to the end of the list of cells to recycle.
 * @param multipole_rec_begin Pointer to the start of the list of multipoles to
 * recycle.
 * @param multipole_rec_end Pointer to the end of the list of multipoles to
 * recycle.
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 */
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void space_rebuild_recycle_rec(struct space *s, struct cell *c,
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                               struct cell **cell_rec_begin,
                               struct cell **cell_rec_end,
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                               struct gravity_tensors **multipole_rec_begin,
                               struct gravity_tensors **multipole_rec_end) {
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  if (c->split)
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    for (int k = 0; k < 8; k++)
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      if (c->progeny[k] != NULL) {
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        space_rebuild_recycle_rec(s, c->progeny[k], cell_rec_begin,
                                  cell_rec_end, multipole_rec_begin,
                                  multipole_rec_end);

        c->progeny[k]->next = *cell_rec_begin;
        *cell_rec_begin = c->progeny[k];
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        if (s->with_self_gravity) {
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          c->progeny[k]->grav.multipole->next = *multipole_rec_begin;
          *multipole_rec_begin = c->progeny[k]->grav.multipole;
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        }
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        if (*cell_rec_end == NULL) *cell_rec_end = *cell_rec_begin;
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        if (s->with_self_gravity && *multipole_rec_end == NULL)
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          *multipole_rec_end = *multipole_rec_begin;

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        c->progeny[k]->grav.multipole = NULL;
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        c->progeny[k] = NULL;
      }
}

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void space_rebuild_recycle_mapper(void *map_data, int num_elements,
                                  void *extra_data) {

  struct space *s = (struct space *)extra_data;
  struct cell *cells = (struct cell *)map_data;

  for (int k = 0; k < num_elements; k++) {
    struct cell *c = &cells[k];
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    struct cell *cell_rec_begin = NULL, *cell_rec_end = NULL;
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    struct gravity_tensors *multipole_rec_begin = NULL,
                           *multipole_rec_end = NULL;
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    space_rebuild_recycle_rec(s, c, &cell_rec_begin, &cell_rec_end,
                              &multipole_rec_begin, &multipole_rec_end);
    if (cell_rec_begin != NULL)
      space_recycle_list(s, cell_rec_begin, cell_rec_end, multipole_rec_begin,
                         multipole_rec_end);
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    c->hydro.sorts = NULL;
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    c->stars.sorts = NULL;
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    c->nr_tasks = 0;
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    c->grav.nr_mm_tasks = 0;
    c->hydro.density = NULL;
    c->hydro.gradient = NULL;
    c->hydro.force = NULL;
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    c->hydro.limiter = NULL;
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    c->grav.grav = NULL;
    c->grav.mm = NULL;
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    c->hydro.dx_max_part = 0.0f;
    c->hydro.dx_max_sort = 0.0f;
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    c->stars.dx_max_part = 0.f;
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    c->stars.dx_max_sort = 0.f;
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    c->hydro.sorted = 0;
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    c->stars.sorted = 0;
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    c->hydro.count = 0;
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    c->hydro.count_total = 0;
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    c->hydro.updated = 0;
    c->hydro.inhibited = 0;
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    c->grav.count = 0;
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    c->grav.count_total = 0;
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    c->grav.updated = 0;
    c->grav.inhibited = 0;
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    c->stars.count = 0;
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    c->stars.count_total = 0;
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    c->stars.updated = 0;
    c->stars.inhibited = 0;
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    c->grav.init = NULL;
    c->grav.init_out = NULL;
    c->hydro.extra_ghost = NULL;
    c->hydro.ghost_in = NULL;
    c->hydro.ghost_out = NULL;
    c->hydro.ghost = NULL;
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    c->stars.ghost_in = NULL;
    c->stars.ghost_out = NULL;
    c->stars.ghost = NULL;
    c->stars.density = NULL;
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    c->stars.feedback = NULL;
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    c->kick1 = NULL;
    c->kick2 = NULL;
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    c->timestep = NULL;
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    c->timestep_limiter = NULL;
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    c->end_force = NULL;
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    c->hydro.drift = NULL;
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    c->grav.drift = NULL;
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    c->grav.drift_out = NULL;
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    c->hydro.cooling = NULL;
    c->grav.long_range = NULL;
    c->grav.down_in = NULL;
    c->grav.down = NULL;
    c->grav.mesh = NULL;
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    c->super = c;
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    c->hydro.super = c;
    c->grav.super = c;
    c->hydro.parts = NULL;
    c->hydro.xparts = NULL;
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    c->grav.parts = NULL;
    c->stars.parts = NULL;
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    c->hydro.do_sub_sort = 0;
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    c->stars.do_sub_sort = 0;
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    c->grav.do_sub_drift = 0;
    c->hydro.do_sub_drift = 0;
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    c->hydro.do_sub_limiter = 0;
    c->hydro.do_limiter = 0;
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    c->hydro.ti_end_min = -1;
    c->hydro.ti_end_max = -1;
    c->grav.ti_end_min = -1;
    c->grav.ti_end_max = -1;
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    c->stars.ti_end_min = -1;
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#ifdef SWIFT_DEBUG_CHECKS
    c->cellID = 0;
#endif
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    if (s->with_self_gravity)
      bzero(c->grav.multipole, sizeof(struct gravity_tensors));
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    for (int i = 0; i < 13; i++) {
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      if (c->hydro.sort[i] != NULL) {
        free(c->hydro.sort[i]);
        c->hydro.sort[i] = NULL;
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      }
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      if (c->stars.sort[i] != NULL) {
        free(c->stars.sort[i]);
        c->stars.sort[i] = NULL;
      }
    }
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#if WITH_MPI
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    c->mpi.tag = -1;

