virtual void SetUp(){
//SetUp is called before every test
LOG_INIT("test.log", NULL, 0);
creator.set_file_name("data/1dc.128.txt");
creator.set_graph_type("DIMACS");
mg = creator.create_mutable_graph();
}
void parmetis_with_metmmd(){
DEBUG("########## Testing Function : %s #################\n", __FUNCTION__);
int size, rank;
MPI_Comm comm;
Graph::GraphEOUtil eoutil;
Graph::VertexWeightedGraph *wmg;
Graph::GraphCreatorFile creator;
int output[] =
{
102,58,128,121,86,64,96,112,103,117,120,87,124,126,127,63,95,108,110,111,91,107,109,119,123,125,115,59,61,62,90,93,122,114,106,118,32,116,55,100,16,79,84,78,24,48,52,56,44,54,60,80,28,30,31,40,46,47,72,76,88,92,94,104,8,101,1,42,4,25,97,81,6,7,3,2,73,49,13,5,9,11,17,33,65,66,67,69,10,18,19,21,34,35,37,41,113,15,68,105,77,50,14,43,20,57,12,70,53,51,23,22,36,38,82,83,98,99,74,26,27,29,39,45,71,75,85,89
};
MPI_Comm_dup(MPI_COMM_WORLD, &comm);
MPI_Comm_size(MPI_COMM_WORLD, &size);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
creator.set_file_name("data/1dc.128.txt");
creator.set_graph_type("DIMACS");
wmg = creator.create_weighted_mutable_graph();
vector<int> ordering(wmg->get_num_nodes(), -1);
eoutil.parmetis_elimination_ordering(wmg, ordering, GD_METIS_MMD, false, comm);
if(rank == 0){
int n = wmg->get_num_nodes();
for(int i = 0; i < n; i++){
assert (output[i] == ordering[i]);
}
cout << "Parmetis Test " << ++testcount << " : Passed" << endl;
}
} // parmetis_with_metmmd
int main(int argc, char **argv){
if((argc != 2) || (strcmp(argv[1],"-h") == 0) || (strcmp(argv[1],"--help") == 0) ){
usage(argv[0]);
}
Graph::VertexWeightedGraph *G;
Graph::GraphCreatorFile creator;
creator.set_file_name(argv[1]);
creator.set_graph_type("DIMACS");
G = creator.create_weighted_mutable_graph();
G->complement();
Graph::GraphWriter writer;
char comp_DIMACS_file[200];
char normalized_comp_DIMACS_file[200];
sprintf(comp_DIMACS_file,"%s.comp",argv[1]);
writer.write_graph(G,comp_DIMACS_file,"DIMACS",true,false);
// Now normalize it
sprintf(normalized_comp_DIMACS_file,"%s.norm",comp_DIMACS_file);
normalize_DIMACS_file(comp_DIMACS_file,normalized_comp_DIMACS_file);
fprintf(stderr,"Complement graph of %s written to %s in normalized DIMACS form\n",
argv[1],normalized_comp_DIMACS_file);
delete G;
return 1;
} // main
virtual void SetUp(){
LOG_INIT("test.log", NULL, 0);
//creator.set_file_name("../data/1dc.128.txt");
creator.set_file_name("data/1dc.128.txt");
creator.set_graph_type("DIMACS");
g = creator.create_graph();
g_five = new Graph::Graph(5);
}
virtual void SetUp(){
//SetUp is called before every test
LOG_INIT("test.log", NULL, 0);
creator.set_file_name("data/1dc.128.adj");
creator.set_graph_type("adjmatrix");
g = creator.create_graph();
in_file = ("data/1dc.128.met");
}
virtual void SetUp()
{
LOG_INIT("test.log", NULL, 0);
gr = factory.create_reader("DIMACS");
gr->read_graph("data/1dc.128.txt");
creator.set_file_name("data/1dc.128.txt");
creator.set_graph_type("DIMACS");
g = creator.create_graph();
}
virtual void SetUp()
{
//SetUp is called before every test
LOG_INIT("test.log", NULL, 0);
creator.set_file_name("../data/1dc.128.adj");
creator.set_graph_type("adjmatrix");
g = creator.create_graph();
string out_file("../data/1dc.128.out");
dim_writer = new Graph::DIMACSGraphWriter(out_file);
}
virtual void SetUp()
{
//SetUp is called before every test
LOG_INIT("test.log", NULL, 0);
creator.set_file_name("data/1dc.128.adj");
creator.set_graph_type("adjmatrix");
g = creator.create_graph();
string in_file("data/1dc.128.met");
mr = new Graph::MetisGraphReader(in_file);
}
int ORD::find_elim_ordering() {
int ws;
int wr;
char eoname[512];
char eoname_other[512];
// Get size and rank from the communicator
