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op_mpi_core.c
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op_mpi_core.c
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/*
* Open source copyright declaration based on BSD open source template:
* http://www.opensource.org/licenses/bsd-license.php
*
* This file is part of the OP2 distribution.
*
* Copyright (c) 2011, Mike Giles and others. Please see the AUTHORS file in
* the main source directory for a full list of copyright holders.
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
* * Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* * Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in the
* documentation and/or other materials provided with the distribution.
* * The name of Mike Giles may not be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY Mike Giles ''AS IS'' AND ANY
* EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL Mike Giles BE LIABLE FOR ANY
* DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
/*
* op_mpi_core.c
*
* Implements the OP2 Distributed memory (MPI) halo creation, halo exchange and
* support utility routines/functions
*
* written by: Gihan R. Mudalige, (Started 01-03-2011)
*/
// mpi header
#include <mpi.h>
//#include <op_lib_core.h>
#include <op_lib_c.h>
#include <op_lib_mpi.h>
#include <op_util.h>
#include <op_mpi_core.h>
//
// MPI Halo related global variables
//
halo_list *OP_export_exec_list; // EEH list
halo_list *OP_import_exec_list; // IEH list
halo_list *OP_import_nonexec_list; // INH list
halo_list *OP_export_nonexec_list; // ENH list
//
// Partial halo exchange lists
//
int *OP_map_partial_exchange; // flag for each map
halo_list *OP_import_nonexec_permap;
halo_list *OP_export_nonexec_permap;
int *set_import_buffer_size;
//
// global array to hold dirty_bits for op_dats
//
/*table holding MPI performance of each loop
(accessed via a hash of loop name) */
op_mpi_kernel *op_mpi_kernel_tab = NULL;
//
// global variables to hold partition information on an MPI rank
//
int OP_part_index = 0;
part *OP_part_list;
//
// Save original partition ranges
//
int **orig_part_range = NULL;
// Sliding planes data structures
int OP_import_index = 0, OP_import_max = 0;
int OP_export_index = 0, OP_export_max = 0;
op_import_handle *OP_import_list = NULL;
op_export_handle *OP_export_list = NULL;
// Timing
double t1, t2, c1, c2;
/*******************************************************************************
* Routine to declare partition information for a given set
*******************************************************************************/
void decl_partition(op_set set, int *g_index, int *partition) {
part p = (part)xmalloc(sizeof(part_core));
p->set = set;
p->g_index = g_index;
p->elem_part = partition;
p->is_partitioned = 0;
OP_part_list[set->index] = p;
OP_part_index++;
}
/*******************************************************************************
* Routine to get partition range on all mpi ranks for all sets
*******************************************************************************/
void get_part_range(int **part_range, int my_rank, int comm_size,
MPI_Comm Comm) {
(void)my_rank;
for (int s = 0; s < OP_set_index; s++) {
op_set set = OP_set_list[s];
int *sizes = (int *)xmalloc(sizeof(int) * comm_size);
MPI_Allgather(&set->size, 1, MPI_INT, sizes, 1, MPI_INT, Comm);
part_range[set->index] = (int *)xmalloc(2 * comm_size * sizeof(int));
int disp = 0;
for (int i = 0; i < comm_size; i++) {
part_range[set->index][2 * i] = disp;
disp = disp + sizes[i] - 1;
part_range[set->index][2 * i + 1] = disp;
disp++;
#ifdef DEBUG
if (my_rank == MPI_ROOT && OP_diags > 5)
printf("range of %10s in rank %d: %d-%d\n", set->name, i,
part_range[set->index][2 * i],
part_range[set->index][2 * i + 1]);
#endif
}
op_free(sizes);
}
}
/*******************************************************************************