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    c->mpi.hydro.recv_xv = NULL;
    c->mpi.hydro.recv_rho = NULL;
    c->mpi.hydro.recv_gradient = NULL;
    c->mpi.grav.recv = NULL;
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    c->mpi.recv_ti = NULL;
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    c->mpi.limiter.recv = NULL;
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    c->mpi.hydro.send_xv = NULL;
    c->mpi.hydro.send_rho = NULL;
    c->mpi.hydro.send_gradient = NULL;
    c->mpi.grav.send = NULL;
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    c->mpi.send_ti = NULL;
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    c->mpi.limiter.send = NULL;
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#endif
  }
}

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/**
 * @brief Free up any allocated cells.
 */
void space_free_cells(struct space *s) {
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  ticks tic = getticks();

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  threadpool_map(&s->e->threadpool, space_rebuild_recycle_mapper, s->cells_top,
                 s->nr_cells, sizeof(struct cell), 0, s);
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  s->maxdepth = 0;
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  if (s->e->verbose)
    message("took %.3f %s.", clocks_from_ticks(getticks() - tic),
            clocks_getunit());
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}

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/**
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 * @brief Re-build the top-level cell grid.
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 *
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 * @param s The #space.
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 * @param verbose Print messages to stdout or not.
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 */
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void space_regrid(struct space *s, int verbose) {
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  const size_t nr_parts = s->nr_parts;
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  const size_t nr_sparts = s->nr_sparts;
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  const ticks tic = getticks();
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  const integertime_t ti_current = (s->e != NULL) ? s->e->ti_current : 0;
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  /* Run through the cells and get the current h_max. */
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  // tic = getticks();
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  float h_max = s->cell_min / kernel_gamma / space_stretch;
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  if (nr_parts > 0) {
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    /* Can we use the list of local non-empty top-level cells? */
    if (s->local_cells_with_particles_top != NULL) {
      for (int k = 0; k < s->nr_local_cells_with_particles; ++k) {
        const struct cell *c =
            &s->cells_top[s->local_cells_with_particles_top[k]];
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        if (c->hydro.h_max > h_max) {
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          h_max = c->hydro.h_max;
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        }
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        if (c->stars.h_max > h_max) {
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          h_max = c->stars.h_max;
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        }
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      }
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      /* Can we instead use all the top-level cells? */
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    } else if (s->cells_top != NULL) {
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      for (int k = 0; k < s->nr_cells; k++) {
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        const struct cell *c = &s->cells_top[k];
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        if (c->nodeID == engine_rank && c->hydro.h_max > h_max) {
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          h_max = c->hydro.h_max;
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        }
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        if (c->nodeID == engine_rank && c->stars.h_max > h_max) {
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          h_max = c->stars.h_max;
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        }
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      }
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      /* Last option: run through the particles */
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    } else {
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      for (size_t k = 0; k < nr_parts; k++) {
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        if (s->parts[k].h > h_max) h_max = s->parts[k].h;
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      }
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      for (size_t k = 0; k < nr_sparts; k++) {
        if (s->sparts[k].h > h_max) h_max = s->sparts[k].h;
      }
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    }
  }

