From f70b07870f788ac5c2e8d8f48b6daf590e1e49d6 Mon Sep 17 00:00:00 2001
From: James Willis <james.s.willis@durham.ac.uk>
Date: Wed, 18 Jul 2018 15:10:20 +0100
Subject: [PATCH] Store fof data in a SoA. Renamed group_id -> group_index.
---
src/fof.c | 186 ++++++++++++++++++++++++++++------------------------
src/space.c | 3 +-
src/space.h | 12 +++-
3 files changed, 113 insertions(+), 88 deletions(-)
diff --git a/src/fof.c b/src/fof.c
index 947e0cf13d..166eb33b8f 100644
--- a/src/fof.c
+++ b/src/fof.c
@@ -57,23 +57,23 @@ void fof_init(struct space *s, long long Ngas, long long Ngparts) {
/* Finds the root ID of the group a particle exists in. */
__attribute__((always_inline)) INLINE static int fof_find(const int i,
- int *group_id) {
+ int *group_index) {
int root = node_offset + i;
if (root < node_offset) return root;
/* TODO: May need this atomic here:
- * while (root != atomic_cas(&group_id[root], group_id[root], group_id[root]))
- * root = atomic_cas(&group_id[root], group_id[root], group_id[root]); */
- while (root != group_id[root - node_offset]) {
- root = group_id[root - node_offset];
+ * while (root != atomic_cas(&group_index[root], group_index[root], group_index[root]))
+ * root = atomic_cas(&group_index[root], group_index[root], group_index[root]); */
+ while (root != group_index[root - node_offset]) {
+ root = group_index[root - node_offset];
if (root < node_offset) break;
}
/* Perform path compression. */
// int index = i;
// while(index != root) {
- // int next = group_id[index];
- // group_id[index] = root;
+ // int next = group_index[index];
+ // group_index[index] = root;
// index = next;
//}
@@ -83,21 +83,21 @@ __attribute__((always_inline)) INLINE static int fof_find(const int i,
#ifdef WITH_MPI
/* Finds the root ID of the group a particle exists in. */
__attribute__((always_inline)) INLINE static int fof_find_global(const int i,
- int *group_id) {
+ int *group_index) {
int root = i;
/* TODO: May need this atomic here:
- * while (root != atomic_cas(&group_id[root], group_id[root], group_id[root]))
- * root = atomic_cas(&group_id[root], group_id[root], group_id[root]); */
- while (root != group_id[root]) {
- root = group_id[root];
+ * while (root != atomic_cas(&group_index[root], group_index[root], group_index[root]))
+ * root = atomic_cas(&group_index[root], group_index[root], group_index[root]); */
+ while (root != group_index[root]) {
+ root = group_index[root];
}
/* Perform path compression. */
// int index = i;
// while(index != root) {
- // int next = group_id[index];
- // group_id[index] = root;
+ // int next = group_index[index];
+ // group_index[index] = root;
// index = next;
//}
@@ -274,7 +274,7 @@ void fof_search_serial(struct space *s) {
struct gpart *gparts = s->gparts;
const double dim[3] = {s->dim[0], s->dim[1], s->dim[2]};
const double l_x2 = s->l_x2;
- int *group_id = s->group_id;
+ int *group_index = s->fof_data.group_index;
int *group_size;
int num_groups = 0;
@@ -296,12 +296,12 @@ void fof_search_serial(struct space *s) {
const double piz = pi->x[2];
/* Find the root of pi. */
- int root_i = fof_find(i, group_id);
+ int root_i = fof_find(i, group_index);
for (size_t j = i + 1; j < nr_gparts; j++) {
/* Find the roots of pi and pj. */
- const int root_j = fof_find(j, group_id);
+ const int root_j = fof_find(j, group_index);
/* Skip particles in the same group. */
if (root_i == root_j) continue;
@@ -329,12 +329,12 @@ void fof_search_serial(struct space *s) {
/* If the root ID of pj is lower than pi's root ID set pi's root to point to pj's.