MPI_Comm_size(comm, &ws);
MPI_Comm_rank(comm, &wr);
double xtime = MPI_Wtime();
sprintf(eoname, "%s.order.%d", this->filename.c_str(), ws);
sprintf(eoname_other, "%s.order_other.%d", this->filename.c_str(), ws);
DEBUG("size: %d, rank %d \n", ws, wr);
int n = G->get_num_nodes();
int x = n/ws;
int xm = n%ws;
int i = 0;
DEBUG("n: %d x: %d xm: %d \n", n, x, xm);
vector<int> xadj;
vector<int> adjncy;
vector<int> vtxdist(ws + 1, 0);
vector<int> sizes(2*ws,0);
vector<int> ordering(x+1, 0);
vector<int> recvcnt(ws, 0);
vector<int> displ(ws, 0);
int numflag = 0;
int options[10];
options[0] = 0;
vtxdist[0] = 0;
for (i = 1; i <= ws; i++)
{
vtxdist[i] = vtxdist[i - 1] + x;
if (i <= xm)
vtxdist[i]++;
}
// prepareing displacement and receive counts to use with MPI_Gatherv
for (i = 0; i < ws; i++)
{
recvcnt[i] = x;
if (i < xm)
recvcnt[i] ++;
if (i > 0)
displ[i] += displ[i - 1] + recvcnt[i - 1];
}
DEBUG("range: %d, %d\n", vtxdist[wr], vtxdist[wr + 1]);
int j = 0;
xadj.push_back(0);
for (i = vtxdist[wr]; i < vtxdist[wr + 1]; i++)
{
Graph::Node *no = G->get_node(i);
list<int> *l = no->get_nbrs_ptr();
list<int>::iterator it = l->begin();
for (; it != l->end(); ++it)
{
adjncy.push_back(*it);
j++;
}
xadj.push_back(j);
}
if (METIS_OK != ParMETIS_V3_NodeND(&vtxdist.front(), &xadj.front(), &adjncy.front(), &numflag, options, &ordering.front(), &sizes.front(), &comm))
{
FERROR("error occured while processing parmetis, aborting\n");
MPI_Abort(MPI_COMM_WORLD, -1);
}
DEBUG("output from ParMETIS\n");
double parmet_time = MPI_Wtime() - xtime;
vector<int> recvbuf;
n = G->get_num_nodes();
if (wr == 0)
{
recvbuf = vector<int>(n, 0);
}
if (MPI_SUCCESS !=
MPI_Gatherv((void *)&ordering.front(), recvcnt[wr], MPI_INT,
(void *)&recvbuf.front(), &recvcnt.front(), &displ.front(), MPI_INT,
0, comm))
{
FERROR("MPI error occured at Gatherv, Abort!\n");
MPI_Abort(comm, -1);
}
vector<int> eo(n, 0);
if (wr == 0)
{
for (int i = 0; i < n; i++)
{
eo[recvbuf[i]] = i;
}
FILE *f = fopen(eoname_other, "w");
for (int i = 0; i < n; i++)
fprintf(f, "%d\n", eo[i] + 1);
fclose(f);
DEBUG("ParMetis NodeND elimination ordering is in : %s\n", eoname_other);
}
ordering.clear();
ordering.resize(recvcnt[wr], 0);
if (MPI_SUCCESS !=
MPI_Scatterv ((void *)&eo.front(), &recvcnt.front(), &displ.front(), MPI_INT,
(void *)&ordering.front(), recvcnt[wr], MPI_INT,
0, comm))
{
FERROR("MPI error occured at Scatterv, Abort! \n");
MPI_Abort(comm, -1);
}
DEBUG("Scatterv completed\n");
Graph::GraphCreatorFile gf;
Graph::VertexWeightedGraph *wg;
Graph::GraphEOUtil eoutil;
Graph::GraphProperties prop;
list<int>members(ordering.begin(), ordering.end());
wg = gf.create_component(G, &members, false);
prop.make_canonical(wg);
vector<int> ord(recvcnt[wr], 0);
vector<int> ordsend(recvcnt[wr, 0]);
double xxtime = MPI_Wtime();
eoutil.find_elimination_ordering(wg, &ord, GD_AMD, false);
DEBUG("eo time : %f\n", MPI_Wtime() - xxtime);
int sz = recvcnt[wr];
for (int i = 0; i < sz; i++)
ordsend[i] = wg->get_node(ord[i])->get_label();
recvbuf.assign(n, -1);
if (MPI_SUCCESS !=
MPI_Gatherv((void *)&ordsend.front(), recvcnt[wr], MPI_INT, (void *)&recvbuf.front(), &recvcnt.front(), &displ.front(), MPI_INT, 0, comm))
{
FERROR("MPI error occured at Gatherv, Abort!\n");
MPI_Abort(comm, -1);
}
double p_amd_time = MPI_Wtime() - xtime;
if (wr == 0)
{
FILE *f = fopen(eoname, "w");
for (int i = 0; i < n && wr == 0; i++)
fprintf(f, "%d\n", recvbuf[i]);
fclose(f);
}
DEBUG("ordering is written into %s\n", eoname);
DEBUG("%f,%f\n", parmet_time, p_amd_time);
return 0;
}
int main(int argc, char **argv){
// This is a utility to generate partial k-trees with specified parameters for use in other applications.
