template<size_t span> struct debruijn_minim_bench { void operator () (Parameter params)
{
size_t kmerSize = params.k;
const Graph& graph = params.graph;
int miniSize = 8;
int NB_REPETITIONS = 2000000;
double unit = 1000000000;
cout.setf(ios_base::fixed);
cout.precision(3);
GraphIterator<Node> nodes = graph.iterator ();
cout << "graph has " << nodes.size() << " nodes" << endl;
if (nodes.size() == 0)
exit(1);
nodes.first ();
/** We get the first node. */
Node node = nodes.item();
typedef typename Kmer<span>::Type Type;
typedef typename Kmer<span>::ModelCanonical ModelCanonical;
typedef typename Kmer<span>::ModelDirect ModelDirect;
typedef typename Kmer<span>::template ModelMinimizer <ModelCanonical> ModelMini;
typedef typename ModelMini::Kmer KmerType;
ModelMini modelMini (kmerSize, miniSize);
/** We get the value of the current minimizer. */
Type kmer = node.kmer.get<Type>();
auto start_t=chrono::system_clock::now();
for (unsigned int i = 0 ; i < NB_REPETITIONS ; i++)
modelMini.getMinimizerValue(kmer, false);
auto end_t=chrono::system_clock::now();
cout << NB_REPETITIONS << " minimizers of length " << miniSize << " on a " << kmerSize << "-mer : " << diff_wtime(start_t, end_t) / unit << " seconds" << endl;
cout << "---- now on all nodes of the graph -----\n";
int times = max((int)(NB_REPETITIONS / nodes.size()), 1);
/* compute a baseline */
start_t=chrono::system_clock::now();
for (int i=0; i < times; i++)
for (nodes.first(); !nodes.isDone(); nodes.next())
modelMini.getMinimizerValueDummy(nodes.item().kmer.get<Type>());
end_t=chrono::system_clock::now();
auto baseline_time = diff_wtime(start_t, end_t) / unit;
cout << "baseline overhead (" << nodes.size() << " nodes, " << times << " times) : " << baseline_time << " seconds" << endl;
/* existing code */
start_t=chrono::system_clock::now();
for (int i=0; i < times; i++)
for (nodes.first(); !nodes.isDone(); nodes.next())
modelMini.getMinimizerValue(nodes.item().kmer.get<Type>(), false);
end_t=chrono::system_clock::now();
cout << nodes.size() << " minimizers of length " << miniSize << " on all nodes (" << kmerSize << "-mers), " << to_string(times) << " times, with existing code : " << (diff_wtime(start_t, end_t) / unit) - baseline_time << " seconds" << endl;
start_t=chrono::system_clock::now();
for (int i=0; i < times; i++)
for (nodes.first(); !nodes.isDone(); nodes.next())
modelMini.getMinimizerValue(nodes.item().kmer.get<Type>(), true);
end_t=chrono::system_clock::now();
cout << nodes.size() << " minimizers of length " << miniSize << " on all nodes (" << kmerSize << "-mers), " << to_string(times) << " times, with new method : " << (diff_wtime(start_t, end_t) / unit) - baseline_time << " seconds" << endl;
//cout << modelMini._invalidMinimizersCounter << "/" << modelMini._minimizersCounter << " normal/fast minimizer computations" << endl,
/* checking agreement between old and new method*/
cout << "checking agreement... ";
for (nodes.first(); !nodes.isDone(); nodes.next())
{
if (modelMini.getMinimizerValue(nodes.item().kmer.get<Type>(), false) != modelMini.getMinimizerValue(nodes.item().kmer.get<Type>(), true))
{
cout << "FAIL! problem with kmer " << graph.toString(nodes.item()) << " : (old) " << modelMini.getMinimizerString(nodes.item().kmer.get<Type>(), false) << " vs (new) " << modelMini.getMinimizerString(nodes.item().kmer.get<Type>(), true) << endl;
cout << "debug: integer representation of new minimizer: " << modelMini.getMinimizerValue(nodes.item().kmer.get<Type>(), true) << endl;
exit(1);
}
if (modelMini.getMinimizerPosition(nodes.item().kmer.get<Type>(), false) != modelMini.getMinimizerPosition(nodes.item().kmer.get<Type>(), true))
{
cout << "FAIL! problem with minimizer positions of kmer " << graph.toString(nodes.item()) << " : (old position) " << modelMini.getMinimizerPosition(nodes.item().kmer.get<Type>(), false) << " vs (new position) " << modelMini.getMinimizerPosition(nodes.item().kmer.get<Type>(), true) << endl;
cout << " minimizer: " << modelMini.getMinimizerString(nodes.item().kmer.get<Type>()) << endl;
exit(1);
