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Commit 647eceac authored by Matthieu Schaller's avatar Matthieu Schaller
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Merge branch 'master' into improved_grackle

parents 55c84bb5 c08467a4
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examples/process_cells
View file @ 647eceac
......@@ -38,7 +38,7 @@ ranks=$(ls -v cells_*.dat | sed 's,cells_\(.*\)_.*.dat,\1,' | sort | uniq | wc -
echo "Number of ranks = $ranks"
# Now construct a list of files ordered by rank, not step.
files=$(ls cells_*.dat | sort -t "_" -k 3,3 -n | xargs -n 4)
files=$(ls cells_*.dat | sort -t "_" -k 3,3 -n | xargs -n $ranks)
# Need number of steps.
nfiles=$(echo $files| wc -w)
......@@ -48,10 +48,10 @@ echo "Number of steps = $steps"
# And process them,
echo "Processing cell dumps files..."
echo $files | xargs -P $NPROCS -n 4 /bin/bash -c "${SCRIPTHOME}/process_cells_helper $NX $NY $NZ \$0 \$1 \$2 \$3"
echo $files | xargs -P $NPROCS -n $ranks ${SCRIPTHOME}/process_cells_helper $NX $NY $NZ
# Create summary.
grep "top cells" step*-active-cells.dat | sort -h > active_cells.log
grep "top cells" step*-active-cells.dat | sort -n -k 1.5 > active_cells.log
# And plot of active cells to edge cells.
stilts plot2plane ifmt=ascii in=active_cells.log xmin=-0.1 xmax=1.1 ymin=0 ymax=$steps grid=1 \
......
src/cell.c
View file @ 647eceac
......@@ -835,11 +835,15 @@ void cell_split(struct cell *c, ptrdiff_t parts_offset, ptrdiff_t sparts_offset,
memswap(&parts[j], &part, sizeof(struct part));
memswap(&xparts[j], &xpart, sizeof(struct xpart));
memswap(&buff[j], &temp_buff, sizeof(struct cell_buff));
if (parts[j].gpart)
parts[j].gpart->id_or_neg_offset = -(j + parts_offset);
bid = temp_buff.ind;
}
parts[k] = part;
xparts[k] = xpart;
buff[k] = temp_buff;
if (parts[k].gpart)
parts[k].gpart->id_or_neg_offset = -(k + parts_offset);
}
bucket_count[bid]++;
}
......@@ -852,10 +856,6 @@ void cell_split(struct cell *c, ptrdiff_t parts_offset, ptrdiff_t sparts_offset,
c->progeny[k]->xparts = &c->xparts[bucket_offset[k]];
}
/* Re-link the gparts. */
if (count > 0 && gcount > 0)
part_relink_gparts_to_parts(parts, count, parts_offset);
#ifdef SWIFT_DEBUG_CHECKS
/* Check that the buffs are OK. */
for (int k = 1; k < count; k++) {
......@@ -952,10 +952,14 @@ void cell_split(struct cell *c, ptrdiff_t parts_offset, ptrdiff_t sparts_offset,
}
memswap(&sparts[j], &spart, sizeof(struct spart));
memswap(&sbuff[j], &temp_buff, sizeof(struct cell_buff));
if (sparts[j].gpart)
sparts[j].gpart->id_or_neg_offset = -(j + sparts_offset);
bid = temp_buff.ind;
}
sparts[k] = spart;
sbuff[k] = temp_buff;
if (sparts[k].gpart)
sparts[k].gpart->id_or_neg_offset = -(k + sparts_offset);
}
bucket_count[bid]++;
}
......@@ -967,10 +971,6 @@ void cell_split(struct cell *c, ptrdiff_t parts_offset, ptrdiff_t sparts_offset,
c->progeny[k]->sparts = &c->sparts[bucket_offset[k]];
}
/* Re-link the gparts. */
if (scount > 0 && gcount > 0)
part_relink_gparts_to_sparts(sparts, scount, sparts_offset);
/* Finally, do the same song and dance for the gparts. */
for (int k = 0; k < 8; k++) bucket_count[k] = 0;
......@@ -1005,10 +1005,23 @@ void cell_split(struct cell *c, ptrdiff_t parts_offset, ptrdiff_t sparts_offset,
}
memswap(&gparts[j], &gpart, sizeof(struct gpart));
memswap(&gbuff[j], &temp_buff, sizeof(struct cell_buff));
if (gparts[j].type == swift_type_gas) {
parts[-gparts[j].id_or_neg_offset - parts_offset].gpart =
&gparts[j];
} else if (gparts[j].type == swift_type_star) {
sparts[-gparts[j].id_or_neg_offset - sparts_offset].gpart =
&gparts[j];
}
bid = temp_buff.ind;
}
gparts[k] = gpart;
gbuff[k] = temp_buff;
if (gparts[k].type == swift_type_gas) {
parts[-gparts[k].id_or_neg_offset - parts_offset].gpart = &gparts[k];
} else if (gparts[k].type == swift_type_star) {
sparts[-gparts[k].id_or_neg_offset - sparts_offset].gpart =
&gparts[k];
}
}
bucket_count[bid]++;
}
......@@ -1019,14 +1032,6 @@ void cell_split(struct cell *c, ptrdiff_t parts_offset, ptrdiff_t sparts_offset,
c->progeny[k]->gcount = bucket_count[k];
c->progeny[k]->gparts = &c->gparts[bucket_offset[k]];
}
/* Re-link the parts. */
if (count > 0 && gcount > 0)
part_relink_parts_to_gparts(gparts, gcount, parts - parts_offset);
/* Re-link the sparts. */
if (scount > 0 && gcount > 0)
part_relink_sparts_to_gparts(gparts, gcount, sparts - sparts_offset);
}
/**
......