* Routine to get partition (i.e. mpi rank) where global_index is located and
* its local index
*******************************************************************************/
int get_partition(int global_index, int *part_range, int *local_index,
int comm_size) {
for (int i = 0; i < comm_size; i++) {
if (global_index >= part_range[2 * i] &&
global_index <= part_range[2 * i + 1]) {
*local_index = global_index - part_range[2 * i];
return i;
}
}
printf("Error: orphan global index\n");
MPI_Abort(OP_MPI_WORLD, 2);
return -1;
}
/*******************************************************************************
* Routine to convert a local index in to a global index
*******************************************************************************/
int get_global_index(int local_index, int partition, int *part_range,
int comm_size) {
(void)comm_size;
int g_index = part_range[2 * partition] + local_index;
#ifdef DEBUG
if (g_index > part_range[2 * (comm_size - 1) + 1] && OP_diags > 2)
printf("Global index larger than set size\n");
#endif
return g_index;
}
/*******************************************************************************
* Routine to find the MPI neighbors given a halo list
*******************************************************************************/
void find_neighbors_set(halo_list List, int *neighbors, int *sizes,
int *ranks_size, int my_rank, int comm_size,
MPI_Comm Comm) {
int *temp = (int *)xmalloc(comm_size * sizeof(int));
int *r_temp = (int *)xmalloc(comm_size * comm_size * sizeof(int));
for (int r = 0; r < comm_size * comm_size; r++)
r_temp[r] = -99;
for (int r = 0; r < comm_size; r++)
temp[r] = -99;
int n = 0;
for (int r = 0; r < comm_size; r++) {
if (List->ranks[r] >= 0)
temp[List->ranks[r]] = List->sizes[r];
}
MPI_Allgather(temp, comm_size, MPI_INT, r_temp, comm_size, MPI_INT, Comm);
for (int i = 0; i < comm_size; i++) {
if (i != my_rank) {
if (r_temp[i * comm_size + my_rank] > 0) {
neighbors[n] = i;
sizes[n] = r_temp[i * comm_size + my_rank];
n++;
}
}
}
*ranks_size = n;
op_free(temp);
op_free(r_temp);
}
/*******************************************************************************
* Routine to create a generic halo list
* (used in both import and export list creation)
*******************************************************************************/
void create_list(int *list, int *ranks, int *disps, int *sizes, int *ranks_size,
int *total, int *temp_list, int size, int comm_size,
int my_rank) {
(void)my_rank;
int index = 0;
int total_size = 0;
if (size < 0)
printf("problem\n");
// negative values set as an initialisation
for (int r = 0; r < comm_size; r++) {
disps[r] = ranks[r] = -99;
sizes[r] = 0;
}
for (int r = 0; r < comm_size; r++) {
sizes[index] = disps[index] = 0;
int *temp = (int *)xmalloc((size / 2) * sizeof(int));
for (int i = 0; i < size; i = i + 2) {
if (temp_list[i] == r)
temp[sizes[index]++] = temp_list[i + 1];
}
if (sizes[index] > 0) {
ranks[index] = r;
// sort temp,
quickSort(temp, 0, sizes[index] - 1);
// eliminate duplicates in temp
sizes[index] = removeDups(temp, sizes[index]);
total_size = total_size + sizes[index];
if (index > 0)
disps[index] = disps[index - 1] + sizes[index - 1];
// add to end of exp_list
for (int e = 0; e < sizes[index]; e++)
list[disps[index] + e] = temp[e];
index++;
}
op_free(temp);
}
*total = total_size;
*ranks_size = index;
}
/*******************************************************************************
* Routine to create an export list
*******************************************************************************/
void create_export_list(op_set set, int *temp_list, halo_list h_list, int size,
int comm_size, int my_rank) {
int *ranks = (int *)xmalloc(comm_size * sizeof(int));
int *list = (int *)xmalloc((size / 2) * sizeof(int));
int *disps = (int *)xmalloc(comm_size * sizeof(int));
int *sizes = (int *)xmalloc(comm_size * sizeof(int));
