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Commit 63c2cae1 authored by Tiago Peixoto's avatar Tiago Peixoto
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Improve performace of random graph generation 

Vectors are used now instead of unordered_sets, which dramatically
improves performace.
parent 42bffcd4
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Inline Side-by-side
Showing with 178 additions and 83 deletions
src/graph/generation/graph_generation.cc
View file @ 63c2cae1
......@@ -52,7 +52,7 @@ void generate_random_graph(GraphInterface& gi, size_t N,
python::object deg_sample,
bool uncorrelated, bool no_parallel,
bool no_self_loops, bool undirected,
size_t seed, bool verbose)
size_t seed, bool verbose, bool verify)
{
typedef graph_tool::detail::get_all_graph_views::apply<
graph_tool::detail::scalar_pairs, mpl::bool_<false>,
......@@ -68,7 +68,7 @@ void generate_random_graph(GraphInterface& gi, size_t N,
(gi, bind<void>(gen_random_graph(), _1, N,
PythonFuncWrap(deg_sample),
no_parallel, no_self_loops,
seed, verbose))();
seed, verbose, verify))();
}
else
{
......@@ -76,7 +76,7 @@ void generate_random_graph(GraphInterface& gi, size_t N,
(gi, bind<void>(gen_random_graph(), _1, N,
PythonFuncWrap(deg_sample),
no_parallel, no_self_loops,
seed, verbose))();
seed, verbose, verify))();
}
gi.ReIndexEdges();
}
......
src/graph/generation/graph_generation.hh
View file @ 63c2cae1
......@@ -55,14 +55,14 @@ size_t hash_value(const dvertex_t& v)
// used for verbose display
void print_progress(size_t current, size_t total, stringstream& str)
{
size_t atom = max(total/100, 1);
if ( (current % atom == 0) || current == total)
size_t atom = (total > 200) ? total/100 : 1;
if ( ( (current+1) % atom == 0) || (current + 1) == total)
{
for (size_t j = 0; j < str.str().length(); ++j)
cout << "\b";
str.str("");
str << current+1 << " of " << total << " (" <<
(current+1)*100/total << "%)";
str << current+1 << " of " << total << " ("
<< (current+1)*100 / total << "%)";
cout << str.str() << flush;
}
}
......@@ -80,6 +80,18 @@ void print_update(size_t current, stringstream& str)
cout << str.str() << flush;
}
template <class Graph>
bool is_adjacent(typename graph_traits<Graph>::vertex_descriptor u,
typename graph_traits<Graph>::vertex_descriptor v,
const Graph& g)
{
typename graph_traits<Graph>::adjacency_iterator a, a_end;
for (tie(a, a_end) = adjacent_vertices(u, g); a != a_end; ++a)
if (*a == v)
return true;
return false;
}
//
// Generation strategies
// =====================
......@@ -173,7 +185,7 @@ public:
(v.in_degree > _max_deg || v.out_degree > _max_deg));
sum_j += v.in_degree;
sum_k += v.out_degree;
if (_no_parallel)
if (_no_parallel || _no_self_loops)
_deg_seq[make_pair(v.in_degree, v.out_degree)]++;
}
......@@ -192,7 +204,7 @@ public:
!is_graphical_parallel(_deg_seq)))
{
dvertex_t& v = vertices[vertex_sample(rng)];
if (_no_parallel || (_no_self_loops && !_no_parallel))
if (_no_parallel || _no_self_loops)
{
typeof(_deg_seq.begin()) iter =
_deg_seq.find(make_pair(v.in_degree, v.out_degree));
......@@ -211,10 +223,10 @@ public:
(v.in_degree > _max_deg || v.out_degree > _max_deg));
sum_j += v.in_degree;
sum_k += v.out_degree;
if (_no_parallel || (_no_self_loops && !_no_parallel))
if (_no_parallel || _no_self_loops)
_deg_seq[make_pair(v.in_degree, v.out_degree)]++;
if (verbose && (count % 100 == 0 || sum_j == sum_k))
print_update(min(sum_j-sum_k, sum_k-sum_j), str);
print_update(min(sum_j-sum_k, sum_k-sum_j), str);
count++;
}
return sum_k;
......@@ -332,7 +344,7 @@ public:
!is_graphical_parallel(_deg_seq)))
{
dvertex_t& v = vertices[vertex_sample(rng)];
