int main(int argc, char *argv[]) {
// set up MPI
//MPI_Init(&argc, &argv);
//int rank, p;
//MPI_Comm_rank(MPI_COMM_WORLD, &rank);
//MPI_Comm_size(MPI_COMM_WORLD, &p);
mxx::env e(argc, argv);
mxx::env::set_exception_on_error();
mxx::comm comm = mxx::comm();
try {
// define commandline usage
TCLAP::CmdLine cmd("Parallel distirbuted suffix array and LCP construction.");
TCLAP::ValueArg<std::string> fileArg("f", "file", "Input filename.", true, "", "filename");
TCLAP::ValueArg<std::size_t> randArg("r", "random", "Random input size", true, 0, "size");
cmd.xorAdd(fileArg, randArg);
TCLAP::ValueArg<int> seedArg("s", "seed", "Sets the seed for the ranom input generation", false, 0, "int");
cmd.add(seedArg);
TCLAP::SwitchArg lcpArg("l", "lcp", "Construct the LCP alongside the SA.", false);
cmd.add(lcpArg);
TCLAP::SwitchArg checkArg("c", "check", "Check correctness of SA (and LCP).", false);
cmd.add(checkArg);
cmd.parse(argc, argv);
// read input file or generate input on master processor
// block decompose input file
std::string local_str;
if (fileArg.getValue() != "") {
local_str = mxx::file_block_decompose(fileArg.getValue().c_str(), MPI_COMM_WORLD);
} else {
// TODO proper distributed random!
local_str = rand_dna(randArg.getValue()/comm.size(), seedArg.getValue() * comm.rank());
}
// TODO differentiate between index types
// run our distributed suffix array construction
mxx::timer t;
double start = t.elapsed();
if (lcpArg.getValue()) {
// construct with LCP
suffix_array<std::string::iterator, index_t, true> sa(local_str.begin(), local_str.end(), MPI_COMM_WORLD);
// TODO choose construction method
sa.construct(true);
double end = t.elapsed() - start;
if (comm.rank() == 0)
std::cerr << "PSAC time: " << end << " ms" << std::endl;
if (checkArg.getValue()) {
gl_check_correct(sa, local_str.begin(), local_str.end(), MPI_COMM_WORLD);
}
} else {
// construct without LCP
suffix_array<std::string::iterator, index_t, false> sa(local_str.begin(), local_str.end(), MPI_COMM_WORLD);
// TODO choose construction method
sa.construct_arr<2>(true);
double end = t.elapsed() - start;
if (comm.rank() == 0)
std::cerr << "PSAC time: " << end << " ms" << std::endl;
if (checkArg.getValue()) {
gl_check_correct(sa, local_str.begin(), local_str.end(), MPI_COMM_WORLD);
}
}
// catch any TCLAP exception
} catch (TCLAP::ArgException& e) {
std::cerr << "error: " << e.error() << " for arg " << e.argId() << std::endl;
exit(EXIT_FAILURE);
}
// finalize MPI
//MPI_Finalize();
return 0;
}
int main(int argc, char* argv[])
{
double high = DEFAULT_MAX_WEIGHT;
double low = DEFAULT_MIN_WEIGHT;
unsigned width = DEFAULT_GRID_WIDTH;
unsigned height = DEFAULT_GRID_HEIGHT;
double equalWeight = MIN_EQUAL_WEIGHT;
double heuristicWeight = MIN_WEIGHTED_HEURISTIC;
try
{
TCLAP::CmdLine cmd("command line for astar demo", ' ' , "0.1");
TCLAP::ValueArg<unsigned> seedArg("s", "seed", "Initial seed value for the Random Number Generator",
false, 0, "unsigned integer: seed value for the RNG.");
TCLAP::ValueArg<double> lowArg("l", "low", "Low value for path weights",
false, DEFAULT_MIN_WEIGHT, "double 0, less than or equal to high");
TCLAP::ValueArg<double> highArg("i", "high", "High value for path weights",
false, DEFAULT_MAX_WEIGHT, "double 0, greater than or equal low");
TCLAP::ValueArg<unsigned> widthArg("w", "width", "Width of the grid in cells",
false, DEFAULT_GRID_WIDTH, "unsigned, between 2 and 9");
TCLAP::ValueArg<unsigned> heightArg("e", "height", "Height of the grid in cells",
false, DEFAULT_GRID_HEIGHT, "unsigned, between 2 and 9");
TCLAP::ValueArg<double> equidistantArg("q", "equal", "Vertical and Horizontal weights are equal. Diagonal weights are 1.414 times Vertical weights",
false, MIN_EQUAL_WEIGHT, "double, between 0 and 7");
TCLAP::ValueArg<double> weightedHeuristicArg("u", "weighted_heuristic", "Heuristcs are weighted on the manhattan distance and a proportion of the path weight",
false, MIN_WEIGHTED_HEURISTIC, "double, between 0.0 and 1.0");
cmd.add(seedArg);