int ranks_size = 0;
int total_size = 0;
create_list(list, ranks, disps, sizes, &ranks_size, &total_size, temp_list,
size, comm_size, my_rank);
h_list->set = set;
h_list->size = total_size;
h_list->ranks = ranks;
h_list->ranks_size = ranks_size;
h_list->disps = disps;
h_list->sizes = sizes;
h_list->list = list;
}
/*******************************************************************************
* Routine to create an import list
*******************************************************************************/
void create_import_list(op_set set, int *temp_list, halo_list h_list,
int total_size, int *ranks, int *sizes, int ranks_size,
int comm_size, int my_rank) {
(void)my_rank;
int *disps = (int *)xmalloc(comm_size * sizeof(int));
disps[0] = 0;
for (int i = 0; i < ranks_size; i++) {
if (i > 0)
disps[i] = disps[i - 1] + sizes[i - 1];
}
h_list->set = set;
h_list->size = total_size;
h_list->ranks = ranks;
h_list->ranks_size = ranks_size;
h_list->disps = disps;
h_list->sizes = sizes;
h_list->list = temp_list;
}
/*******************************************************************************
* Routine to create an nonexec-import list (only a wrapper)
*******************************************************************************/
static void create_nonexec_import_list(op_set set, int *temp_list,
halo_list h_list, int size,
int comm_size, int my_rank) {
create_export_list(set, temp_list, h_list, size, comm_size, my_rank);
}
/*******************************************************************************
* Routine to create an nonexec-export list (only a wrapper)
*******************************************************************************/
static void create_nonexec_export_list(op_set set, int *temp_list,
halo_list h_list, int total_size,
int *ranks, int *sizes, int ranks_size,
int comm_size, int my_rank) {
create_import_list(set, temp_list, h_list, total_size, ranks, sizes,
ranks_size, comm_size, my_rank);
}
/*******************************************************************************
* Check if a given op_map is an on-to map from the from-set to the to-set
* note: on large meshes this routine takes up a lot of memory due to memory
* allocated for MPI_Allgathers, thus use only when debugging code
*******************************************************************************/
int is_onto_map(op_map map) {
// create new communicator
int my_rank, comm_size;
MPI_Comm OP_CHECK_WORLD;
MPI_Comm_dup(OP_MPI_WORLD, &OP_CHECK_WORLD);
MPI_Comm_rank(OP_CHECK_WORLD, &my_rank);
MPI_Comm_size(OP_CHECK_WORLD, &comm_size);
// Compute global partition range information for each set
int **part_range = (int **)xmalloc(OP_set_index * sizeof(int *));
get_part_range(part_range, my_rank, comm_size, OP_CHECK_WORLD);
// mak a copy of the to-set elements of the map
int *to_elem_copy = (int *)xmalloc(map->from->size * map->dim * sizeof(int));
memcpy(to_elem_copy, (void *)map->map,
map->from->size * map->dim * sizeof(int));
// sort and remove duplicates from to_elem_copy
quickSort(to_elem_copy, 0, map->from->size * map->dim - 1);
int to_elem_copy_size = removeDups(to_elem_copy, map->from->size * map->dim);
to_elem_copy = (int *)xrealloc(to_elem_copy, to_elem_copy_size * sizeof(int));
// go through the to-set element range that this local MPI process holds
// and collect the to-set elements not found in to_elem_copy
int cap = 100;
int count = 0;
int *not_found = (int *)xmalloc(sizeof(int) * cap);
for (int i = 0; i < map->to->size; i++) {
int g_index =
get_global_index(i, my_rank, part_range[map->to->index], comm_size);
if (binary_search(to_elem_copy, i, 0, to_elem_copy_size - 1) < 0) {
// add to not_found list
if (count >= cap) {
cap = cap * 2;
not_found = (int *)xrealloc(not_found, cap * sizeof(int));
}
not_found[count++] = g_index;
}
}
//
// allreduce this not_found to form a global_not_found list
