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graph.hpp
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graph.hpp
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#pragma once
#ifndef GRAPH_HPP
#define GRAPH_HPP
#include <iostream>
#include <algorithm>
#include <vector>
#include <string>
#include <fstream>
#include <sstream>
#include <climits>
#include <array>
#include <unordered_map>
#include <mpi.h>
#include "utils.hpp"
unsigned seed;
// (vite) graph converter ensures
// weights are 1.0 if not provided
struct Edge
{
GraphElem tail_;
GraphWeight weight_;
Edge(): tail_(-1), weight_(0.0) {}
};
struct EdgeActive
{
Edge const& edge_;
bool active_;
EdgeActive(Edge const& edge): edge_(edge), active_(true) {}
};
struct EdgeTuple
{
GraphElem ij_[2];
GraphWeight w_;
EdgeTuple(GraphElem i, GraphElem j, GraphWeight w):
ij_{i, j}, w_(w)
{}
EdgeTuple(GraphElem i, GraphElem j):
ij_{i, j}, w_(1.0)
{}
EdgeTuple():
ij_{-1, -1}, w_(0.0)
{}
};
// per process graph instance
class Graph
{
public:
Graph():
lnv_(-1), lne_(-1), nv_(-1),
ne_(-1), comm_(MPI_COMM_WORLD)
{
MPI_Comm_size(comm_, &size_);
MPI_Comm_rank(comm_, &rank_);
}
// 1D distribution: vertex based distribution
// assumed with equal number of vertices per
// process
// edges could be set in this ctor
// or later using set_nedges
Graph(GraphElem lnv, GraphElem lne,
GraphElem nv, GraphElem ne,
MPI_Comm comm=MPI_COMM_WORLD):
lnv_(lnv), lne_(lne),
nv_(nv), ne_(ne),
comm_(comm)
{
MPI_Comm_size(comm_, &size_);
MPI_Comm_rank(comm_, &rank_);
edge_indices_.resize(lnv_+1, 0);
parts_.resize(size_+1);
parts_[0] = 0;
for (GraphElem i = 1; i < size_+1; i++)
parts_[i]=((nv_ * i) / size_);
set_nedges(lne_);
}
// edge based distribution, irregular
// number of vertices per node
Graph(GraphElem lne,
GraphElem nv, GraphElem ne,
MPI_Comm comm=MPI_COMM_WORLD):
lnv_(0), lne_(lne),
nv_(nv), ne_(ne),
comm_(comm)
{
MPI_Comm_size(comm_, &size_);
MPI_Comm_rank(comm_, &rank_);
set_nedges(ne);
}
~Graph()
{
edge_active_.clear();
edge_list_.clear();
edge_indices_.clear();
parts_.clear();
}
// update vertex partition information
void repart(std::vector<GraphElem> const& parts)
{ memcpy(parts_.data(), parts.data(), sizeof(GraphElem)*(size_+1)); }
// TODO FIXME put asserts like the following
// everywhere function member of Graph class
void set_edge_index(GraphElem const vertex, GraphElem const e0)
{
#if defined(DEBUG_BUILD)
assert((vertex >= 0) && (vertex <= lnv_));
assert((e0 >= 0) && (e0 <= lne_));
edge_indices_.at(vertex) = e0;
#else
edge_indices_[vertex] = e0;
#endif
}
void edge_range(GraphElem const vertex, GraphElem& e0,
GraphElem& e1) const
{
e0 = edge_indices_[vertex];
e1 = edge_indices_[vertex+1];
}
// collective
void set_nedges(GraphElem lne)
{
lne_ = lne;
edge_list_.resize(lne_);
// compute total number of edges
ne_ = 0;
MPI_Allreduce(&lne_, &ne_, 1, MPI_GRAPH_TYPE, MPI_SUM, comm_);
}
void set_nvertices(GraphElem lnv)
{
lnv_ = lnv;
edge_indices_.resize(lnv_+1, 0);
std::vector<GraphElem> counts(size_);
parts_.resize(size_+1);
MPI_Allgather(&lnv_, 1, MPI_GRAPH_TYPE, counts.data(),
1, MPI_GRAPH_TYPE, comm_);
GraphElem disp = parts_[0] = 0;
for (GraphElem i = 1; i < size_+1; i++)
{
parts_[i] = disp;
disp += counts[i-1];
}
}
GraphElem get_base(const int rank) const