/* 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)
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      error("Failed to aggregate the rebuild flag across nodes.");
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    h_max = buff;
  }
#endif
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  if (verbose) message("h_max is %.3e (cell_min=%.3e).", h_max, s->cell_min);
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  /* Get the new putative cell dimensions. */
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  const int cdim[3] = {
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      (int)floor(s->dim[0] /
                 fmax(h_max * kernel_gamma * space_stretch, s->cell_min)),
      (int)floor(s->dim[1] /
                 fmax(h_max * kernel_gamma * space_stretch, s->cell_min)),
      (int)floor(s->dim[2] /
                 fmax(h_max * kernel_gamma * space_stretch, s->cell_min))};
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  /* 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 "
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        "is switched on.\nThis error is often caused by any of the "
        "followings:\n"
        " - too few particles to generate a sensible grid,\n"
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        " - the initial value of 'Scheduler:max_top_level_cells' is too "
        "small,\n"
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        " - the (minimal) time-step is too large leading to particles with "
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        "predicted smoothing lengths too large for the box size,\n"
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        " - particles with velocities so large that they move by more than two "
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        "box sizes per time-step.\n");
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/* 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. */
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#ifdef WITH_MPI
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  double oldwidth[3];
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  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];
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    oldwidth[0] = s->width[0];
    oldwidth[1] = s->width[1];
    oldwidth[2] = s->width[2];
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    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);
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          oldnodeIDs[cid] = s->cells_top[cid].nodeID;
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        }
      }
    }
  }

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  /* Are we about to allocate new top level cells without a regrid?
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   * Can happen when restarting the application. */
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  const int no_regrid = (s->cells_top == NULL && oldnodeIDs == NULL);
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#endif

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

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

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    /* Free the old cells, if they were allocated. */
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    if (s->cells_top != NULL) {
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      space_free_cells(s);
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      free(s->local_cells_with_tasks_top);
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      free(s->local_cells_top);
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      free(s->cells_with_particles_top);
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      free(s->local_cells_with_particles_top);
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      free(s->cells_top);
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      free(s->multipoles_top);
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    }

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    /* Also free the task arrays, these will be regenerated and we can use the
     * memory while copying the particle arrays. */
    if (s->e != NULL) scheduler_free_tasks(&s->e->sched);

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    /* Set the new cell dimensions only if smaller. */
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    for (int k = 0; k < 3; k++) {
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      s->cdim[k] = cdim[k];
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      s->width[k] = s->dim[k] / cdim[k];
      s->iwidth[k] = 1.0 / s->width[k];
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    }
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    const float dmin = min3(s->width[0], s->width[1], s->width[2]);
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    /* Allocate the highest level of cells. */
    s->tot_cells = s->nr_cells = cdim[0] * cdim[1] * cdim[2];
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    if (posix_memalign((void **)&s->cells_top, cell_align,
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                       s->nr_cells * sizeof(struct cell)) != 0)
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      error("Failed to allocate top-level cells.");
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    bzero(s->cells_top, s->nr_cells * sizeof(struct cell));
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    /* Allocate the multipoles for the top-level cells. */
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    if (s->with_self_gravity) {
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      if (posix_memalign((void **)&s->multipoles_top, multipole_align,
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                         s->nr_cells * sizeof(struct gravity_tensors)) != 0)
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        error("Failed to allocate top-level multipoles.");
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      bzero(s->multipoles_top, s->nr_cells * sizeof(struct gravity_tensors));
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    }

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    /* Allocate the indices of local cells */
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    if (posix_memalign((void **)&s->local_cells_top, SWIFT_STRUCT_ALIGNMENT,
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                       s->nr_cells * sizeof(int)) != 0)
      error("Failed to allocate indices of local top-level cells.");
    bzero(s->local_cells_top, s->nr_cells * sizeof(int));

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    /* Allocate the indices of local cells with tasks */
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    if (posix_memalign((void **)&s->local_cells_with_tasks_top,
                       SWIFT_STRUCT_ALIGNMENT, s->nr_cells * sizeof(int)) != 0)
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      error("Failed to allocate indices of local top-level cells with tasks.");
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    bzero(s->local_cells_with_tasks_top, s->nr_cells * sizeof(int));