//
int recv_count[comm_size];
MPI_Allgather(&count, 1, MPI_INT, recv_count, 1, MPI_INT, OP_CHECK_WORLD);
// discover global size of the not_found_list
int g_count = 0;
for (int i = 0; i < comm_size; i++)
g_count += recv_count[i];
// prepare for an allgatherv
int disp = 0;
int *displs = (int *)xmalloc(comm_size * sizeof(int));
for (int i = 0; i < comm_size; i++) {
displs[i] = disp;
disp = disp + recv_count[i];
}
// allocate memory to hold the global_not_found list
int *global_not_found = (int *)xmalloc(sizeof(int) * g_count);
MPI_Allgatherv(not_found, count, MPI_INT, global_not_found, recv_count,
displs, MPI_INT, OP_CHECK_WORLD);
op_free(not_found);
op_free(displs);
// sort and remove duplicates of the global_not_found list
if (g_count > 0) {
quickSort(global_not_found, 0, g_count - 1);
g_count = removeDups(global_not_found, g_count);
global_not_found = (int *)xrealloc(global_not_found, g_count * sizeof(int));
} else {
// nothing in the global_not_found list .. i.e. this is an on to map
op_free(global_not_found);
op_free(to_elem_copy); // op_free(displs);
for (int i = 0; i < OP_set_index; i++)
op_free(part_range[i]);
op_free(part_range);
return 1;
}
// see if any element in the global_not_found is found in the local map-copy
// and add it to a "found" list
cap = 100;
count = 0;
int *found = (int *)xmalloc(sizeof(int) * cap);
for (int i = 0; i < g_count; i++) {
if (binary_search(to_elem_copy, global_not_found[i], 0,
to_elem_copy_size - 1) >= 0) {
// add to found list
if (count >= cap) {
cap = cap * 2;
found = (int *)xrealloc(found, cap * sizeof(int));
}
found[count++] = global_not_found[i];
}
}
op_free(global_not_found);
//
// allreduce the "found" elements to form a global_found list
//
// recv_count[comm_size];
MPI_Allgather(&count, 1, MPI_INT, recv_count, 1, MPI_INT, OP_CHECK_WORLD);
// discover global size of the found_list
int g_found_count = 0;
for (int i = 0; i < comm_size; i++)
g_found_count += recv_count[i];
// prepare for an allgatherv
disp = 0;
displs = (int *)xmalloc(comm_size * sizeof(int));
for (int i = 0; i < comm_size; i++) {
displs[i] = disp;
disp = disp + recv_count[i];
}
// allocate memory to hold the global_found list
int *global_found = (int *)xmalloc(sizeof(int) * g_found_count);
MPI_Allgatherv(found, count, MPI_INT, global_found, recv_count, displs,
MPI_INT, OP_CHECK_WORLD);
op_free(found);
// sort global_found list and remove duplicates
if (g_count > 0) {
quickSort(global_found, 0, g_found_count - 1);
g_found_count = removeDups(global_found, g_found_count);
global_found = (int *)xrealloc(global_found, g_found_count * sizeof(int));
}
// if the global_found list size is smaller than the globla_not_found list
// size
// then map is not an on_to map
int result = 0;
if (g_found_count == g_count)
result = 1;
op_free(global_found);
op_free(displs);
for (int i = 0; i < OP_set_index; i++)
op_free(part_range[i]);
op_free(part_range);
MPI_Comm_free(&OP_CHECK_WORLD);
op_free(to_elem_copy);
return result;
}
/*******************************************************************************
* Main MPI halo creation routine
*******************************************************************************/
void op_halo_create() {
// declare timers
double cpu_t1, cpu_t2, wall_t1, wall_t2;
double time;
double max_time;
op_timers(&cpu_t1, &wall_t1); // timer start for list create
// create new communicator for OP mpi operation
int my_rank, comm_size;
// MPI_Comm_dup(OP_MPI_WORLD, &OP_MPI_WORLD);
MPI_Comm_rank(OP_MPI_WORLD, &my_rank);
MPI_Comm_size(OP_MPI_WORLD, &comm_size);
/* Compute global partition range information for each set*/
int **part_range = (int **)xmalloc(OP_set_index * sizeof(int *));
get_part_range(part_range, my_rank, comm_size, OP_MPI_WORLD);
// save this partition range information if it is not already saved during
// a call to some partitioning routine