{ return parts_[rank]; }
GraphElem get_bound(const int rank) const
{ return parts_[rank+1]; }
GraphElem get_range(const int rank) const
{ return (parts_[rank+1] - parts_[rank] + 1); }
int get_owner(const GraphElem vertex) const
{
const std::vector<GraphElem>::const_iterator iter =
std::upper_bound(parts_.begin(), parts_.end(), vertex);
return (iter - parts_.begin() - 1);
}
GraphElem get_lnv() const { return lnv_; }
GraphElem get_lne() const { return lne_; }
GraphElem get_nv() const { return nv_; }
GraphElem get_ne() const { return ne_; }
MPI_Comm get_comm() const { return comm_; }
// return edge and active info
// ----------------------------
Edge const& get_edge(GraphElem const index) const
{ return edge_list_[index]; }
EdgeActive& get_active_edge(GraphElem const index)
{ return edge_active_[index]; }
Edge& set_edge(GraphElem const index)
{ return edge_list_[index]; }
// local <--> global index translation
// -----------------------------------
GraphElem local_to_global(GraphElem idx)
{ return (idx + get_base(rank_)); }
GraphElem global_to_local(GraphElem idx)
{ return (idx - get_base(rank_)); }
// w.r.t passed rank
GraphElem local_to_global(GraphElem idx, int rank)
{ return (idx + get_base(rank)); }
GraphElem global_to_local(GraphElem idx, int rank)
{ return (idx - get_base(rank)); }
// print edge list (with weights)
void print(bool print_weight = true) const
{
if (lne_ < MAX_PRINT_NEDGE)
{
for (int p = 0; p < size_; p++)
{
MPI_Barrier(comm_);
if (p == rank_)
{
std::cout << "###############" << std::endl;
std::cout << "Process #" << p << ": " << std::endl;
std::cout << "###############" << std::endl;
GraphElem base = get_base(p);
for (GraphElem i = 0; i < lnv_; i++)
{
GraphElem e0, e1;
edge_range(i, e0, e1);
if (print_weight) { // print weights (default)
for (GraphElem e = e0; e < e1; e++)
{
Edge const& edge = get_edge(e);
std::cout << i+base << " " << edge.tail_ << " " << edge.weight_ << std::endl;
}
}
else { // don't print weights
for (GraphElem e = e0; e < e1; e++)
{
Edge const& edge = get_edge(e);
std::cout << i+base << " " << edge.tail_ << std::endl;
}
}
}
MPI_Barrier(comm_);
}
}
}
else
{
if (rank_ == 0)
std::cout << "Graph size per process is {" << lnv_ << ", " << lne_ <<
"}, which will overwhelm STDOUT." << std::endl;
}
}
// print statistics about edge distribution
// TODO FIXME check the data types
void print_dist_stats()
{
GraphElem sumdeg = 0, maxdeg = 0;
MPI_Reduce(&lne_, &sumdeg, 1, MPI_GRAPH_TYPE, MPI_SUM, 0, comm_);
MPI_Reduce(&lne_, &maxdeg, 1, MPI_GRAPH_TYPE, MPI_MAX, 0, comm_);
GraphElem my_sq = lne_*lne_;
GraphElem sum_sq = 0;
MPI_Reduce(&my_sq, &sum_sq, 1, MPI_GRAPH_TYPE, MPI_SUM, 0, comm_);
GraphWeight average = (GraphWeight) sumdeg / size_;
GraphWeight avg_sq = (GraphWeight) sum_sq / size_;
GraphWeight var = avg_sq - (average*average);
GraphWeight stddev = sqrt(var);
MPI_Barrier(comm_);
if (rank_ == 0)
{
std::cout << std::endl;
std::cout << "-------------------------------------------------------" << std::endl;
std::cout << "Graph edge distribution characteristics" << std::endl;
std::cout << "-------------------------------------------------------" << std::endl;
std::cout << "Number of vertices: " << nv_ << std::endl;
std::cout << "Number of edges: " << ne_ << std::endl;