* Otherwise set pj's to root to point to pi's.*/
if (root_j < root_i) {
- group_id[root_i] = root_j;
+ group_index[root_i] = root_j;
/* Update root_i on the fly. */
root_i = root_j;
}
else
- group_id[root_j] = root_i;
+ group_index[root_j] = root_i;
}
}
@@ -342,20 +342,20 @@ void fof_search_serial(struct space *s) {
/* Calculate the total number of particles in each group and total number of groups. */
for (size_t i = 0; i < nr_gparts; i++) {
- group_size[fof_find(i, group_id)]++;
- if(group_id[i] == i) num_groups++;
+ group_size[fof_find(i, group_index)]++;
+ if(group_index[i] == i) num_groups++;
}
- fof_dump_group_data("fof_output_serial.dat", nr_gparts, group_id, group_size);
+ fof_dump_group_data("fof_output_serial.dat", nr_gparts, group_index, group_size);
int num_parts_in_groups = 0;
- int max_group_size = 0, max_group_id = 0;
+ int max_group_size = 0, max_group_index = 0;
for (size_t i = 0; i < nr_gparts; i++) {
if (group_size[i] > 1) num_parts_in_groups += group_size[i];
if (group_size[i] > max_group_size) {
max_group_size = group_size[i];
- max_group_id = i;
+ max_group_index = i;
}
}
@@ -363,7 +363,7 @@ void fof_search_serial(struct space *s) {
"No. of groups: %d. No. of particles in groups: %d. No. of particles not "
"in groups: %zu.",
num_groups, num_parts_in_groups, nr_gparts - num_parts_in_groups);
- message("Biggest group size: %d with ID: %d", max_group_size, max_group_id);
+ message("Biggest group size: %d with ID: %d", max_group_size, max_group_index);
free(group_size);
}
@@ -374,10 +374,10 @@ void fof_search_cell(struct space *s, struct cell *c) {
const size_t count = c->gcount;
struct gpart *gparts = c->gparts;
const double l_x2 = s->l_x2;
- int *group_id = s->group_id;
+ int *group_index = s->fof_data.group_index;
/* Make a list of particle offsets into the global gparts array. */
- int *const offset = group_id + (ptrdiff_t)(gparts - s->gparts);
+ int *const offset = group_index + (ptrdiff_t)(gparts - s->gparts);
/* Loop over particles and find which particles belong in the same group. */
for (size_t i = 0; i < count; i++) {
@@ -388,12 +388,12 @@ void fof_search_cell(struct space *s, struct cell *c) {
const double piz = pi->x[2];
/* Find the root of pi. */
- int root_i = fof_find(offset[i] - node_offset, group_id);
+ int root_i = fof_find(offset[i] - node_offset, group_index);
for (size_t j = i + 1; j < count; j++) {
/* Find the root of pj. */
- const int root_j = fof_find(offset[j] - node_offset, group_id);
+ const int root_j = fof_find(offset[j] - node_offset, group_index);
/* Skip particles in the same group. */
if (root_i == root_j) continue;
@@ -417,12 +417,12 @@ void fof_search_cell(struct space *s, struct cell *c) {
/* If the root ID of pj is lower than pi's root ID set pi's root to point to pj's.
* Otherwise set pj's to root to point to pi's.*/
if (root_j < root_i) {
- atomic_min(&group_id[root_i - node_offset], root_j);
+ atomic_min(&group_index[root_i - node_offset], root_j);
/* Update root_i on the fly. */
root_i = root_j;
}
else
- atomic_min(&group_id[root_j - node_offset], root_i);
+ atomic_min(&group_index[root_j - node_offset], root_i);
}
}
@@ -438,11 +438,11 @@ void fof_search_pair_cells(struct space *s, struct cell *ci, struct cell *cj) {
struct gpart *gparts_j = cj->gparts;
const double dim[3] = {s->dim[0], s->dim[1], s->dim[2]};
const double l_x2 = s->l_x2;
- int *group_id = s->group_id;
+ int *group_index = s->fof_data.group_index;
/* Make a list of particle offsets into the global gparts array. */
- int *const offset_i = group_id + (ptrdiff_t)(gparts_i - s->gparts);
- int *const offset_j = group_id + (ptrdiff_t)(gparts_j - s->gparts);
+ int *const offset_i = group_index + (ptrdiff_t)(gparts_i - s->gparts);
+ int *const offset_j = group_index + (ptrdiff_t)(gparts_j - s->gparts);
/* Account for boundary conditions.*/
double shift[3] = {0.0, 0.0, 0.0};
@@ -470,12 +470,12 @@ void fof_search_pair_cells(struct space *s, struct cell *ci, struct cell *cj) {
const double piz = pi->x[2] - shift[2];
/* Find the root of pi. */
- int root_i = fof_find(offset_i[i] - node_offset, group_id);
+ int root_i = fof_find(offset_i[i] - node_offset, group_index);
for (size_t j = 0; j < count_j; j++) {
/* Find the root of pj. */
- const int root_j = fof_find(offset_j[j] - node_offset, group_id);
+ const int root_j = fof_find(offset_j[j] - node_offset, group_index);
/* Skip particles in the same group. */
if (root_i == root_j) continue;
@@ -500,12 +500,12 @@ void fof_search_pair_cells(struct space *s, struct cell *ci, struct cell *cj) {
/* If the root ID of pj is lower than pi's root ID set pi's root to point to pj's.