src/debug.c
View file @ 647eceac
......@@ -326,8 +326,7 @@ static void dumpCells_map(struct cell *c, void *data) {
/* So output local super cells that are active and have MPI
* tasks as requested. */
if (c->nodeID == e->nodeID && (!super || (super && c->super == c)) &&
active && mpiactive) {
if (c->nodeID == e->nodeID && (!super ||((super && c->super == c) || (c->parent == NULL))) && active && mpiactive) {
/* If requested we work out how many particles are active in this cell. */
int pactcount = 0;
......
src/engine.c
View file @ 647eceac
......@@ -565,7 +565,8 @@ void engine_redistribute(struct engine *e) {
/* Sort the particles according to their cell index. */
if (s->nr_parts > 0)
space_parts_sort(s, dest, s->nr_parts, 0, nr_nodes - 1, e->verbose);
space_parts_sort(s->parts, s->xparts, dest, &counts[nodeID * nr_nodes],
nr_nodes, 0);
#ifdef SWIFT_DEBUG_CHECKS
/* Verify that the part have been sorted correctly. */
......@@ -656,7 +657,8 @@ void engine_redistribute(struct engine *e) {
/* Sort the particles according to their cell index. */
if (s->nr_sparts > 0)
space_sparts_sort(s, s_dest, s->nr_sparts, 0, nr_nodes - 1, e->verbose);
space_sparts_sort(s->sparts, s_dest, &s_counts[nodeID * nr_nodes], nr_nodes,
0);
#ifdef SWIFT_DEBUG_CHECKS
/* Verify that the spart have been sorted correctly. */
......@@ -748,7 +750,8 @@ void engine_redistribute(struct engine *e) {
/* Sort the gparticles according to their cell index. */
if (s->nr_gparts > 0)
space_gparts_sort(s, g_dest, s->nr_gparts, 0, nr_nodes - 1, e->verbose);
space_gparts_sort(s->gparts, s->parts, s->sparts, g_dest,
&g_counts[nodeID * nr_nodes], nr_nodes);
#ifdef SWIFT_DEBUG_CHECKS
/* Verify that the gpart have been sorted correctly. */
......@@ -3678,6 +3681,11 @@ void engine_rebuild(struct engine *e, int clean_smoothing_length_values) {
/* Re-build the space. */
space_rebuild(e->s, e->verbose);
#ifdef SWIFT_DEBUG_CHECKS
part_verify_links(e->s->parts, e->s->gparts, e->s->sparts, e->s->nr_parts,
e->s->nr_gparts, e->s->nr_sparts, e->verbose);
#endif
/* Initial cleaning up session ? */
if (clean_smoothing_length_values) space_sanitize(e->s);
......@@ -4151,7 +4159,7 @@ void engine_first_init_particles(struct engine *e) {
const ticks tic = getticks();
/* Set the particles in a state where they are ready for a run */
/* Set the particles in a state where they are ready for a run. */
space_first_init_parts(e->s, e->chemistry, e->cooling_func);
space_first_init_gparts(e->s, e->gravity_properties);
space_first_init_sparts(e->s);
......
src/part.c
View file @ 647eceac
......@@ -94,6 +94,26 @@ void part_relink_sparts_to_gparts(struct gpart *gparts, size_t N,
}
}
/**
* @brief Re-link both the #part%s and #spart%s associated with the list of
* #gpart%s.
*
* @param gparts The list of #gpart.
* @param N The number of particles to re-link;
* @param parts The global #part array in which to find the #gpart offsets.
* @param sparts The global #spart array in which to find the #gpart offsets.