std::cout << "Maximum number of edges: " << maxdeg << std::endl;
std::cout << "Average number of edges: " << average << std::endl;
std::cout << "Expected value of X^2: " << avg_sq << std::endl;
std::cout << "Variance: " << var << std::endl;
std::cout << "Standard deviation: " << stddev << std::endl;
std::cout << "-------------------------------------------------------" << std::endl;
}
}
// public variables
std::vector<EdgeActive> edge_active_;
std::vector<GraphElem> edge_indices_;
std::vector<Edge> edge_list_;
private:
GraphElem lnv_, lne_, nv_, ne_;
std::vector<GraphElem> parts_;
MPI_Comm comm_;
int rank_, size_;
};
// read in binary edge list files
// using MPI I/O
class BinaryEdgeList
{
public:
BinaryEdgeList() :
M_(-1), N_(-1),
M_local_(-1), N_local_(-1),
comm_(MPI_COMM_WORLD)
{}
BinaryEdgeList(MPI_Comm comm) :
M_(-1), N_(-1),
M_local_(-1), N_local_(-1),
comm_(comm)
{}
// the input binary file will be sorted by
// vertices
// read a file and return a graph
Graph* read(int me, int nprocs, int ranks_per_node, std::string file)
{
int file_open_error;
MPI_File fh;
MPI_Status status;
// specify the number of aggregates
MPI_Info info;
MPI_Info_create(&info);
int naggr = (ranks_per_node > 1) ? (nprocs/ranks_per_node) : ranks_per_node;
if (naggr >= nprocs)
naggr = 1;
std::stringstream tmp_str;
tmp_str << naggr;
std::string str = tmp_str.str();
MPI_Info_set(info, "cb_nodes", str.c_str());
file_open_error = MPI_File_open(comm_, file.c_str(), MPI_MODE_RDONLY, info, &fh);
MPI_Info_free(&info);
if (file_open_error != MPI_SUCCESS)
{
std::cout << " Error opening file! " << std::endl;
MPI_Abort(comm_, -99);
}
// read the dimensions
MPI_File_read_all(fh, &M_, sizeof(GraphElem), MPI_BYTE, &status);
MPI_File_read_all(fh, &N_, sizeof(GraphElem), MPI_BYTE, &status);
// local graph
M_local_ = ((M_*(me + 1)) / nprocs) - ((M_*me) / nprocs);
Graph* g = new Graph(M_local_, 0, M_, N_);
// Let N = array length and P = number of processors.
// From j = 0 to P-1,
// Starting point of array on processor j = floor(N * j / P)
// Length of array on processor j = floor(N * (j + 1) / P) - floor(N * j / P)
uint64_t tot_bytes=(M_local_+1)*sizeof(GraphElem);
MPI_Offset offset = 2*sizeof(GraphElem) + ((M_*me) / nprocs)*sizeof(GraphElem);
// read in INT_MAX increments if total byte size is > INT_MAX
if (tot_bytes < INT_MAX)
MPI_File_read_at(fh, offset, &g->edge_indices_[0], tot_bytes, MPI_BYTE, &status);
else
{
int chunk_bytes=INT_MAX;
uint8_t *curr_pointer = (uint8_t*) &g->edge_indices_[0];
uint64_t transf_bytes = 0;
while (transf_bytes < tot_bytes)
{
MPI_File_read_at(fh, offset, curr_pointer, chunk_bytes, MPI_BYTE, &status);
transf_bytes += chunk_bytes;
offset += chunk_bytes;
curr_pointer += chunk_bytes;
if ((tot_bytes - transf_bytes) < INT_MAX)
chunk_bytes = tot_bytes - transf_bytes;
}
}
N_local_ = g->edge_indices_[M_local_] - g->edge_indices_[0];
g->set_nedges(N_local_);
tot_bytes = N_local_*(sizeof(Edge));
offset = 2*sizeof(GraphElem) + (M_+1)*sizeof(GraphElem) + g->edge_indices_[0]*(sizeof(Edge));
if (tot_bytes < INT_MAX)
MPI_File_read_at(fh, offset, &g->edge_list_[0], tot_bytes, MPI_BYTE, &status);
else
{
int chunk_bytes=INT_MAX;
uint8_t *curr_pointer = (uint8_t*)&g->edge_list_[0];
uint64_t transf_bytes = 0;
while (transf_bytes < tot_bytes)
{