* Otherwise set pj's to root to point to pi's.*/
if (root_j < root_i) {
- atomic_min(&group_id[root_i - node_offset], root_j);
+ atomic_min(&group_index[root_i - node_offset], root_j);
/* Update root_i on the fly. */
root_i = root_j;
}
else
- atomic_min(&group_id[root_j - node_offset], root_i);
+ atomic_min(&group_index[root_j - node_offset], root_i);
}
}
@@ -522,11 +522,11 @@ void fof_search_pair_cells_foreign(struct space *s, struct cell *ci, struct cell
struct gpart *gparts_j = cj->gparts;
const double dim[3] = {s->dim[0], s->dim[1], s->dim[2]};
const double l_x2 = s->l_x2;
- int *group_id = s->group_id;
+ int *group_index = s->fof_data.group_index;
/* Make a list of particle offsets into the global gparts array. */
- int *const offset_i = group_id + (ptrdiff_t)(gparts_i - s->gparts);
- int *const offset_j = group_id + (ptrdiff_t)(gparts_j - s->gparts);
+ int *const offset_i = group_index + (ptrdiff_t)(gparts_i - s->gparts);
+ int *const offset_j = group_index + (ptrdiff_t)(gparts_j - s->gparts);
/* Account for boundary conditions.*/
double shift[3] = {0.0, 0.0, 0.0};
@@ -565,7 +565,7 @@ void fof_search_pair_cells_foreign(struct space *s, struct cell *ci, struct cell
const double piz = pi->x[2] - shift[2];
/* Find the root of pi. */
- int root_i = fof_find(offset_i[i] - node_offset, group_id);
+ int root_i = fof_find(offset_i[i] - node_offset, group_index);
for (size_t j = 0; j < count_j; j++) {
@@ -622,7 +622,7 @@ void fof_search_pair_cells_foreign(struct space *s, struct cell *ci, struct cell
const double pjz = pj->x[2] - shift[2];
/* Find the root of pj. */
- int root_j = fof_find(offset_j[j] - node_offset, group_id);
+ int root_j = fof_find(offset_j[j] - node_offset, group_index);
for (size_t i = 0; i < count_i; i++) {
@@ -674,7 +674,7 @@ void fof_search_tree_serial(struct space *s) {
const size_t nr_gparts = s->nr_gparts;
const size_t nr_cells = s->nr_cells;
struct gpart *gparts = s->gparts;
- int *group_id;
+ int *group_index;
int *group_size;
float *group_mass;
int num_groups = 0;
@@ -686,17 +686,17 @@ void fof_search_tree_serial(struct space *s) {
s->l_x2);
/* Allocate and initialise array of particle group IDs. */
- if(s->group_id != NULL) free(s->group_id);
+ if(s->fof_data.group_index != NULL) free(s->fof_data.group_index);
- if (posix_memalign((void **)&s->group_id, 32, nr_gparts * sizeof(int)) != 0)
+ if (posix_memalign((void **)&s->fof_data.group_index, 32, nr_gparts * sizeof(int)) != 0)
error("Failed to allocate list of particle group IDs for FOF search.");
/* Initial group ID is particle offset into array. */
- for (size_t i = 0; i < nr_gparts; i++) s->group_id[i] = i;
+ for (size_t i = 0; i < nr_gparts; i++) s->fof_data.group_index[i] = i;
- group_id = s->group_id;
+ group_index = s->fof_data.group_index;
- message("Rank: %d, Allocated group_id array of size %zu", engine_rank, s->nr_gparts);
+ message("Rank: %d, Allocated group_index array of size %zu", engine_rank, s->nr_gparts);
/* Allocate and initialise a group size array. */
if (posix_memalign((void **)&group_size, 32, nr_gparts * sizeof(int)) != 0)
@@ -743,17 +743,17 @@ void fof_search_tree_serial(struct space *s) {
/* Calculate the total number of particles in each group, group mass and the total number of groups. */
for (size_t i = 0; i < nr_gparts; i++) {
- const int root = fof_find(i, group_id);