if (orig_part_range == NULL) {
orig_part_range = (int **)xmalloc(OP_set_index * sizeof(int *));
for (int s = 0; s < OP_set_index; s++) {
op_set set = OP_set_list[s];
orig_part_range[set->index] = (int *)xmalloc(2 * comm_size * sizeof(int));
for (int j = 0; j < comm_size; j++) {
orig_part_range[set->index][2 * j] = part_range[set->index][2 * j];
orig_part_range[set->index][2 * j + 1] =
part_range[set->index][2 * j + 1];
}
}
}
OP_export_exec_list = (halo_list *)xmalloc(OP_set_index * sizeof(halo_list));
/*----- STEP 1 - Construct export lists for execute set elements and related
mapping table entries -----*/
// declare temporaty scratch variables to hold set export lists and mapping
// table export lists
int s_i;
int *set_list;
int cap_s = 1000; // keep track of the temp array capacities
for (int s = 0; s < OP_set_index; s++) { // for each set
op_set set = OP_set_list[s];
// create a temporaty scratch space to hold export list for this set
s_i = 0;
cap_s = 1000;
set_list = (int *)xmalloc(cap_s * sizeof(int));
for (int e = 0; e < set->size; e++) { // for each elment of this set
for (int m = 0; m < OP_map_index; m++) { // for each maping table
op_map map = OP_map_list[m];
if (compare_sets(map->from, set) == 1) { // need to select mappings
// FROM this set
int part, local_index;
for (int j = 0; j < map->dim; j++) { // for each element
// pointed at by this entry
part = get_partition(map->map[e * map->dim + j],
part_range[map->to->index], &local_index,
comm_size);
if (s_i >= cap_s) {
cap_s = cap_s * 2;
set_list = (int *)xrealloc(set_list, cap_s * sizeof(int));
}
if (part != my_rank) {
set_list[s_i++] = part; // add to set export list
set_list[s_i++] = e;
}
}
}
}
}
// create set export list
// printf("creating set export list for set %10s of size %d\n",
// set->name,s_i);
halo_list h_list = (halo_list)xmalloc(sizeof(halo_list_core));
create_export_list(set, set_list, h_list, s_i, comm_size, my_rank);
OP_export_exec_list[set->index] = h_list;
op_free(set_list); // free temp list
}
/*---- STEP 2 - construct import lists for mappings and execute sets------*/
OP_import_exec_list = (halo_list *)xmalloc(OP_set_index * sizeof(halo_list));
int *neighbors, *sizes;
int ranks_size;
for (int s = 0; s < OP_set_index; s++) { // for each set
op_set set = OP_set_list[s];
//-----Discover neighbors-----
ranks_size = 0;
neighbors = (int *)xmalloc(comm_size * sizeof(int));
sizes = (int *)xmalloc(comm_size * sizeof(int));
halo_list list = OP_export_exec_list[set->index];
find_neighbors_set(list, neighbors, sizes, &ranks_size, my_rank, comm_size,
OP_MPI_WORLD);
MPI_Request request_send[list->ranks_size];
int *rbuf, cap = 0, index = 0;
for (int i = 0; i < list->ranks_size; i++) {
// printf("export from %d to %d set %10s, list of size %d \n",
// my_rank,list->ranks[i],set->name,list->sizes[i]);
int *sbuf = &list->list[list->disps[i]];
MPI_Isend(sbuf, list->sizes[i], MPI_INT, list->ranks[i], s, OP_MPI_WORLD,
&request_send[i]);
}
for (int i = 0; i < ranks_size; i++)
cap = cap + sizes[i];
int *temp = (int *)xmalloc(cap * sizeof(int));
// import this list from those neighbors
for (int i = 0; i < ranks_size; i++) {
// printf("import from %d to %d set %10s, list of size %d\n",
// neighbors[i], my_rank, set->name, sizes[i]);
rbuf = (int *)xmalloc(sizes[i] * sizeof(int));
MPI_Recv(rbuf, sizes[i], MPI_INT, neighbors[i], s, OP_MPI_WORLD,
MPI_STATUS_IGNORE);
memcpy(&temp[index], (void *)&rbuf[0], sizes[i] * sizeof(int));
index = index + sizes[i];
op_free(rbuf);
}
MPI_Waitall(list->ranks_size, request_send, MPI_STATUSES_IGNORE);
// create import lists
// printf("creating importlist with number of neighbors %d\n",ranks_size);
halo_list h_list = (halo_list)xmalloc(sizeof(halo_list_core));
create_import_list(set, temp, h_list, index, neighbors, sizes, ranks_size,
comm_size, my_rank);
OP_import_exec_list[set->index] = h_list;
}