MPI_File_read_at(fh, offset, curr_pointer, chunk_bytes, MPI_BYTE, &status);
transf_bytes += chunk_bytes;
offset += chunk_bytes;
curr_pointer += chunk_bytes;
if ((tot_bytes - transf_bytes) < INT_MAX)
chunk_bytes = (tot_bytes - transf_bytes);
}
}
MPI_File_close(&fh);
for(GraphElem i=1; i < M_local_+1; i++)
g->edge_indices_[i] -= g->edge_indices_[0];
g->edge_indices_[0] = 0;
// store reference to edge and active info
// and ensure weights are positive
for (GraphElem i=0; i < g->edge_list_.size(); i++)
{
//g->edge_list_[i].weight_ = std::fabs(g->edge_list_[i].weight_);
g->edge_active_.emplace_back(g->edge_list_[i]);
}
/*
for (GraphElem i = 0; i < g->get_lnv(); i++)
{
GraphElem e0, e1;
g->edge_range(i, e0, e1);
GraphElem base = g->get_base(me);
for (GraphElem e = e0; e < e1; e++)
{
Edge const& cedge = g->get_edge(e);
Edge& edge = g->set_edge(e);
if ((i + base) != edge.tail_) // no self loops
{
edge.weight_ = std::fabs(edge.weight_);
g->edge_active_.emplace_back(cedge);
}
}
}
*/
return g;
}
// find a distribution such that every
// process own equal number of edges (serial)
void find_balanced_num_edges(int nprocs, std::string file, std::vector<GraphElem>& mbins)
{
FILE *fp;
GraphElem nv, ne; // #vertices, #edges
std::vector<GraphElem> nbins(nprocs,0);
fp = fopen(file.c_str(), "rb");
if (fp == NULL)
{
std::cout<< " Error opening file! " << std::endl;
return;
}
// read nv and ne
fread(&nv, sizeof(GraphElem), 1, fp);
fread(&ne, sizeof(GraphElem), 1, fp);
// bin capacity
GraphElem nbcap = (ne / nprocs), ecount_idx, past_ecount_idx = 0;
int p = 0;
for (GraphElem m = 0; m < nv; m++)
{
fread(&ecount_idx, sizeof(GraphElem), 1, fp);
// bins[p] >= capacity only for the last process
if ((nbins[p] < nbcap) || (p == (nprocs - 1)))
nbins[p] += (ecount_idx - past_ecount_idx);
// increment p as long as p is not the last process
// worst case: excess edges piled up on (p-1)
if ((nbins[p] >= nbcap) && (p < (nprocs - 1)))
p++;
mbins[p+1]++;
past_ecount_idx = ecount_idx;
}
fclose(fp);
// prefix sum to store indices
for (int k = 1; k < nprocs+1; k++)
mbins[k] += mbins[k-1];
nbins.clear();
}
// read a file and return a graph
// uses a balanced distribution
// (approximately equal #edges per process)
Graph* read_balanced(int me, int nprocs, int ranks_per_node, std::string file)
{
int file_open_error;
MPI_File fh;
MPI_Status status;
std::vector<GraphElem> mbins(nprocs+1,0);
// find #vertices per process such that
// each process roughly owns equal #edges
if (me == 0)
{
find_balanced_num_edges(nprocs, file, mbins);
std::cout << "Trying to achieve equal edge distribution across processes." << std::endl;
}
MPI_Barrier(comm_);
MPI_Bcast(mbins.data(), nprocs+1, MPI_GRAPH_TYPE, 0, comm_);
// specify the number of aggregates
MPI_Info info;
MPI_Info_create(&info);
int naggr = (ranks_per_node > 1) ? (nprocs/ranks_per_node) : ranks_per_node;
if (naggr >= nprocs)
naggr = 1;
std::stringstream tmp_str;
tmp_str << naggr;
std::string str = tmp_str.str();
MPI_Info_set(info, "cb_nodes", str.c_str());
file_open_error = MPI_File_open(comm_, file.c_str(), MPI_MODE_RDONLY, info, &fh);
MPI_Info_free(&info);
if (file_open_error != MPI_SUCCESS)
{
std::cout << " Error opening file! " << std::endl;
MPI_Abort(comm_, -99);
}
// read the dimensions
MPI_File_read_all(fh, &M_, sizeof(GraphElem), MPI_BYTE, &status);