+ const int root = fof_find(i, group_index);
group_size[root]++;
group_mass[root] += gparts[i].mass;
- if(group_id[i] == i) num_groups++;
+ if(group_index[i] == i) num_groups++;
}
- fof_dump_group_data("fof_output_tree_serial.dat", nr_gparts, group_id,
+ fof_dump_group_data("fof_output_tree_serial.dat", nr_gparts, group_index,
group_size);
int num_parts_in_groups = 0;
- int max_group_size = 0, max_group_id = 0, max_group_mass_id = 0;
+ int max_group_size = 0, max_group_index = 0, max_group_mass_id = 0;
float max_group_mass = 0;
for (size_t i = 0; i < nr_gparts; i++) {
@@ -763,7 +763,7 @@ void fof_search_tree_serial(struct space *s) {
/* Find the largest group. */
if (group_size[i] > max_group_size) {
max_group_size = group_size[i];
- max_group_id = i;
+ max_group_index = i;
}
/* Find the largest group by mass. */
@@ -777,7 +777,7 @@ void fof_search_tree_serial(struct space *s) {
"No. of groups: %d. No. of particles in groups: %d. No. of particles not "
"in groups: %zu.",
num_groups, num_parts_in_groups, nr_gparts - num_parts_in_groups);
- message("Biggest group size: %d with ID: %d", max_group_size, max_group_id);
+ message("Biggest group size: %d with ID: %d", max_group_size, max_group_index);
message("Biggest group by mass: %f with ID: %d", max_group_mass, max_group_mass_id);
free(group_size);
@@ -1025,7 +1025,7 @@ void fof_search_foreign_cells(struct space *s) {
struct gpart *gparts = c->gparts;
/* Make a list of particle offsets into the global gparts array. */
- int *const offset = s->group_id + (ptrdiff_t)(gparts - s->gparts);
+ int *const offset = s->fof_data.group_index + (ptrdiff_t)(gparts - s->gparts);
for(int k=0; k<c->gcount; k++) {
@@ -1036,13 +1036,13 @@ void fof_search_foreign_cells(struct space *s) {
found_count++;
found = 1;
- int local_root = fof_find(offset[k] - node_offset, s->group_id);
+ int local_root = fof_find(offset[k] - node_offset, s->fof_data.group_index);
if(local_root == fof_recv[i].root_i) continue;
if(fof_recv[i].root_i < local_root) {
- s->group_id[local_root - node_offset] = fof_recv[i].root_i;
+ s->fof_data.group_index[local_root - node_offset] = fof_recv[i].root_i;
//message("Rank: %d Particle %lld found new group with root: %d, previous group: %d, i=%d, j=%d, k=%d", engine_rank, gp->id_or_neg_offset, fof_recv[i].root_i, local_root, i,j,k);
@@ -1077,7 +1077,8 @@ void fof_search_tree(struct space *s) {
const size_t nr_gparts = s->nr_gparts;
const size_t nr_cells = s->nr_cells;
struct gpart *gparts = s->gparts;
- int *group_id;
+ //long long *group_id;
+ int *group_index;
int *group_size;
float *group_mass;
int num_groups = 0;
@@ -1115,17 +1116,17 @@ void fof_search_tree(struct space *s) {
message("Node offset: %d", node_offset);
/* Allocate and initialise array of particle group IDs. */
- if(s->group_id != NULL) free(s->group_id);
+ if(s->fof_data.group_index != NULL) free(s->fof_data.group_index);
- if (posix_memalign((void **)&s->group_id, 32, nr_gparts * sizeof(int)) != 0)
+ if (posix_memalign((void **)&s->fof_data.group_index, 32, nr_gparts * sizeof(int)) != 0)
error("Failed to allocate list of particle group IDs for FOF search.");
/* Initial group ID is particle offset into array. */
- for (size_t i = 0; i < nr_gparts; i++) s->group_id[i] = node_offset + i;
+ for (size_t i = 0; i < nr_gparts; i++) s->fof_data.group_index[i] = node_offset + i;
- group_id = s->group_id;