/*--STEP 3 -Exchange mapping table entries using the import/export lists--*/
for (int m = 0; m < OP_map_index; m++) { // for each maping table
op_map map = OP_map_list[m];
halo_list i_list = OP_import_exec_list[map->from->index];
halo_list e_list = OP_export_exec_list[map->from->index];
MPI_Request request_send[e_list->ranks_size];
// prepare bits of the mapping tables to be exported
int **sbuf = (int **)xmalloc(e_list->ranks_size * sizeof(int *));
for (int i = 0; i < e_list->ranks_size; i++) {
sbuf[i] = (int *)xmalloc(e_list->sizes[i] * map->dim * sizeof(int));
for (int j = 0; j < e_list->sizes[i]; j++) {
for (int p = 0; p < map->dim; p++) {
sbuf[i][j * map->dim + p] =
map->map[map->dim * (e_list->list[e_list->disps[i] + j]) + p];
}
}
// printf("\n export from %d to %d map %10s, number of elements of size %d
// | sending:\n ",
// my_rank,e_list.ranks[i],map.name,e_list.sizes[i]);
MPI_Isend(sbuf[i], map->dim * e_list->sizes[i], MPI_INT, e_list->ranks[i],
m, OP_MPI_WORLD, &request_send[i]);
}
// prepare space for the incomming mapping tables - realloc each
// mapping tables in each mpi process
OP_map_list[map->index]->map = (int *)xrealloc(
OP_map_list[map->index]->map,
(map->dim * (map->from->size + i_list->size)) * sizeof(int));
int init = map->dim * (map->from->size);
for (int i = 0; i < i_list->ranks_size; i++) {
// printf("\n imported on to %d map %10s, number of elements of size %d |
// recieving: ",
// my_rank, map->name, i_list->size);
MPI_Recv(
&(OP_map_list[map->index]->map[init + i_list->disps[i] * map->dim]),
map->dim * i_list->sizes[i], MPI_INT, i_list->ranks[i], m,
OP_MPI_WORLD, MPI_STATUS_IGNORE);
}
MPI_Waitall(e_list->ranks_size, request_send, MPI_STATUSES_IGNORE);
for (int i = 0; i < e_list->ranks_size; i++)
op_free(sbuf[i]);
op_free(sbuf);
}
/*-- STEP 4 - Create import lists for non-execute set elements using mapping
table entries including the additional mapping table entries --*/
OP_import_nonexec_list =
(halo_list *)xmalloc(OP_set_index * sizeof(halo_list));
OP_export_nonexec_list =
(halo_list *)xmalloc(OP_set_index * sizeof(halo_list));
// declare temporaty scratch variables to hold non-exec set export lists
s_i = 0;
set_list = NULL;
cap_s = 1000; // keep track of the temp array capacity
for (int s = 0; s < OP_set_index; s++) { // for each set
op_set set = OP_set_list[s];
halo_list exec_set_list = OP_import_exec_list[set->index];
// create a temporaty scratch space to hold nonexec export list for this set
s_i = 0;
set_list = (int *)xmalloc(cap_s * sizeof(int));
for (int m = 0; m < OP_map_index; m++) { // for each maping table
op_map map = OP_map_list[m];
halo_list exec_map_list = OP_import_exec_list[map->from->index];
if (compare_sets(map->to, set) == 1) { // need to select
// mappings TO this set
// for each entry in this mapping table: original+execlist
int len = map->from->size + exec_map_list->size;
for (int e = 0; e < len; e++) {
int part;
int local_index;
for (int j = 0; j < map->dim; j++) { // for each element pointed
// at by this entry
part = get_partition(map->map[e * map->dim + j],
part_range[map->to->index], &local_index,
comm_size);
if (s_i >= cap_s) {
cap_s = cap_s * 2;
set_list = (int *)xrealloc(set_list, cap_s * sizeof(int));
}
if (part != my_rank) {
int found = -1;
// check in exec list
int rank = binary_search(exec_set_list->ranks, part, 0,
exec_set_list->ranks_size - 1);
if (rank >= 0) {
found = binary_search(exec_set_list->list, local_index,
exec_set_list->disps[rank],
exec_set_list->disps[rank] +
exec_set_list->sizes[rank] - 1);
}
if (found < 0) {
// not in this partition and not found in
// exec list
// add to non-execute set_list
set_list[s_i++] = part;
set_list[s_i++] = local_index;
}
}
}
}
}
}
// create non-exec set import list
// printf("creating non-exec import list of size %d\n",s_i);
halo_list h_list = (halo_list)xmalloc(sizeof(halo_list_core));