}
}
cout << "all good." << endl;
}
template<size_t span> struct debruijn_mphf_bench { void operator () (Parameter params)
{
typedef NodeFast<span> NodeFastT;
typedef GraphTemplate<NodeFastT,EdgeFast<span>,GraphDataVariantFast<span>> GraphFast;
size_t kmerSize = params.k;
Graph graph;
GraphFast graphFast;
if (params.seq == "")
{
graph = Graph::create (params.args.c_str());
graphFast = GraphFast::create (params.args.c_str());
}
else
{
graph = Graph::create (new BankStrings (params.seq.c_str(), 0), params.args.c_str());
graphFast = GraphFast::create (new BankStrings (params.seq.c_str(), 0), params.args.c_str());
}
cout << "graph built, benchmarking.." << endl;
int miniSize = 8;
int NB_REPETITIONS = 2000000;
double unit = 1000000000;
cout.setf(ios_base::fixed);
cout.precision(3);
Graph::Iterator<Node> nodes = graph.iterator();
typename GraphFast::template Iterator<NodeFastT> nodesFast = graphFast.iterator();
nodes.first ();
/** We get the first node. */
Node node = nodes.item();
typedef typename Kmer<span>::Type Type;
typedef typename Kmer<span>::ModelCanonical ModelCanonical;
typedef typename Kmer<span>::ModelDirect ModelDirect;
typedef typename Kmer<span>::template ModelMinimizer <ModelCanonical> ModelMini;
typedef typename ModelMini::Kmer KmerType;
ModelMini modelMini (kmerSize, miniSize);
ModelCanonical modelCanonical (kmerSize);
// for some reason.. if *compiled*, this code confuses makes later MPHF queries 3x slower. really? yes. try to replace "if (confuse_mphf)" by "if (confuse_mphf && 0)" and re-run, you will see.
{
bool confuse_mphf = false;
if (confuse_mphf)
{
//Type b; b.setVal(0);
//modelCanonical.emphf_hasher(modelCanonical.adaptor(b));
//typedef std::pair<u_int8_t const*, u_int8_t const*> byte_range_t;
//int c = 0;
//byte_range_t brange( reinterpret_cast <u_int8_t const*> (&c), reinterpret_cast <u_int8_t const*> (&c) + 2 );
//byte_range_t brange( (u_int8_t const*) 1,(u_int8_t const*)33);
//auto hashes = modelCanonical.empfh_hasher(brange);
}
for (int i = 0; i < 0; i++)
{
auto start_tt=chrono::system_clock::now();
for (nodes.first(); !nodes.isDone(); nodes.next())
modelCanonical.EMPHFhash(nodes.item().kmer.get<Type>());
auto end_tt=chrono::system_clock::now();
cout << "time to do " << nodes.size() << " computing EMPHFhash of kmers on all nodes (" << kmerSize << "-mers) : " << (diff_wtime(start_tt, end_tt) / unit) << " seconds" << endl;
}
// it's slow. i don't understand why. see above for the "confuse mphf" part
//return; //FIXME
}
/** We get the value of the first node (just an example, it's not used later). */
Type kmer = node.kmer.get<Type>();
auto start_t=chrono::system_clock::now();
auto end_t=chrono::system_clock::now();
cout << "----\non all nodes of the graph\n-----\n";
/* disable node state (because we don't want to pay the price for overhea of checking whether a node is deleted or not in contain() */
std::cout<< "PAY ATTENTION: this neighbor() benchmark, in the Bloom flavor, is without performing a MPHF query for each found node" << std::endl;
graph.disableNodeState();
graphFast.disableNodeState();
/* compute baseline times (= overheads we're not interested in) */
start_t=chrono::system_clock::now();
for (nodes.first(); !nodes.isDone(); nodes.next())
{}
end_t=chrono::system_clock::now();
auto baseline_graph_time = diff_wtime(start_t, end_t) / unit;
cout << "baseline overhead for graph nodes enumeration (" << nodes.size() << " nodes) : " << baseline_graph_time << " seconds" << endl;
start_t=chrono::system_clock::now();
for (nodesFast.first(); !nodesFast.isDone(); nodesFast.next())
{}
end_t=chrono::system_clock::now();
auto baseline_graphfast_time = diff_wtime(start_t, end_t) / unit;
cout << "baseline overhead for graph NodeFast enumeration (" << nodes.size() << " nodes) : " << baseline_graphfast_time << " seconds" << endl;
start_t=chrono::system_clock::now();
for (nodes.first(); !nodes.isDone(); nodes.next())
modelMini.getMinimizerValueDummy(nodes.item().kmer.get<Type>());
end_t=chrono::system_clock::now();
auto baseline_minim_time = diff_wtime(start_t, end_t) / unit;