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    /* Allocate the indices of cells with particles */
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    if (posix_memalign((void **)&s->cells_with_particles_top,
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                       SWIFT_STRUCT_ALIGNMENT, s->nr_cells * sizeof(int)) != 0)
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      error("Failed to allocate indices of top-level cells with particles.");
    bzero(s->cells_with_particles_top, s->nr_cells * sizeof(int));
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    /* Allocate the indices of local cells with particles */
    if (posix_memalign((void **)&s->local_cells_with_particles_top,
                       SWIFT_STRUCT_ALIGNMENT, s->nr_cells * sizeof(int)) != 0)
      error(
          "Failed to allocate indices of local top-level cells with "
          "particles.");
    bzero(s->local_cells_with_particles_top, s->nr_cells * sizeof(int));

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    /* Set the cells' locks */
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    for (int k = 0; k < s->nr_cells; k++) {
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      if (lock_init(&s->cells_top[k].hydro.lock) != 0)
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        error("Failed to init spinlock for hydro.");
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      if (lock_init(&s->cells_top[k].grav.plock) != 0)
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        error("Failed to init spinlock for gravity.");
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      if (lock_init(&s->cells_top[k].grav.mlock) != 0)
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        error("Failed to init spinlock for multipoles.");
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      if (lock_init(&s->cells_top[k].stars.lock) != 0)
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        error("Failed to init spinlock for stars.");
    }
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    /* Set the cell location and sizes. */
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    for (int i = 0; i < cdim[0]; i++)
      for (int j = 0; j < cdim[1]; j++)
        for (int k = 0; k < cdim[2]; k++) {
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          const size_t cid = cell_getid(cdim, i, j, k);
          struct cell *restrict c = &s->cells_top[cid];
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          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];
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          c->dmin = dmin;
          c->depth = 0;
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          c->split = 0;
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          c->hydro.count = 0;
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          c->grav.count = 0;
          c->stars.count = 0;
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          c->super = c;
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          c->hydro.super = c;
          c->grav.super = c;
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          c->hydro.ti_old_part = ti_current;
          c->grav.ti_old_part = ti_current;
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          c->grav.ti_old_multipole = ti_current;
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#ifdef WITH_MPI
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          c->mpi.tag = -1;
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          c->mpi.hydro.recv_xv = NULL;
          c->mpi.hydro.recv_rho = NULL;
          c->mpi.hydro.recv_gradient = NULL;
          c->mpi.hydro.send_xv = NULL;
          c->mpi.hydro.send_rho = NULL;
          c->mpi.hydro.send_gradient = NULL;
          c->mpi.grav.recv = NULL;
          c->mpi.grav.send = NULL;
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#endif  // WITH_MPI
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          if (s->with_self_gravity) c->grav.multipole = &s->multipoles_top[cid];
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#ifdef SWIFT_DEBUG_CHECKS
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          c->cellID = -last_cell_id;
          last_cell_id++;
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#endif
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        }
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    /* Be verbose about the change. */
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    if (verbose)
      message("set cell dimensions to [ %i %i %i ].", cdim[0], cdim[1],
              cdim[2]);
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#ifdef WITH_MPI
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    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)
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        message(
            "basic cell dimensions have increased - recalculating the "
            "global partition.");
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      if (!partition_space_to_space(oldwidth, oldcdim, oldnodeIDs, s)) {
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        /* Failed, try another technique that requires no settings. */
        message("Failed to get a new partition, trying less optimal method");
        struct partition initial_partition;
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#if defined(HAVE_PARMETIS) || defined(HAVE_METIS)
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        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);
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      /* Finished with these. */
      free(oldnodeIDs);
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    } else if (no_regrid && s->e != NULL) {
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      /* If we have created the top-levels cells and not done an initial
       * partition (can happen when restarting), then the top-level cells
       * are not assigned to a node, we must do that and then associate the
       * particles with the cells. Note requires that
       * partition_store_celllist() was called once before, or just before
       * dumping the restart files.*/
      partition_restore_celllist(s, s->e->reparttype);

      /* Now re-distribute the particles, should just add to cells? */
      engine_redistribute(s->e);

      /* Make the proxies. */
      engine_makeproxies(s->e);
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    }
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#endif /* WITH_MPI */
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    // message( "rebuilding upper-level cells took %.3f %s." ,
    // clocks_from_ticks(double)(getticks() - tic), clocks_getunit());