+ group_index = s->fof_data.group_index;
- message("Rank: %d, Allocated group_id array of size %zu", engine_rank, s->nr_gparts);
+ message("Rank: %d, Allocated group_index array of size %zu", engine_rank, s->nr_gparts);
/* Allocate and initialise a group size array. */
if (posix_memalign((void **)&group_size, 32, nr_gparts * sizeof(int)) != 0)
@@ -1151,56 +1152,56 @@ void fof_search_tree(struct space *s) {
/* Calculate the total number of particles in each group, group mass and the total number of groups. */
for (size_t i = 0; i < nr_gparts; i++) {
- const int root = fof_find(i, group_id);
+ const int root = fof_find(i, group_index);
group_size[root - node_offset]++;
group_mass[root - node_offset] += gparts[i].mass;
- if(group_id[i] == i + node_offset) num_groups++;
+ if(group_index[i] == i + node_offset) num_groups++;
}
- fof_dump_group_data("fof_search_tree_local.dat", nr_gparts, group_id,
+ fof_dump_group_data("fof_search_tree_local.dat", nr_gparts, group_index,
group_size);
#ifdef WITH_MPI
- int *global_group_id, *global_group_size;
+ int *global_group_index, *global_group_size;
int total_num_groups = 0;
if (s->e->nr_nodes > 1) {
MPI_Reduce(&num_groups, &total_num_groups, 1, MPI_INT, MPI_SUM, 0, MPI_COMM_WORLD);
- if (posix_memalign((void **)&global_group_id, 32, s->e->total_nr_gparts * sizeof(int)) != 0)
+ if (posix_memalign((void **)&global_group_index, 32, s->e->total_nr_gparts * sizeof(int)) != 0)
error("Failed to allocate list of global group IDs for FOF search.");
if (posix_memalign((void **)&global_group_size, 32, s->e->total_nr_gparts * sizeof(int)) != 0)
error("Failed to allocate list of global group sizes for FOF search.");
- bzero(global_group_id, s->e->total_nr_gparts * sizeof(int));
+ bzero(global_group_index, s->e->total_nr_gparts * sizeof(int));
bzero(global_group_size, s->e->total_nr_gparts * sizeof(int));
int displ[2] = {0, nr_gparts};
- MPI_Gatherv(group_id, nr_gparts, MPI_INT, global_group_id, global_nr_gparts, displ, MPI_INT, 0, MPI_COMM_WORLD);
+ MPI_Gatherv(group_index, nr_gparts, MPI_INT, global_group_index, global_nr_gparts, displ, MPI_INT, 0, MPI_COMM_WORLD);
total_num_groups = 0;
for (size_t i = 0; i < s->e->total_nr_gparts; i++) {
- const int root = fof_find_global(i, global_group_id);
- //const int root = fof_find(i, global_group_id);
+ const int root = fof_find_global(i, global_group_index);
+ //const int root = fof_find(i, global_group_index);
global_group_size[root]++;
- if(global_group_id[i] == i) total_num_groups++;
+ if(global_group_index[i] == i) total_num_groups++;
}
if(engine_rank == 0) {
- fof_file = fopen("global_group_id.dat", "w");
+ fof_file = fopen("global_group_index.dat", "w");
fprintf(fof_file, "# %7s %7s\n", "Index", "Group ID");
fprintf(fof_file, "#-------------------------------\n");
for (size_t i = 0; i < s->e->total_nr_gparts; i++) {
- fprintf(fof_file, " %7zu %7d \n", i, global_group_id[i]);
+ fprintf(fof_file, " %7zu %7d \n", i, global_group_index[i]);
}
- fof_dump_group_data(output_file_name, s->e->total_nr_gparts, global_group_id,
+ fof_dump_group_data(output_file_name, s->e->total_nr_gparts, global_group_index,
global_group_size);
}
@@ -1208,7 +1209,7 @@ void fof_search_tree(struct space *s) {
#endif /* WITH_MPI */
int num_parts_in_groups = 0;
- int max_group_size = 0, max_group_id = 0, max_group_mass_id = 0;