MPI_File_read_all(fh, &N_, sizeof(GraphElem), MPI_BYTE, &status);
M_local_ = mbins[me+1] - mbins[me];
// create local graph
Graph *g = new Graph(M_local_, 0, M_, N_);
// readjust parts with new vertex partition
g->repart(mbins);
uint64_t tot_bytes=(M_local_+1)*sizeof(GraphElem);
MPI_Offset offset = 2*sizeof(GraphElem) + mbins[me]*sizeof(GraphElem);
// read in INT_MAX increments if total byte size is > INT_MAX
if (tot_bytes < INT_MAX)
MPI_File_read_at(fh, offset, &g->edge_indices_[0], tot_bytes, MPI_BYTE, &status);
else
{
int chunk_bytes=INT_MAX;
uint8_t *curr_pointer = (uint8_t*) &g->edge_indices_[0];
uint64_t transf_bytes = 0;
while (transf_bytes < tot_bytes)
{
MPI_File_read_at(fh, offset, curr_pointer, chunk_bytes, MPI_BYTE, &status);
transf_bytes += chunk_bytes;
offset += chunk_bytes;
curr_pointer += chunk_bytes;
if ((tot_bytes - transf_bytes) < INT_MAX)
chunk_bytes = tot_bytes - transf_bytes;
}
}
N_local_ = g->edge_indices_[M_local_] - g->edge_indices_[0];
g->set_nedges(N_local_);
tot_bytes = N_local_*(sizeof(Edge));
offset = 2*sizeof(GraphElem) + (M_+1)*sizeof(GraphElem) + g->edge_indices_[0]*(sizeof(Edge));
if (tot_bytes < INT_MAX)
MPI_File_read_at(fh, offset, &g->edge_list_[0], tot_bytes, MPI_BYTE, &status);
else
{
int chunk_bytes=INT_MAX;
uint8_t *curr_pointer = (uint8_t*)&g->edge_list_[0];
uint64_t transf_bytes = 0;
while (transf_bytes < tot_bytes)
{
MPI_File_read_at(fh, offset, curr_pointer, chunk_bytes, MPI_BYTE, &status);
transf_bytes += chunk_bytes;
offset += chunk_bytes;
curr_pointer += chunk_bytes;
if ((tot_bytes - transf_bytes) < INT_MAX)
chunk_bytes = (tot_bytes - transf_bytes);
}
}
MPI_File_close(&fh);
for(GraphElem i=1; i < M_local_+1; i++)
g->edge_indices_[i] -= g->edge_indices_[0];
g->edge_indices_[0] = 0;
// store reference to edge and active info
// and ensure weights are positive
for (GraphElem i=0; i < g->edge_list_.size(); i++)
{
//g->edge_list_[i].weight_ = std::fabs(g->edge_list_[i].weight_);
g->edge_active_.emplace_back(g->edge_list_[i]);
}
mbins.clear();
return g;
}
private:
GraphElem M_;
GraphElem N_;
GraphElem M_local_;
GraphElem N_local_;
MPI_Comm comm_;
};
// RGG graph
// 1D vertex distribution
class GenerateRGG
{
public:
GenerateRGG(GraphElem nv, MPI_Comm comm = MPI_COMM_WORLD)
{
nv_ = nv;
comm_ = comm;
MPI_Comm_rank(comm_, &rank_);
MPI_Comm_size(comm_, &nprocs_);
// neighbors
up_ = down_ = MPI_PROC_NULL;
if (nprocs_ > 1) {
if (rank_ > 0 && rank_ < (nprocs_ - 1)) {
up_ = rank_ - 1;
down_ = rank_ + 1;
}
if (rank_ == 0)
down_ = 1;
if (rank_ == (nprocs_ - 1))
up_ = rank_ - 1;
}
n_ = nv_ / nprocs_;
// check if number of nodes is divisible by #processes
if ((nv_ % nprocs_) != 0) {
if (rank_ == 0) {
std::cout << "[ERROR] Number of vertices must be perfectly divisible by number of processes." << std::endl;
std::cout << "Exiting..." << std::endl;
}
MPI_Abort(comm_, -99);
}
// check if processes are power of 2
if (!is_pwr2(nprocs_)) {
if (rank_ == 0) {
std::cout << "[ERROR] Number of processes must be a power of 2." << std::endl;
std::cout << "Exiting..." << std::endl;
}
MPI_Abort(comm_, -99);
}
// calculate r(n)
GraphWeight rc = sqrt((GraphWeight)log(nv)/(GraphWeight)(PI*nv));
GraphWeight rt = sqrt((GraphWeight)2.0736/(GraphWeight)nv);