cmd.add(lowArg);
cmd.add(highArg);
cmd.add(widthArg);
cmd.add(heightArg);
cmd.add(equidistantArg);
cmd.add(weightedHeuristicArg);
cmd.parse(argc, argv);
RandGen::setSeed(seedArg.getValue());
low = lowArg.getValue();
low = low < 0 ? 0 : low;
high = highArg.getValue();
high = high < low ? low : high;
width = widthArg.getValue();
width = width > MAX_GRID_DIMENSION ? MAX_GRID_DIMENSION : width;
width = width < MIN_GRID_DIMENSION ? MIN_GRID_DIMENSION : width;
height = heightArg.getValue();
height = height > MAX_GRID_DIMENSION ? MAX_GRID_DIMENSION : height;
height = height < MIN_GRID_DIMENSION ? MIN_GRID_DIMENSION : height;
equalWeight = equidistantArg.getValue();
equalWeight = equalWeight > MAX_EQUAL_WEIGHT ? MAX_EQUAL_WEIGHT : equalWeight;
equalWeight = equalWeight < MIN_EQUAL_WEIGHT ? MIN_EQUAL_WEIGHT : equalWeight;
heuristicWeight = weightedHeuristicArg.getValue();
heuristicWeight = heuristicWeight > MAX_WEIGHTED_HEURISTIC ? MAX_WEIGHTED_HEURISTIC : heuristicWeight;
heuristicWeight = heuristicWeight < MIN_WEIGHTED_HEURISTIC ? MIN_WEIGHTED_HEURISTIC : heuristicWeight;
}
catch(TCLAP::ArgException& e)
{
std::cerr << "error: " << e.error() << " for argument " << e.argId() << std::endl;
return 1;
}
Board board(width, height, low, high, equalWeight, heuristicWeight);
do
{
board.show(std::cout);
std::cout << "Press <enter> to continue.....";
std::cin.get();
}while(board.next(std::cout) == false);
std::cin.get();
return 0;
}
int main(int argc, char *argv[])
{
// set up MPI
MPI_Init(&argc, &argv);
int rank;
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
try {
// define commandline usage
TCLAP::CmdLine cmd("Compare our parallel implementation with divsufsort.");
TCLAP::ValueArg<std::string> fileArg("f", "file", "Input filename.", true, "", "filename");
TCLAP::ValueArg<std::size_t> randArg("r", "random", "Random input size", true, 0, "size");
TCLAP::ValueArg<int> seedArg("s", "seed", "Sets the seed for the ranom input generation", false, 0, "int");
cmd.add(seedArg);
cmd.xorAdd(fileArg, randArg);
TCLAP::SwitchArg checkArg("c", "check", "Check correctness of SA for PSAC using divsufsort `sufcheck()`.", false);
cmd.add(checkArg);
cmd.parse(argc, argv);
// read input file or generate input on master processor
std::string input_str;
if (rank == 0) {
if (fileArg.getValue() != "") {
std::ifstream t(fileArg.getValue().c_str());
std::stringstream buffer;
buffer << t.rdbuf();
input_str = buffer.str();
} else {
input_str = rand_dna(randArg.getValue(), seedArg.getValue());
}
}
// TODO differentiate between index types
// run our distributed suffix array construction
std::string local_str = mxx::stable_distribute(input_str, MPI_COMM_WORLD);
mxx::timer t;
double start = t.elapsed();
suffix_array<std::string::iterator, index_t, false> sa(local_str.begin(), local_str.end(), MPI_COMM_WORLD);
// TODO: choose construction method!
sa.construct_arr<2>(true);
//sa.construct_arr<2>();
double end = t.elapsed() - start;
if (rank == 0)
std::cerr << "PSAC time: " << end << " ms" << std::endl;
std::vector<index_t> glSA = mxx::gatherv(sa.local_SA, 0);
// run construction with divsufsort locally on rank 0
if (rank == 0) {
mxx::timer t;
std::vector<index_t> SA;
double start = t.elapsed();
dss::construct(input_str.begin(), input_str.end(), SA);
double end = t.elapsed() - start;
std::cerr << "divsufsort time: " << end << " ms" << std::endl;
// check correctness if we should do so!
if (checkArg.getValue()) {
std::cerr << "Checking for correctness..." << std::endl;
if(!dss::check(input_str.begin(), input_str.end(), glSA)) {
std::cerr << "ERROR: wrong suffix array from PSAC" << std::endl;
return false;
}
if(!dss::check(input_str.begin(), input_str.end(), SA)) {
std::cerr << "ERROR: wrong suffix array from divsufsort" << std::endl;
}
}
}
// catch any TCLAP exception
} catch (TCLAP::ArgException& e) {
std::cerr << "error: " << e.error() << " for arg " << e.argId() << std::endl;
exit(EXIT_FAILURE);
}
// finalize MPI
MPI_Finalize();
return 0;
}