+ int max_group_size = 0, max_group_index = 0, max_group_mass_id = 0;
float max_group_mass = 0;
for (size_t i = 0; i < nr_gparts; i++) {
@@ -1218,7 +1219,7 @@ void fof_search_tree(struct space *s) {
/* Find the largest group. */
if (group_size[i] > max_group_size) {
max_group_size = group_size[i];
- max_group_id = i;
+ max_group_index = i;
}
/* Find the largest group by mass. */
@@ -1233,7 +1234,7 @@ void fof_search_tree(struct space *s) {
"in groups: %zu.",
num_groups, num_parts_in_groups, nr_gparts - num_parts_in_groups);
- message("Biggest group size: %d with ID: %d", max_group_size, max_group_id);
+ message("Biggest group size: %d with ID: %d", max_group_size, max_group_index);
message("Biggest group by mass: %f with ID: %d", max_group_mass, max_group_mass_id);
free(group_size);
@@ -1243,7 +1244,7 @@ void fof_search_tree(struct space *s) {
if (s->e->nr_nodes > 1) {
if(engine_rank == 0) message("Total number of groups: %d", total_num_groups);
free(global_nr_gparts);
- free(global_group_id);
+ free(global_group_index);
}
#endif /* WITH_MPI */
@@ -1251,18 +1252,33 @@ void fof_search_tree(struct space *s) {
clocks_from_ticks(getticks() - tic), clocks_getunit());
}
-/* Dump FOF group data. */
-void fof_dump_group_data(char *out_file, const size_t nr_gparts, int *group_id,
+void fof_dump_group_data(char *out_file, const size_t nr_gparts, int *group_index,
int *group_size) {
FILE *file = fopen(out_file, "w");
fprintf(file, "# %7s %7s %7s\n", "ID", "Root ID", "Group Size");
- fprintf(file, "#-------------------------------\n");
+ fprintf(file, "#---------------------------------------\n");
for (size_t i = 0; i < nr_gparts; i++) {
- const int root = fof_find(i, group_id);
+ const int root = fof_find(i, group_index);
fprintf(file, " %7zu %7d %7d\n", i, root, group_size[i]);
}
fclose(file);
}
+
+/* Dump FOF group data. */
+//void fof_dump_group_data(char *out_file, const size_t nr_gparts, int *group_index,
+// int *group_size, struct gpart *gparts) {
+//
+// FILE *file = fopen(out_file, "w");
+// fprintf(file, "# %7s %7s %7s %7s\n", "ID", "Root ID", "Group Size", "Group ID");
+// fprintf(file, "#---------------------------------------\n");
+//
+// for (size_t i = 0; i < nr_gparts; i++) {
+// const int root = fof_find(i, group_index);
+// fprintf(file, " %7zu %7d %7d %10lld\n", i, root, group_size[i], gparts[root].id_or_neg_offset);
+// }
+//
+// fclose(file);
+//}
diff --git a/src/space.c b/src/space.c
index 90f4722ce9..3f25954cb7 100644
--- a/src/space.c
+++ b/src/space.c
@@ -3213,7 +3213,8 @@ void space_clean(struct space *s) {
free(s->xparts);
free(s->gparts);
free(s->sparts);
- free(s->group_id);
+ free(s->fof_data.group_id);
+ free(s->fof_data.group_index);
}
/**
diff --git a/src/space.h b/src/space.h
index c6b695a060..16fc15b32e 100644
--- a/src/space.h
+++ b/src/space.h
@@ -35,11 +35,19 @@
#include "lock.h"
#include "parser.h"
#include "part.h"
+//#include "fof.h"
/* Avoid cyclic inclusions */
struct cell;
struct cosmology;
+struct fof {
+
+ long long *group_id;
+ int *group_index;
+
+} SWIFT_STRUCT_ALIGN;
+
/* Some constants. */
#define space_cellallocchunk 1000
#define space_splitsize_default 400
@@ -177,8 +185,8 @@ struct space {
double l_x2;
/*! The FOF group data. */
- int *group_id;
-
+ struct fof fof_data;
+
/*! List of cell indices. */
int *cell_index;
--
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