create_nonexec_import_list(set, set_list, h_list, s_i, comm_size, my_rank);
op_free(set_list); // free temp list
OP_import_nonexec_list[set->index] = h_list;
}
/*----------- STEP 5 - construct non-execute set export lists -------------*/
for (int s = 0; s < OP_set_index; s++) { // for each set
op_set set = OP_set_list[s];
//-----Discover neighbors-----
ranks_size = 0;
neighbors = (int *)xmalloc(comm_size * sizeof(int));
sizes = (int *)xmalloc(comm_size * sizeof(int));
halo_list list = OP_import_nonexec_list[set->index];
find_neighbors_set(list, neighbors, sizes, &ranks_size, my_rank, comm_size,
OP_MPI_WORLD);
MPI_Request request_send[list->ranks_size];
int *rbuf, cap = 0, index = 0;
for (int i = 0; i < list->ranks_size; i++) {
// printf("import to %d from %d set %10s, nonexec list of size %d |
// sending:\n",
// my_rank,list->ranks[i],set->name,list->sizes[i]);
int *sbuf = &list->list[list->disps[i]];
MPI_Isend(sbuf, list->sizes[i], MPI_INT, list->ranks[i], s, OP_MPI_WORLD,
&request_send[i]);
}
for (int i = 0; i < ranks_size; i++)
cap = cap + sizes[i];
int *temp = (int *)xmalloc(cap * sizeof(int));
// export this list to those neighbors
for (int i = 0; i < ranks_size; i++) {
// printf("export to %d from %d set %10s, list of size %d | recieving:\n",
// neighbors[i], my_rank, set->name, sizes[i]);
rbuf = (int *)xmalloc(sizes[i] * sizeof(int));
MPI_Recv(rbuf, sizes[i], MPI_INT, neighbors[i], s, OP_MPI_WORLD,
MPI_STATUS_IGNORE);
memcpy(&temp[index], (void *)&rbuf[0], sizes[i] * sizeof(int));
index = index + sizes[i];
op_free(rbuf);
}
MPI_Waitall(list->ranks_size, request_send, MPI_STATUSES_IGNORE);
// create import lists
// printf("creating nonexec set export list with number of neighbors
// %d\n",ranks_size);
halo_list h_list = (halo_list)xmalloc(sizeof(halo_list_core));
create_nonexec_export_list(set, temp, h_list, index, neighbors, sizes,
ranks_size, comm_size, my_rank);
OP_export_nonexec_list[set->index] = h_list;
}
/*-STEP 6 - Exchange execute set elements/data using the import/export
* lists--*/
for (int s = 0; s < OP_set_index; s++) { // for each set
op_set set = OP_set_list[s];
halo_list i_list = OP_import_exec_list[set->index];
halo_list e_list = OP_export_exec_list[set->index];
// for each data array
op_dat_entry *item;
int d = -1; // d is just simply the tag for mpi comms
TAILQ_FOREACH(item, &OP_dat_list, entries) {
d++; // increase tag to do mpi comm for the next op_dat
op_dat dat = item->dat;
if (compare_sets(set, dat->set) == 1) { // if this data array
// is defined on this set
// printf("on rank %d, The data array is %10s\n",my_rank,dat->name);
MPI_Request request_send[e_list->ranks_size];
// prepare execute set element data to be exported
char **sbuf = (char **)xmalloc(e_list->ranks_size * sizeof(char *));
for (int i = 0; i < e_list->ranks_size; i++) {
sbuf[i] = (char *)xmalloc(e_list->sizes[i] * dat->size);
for (int j = 0; j < e_list->sizes[i]; j++) {
int set_elem_index = e_list->list[e_list->disps[i] + j];
memcpy(&sbuf[i][j * dat->size],
(void *)&dat->data[dat->size * (set_elem_index)], dat->size);
}
// printf("export from %d to %d data %10s, number of elements of size
// %d | sending:\n ",
// my_rank,e_list->ranks[i],dat->name,e_list->sizes[i]);
MPI_Isend(sbuf[i], dat->size * e_list->sizes[i], MPI_CHAR,
e_list->ranks[i], d, OP_MPI_WORLD, &request_send[i]);
}
// prepare space for the incomming data - realloc each
// data array in each mpi process
dat->data =
(char *)xrealloc(dat->data, (set->size + i_list->size) * dat->size);
int init = set->size * dat->size;
for (int i = 0; i < i_list->ranks_size; i++) {
MPI_Recv(&(dat->data[init + i_list->disps[i] * dat->size]),
dat->size * i_list->sizes[i], MPI_CHAR, i_list->ranks[i], d,
OP_MPI_WORLD, MPI_STATUS_IGNORE);
}
MPI_Waitall(e_list->ranks_size, request_send, MPI_STATUSES_IGNORE);
for (int i = 0; i < e_list->ranks_size; i++)
op_free(sbuf[i]);