if (_no_parallel || (_no_self_loops && !_no_parallel))
if (_no_parallel || _no_self_loops)
{
typeof(_deg_seq.begin()) iter = _deg_seq.find(v.out_degree);
iter->second--;
......@@ -346,7 +358,7 @@ public:
}
while (_no_parallel && (v.out_degree > _max_deg));
sum_k += v.out_degree;
if (_no_parallel || (_no_self_loops && !_no_parallel))
if (_no_parallel || _no_self_loops)
_deg_seq[v.out_degree]++;
if (verbose && (count % 100 || sum_k % 2 == 0))
print_update(sum_k, str);
......@@ -402,11 +414,39 @@ pair<size_t, size_t> get_deg(dvertex_t& v, Graph& g)
v.out_degree - out_degree(vertex(v.index, g), g));
}
template <class Graph>
bool is_source(const pair<size_t, size_t>& deg)
{
return deg.second > 0;
}
template <class Graph>
bool is_target(const pair<size_t, size_t>& deg)
{
if (is_directed::apply<Graph>::type::value)
return deg.first > 0;
else
return is_source<Graph>(deg);
}
template <class Vset, class Targets, class Sources, class Graph>
bool update_deg(size_t t_i, const pair<size_t, size_t>& deg, Vset& vset,
Targets& targets, Sources& sources, Graph& g)
{
if (is_source<Graph>(deg))
sources.insert(deg);
if (is_target<Graph>(deg))
targets.insert(deg);
vset[deg].push_back(t_i);
return true;
}
struct gen_random_graph
{
template <class Graph, class DegSample>
void operator()(Graph& g, size_t N, DegSample& deg_sample, bool no_parallel,
bool no_self_loops, size_t seed, bool verbose)
bool no_self_loops, size_t seed, bool verbose, bool verify)
const
{
rng_t rng(static_cast<rng_t::result_type>(seed));
......@@ -431,18 +471,26 @@ struct gen_random_graph
// sample the N (j,k) pairs
size_t E = gen_strat.SampleDegrees(vertices, deg_sample, rng, verbose);
// source and target degree lists
typedef pair<size_t, size_t> deg_t;
set<deg_t, cmp_out<greater<size_t> > > sources;
set<deg_t, cmp_in<greater<size_t> > > targets;
tr1::unordered_map<deg_t, tr1::unordered_set<size_t>,
// vertices with a given degree
tr1::unordered_map<deg_t, vector<size_t>,
boost::hash<deg_t> > vset;
size_t num_e = 0;
for (size_t i = 0; i < vertices.size(); ++i)
{
deg_t deg = get_deg(vertices[i], g);
sources.insert(deg);
targets.insert(deg);
vset[deg].insert(i);
if (is_source<Graph>(deg))
sources.insert(deg);
if (is_target<Graph>(deg))
targets.insert(deg);
if (is_target<Graph>(deg) || is_source<Graph>(deg))
vset[deg].push_back(i);
}
if (verbose)
......@@ -451,7 +499,7 @@ struct gen_random_graph
str.str("");
}
size_t num_e = 0;
vector<size_t> skip;
// connect edges: from sources with the largest in-degree to the ones
// with largest out-degree
......@@ -460,103 +508,150 @@ struct gen_random_graph
// find source. The out-degree must be non-zero, and there must be a
// vertex with the chosen degree.
deg_t s_deg = *sources.begin();
typeof(vset.begin()) v_iter = vset.find(s_deg);
if (s_deg.second == 0 || v_iter == vset.end())
typeof(vset.begin()) sv_iter = vset.find(s_deg);
if (s_deg.second == 0 || sv_iter == vset.end() ||
sv_iter->second.empty())
{
sources.erase(sources.begin());
continue;
}
size_t s_i = *v_iter->second.begin();
vector<size_t>& s_list = sv_iter->second;
size_t s_i = s_list.front();
typename graph_traits<Graph>::vertex_descriptor s =
vertex(vertices[s_i].index, g);
// find the targets. Skipped targets will be removed from the main
// set, and kept temporarily in the skip set.
vector<pair<deg_t, size_t> > skip;
skip.reserve(s_deg.second+1);
skip.push_back(make_pair(s_deg, s_i));
deg_t ns_deg = get_deg(vertices[s_i], g);
if (ns_deg != s_deg)
{
swap(s_list.back(), s_list.front());
s_list.pop_back();
update_deg(s_i, ns_deg, vset, targets, sources, g);
continue;
}
// find the targets.