// Check for a cry for help
if((argc == 1) || ((argc == 2) && (strcmp(argv[1],"-h") == 0)) || ((argc == 2) && (strcmp(argv[1],"--help") == 0))
|| ((argc == 2) && (strcmp(argv[1],"--h") == 0) ) ){
usage(argv[0]);
exit(-1);
}
ORB_t t1=0, t2=0, t3=0;
int i;
int t = 1;
int ktree_n = -1, ktree_k = -1, ktree_p = -1;
int seed = 0;
Graph::VertexWeightedGraph *G = NULL, *H = NULL;
time_t start, stop;
char filename[100];
char *prefix = (char *)"pkt";
string out_format = "DIMACS";
bool random = false;
bool timings = false;
bool exact_filename = false;
char lfname[100];
char efname[100];
sprintf(lfname, "genpkt.log");
sprintf(efname, "genpkt.log");
//0: debug, 5: critical
LOG_INIT(lfname, efname, 0);
// Parse arguments
for(i = 0; i < argc; i++){
if(strcmp(argv[i],"-t") == 0){
t = atoi(argv[i + 1]);
}
if(strcmp(argv[i],"-k") == 0){
ktree_k = atoi(argv[i + 1]);
}
if(strcmp(argv[i],"-n") == 0){
ktree_n = atoi(argv[i + 1]);
}
if(strcmp(argv[i],"-p") == 0){
ktree_p = atoi(argv[i + 1]);
}
if(strcmp(argv[i],"-o") == 0){
out_format = string(argv[i + 1]);
}
if(strcmp(argv[i],"-s") == 0){
seed = atoi(argv[i + 1]);
}
if(strcmp(argv[i],"-fn") == 0){
prefix = argv[i + 1];
}
if(strcmp(argv[i],"-fe") == 0){
prefix = argv[i + 1];
exact_filename = true;
}
if(strcmp(argv[i],"-m") == 0){
timings = true;
}
if(strcmp(argv[i],"-r") == 0){
random = true;
}
}
if((true == exact_filename) && (t != 1)){
cerr << "Error: cannot specify both -t and -fe flags\n";
exit(1);
}
if(("adjlist" != out_format) && ("dimacs" != out_format)){
cerr << "Error: only allowed output formats are: adjlist, dimacs\n";
exit(1);
}
// Spin the RNG seed times
for(int ss = 0; ss < seed; ss++){
Graph::lcgrand(0);
}
//Make sure we set all the parameters to viable values.