op_free(sbuf);
// printf("imported on to %d data %10s, number of elements of size %d |
// recieving:\n ",
// my_rank, dat->name, i_list->size);
}
}
}
/*-STEP 7 - Exchange non-execute set elements/data using the import/export
* lists--*/
for (int s = 0; s < OP_set_index; s++) { // for each set
op_set set = OP_set_list[s];
halo_list i_list = OP_import_nonexec_list[set->index];
halo_list e_list = OP_export_nonexec_list[set->index];
// for each data array
op_dat_entry *item;
int d = -1; // d is just simply the tag for mpi comms
TAILQ_FOREACH(item, &OP_dat_list, entries) {
d++; // increase tag to do mpi comm for the next op_dat
op_dat dat = item->dat;
if (compare_sets(set, dat->set) == 1) { // if this data array is
// defined on this set
// printf("on rank %d, The data array is %10s\n",my_rank,dat->name);
MPI_Request request_send[e_list->ranks_size];
// prepare non-execute set element data to be exported
char **sbuf = (char **)xmalloc(e_list->ranks_size * sizeof(char *));
for (int i = 0; i < e_list->ranks_size; i++) {
sbuf[i] = (char *)xmalloc(e_list->sizes[i] * dat->size);
for (int j = 0; j < e_list->sizes[i]; j++) {
int set_elem_index = e_list->list[e_list->disps[i] + j];
memcpy(&sbuf[i][j * dat->size],
(void *)&dat->data[dat->size * (set_elem_index)], dat->size);
}
MPI_Isend(sbuf[i], dat->size * e_list->sizes[i], MPI_CHAR,
e_list->ranks[i], d, OP_MPI_WORLD, &request_send[i]);
}
// prepare space for the incomming nonexec-data - realloc each
// data array in each mpi process
halo_list exec_i_list = OP_import_exec_list[set->index];
dat->data = (char *)xrealloc(
dat->data,
(set->size + exec_i_list->size + i_list->size) * dat->size);
int init = (set->size + exec_i_list->size) * dat->size;
for (int i = 0; i < i_list->ranks_size; i++) {
MPI_Recv(&(dat->data[init + i_list->disps[i] * dat->size]),
dat->size * i_list->sizes[i], MPI_CHAR, i_list->ranks[i], d,
OP_MPI_WORLD, MPI_STATUS_IGNORE);
}
MPI_Waitall(e_list->ranks_size, request_send, MPI_STATUSES_IGNORE);
for (int i = 0; i < e_list->ranks_size; i++)
op_free(sbuf[i]);
op_free(sbuf);
}
}
}
/*-STEP 8 ----------------- Renumber Mapping tables-----------------------*/
for (int s = 0; s < OP_set_index; s++) { // for each set
op_set set = OP_set_list[s];
for (int m = 0; m < OP_map_index; m++) { // for each maping table
op_map map = OP_map_list[m];
if (compare_sets(map->to, set) == 1) { // need to select
// mappings TO this set
halo_list exec_set_list = OP_import_exec_list[set->index];
halo_list nonexec_set_list = OP_import_nonexec_list[set->index];
halo_list exec_map_list = OP_import_exec_list[map->from->index];
// for each entry in this mapping table: original+execlist
int len = map->from->size + exec_map_list->size;
for (int e = 0; e < len; e++) {
for (int j = 0; j < map->dim; j++) { // for each element
// pointed at by this entry
int part;
int local_index = 0;
part = get_partition(map->map[e * map->dim + j],
part_range[map->to->index], &local_index,
comm_size);
if (part == my_rank) {
OP_map_list[map->index]->map[e * map->dim + j] = local_index;
} else {
int found = -1;
// check in exec list
int rank1 = binary_search(exec_set_list->ranks, part, 0,
exec_set_list->ranks_size - 1);
// check in nonexec list
int rank2 = binary_search(nonexec_set_list->ranks, part, 0,
nonexec_set_list->ranks_size - 1);
if (rank1 >= 0) {
found = binary_search(exec_set_list->list, local_index,
exec_set_list->disps[rank1],
exec_set_list->disps[rank1] +
exec_set_list->sizes[rank1] - 1);
if (found >= 0) {
OP_map_list[map->index]->map[e * map->dim + j] =
found + map->to->size;
}
}
if (rank2 >= 0 && found < 0) {
found = binary_search(nonexec_set_list->list, local_index,
nonexec_set_list->disps[rank2],
nonexec_set_list->disps[rank2] +
nonexec_set_list->sizes[rank2] - 1);
if (found >= 0) {
OP_map_list[map->index]->map[e * map->dim + j] =
found + set->size + exec_set_list->size;