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  }      /* re-build upper-level cells? */
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  else { /* Otherwise, just clean up the cells. */
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    /* Free the old cells, if they were allocated. */
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    space_free_cells(s);
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  }
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  if (verbose)
    message("took %.3f %s.", clocks_from_ticks(getticks() - tic),
            clocks_getunit());
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}
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/**
 * @brief Allocate memory for the extra particles used for on-the-fly creation.
 *
 * This rarely actually allocates memory. Most of the time, we convert
 * pre-allocated memory inot extra particles.
 *
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 * This function also sets the extra particles' location to their top-level
 * cells. They can then be sorted into their correct memory position later on.
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 *
 * @param s The current #space.
 * @param verbose Are we talkative?
 */
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void space_allocate_extras(struct space *s, int verbose) {

  const int local_nodeID = s->e->nodeID;

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  /* Anything to do here? (Abort if we don't want extras)*/
  if (space_extra_parts == 0 && space_extra_gparts == 0 &&
      space_extra_sparts == 0)
    return;

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  /* The top-level cells */
  const struct cell *cells = s->cells_top;
  const double half_cell_width[3] = {0.5 * cells[0].width[0],
                                     0.5 * cells[0].width[1],
                                     0.5 * cells[0].width[2]};

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  /* The current number of particles (including spare ones) */
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  size_t nr_parts = s->nr_parts;
  size_t nr_gparts = s->nr_gparts;
  size_t nr_sparts = s->nr_sparts;

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  /* The current number of actual particles */
  size_t nr_actual_parts = nr_parts - s->nr_extra_parts;
  size_t nr_actual_gparts = nr_gparts - s->nr_extra_gparts;
  size_t nr_actual_sparts = nr_sparts - s->nr_extra_sparts;

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  /* The number of particles we allocated memory for (MPI overhead) */
  size_t size_parts = s->size_parts;
  size_t size_gparts = s->size_gparts;
  size_t size_sparts = s->size_sparts;

  int local_cells = 0;
  for (int i = 0; i < s->nr_cells; ++i)
    if (s->cells_top[i].nodeID == local_nodeID) local_cells++;

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  /* Number of extra particles we want for each type */
  const size_t expected_num_extra_parts = local_cells * space_extra_parts;
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  const size_t expected_num_extra_gparts = local_cells * space_extra_gparts;
  const size_t expected_num_extra_sparts = local_cells * space_extra_sparts;
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  if (verbose) {
    message("Currently have %zd/%zd/%zd real particles.", nr_actual_parts,
            nr_actual_gparts, nr_actual_sparts);
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    message("Currently have %zd/%zd/%zd spaces for extra particles.",
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            s->nr_extra_parts, s->nr_extra_gparts, s->nr_extra_sparts);
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    message("Requesting space for future %zd/%zd/%zd part/gpart/sparts.",
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            expected_num_extra_parts, expected_num_extra_gparts,
            expected_num_extra_sparts);
  }
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  if (expected_num_extra_parts < s->nr_extra_parts)
    error("Reduction in top-level cells number not handled.");
  if (expected_num_extra_gparts < s->nr_extra_gparts)
    error("Reduction in top-level cells number not handled.");
  if (expected_num_extra_sparts < s->nr_extra_sparts)
    error("Reduction in top-level cells number not handled.");

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  /* Do we have enough space for the extra gparts (i.e. we haven't used up any)
   * ? */
  if (nr_gparts + expected_num_extra_gparts > size_gparts) {

    /* Ok... need to put some more in the game */

    /* Do we need to reallocate? */
    if (nr_actual_gparts + expected_num_extra_gparts > size_gparts) {

      size_gparts = (nr_actual_gparts + expected_num_extra_gparts) *
                    engine_redistribute_alloc_margin;

      if (verbose)
        message("Re-allocating gparts array from %zd to %zd", s->size_gparts,
                size_gparts);

      /* Create more space for parts */
      struct gpart *gparts_new = NULL;
      if (posix_memalign((void **)&gparts_new, gpart_align,
                         sizeof(struct gpart) * size_gparts) != 0)
        error("Failed to allocate new gpart data");
      const ptrdiff_t delta = gparts_new - s->gparts;
      memcpy(gparts_new, s->gparts, sizeof(struct gpart) * s->size_gparts);
      free(s->gparts);
      s->gparts = gparts_new;

      /* Update the counter */
      s->size_gparts = size_gparts;