cout << "baseline overhead for graph nodes enumeration and minimizer computation setup (" << nodes.size() << " nodes) : " << baseline_minim_time << " seconds" << endl;
start_t=chrono::system_clock::now();
for (nodes.first(); !nodes.isDone(); nodes.next())
nodes.item().getKmer<Type>();
end_t=chrono::system_clock::now();
auto baseline_hash_time = diff_wtime(start_t, end_t) / unit;
cout << "baseline overhead for graph nodes enumeration and hash computation setup (" << nodes.size() << " nodes) : " << baseline_hash_time << " seconds" << endl;
start_t=chrono::system_clock::now();
for (nodesFast.first(); !nodesFast.isDone(); nodesFast.next())
nodesFast.item().kmer;
end_t=chrono::system_clock::now();
auto baseline_hashfast_time = diff_wtime(start_t, end_t) / unit;
cout << "baseline overhead for graph NodeFast enumeration and hash computation setup (" << nodes.size() << " nodes) : " << baseline_hashfast_time << " seconds" << endl;
start_t=chrono::system_clock::now();
for (nodes.first(); !nodes.isDone(); nodes.next())
graph.nodeMPHFIndexDummy(nodes.item());
end_t=chrono::system_clock::now();
auto baseline_mphf_time = diff_wtime(start_t, end_t) / unit;
cout << "baseline overhead for graph nodes enumeration and mphf query setup (" << nodes.size() << " nodes) : " << baseline_mphf_time << " seconds" << endl;
start_t=chrono::system_clock::now();
for (nodesFast.first(); !nodesFast.isDone(); nodesFast.next())
graphFast.nodeMPHFIndexDummy(nodesFast.item());
end_t=chrono::system_clock::now();
auto baseline_mphffast_time = diff_wtime(start_t, end_t) / unit;
cout << "baseline overhead for graph NodeFast enumeration and mphf query setup (" << nodes.size() << " nodes) : " << baseline_mphffast_time << " seconds" << endl;
/* do actual benchmark */
start_t=chrono::system_clock::now();
for (nodes.first(); !nodes.isDone(); nodes.next())
modelMini.getMinimizerValue(nodes.item().kmer.get<Type>(), true);
end_t=chrono::system_clock::now();
cout << "time to do " << nodes.size() << " computations of minimizers (fast method) of length " << miniSize << " on all nodes (" << kmerSize << "-mers) : " << (diff_wtime(start_t, end_t) / unit) - baseline_minim_time << " seconds" << endl;
start_t=chrono::system_clock::now();
for (nodes.first(); !nodes.isDone(); nodes.next())
graph.nodeMPHFIndex(nodes.item());
end_t=chrono::system_clock::now();
cout << "time to do " << nodes.size() << " computations of MPHF index on all nodes (" << kmerSize << "-mers) : " << (diff_wtime(start_t, end_t) / unit) - baseline_mphf_time << " seconds" << endl;
start_t=chrono::system_clock::now();
for (nodesFast.first(); !nodesFast.isDone(); nodesFast.next())
graphFast.nodeMPHFIndex(nodesFast.item());
end_t=chrono::system_clock::now();
cout << "time to do " << nodes.size() << " computations of MPHF index on all NodeFast (" << kmerSize << "-mers) : " << (diff_wtime(start_t, end_t) / unit) - baseline_mphffast_time << " seconds" << endl;
start_t=chrono::system_clock::now();
for (nodes.first(); !nodes.isDone(); nodes.next())
modelCanonical.getHash(nodes.item().kmer.get<Type>());
end_t=chrono::system_clock::now();
cout << "time to do " << nodes.size() << " computing hash1 of kmers on all nodes (" << kmerSize << "-mers) : " << (diff_wtime(start_t, end_t) / unit) - baseline_hash_time << " seconds" << endl;
start_t=chrono::system_clock::now();
for (nodes.first(); !nodes.isDone(); nodes.next())
modelCanonical.getHash2(nodes.item().kmer.get<Type>());
end_t=chrono::system_clock::now();
cout << "time to do " << nodes.size() << " computing hash2 of kmers on all nodes (" << kmerSize << "-mers) : " << (diff_wtime(start_t, end_t) / unit) - baseline_hash_time << " seconds" << endl;
start_t=chrono::system_clock::now();
for (nodesFast.first(); !nodesFast.isDone(); nodesFast.next())
modelCanonical.getHash2(nodesFast.item().kmer);
end_t=chrono::system_clock::now();
cout << "time to do " << nodes.size() << " computing hash2 of kmers on all NodeFast (" << kmerSize << "-mers) : " << (diff_wtime(start_t, end_t) / unit) - baseline_hashfast_time << " seconds" << endl;