rn_ = (rc + rt)/(GraphWeight)2.0;
assert(((GraphWeight)1.0/(GraphWeight)nprocs_) > rn_);
MPI_Barrier(comm_);
}
// create RGG and returns Graph
// TODO FIXME use OpenMP wherever possible
// use Euclidean distance as edge weight
// for random edges, choose from (0,1)
// otherwise, use unit weight throughout
Graph* generate(bool isLCG, bool unitEdgeWeight = true, GraphWeight randomEdgePercent = 0.0)
{
// Generate random coordinate points
std::vector<GraphWeight> X, Y, X_up, Y_up, X_down, Y_down;
if (isLCG)
X.resize(2*n_);
else
X.resize(n_);
Y.resize(n_);
if (up_ != MPI_PROC_NULL) {
X_up.resize(n_);
Y_up.resize(n_);
}
if (down_ != MPI_PROC_NULL) {
X_down.resize(n_);
Y_down.resize(n_);
}
// create local graph
Graph *g = new Graph(n_, 0, nv_, nv_);
// generate random number within range
// X: 0, 1
// Y: rank_*1/p, (rank_+1)*1/p,
GraphWeight rec_np = (GraphWeight)(1.0/(GraphWeight)nprocs_);
GraphWeight lo = rank_* rec_np;
GraphWeight hi = lo + rec_np;
assert(hi > lo);
// measure the time to generate random numbers
MPI_Barrier(MPI_COMM_WORLD);
double st = MPI_Wtime();
if (!isLCG) {
// set seed (declared an extern in utils)
seed = (unsigned)reseeder(1);
#if defined(PRINT_RANDOM_XY_COORD)
for (int k = 0; k < nprocs_; k++) {
if (k == rank_) {
std::cout << "Random number generated on Process#" << k << " :" << std::endl;
for (GraphElem i = 0; i < n_; i++) {
X[i] = genRandom<GraphWeight>(0.0, 1.0);
Y[i] = genRandom<GraphWeight>(lo, hi);
std::cout << "X, Y: " << X[i] << ", " << Y[i] << std::endl;
}
}
MPI_Barrier(comm_);
}
#else
for (GraphElem i = 0; i < n_; i++) {
X[i] = genRandom<GraphWeight>(0.0, 1.0);
Y[i] = genRandom<GraphWeight>(lo, hi);
}
#endif
}
else { // LCG
// X | Y
// e.g seeds: 1741, 3821
// create LCG object
// seed to generate x0
LCG xr(/*seed*/1, X.data(), 2*n_, comm_);
// generate random numbers between 0-1
xr.generate();
// rescale xr further between lo-hi
// and put the numbers in Y taking
// from X[n]
xr.rescale(Y.data(), n_, lo);
#if defined(PRINT_RANDOM_XY_COORD)
for (int k = 0; k < nprocs_; k++) {
if (k == rank_) {
std::cout << "Random number generated on Process#" << k << " :" << std::endl;
for (GraphElem i = 0; i < n_; i++) {
std::cout << "X, Y: " << X[i] << ", " << Y[i] << std::endl;
}
}
MPI_Barrier(comm_);
}
#endif
}
double et = MPI_Wtime();
double tt = et - st;
double tot_tt = 0.0;
MPI_Reduce(&tt, &tot_tt, 1, MPI_DOUBLE, MPI_SUM, 0, comm_);
if (rank_ == 0) {
double tot_avg = (tot_tt/nprocs_);
std::cout << "Average time to generate " << 2*n_
<< " random numbers using LCG (in s): "
<< tot_avg << std::endl;
}
// ghost(s)
// cross edges, each processor
// communicates with up or/and down
// neighbor only
std::vector<EdgeTuple> sendup_edges, senddn_edges;
std::vector<EdgeTuple> recvup_edges, recvdn_edges;
std::vector<EdgeTuple> edgeList;
// counts, indexing: [2] = {up - 0, down - 1}
// TODO can't we use MPI_INT
std::array<GraphElem, 2> send_sizes = {0, 0}, recv_sizes = {0, 0};
#if defined(CHECK_NUM_EDGES)
GraphElem numEdges = 0;
#endif
// local
for (GraphElem i = 0; i < n_; i++) {
for (GraphElem j = i + 1; j < n_; j++) {
// euclidean distance:
// 2D: sqrt((px-qx)^2 + (py-qy)^2)
GraphWeight dx = X[i] - X[j];
GraphWeight dy = Y[i] - Y[j];
GraphWeight ed = sqrt(dx*dx + dy*dy);
// are the two vertices within the range?