      /* We now need to reset all the part and spart pointers */
      for (size_t i = 0; i < nr_parts; ++i) {
        if (s->parts[i].time_bin != time_bin_not_created)
          s->parts[i].gpart += delta;
      }
      for (size_t i = 0; i < nr_sparts; ++i) {
        if (s->sparts[i].time_bin != time_bin_not_created)
          s->sparts[i].gpart += delta;
      }
    }

    /* Turn some of the allocated spares into particles we can use */
    for (size_t i = nr_gparts; i < nr_actual_gparts + expected_num_extra_gparts;
         ++i) {
      bzero(&s->gparts[i], sizeof(struct gpart));
      s->gparts[i].time_bin = time_bin_not_created;
      s->gparts[i].type = swift_type_dark_matter;
      s->gparts[i].id_or_neg_offset = -1;
    }

      /* Put the spare particles in their correct cell */
#ifdef WITH_MPI
    error("Need to do this correctly over MPI for only the local cells.");
#endif
    int count_in_cell = 0, current_cell = 0;
    size_t count_extra_gparts = 0;
    for (size_t i = 0; i < nr_actual_gparts + expected_num_extra_gparts; ++i) {

#ifdef SWIFT_DEBUG_CHECKS
      if (current_cell == s->nr_cells)
        error("Cell counter beyond the maximal nr. cells.");
#endif

      if (s->gparts[i].time_bin == time_bin_not_created) {

        /* We want the extra particles to be at the centre of their cell */
        s->gparts[i].x[0] = cells[current_cell].loc[0] + half_cell_width[0];
        s->gparts[i].x[1] = cells[current_cell].loc[1] + half_cell_width[1];
        s->gparts[i].x[2] = cells[current_cell].loc[2] + half_cell_width[2];
        ++count_in_cell;
        count_extra_gparts++;
      }

      /* Once we have reached the number of extra gpart per cell, we move to the
       * next */
      if (count_in_cell == space_extra_gparts) {
        ++current_cell;
        count_in_cell = 0;
      }
    }

#ifdef SWIFT_DEBUG_CHECKS
    if (count_extra_gparts != expected_num_extra_gparts)
      error("Constructed the wrong number of extra gparts (%zd vs. %zd)",
            count_extra_gparts, expected_num_extra_gparts);
#endif

    /* Update the counters */
    s->nr_gparts = nr_actual_gparts + expected_num_extra_gparts;
    s->nr_extra_gparts = expected_num_extra_gparts;
  }

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  /* Do we have enough space for the extra parts (i.e. we haven't used up any) ?
   */
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  if (expected_num_extra_parts > s->nr_extra_parts) {

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    /* Ok... need to put some more in the game */

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    /* Do we need to reallocate? */
    if (nr_actual_parts + expected_num_extra_parts > size_parts) {

      size_parts = (nr_actual_parts + expected_num_extra_parts) *
                   engine_redistribute_alloc_margin;

      if (verbose)
        message("Re-allocating parts array from %zd to %zd", s->size_parts,
                size_parts);

      /* Create more space for parts */
      struct part *parts_new = NULL;
      if (posix_memalign((void **)&parts_new, part_align,
                         sizeof(struct part) * size_parts) != 0)
        error("Failed to allocate new part data");
      memcpy(parts_new, s->parts, sizeof(struct part) * s->size_parts);
      free(s->parts);
      s->parts = parts_new;

      /* Same for xparts */
      struct xpart *xparts_new = NULL;
      if (posix_memalign((void **)&xparts_new, xpart_align,
                         sizeof(struct xpart) * size_parts) != 0)
        error("Failed to allocate new xpart data");
      memcpy(xparts_new, s->xparts, sizeof(struct xpart) * s->size_parts);
      free(s->xparts);
      s->xparts = xparts_new;

      /* Update the counter */
      s->size_parts = size_parts;
    }

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    /* Turn some of the allocated spares into particles we can use */
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    for (size_t i = nr_parts; i < nr_actual_parts + expected_num_extra_parts;
         ++i) {
      bzero(&s->parts[i], sizeof(struct part));
      bzero(&s->xparts[i], sizeof(struct xpart));
      s->parts[i].time_bin = time_bin_not_created;
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      s->parts[i].id = -1;
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    }