start_t=chrono::system_clock::now();
for (nodes.first(); !nodes.isDone(); nodes.next())
modelCanonical.EMPHFhash(nodes.item().kmer.get<Type>());
end_t=chrono::system_clock::now();
cout << "time to do " << nodes.size() << " computing EMPHFhash of kmers on all nodes (" << kmerSize << "-mers) : " << (diff_wtime(start_t, end_t) / unit) - baseline_hash_time << " seconds" << endl;
// it's slow. i don't understand why. see above for the "confuse mphf" part
start_t=chrono::system_clock::now();
for (nodes.first(); !nodes.isDone(); nodes.next())
graph.neighborsDummy(nodes.item());
end_t=chrono::system_clock::now();
cout << "time to do " << nodes.size() << " dummy neighbors() query on all nodes (" << kmerSize << "-mers) : " << (diff_wtime(start_t, end_t) / unit) - baseline_graph_time << " seconds" << endl;
start_t=chrono::system_clock::now();
for (nodes.first(); !nodes.isDone(); nodes.next())
graph.neighbors(nodes.item());
end_t=chrono::system_clock::now();
cout << "time to do " << nodes.size() << " neighbors() query on all nodes (" << kmerSize << "-mers) : " << (diff_wtime(start_t, end_t) / unit) - baseline_graph_time << " seconds" << endl;
start_t=chrono::system_clock::now();
for (nodesFast.first(); !nodesFast.isDone(); nodesFast.next())
graphFast.neighbors(nodesFast.item());
end_t=chrono::system_clock::now();
cout << "time to do " << nodes.size() << " neighbors() query on all NodeFast (" << kmerSize << "-mers) : " << (diff_wtime(start_t, end_t) / unit) - baseline_graphfast_time << " seconds" << endl;
/* isBranching */
start_t=chrono::system_clock::now();
for (nodes.first(); !nodes.isDone(); nodes.next())
graph.isBranching(nodes.item());
end_t=chrono::system_clock::now();
cout << "time to do " << nodes.size() << " isBranching() query on all nodes (" << kmerSize << "-mers) : " << (diff_wtime(start_t, end_t) / unit) - baseline_graph_time << " seconds" << endl;
start_t=chrono::system_clock::now();
for (nodesFast.first(); !nodesFast.isDone(); nodesFast.next())
graphFast.isBranching(nodesFast.item());
end_t=chrono::system_clock::now();
cout << "time to do " << nodes.size() << " isBranching() query on all NodeFast (" << kmerSize << "-mers) : " << (diff_wtime(start_t, end_t) / unit) - baseline_graphfast_time << " seconds" << endl;
/* now, compute adjacency! */
graph.precomputeAdjacency();
graphFast.precomputeAdjacency();
cout << "adjacency precomputed" << endl;
start_t=chrono::system_clock::now();
for (nodes.first(); !nodes.isDone(); nodes.next())
graph.neighbors(nodes.item());
end_t=chrono::system_clock::now();
cout << "time to do " << nodes.size() << " neighbors() query on all nodes (" << kmerSize << "-mers) using adjacency : " << (diff_wtime(start_t, end_t) / unit) - baseline_graph_time << " seconds" << endl;
start_t=chrono::system_clock::now();
for (nodesFast.first(); !nodesFast.isDone(); nodesFast.next())
graphFast.neighbors(nodesFast.item());
end_t=chrono::system_clock::now();
cout << "time to do " << nodes.size() << " fast neighbors() query on all NodeFast (" << kmerSize << "-mers) using adjacency : " << (diff_wtime(start_t, end_t) / unit) - baseline_graphfast_time << " seconds" << endl;
/* isBranching */
start_t=chrono::system_clock::now();
for (nodes.first(); !nodes.isDone(); nodes.next())
graph.isBranching(nodes.item());
end_t=chrono::system_clock::now();
cout << "time to do " << nodes.size() << " isBranching() query on all nodes (" << kmerSize << "-mers) using adjacency : " << (diff_wtime(start_t, end_t) / unit) - baseline_graph_time << " seconds" << endl;
start_t=chrono::system_clock::now();
for (nodesFast.first(); !nodesFast.isDone(); nodesFast.next())
graphFast.isBranching(nodesFast.item());
end_t=chrono::system_clock::now();
cout << "time to do " << nodes.size() << " fast isBranching() query on all NodeFast (" << kmerSize << "-mers) using adjacency : " << (diff_wtime(start_t, end_t) / unit) - baseline_graphfast_time << " seconds" << endl;
/** We remove the graph. */
//graph.remove ();
//graphFast.remove (); // no actually, I want to keep the .h5 file
}