if (ed <= rn_) {
// local to global index
const GraphElem g_i = g->local_to_global(i);
const GraphElem g_j = g->local_to_global(j);
if (!unitEdgeWeight) {
edgeList.emplace_back(i, g_j, ed);
edgeList.emplace_back(j, g_i, ed);
}
else {
edgeList.emplace_back(i, g_j);
edgeList.emplace_back(j, g_i);
}
#if defined(CHECK_NUM_EDGES)
numEdges += 2;
#endif
g->edge_indices_[i+1]++;
g->edge_indices_[j+1]++;
}
}
}
MPI_Barrier(comm_);
// communicate ghost coordinates with neighbors
const int x_ndown = X_down.empty() ? 0 : n_;
const int y_ndown = Y_down.empty() ? 0 : n_;
const int x_nup = X_up.empty() ? 0 : n_;
const int y_nup = Y_up.empty() ? 0 : n_;
MPI_Sendrecv(X.data(), n_, MPI_WEIGHT_TYPE, up_, SR_X_UP_TAG,
X_down.data(), x_ndown, MPI_WEIGHT_TYPE, down_, SR_X_UP_TAG,
comm_, MPI_STATUS_IGNORE);
MPI_Sendrecv(X.data(), n_, MPI_WEIGHT_TYPE, down_, SR_X_DOWN_TAG,
X_up.data(), x_nup, MPI_WEIGHT_TYPE, up_, SR_X_DOWN_TAG,
comm_, MPI_STATUS_IGNORE);
MPI_Sendrecv(Y.data(), n_, MPI_WEIGHT_TYPE, up_, SR_Y_UP_TAG,
Y_down.data(), y_ndown, MPI_WEIGHT_TYPE, down_, SR_Y_UP_TAG,
comm_, MPI_STATUS_IGNORE);
MPI_Sendrecv(Y.data(), n_, MPI_WEIGHT_TYPE, down_, SR_Y_DOWN_TAG,
Y_up.data(), y_nup, MPI_WEIGHT_TYPE, up_, SR_Y_DOWN_TAG,
comm_, MPI_STATUS_IGNORE);
// exchange ghost vertices / cross edges
if (nprocs_ > 1) {
if (up_ != MPI_PROC_NULL) {
for (GraphElem i = 0; i < n_; i++) {
for (GraphElem j = i + 1; j < n_; j++) {
GraphWeight dx = X[i] - X_up[j];
GraphWeight dy = Y[i] - Y_up[j];
GraphWeight ed = sqrt(dx*dx + dy*dy);
if (ed <= rn_) {
const GraphElem g_i = g->local_to_global(i);
const GraphElem g_j = j + up_*n_;
if (!unitEdgeWeight) {
sendup_edges.emplace_back(j, g_i, ed);
edgeList.emplace_back(i, g_j, ed);
}
else {
sendup_edges.emplace_back(j, g_i);
edgeList.emplace_back(i, g_j);
}
#if defined(CHECK_NUM_EDGES)
numEdges++;
#endif
g->edge_indices_[i+1]++;
}
}
}
// send up sizes
send_sizes[0] = sendup_edges.size();
}
if (down_ != MPI_PROC_NULL) {
for (GraphElem i = 0; i < n_; i++) {
for (GraphElem j = i + 1; j < n_; j++) {
GraphWeight dx = X[i] - X_down[j];
GraphWeight dy = Y[i] - Y_down[j];
GraphWeight ed = sqrt(dx*dx + dy*dy);
if (ed <= rn_) {
const GraphElem g_i = g->local_to_global(i);
const GraphElem g_j = j + down_*n_;