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      /* Put the spare particles in their correct cell */
#ifdef WITH_MPI
    error("Need to do this correctly over MPI for only the local cells.");
#endif
    int count_in_cell = 0, current_cell = 0;
    size_t count_extra_parts = 0;
    for (size_t i = 0; i < nr_actual_parts + expected_num_extra_parts; ++i) {
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#ifdef SWIFT_DEBUG_CHECKS
      if (current_cell == s->nr_cells)
        error("Cell counter beyond the maximal nr. cells.");
#endif

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      if (s->parts[i].time_bin == time_bin_not_created) {

        /* We want the extra particles to be at the centre of their cell */
        s->parts[i].x[0] = cells[current_cell].loc[0] + half_cell_width[0];
        s->parts[i].x[1] = cells[current_cell].loc[1] + half_cell_width[1];
        s->parts[i].x[2] = cells[current_cell].loc[2] + half_cell_width[2];
        ++count_in_cell;
        count_extra_parts++;
      }

      /* Once we have reached the number of extra part per cell, we move to the
       * next */
      if (count_in_cell == space_extra_parts) {
        ++current_cell;
        count_in_cell = 0;
      }
    }

#ifdef SWIFT_DEBUG_CHECKS
    if (count_extra_parts != expected_num_extra_parts)
      error("Constructed the wrong number of extra parts (%zd vs. %zd)",
            count_extra_parts, expected_num_extra_parts);
#endif

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    /* Update the counters */
    s->nr_parts = nr_actual_parts + expected_num_extra_parts;
    s->nr_extra_parts = expected_num_extra_parts;
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  }
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  /* Do we have enough space for the extra sparts (i.e. we haven't used up any)
   * ? */
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  if (nr_actual_sparts + expected_num_extra_sparts > nr_sparts) {
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    /* Ok... need to put some more in the game */

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    /* Do we need to reallocate? */
    if (nr_actual_sparts + expected_num_extra_sparts > size_sparts) {

      size_sparts = (nr_actual_sparts + expected_num_extra_sparts) *
                    engine_redistribute_alloc_margin;

      if (verbose)
        message("Re-allocating sparts array from %zd to %zd", s->size_sparts,
                size_sparts);

      /* Create more space for parts */
      struct spart *sparts_new = NULL;
      if (posix_memalign((void **)&sparts_new, spart_align,
                         sizeof(struct spart) * size_sparts) != 0)
        error("Failed to allocate new spart data");
      memcpy(sparts_new, s->sparts, sizeof(struct spart) * s->size_sparts);
      free(s->sparts);
      s->sparts = sparts_new;

      /* Update the counter */
      s->size_sparts = size_sparts;
    }

    /* Turn some of the allocated spares into particles we can use */
    for (size_t i = nr_sparts; i < nr_actual_sparts + expected_num_extra_sparts;
         ++i) {
      bzero(&s->sparts[i], sizeof(struct spart));
      s->sparts[i].time_bin = time_bin_not_created;
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      s->sparts[i].id = -42;
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    }

      /* Put the spare particles in their correct cell */
#ifdef WITH_MPI
    error("Need to do this correctly over MPI for only the local cells.");
#endif
    int count_in_cell = 0, current_cell = 0;
    size_t count_extra_sparts = 0;
    for (size_t i = 0; i < nr_actual_sparts + expected_num_extra_sparts; ++i) {

#ifdef SWIFT_DEBUG_CHECKS
      if (current_cell == s->nr_cells)
        error("Cell counter beyond the maximal nr. cells.");
#endif

      if (s->sparts[i].time_bin == time_bin_not_created) {

        /* We want the extra particles to be at the centre of their cell */
        s->sparts[i].x[0] = cells[current_cell].loc[0] + half_cell_width[0];
        s->sparts[i].x[1] = cells[current_cell].loc[1] + half_cell_width[1];
        s->sparts[i].x[2] = cells[current_cell].loc[2] + half_cell_width[2];
        ++count_in_cell;
        count_extra_sparts++;
      }

      /* Once we have reached the number of extra spart per cell, we move to the
       * next */
      if (count_in_cell == space_extra_sparts) {
        ++current_cell;
        count_in_cell = 0;
      }
    }

#ifdef SWIFT_DEBUG_CHECKS
    if (count_extra_sparts != expected_num_extra_sparts)
      error("Constructed the wrong number of extra sparts (%zd vs. %zd)",
            count_extra_sparts, expected_num_extra_sparts);
#endif