// we will keep an iterator to the current target degree
typeof(targets.begin()) t_iter = targets.begin();
typeof(vset.begin()) v_iter = vset.find(*t_iter);
while (v_iter == vset.end() || v_iter->second.empty())
{
targets.erase(t_iter);
t_iter = targets.begin();
v_iter = vset.find(*t_iter);
}
skip.clear();
skip.push_back(s_i);
if (no_self_loops)
{
swap(s_list.back(), s_list.front());
s_list.pop_back();
}
while (s_deg.second > 0)
{
assert(!targets.empty());
deg_t t_deg = *targets.begin();
v_iter = vset.find(t_deg);
if (v_iter == vset.end() ||
(is_directed::apply<Graph>::type::value &&
t_deg.first == 0))
//assert(!targets.empty());
//assert(t_iter != targets.end());
while (v_iter == vset.end() || v_iter->second.empty())
{
targets.erase(targets.begin());
continue;
++t_iter;
v_iter = vset.find(*t_iter);
}
size_t t_i = *v_iter->second.begin();
// remove target from vertex list temporarily
v_iter->second.erase(t_i);
if (v_iter->second.empty())
vset.erase(v_iter);
skip.push_back(make_pair(t_deg, t_i));
deg_t t_deg = *t_iter;
if (!no_parallel)
vector<size_t>& v_list = v_iter->second;
size_t t_i = v_list.front();
deg_t nt_deg = get_deg(vertices[t_i], g);
if (nt_deg != t_deg)
{
v_iter = vset.find(s_deg);
if (v_iter != vset.end())
{
v_iter->second.erase(s_i);
if (v_iter->second.empty())
vset.erase(v_iter);
}
swap(v_list.back(), v_list.front());
v_list.pop_back();
update_deg(t_i, nt_deg, vset, targets, sources, g);
//t_iter = targets.begin();
//v_iter = vset.find(*t_iter);
continue;
}
// remove target from vertex list, and get new t_i
skip.push_back(t_i);
swap(v_list.back(), v_list.front());
v_list.pop_back();
typename graph_traits<Graph>::vertex_descriptor t =
vertex(vertices[t_i].index, g);
if ((s == t) && (no_self_loops ||
(!is_directed::apply<Graph>::type::value
&& s_deg.second < 2)))
continue; // no self-loops
if ((s == t) && (!is_directed::apply<Graph>::type::value &&
s_deg.second < 2))
continue;
add_edge(s, t, g);
s_deg = get_deg(vertices[s_i], g);
// if parallel edges are allowed, we should put the target back
// in the set right away
// if parallel edges are allowed, we should update the target
// list right away
if (!no_parallel)
{
skip.pop_back();
deg_t deg = get_deg(vertices[t_i], g);
vset[deg].insert(t_i);
targets.insert(deg);
sources.insert(deg);
deg = get_deg(vertices[s_i], g);
vset[deg].insert(s_i);
targets.insert(deg);
sources.insert(deg);
for (size_t i = 0; i < skip.size(); ++i)
{
if (no_self_loops && skip[i] == s_i)
continue;
update_deg(skip[i],
get_deg(vertices[skip[i]], g), vset,
targets, sources, g);
}
skip.clear();
if (no_self_loops)
skip.push_back(s_i);
}
s_deg = get_deg(vertices[s_i], g);
if (verbose)
print_progress(num_e++, E, str);
}
// put back modified targets
for (int i = skip.size() - 1; i >= 0; --i)
if (!s_list.empty() && s_list.front() == s_i)
{
v_iter = vset.find(skip[i].first);
if (v_iter != vset.end())
{
v_iter->second.erase(skip[i].second);
if (v_iter->second.empty())
vset.erase(v_iter);
}
deg_t deg = get_deg(vertices[skip[i].second], g);
targets.insert(targets.begin(), deg);
sources.insert(deg);
vset[deg].insert(skip[i].second);
swap(s_list.back(), s_list.front());
s_list.pop_back();
}
}
// update modified degrees
for (size_t i = 0; i < skip.size(); ++i)
update_deg(skip[i],
get_deg(vertices[skip[i]], g),
vset, targets, sources, g);
}
if (verbose)
cout << endl;
if (verify)
{
for (size_t i = 0; i < vertices.size(); ++i)
{
deg_t dseq = make_pair(vertices[i].in_degree,
vertices[i].out_degree);
deg_t deg = make_pair(in_degreeS()(vertex(i, g), g),
out_degree(vertex(i, g), g));
if (deg != dseq)
throw GraphException("Graph does not match the desired "
"sequence! Vertex " +
lexical_cast<string>(i) +
", wanted: " +
lexical_cast<string>(dseq.first) +
" " +
lexical_cast<string>(dseq.second) +
", got: " +
lexical_cast<string>(deg.first) +
" " +
lexical_cast<string>(deg.second) +
" This is a bug.");
}
}
}
};
......
src/graph_tool/generation/__init__.py
View file @ 63c2cae1
......@@ -237,7 +237,7 @@ def random_graph(N, deg_sampler, deg_corr=None, directed=True,
libgraph_tool_generation.gen_random_graph(g._Graph__graph, N, deg_sampler,
uncorrelated, not parallel_edges,
not self_loops, not directed,
seed, verbose)
seed, verbose, True)
g.set_directed(directed)
if random:
random_rewire(g, parallel_edges=parallel_edges,
......
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