if (!unitEdgeWeight) {
senddn_edges.emplace_back(j, g_i, ed);
edgeList.emplace_back(i, g_j, ed);
}
else {
senddn_edges.emplace_back(j, g_i);
edgeList.emplace_back(i, g_j);
}
#if defined(CHECK_NUM_EDGES)
numEdges++;
#endif
g->edge_indices_[i+1]++;
}
}
}
// send down sizes
send_sizes[1] = senddn_edges.size();
}
}
MPI_Barrier(comm_);
// communicate ghost vertices with neighbors
// send/recv buffer sizes
MPI_Sendrecv(&send_sizes[0], 1, MPI_GRAPH_TYPE, up_, SR_SIZES_UP_TAG,
&recv_sizes[1], 1, MPI_GRAPH_TYPE, down_, SR_SIZES_UP_TAG,
comm_, MPI_STATUS_IGNORE);
MPI_Sendrecv(&send_sizes[1], 1, MPI_GRAPH_TYPE, down_, SR_SIZES_DOWN_TAG,
&recv_sizes[0], 1, MPI_GRAPH_TYPE, up_, SR_SIZES_DOWN_TAG,
comm_, MPI_STATUS_IGNORE);
// resize recv buffers
if (recv_sizes[0] > 0)
recvup_edges.resize(recv_sizes[0]);
if (recv_sizes[1] > 0)
recvdn_edges.resize(recv_sizes[1]);
// send/recv both up and down
MPI_Sendrecv(sendup_edges.data(), send_sizes[0]*sizeof(struct EdgeTuple), MPI_BYTE,
up_, SR_UP_TAG, recvdn_edges.data(), recv_sizes[1]*sizeof(struct EdgeTuple),
MPI_BYTE, down_, SR_UP_TAG, comm_, MPI_STATUS_IGNORE);
MPI_Sendrecv(senddn_edges.data(), send_sizes[1]*sizeof(struct EdgeTuple), MPI_BYTE,
down_, SR_DOWN_TAG, recvup_edges.data(), recv_sizes[0]*sizeof(struct EdgeTuple),
MPI_BYTE, up_, SR_DOWN_TAG, comm_, MPI_STATUS_IGNORE);
// update local #edges
// down
if (down_ != MPI_PROC_NULL) {
for (GraphElem i = 0; i < recv_sizes[1]; i++) {
#if defined(CHECK_NUM_EDGES)
numEdges++;
#endif
if (!unitEdgeWeight)
edgeList.emplace_back(recvdn_edges[i].ij_[0], recvdn_edges[i].ij_[1], recvdn_edges[i].w_);
else
edgeList.emplace_back(recvdn_edges[i].ij_[0], recvdn_edges[i].ij_[1]);
g->edge_indices_[recvdn_edges[i].ij_[0]+1]++;
}
}
// up
if (up_ != MPI_PROC_NULL) {
for (GraphElem i = 0; i < recv_sizes[0]; i++) {
#if defined(CHECK_NUM_EDGES)
numEdges++;
#endif
if (!unitEdgeWeight)
edgeList.emplace_back(recvup_edges[i].ij_[0], recvup_edges[i].ij_[1], recvup_edges[i].w_);
else
edgeList.emplace_back(recvup_edges[i].ij_[0], recvup_edges[i].ij_[1]);
g->edge_indices_[recvup_edges[i].ij_[0]+1]++;
}
}
// add random edges based on
// randomEdgePercent
if (randomEdgePercent > 0) {
const GraphElem pnedges = (edgeList.size()/2);
GraphElem tot_pnedges = 0;