    /* Update the counters */
    s->nr_sparts = nr_actual_sparts + expected_num_extra_sparts;
    s->nr_extra_sparts = expected_num_extra_sparts;
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  }
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#ifdef SWIFT_DEBUG_CHECKS
  /* Verify that the links are correct */
  if ((nr_gparts > 0 && nr_parts > 0) || (nr_gparts > 0 && nr_sparts > 0))
    part_verify_links(s->parts, s->gparts, s->sparts, nr_parts, nr_gparts,
                      nr_sparts, verbose);
#endif
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}

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/**
 * @brief Re-build the cells as well as the tasks.
 *
 * @param s The #space in which to update the cells.
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 * @param repartitioned Did we just repartition?
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 * @param verbose Print messages to stdout or not
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void space_rebuild(struct space *s, int repartitioned, int verbose) {
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  const ticks tic = getticks();
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/* Be verbose about this. */
#ifdef SWIFT_DEBUG_CHECKS
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  if (s->e->nodeID == 0 || verbose) message("(re)building space");
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  fflush(stdout);
#endif
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  /* Re-grid if necessary, or just re-set the cell data. */
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  space_regrid(s, verbose);
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  /* Allocate extra space for particles that will be created */
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  if (s->with_star_formation) space_allocate_extras(s, verbose);
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  struct cell *cells_top = s->cells_top;
  const integertime_t ti_current = (s->e != NULL) ? s->e->ti_current : 0;
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  const int local_nodeID = s->e->nodeID;
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  /* The current number of particles */
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  size_t nr_parts = s->nr_parts;
  size_t nr_gparts = s->nr_gparts;
996
  size_t nr_sparts = s->nr_sparts;
997

998
999
1000
1001
1002
  /* The number of particles we allocated memory for */
  size_t size_parts = s->size_parts;
  size_t size_gparts = s->size_gparts;
  size_t size_sparts = s->size_sparts;

1003
  /* Counter for the number of inhibited particles found on the node */
1004
1005
1006
1007
  size_t count_inhibited_parts = 0;
  size_t count_inhibited_gparts = 0;
  size_t count_inhibited_sparts = 0;

1008
  /* Counter for the number of extra particles found on the node */
1009
1010
1011
  size_t count_extra_parts = 0;
  size_t count_extra_gparts = 0;
  size_t count_extra_sparts = 0;
1012
1013
1014
1015
1016

  /* Number of particles we expect to have after strays exchange */
  const size_t h_index_size = size_parts + space_expected_max_nr_strays;
  const size_t g_index_size = size_gparts + space_expected_max_nr_strays;
  const size_t s_index_size = size_sparts + space_expected_max_nr_strays;
1017

1018
1019
1020
  /* Allocate arrays to store the indices of the cells where particles
     belong. We allocate extra space to allow for particles we may
     receive from other nodes */
1021
  int *h_index = (int *)malloc(sizeof(int) * h_index_size);
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
  int *g_index = (int *)malloc(sizeof(int) * g_index_size);
  int *s_index = (int *)malloc(sizeof(int) * s_index_size);
  if (h_index == NULL || g_index == NULL || s_index == NULL)
    error("Failed to allocate temporary particle indices.");

  /* Allocate counters of particles that will land in each cell */
  int *cell_part_counts = (int *)malloc(sizeof(int) * s->nr_cells);
  int *cell_gpart_counts = (int *)malloc(sizeof(int) * s->nr_cells);
  int *cell_spart_counts = (int *)malloc(sizeof(int) * s->nr_cells);
  if (cell_part_counts == NULL || cell_gpart_counts == NULL ||
      cell_spart_counts == NULL)
    error("Failed to allocate cell particle count buffer.");

  /* Initialise the counters, including buffer space for future particles */
  for (int i = 0; i < s->nr_cells; ++i) {
1037
1038
1039
    cell_part_counts[i] = 0;
    cell_gpart_counts[i] = 0;
    cell_spart_counts[i] = 0;
1040
  }
1041

1042
  /* Run through the particles and get their cell index. */
1043
  if (nr_parts > 0)
1044
    space_parts_get_cell_index(s, h_index, cell_part_counts,
1045
1046
1047
                               &count_inhibited_parts, &count_extra_parts,
                               verbose);
  if (nr_gparts > 0)
1048
    space_gparts_get_cell_index(s, g_index, cell_gpart_counts,
1049
1050
1051
                                &count_inhibited_gparts, &count_extra_gparts,
                                verbose);
  if (nr_sparts > 0)
1052
    spa