*/
void part_relink_all_parts_to_gparts(struct gpart *gparts, size_t N,
struct part *parts, struct spart *sparts) {
for (size_t k = 0; k < N; k++) {
if (gparts[k].type == swift_type_gas) {
parts[-gparts[k].id_or_neg_offset].gpart = &gparts[k];
} else if (gparts[k].type == swift_type_star) {
sparts[-gparts[k].id_or_neg_offset].gpart = &gparts[k];
}
}
}
/**
* @brief Verifies that the #gpart, #part and #spart are correctly linked
* together
......@@ -128,19 +148,19 @@ void part_verify_links(struct part *parts, struct gpart *gparts,
/* Check that it is linked */
if (gparts[k].id_or_neg_offset > 0)
error("Gas gpart not linked to anything !");
error("Gas gpart not linked to anything!");
/* Find its link */
const struct part *part = &parts[-gparts[k].id_or_neg_offset];
/* Check the reverse link */
if (part->gpart != &gparts[k]) error("Linking problem !");
if (part->gpart != &gparts[k]) error("Linking problem!");
/* Check that the particles are at the same place */
if (gparts[k].x[0] != part->x[0] || gparts[k].x[1] != part->x[1] ||
gparts[k].x[2] != part->x[2])
error(
"Linked particles are not at the same position !\n"
"Linked particles are not at the same position!\n"
"gp->x=[%e %e %e] p->x=[%e %e %e] diff=[%e %e %e]",
gparts[k].x[0], gparts[k].x[1], gparts[k].x[2], part->x[0],
part->x[1], part->x[2], gparts[k].x[0] - part->x[0],
......
src/part.h
View file @ 647eceac
......@@ -80,6 +80,8 @@ void part_relink_parts_to_gparts(struct gpart *gparts, size_t N,
struct part *parts);
void part_relink_sparts_to_gparts(struct gpart *gparts, size_t N,
struct spart *sparts);
void part_relink_all_parts_to_gparts(struct gpart *gparts, size_t N,
struct part *parts, struct spart *sparts);
void part_verify_links(struct part *parts, struct gpart *gparts,
struct spart *sparts, size_t nr_parts, size_t nr_gparts,
size_t nr_sparts, int verbose);
......
src/space.c
View file @ 647eceac
This diff is collapsed.
src/space.h
View file @ 647eceac
......@@ -173,12 +173,14 @@ struct space {
};
/* function prototypes. */
void space_parts_sort(struct space *s, int *ind, size_t N, int min, int max,
int verbose);
void space_gparts_sort(struct space *s, int *ind, size_t N, int min, int max,
int verbose);
void space_sparts_sort(struct space *s, int *ind, size_t N, int min, int max,
int verbose);
void space_free_buff_sort_indices(struct space *s);
void space_parts_sort(struct part *parts, struct xpart *xparts, int *ind,
int *counts, int num_bins, ptrdiff_t parts_offset);
void space_gparts_sort(struct gpart *gparts, struct part *parts,
struct spart *sparts, int *ind, int *counts,
int num_bins);
void space_sparts_sort(struct spart *sparts, int *ind, int *counts,
int num_bins, ptrdiff_t sparts_offset);
void space_getcells(struct space *s, int nr_cells, struct cell **cells);
int space_getsid(struct space *s, struct cell **ci, struct cell **cj,
double *shift);
......@@ -199,12 +201,6 @@ void space_map_parts_xparts(struct space *s,
struct cell *c));
void space_map_cells_post(struct space *s, int full,
void (*fun)(struct cell *c, void *data), void *data);
void space_parts_sort_mapper(void *map_data, int num_elements,
void *extra_data);
void space_gparts_sort_mapper(void *map_data, int num_elements,
void *extra_data);
void space_sparts_sort_mapper(void *map_data, int num_elements,
void *extra_data);
void space_rebuild(struct space *s, int verbose);
void space_recycle(struct space *s, struct cell *c);
void space_recycle_list(struct space *s, struct cell *cell_list_begin,
......@@ -215,12 +211,12 @@ void space_split(struct space *s, struct cell *cells, int nr_cells,
int verbose);
void space_split_mapper(void *map_data, int num_elements, void *extra_data);
void space_list_cells_with_tasks(struct space *s);
void space_parts_get_cell_index(struct space *s, int *ind, struct cell *cells,
int verbose);
void space_gparts_get_cell_index(struct space *s, int *gind, struct cell *cells,
int verbose);
void space_sparts_get_cell_index(struct space *s, int *sind, struct cell *cells,
int verbose);
void space_parts_get_cell_index(struct space *s, int *ind, int *cell_counts,
struct cell *cells, int verbose);
void space_gparts_get_cell_index(struct space *s, int *gind, int *cell_counts,
struct cell *cells, int verbose);
void space_sparts_get_cell_index(struct space *s, int *sind, int *cell_counts,
struct cell *cells, int verbose);
void space_synchronize_particle_positions(struct space *s);
void space_do_parts_sort();
void space_do_gparts_sort();
......
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