if((ktree_k < 0) || (ktree_n < 0) || (ktree_p < 0)){
fatal_error("Failed to input viable parameters for n, k, p (%d,%d,%d)\n",
ktree_k, ktree_n, ktree_p);
}
Graph::GraphCreatorFile creator;
Graph::GraphProperties prop;
Graph::GraphWriter writer;
//ORB_calibrate();
DEBUG("Graph generation loop\n");
DEBUG("n : %d k: %d\n", ktree_n, ktree_p);
for(i = 0; i < t; i++){
// Create the Ktree
//H = new Graph::Graph(ktree_n, ktree_k);
cout << "Generating k-tree\n";
H = creator.initialize_ktree(ktree_n, ktree_k);
// Generate an n-node Graph G that is a partial k-tree derived from the k-tree
start = clock();
cout << "Deriving partial k-tree\n";
//ORB_read(t1);
G = creator.create_random_edge_subgraph(H, ktree_p);
//ORB_read(t2);
stop = clock();
if(timings){
print_time("Generation time", t1, t2);
}
fprintf(stderr,"Generated random partial k-tree (%d,%d) in %f sec.\n",
ktree_n, ktree_k, ((double)(stop - start)) / CLOCKS_PER_SEC);
//write it to a file
if(!exact_filename){
sprintf(filename, "%s.%d.%d.%d_%d.dimacs", prefix, ktree_n,ktree_k,ktree_p, i);
}
else {
strncpy(filename,prefix, 99);
}
print_message(0,"Writing file %s\n",filename);
//writer->set_out_file_name(filename);
if(random){
writer.set_shuffle(true);
writer.set_shuffle_seed(seed);
}
//ORB_read(t2);
writer.write_graph(G,filename, out_format);
//ORB_read(t3);
if(timings){
print_time("Output time", t2, t3);
print_time("Total time", t1, t3);
cout << "Output edges: " << G->get_num_edges() << "\nOutput vertices: " << G->get_num_nodes();
cout << "\nOutput format: " << out_format << "\nOutput filename: " << filename << "\n";
}
delete G;
delete H;
}
LOG_CLOSE();
exit(0);
} // main
int main(int argc, char **argv)
{
// This is a utility to generate partial k-trees with specified parameters for use in other applications.
// Check for a cry for help
if(argc==1 || (argc==2 && strcmp(argv[1],"-h")==0) || (argc==2 && strcmp(argv[1],"--help")==0)
|| (argc==2 && strcmp(argv[1],"--h")==0) )
{
usage(argv[0]);
exit(-1);
}
int i;
int t = 1;
int ktree_n=-1, ktree_k=-1, ktree_p=-1;
int seed=0;
Graph::WeightedMutableGraph *G=NULL, *H=NULL;
time_t start, stop;
char filename[100];
char *prefix= (char *)"pkt";
bool random = false, write_scotch=false;
char lfname[100];
char efname[100];
sprintf(lfname, "genpkt.log");
sprintf(efname, "genpkt.log");
//0: debug, 5: critical
LOG_INIT(lfname, efname, 0);
// Parse arguments
for(i=0;i<argc;i++)
{
if(strcmp(argv[i],"-t")==0)
{
t=atoi(argv[i+1]);
}
if(strcmp(argv[i],"-k")==0)
{
ktree_k=atoi(argv[i+1]);
}
if(strcmp(argv[i],"-n")==0)
{
ktree_n=atoi(argv[i+1]);
}
if(strcmp(argv[i],"-p")==0)
{
ktree_p=atoi(argv[i+1]);
}
if(strcmp(argv[i],"-s")==0)
{
seed=atoi(argv[i+1]);
}
if(strcmp(argv[i],"-fn")==0)
prefix = argv[i+1];
if(strcmp(argv[i],"-r")==0)
random = true;
if(strcmp(argv[i],"-scotch")==0)
write_scotch = true;
}
if(!seed)
// Set the seed to a rand int in 0,2^24
seed=Graph::rand_int(0,0xffffff);
// Spin the RNG seed times
for(int ss=0;ss<seed;ss++)
Graph::lcgrand(0);
//Make sure we set all the parameters to viable values.
if(ktree_k < 0 || ktree_n < 0 || ktree_p < 0)
{
fatal_error("Failed to input viable parameters for n, k, p (%d,%d,%d)\n",
ktree_k, ktree_n, ktree_p);
}
Graph::GraphCreatorFile creator;
Graph::GraphWriter *writer;
Graph::GraphReaderWriterFactory rwf;
Graph::GraphProperties prop;
writer = rwf.create_writer("DIMACS", "t");
DEBUG("Graph generation loop\n");
DEBUG("n : %d k: %d\n", ktree_n, ktree_p);
for(i = 0; i < t; i++)
{
// Create the Ktree
//H = new Graph::Graph(ktree_n, ktree_k);
H = creator.initialize_ktree(ktree_n, ktree_k);
// Generate an n-node Graph G that is a partial k-tree derived from the k-tree
start=clock();
G= creator.create_random_edge_subgraph(H, ktree_p);
stop=clock();
fprintf(stderr,"Generated random partial k-tree (%d,%d) in %f sec.\n",
ktree_n, ktree_k, ((double)(stop-start))/CLOCKS_PER_SEC);
//write it to a file
sprintf(filename, "%s.%d.%d.%d_%d.dimacs", prefix, ktree_n,ktree_k,ktree_p, i);
print_message(0,"Writing file %s\n",filename);
writer->set_out_file_name(filename);
if (random)
writer->shuffle(G, seed);
writer->write_graph(G);
delete G;
delete H;
}
LOG_CLOSE();
return 0;
}
