/*************************************************************************
* Let the game begin
**************************************************************************/
main(int argc, char *argv[])
{
int i, j, ne, nn, etype, numflag=0;
idxtype *elmnts, *xadj, *adjncy;
timer IOTmr, DUALTmr;
char fileout[256], etypestr[4][5] = {"TRI", "TET", "HEX", "QUAD"};
if (argc != 2) {
printf("Usage: %s <meshfile>\n",argv[0]);
exit(0);
}
cleartimer(IOTmr);
cleartimer(DUALTmr);
starttimer(IOTmr);
elmnts = ReadMesh(argv[1], &ne, &nn, &etype);
stoptimer(IOTmr);
printf("**********************************************************************\n");
printf("%s", METISTITLE);
printf("Mesh Information ----------------------------------------------------\n");
printf(" Name: %s, #Elements: %d, #Nodes: %d, Etype: %s\n\n", argv[1], ne, nn, etypestr[etype-1]);
printf("Forming Dual Graph... -----------------------------------------------\n");
xadj = idxmalloc(ne+1, "main: xadj");
adjncy = idxmalloc(10*ne, "main: adjncy");
starttimer(DUALTmr);
METIS_MeshToDual(&ne, &nn, elmnts, &etype, &numflag, xadj, adjncy);
stoptimer(DUALTmr);
printf(" Dual Information: #Vertices: %d, #Edges: %d\n", ne, xadj[ne]/2);
sprintf(fileout, "%s.dgraph", argv[1]);
starttimer(IOTmr);
WriteGraph(fileout, ne, xadj, adjncy);
stoptimer(IOTmr);
printf("\nTiming Information --------------------------------------------------\n");
printf(" I/O: \t\t %7.3f\n", gettimer(IOTmr));
printf(" Dual Creation:\t\t %7.3f\n", gettimer(DUALTmr));
printf("**********************************************************************\n");
GKfree(&elmnts, &xadj, &adjncy, LTERM);
}
/***********************************************************************************
* This function is the testing routine for the adaptive multilevel partitioning code.
* It computes a partition from scratch, it then moves the graph and changes some
* of the vertex weights and then call the adaptive code.
************************************************************************************/
void TestParMGridGen(char *filename, int *options, int minsize, int maxsize, MPI_Comm comm)
{
int i, nparts, npes, mype;
MGridGraphType graph;
idxtype *part;
double tmr;
MPI_Comm_size(comm, &npes);
MPI_Comm_rank(comm, &mype);
MGridReadTestGraph(&graph, filename, comm);
part = idxmalloc(graph.nvtxs, "TestParMGridGen: part");
/*======================================================================
/ ParMETIS_AspectRatio
/=======================================================================*/
if (mype==0)
printf("------------------------ PARAMETERS --------------------------------------\n");
for (i=0; i<npes; i++)
if (mype == i)
printf("%s, Dim=%d [%2d %2d] CType=%d RType=%d Nvtxs=%d Nedges=%d\n", filename,
options[OPTION_DIM], minsize, maxsize, options[OPTION_CTYPE],
options[OPTION_RTYPE], graph.nvtxs, graph.nedges);
cleartimer(tmr);
MPI_Barrier(comm);
starttimer(tmr);
ParMGridGen(graph.vtxdist, graph.xadj, graph.vvol, graph.vsurf, graph.adjncy,
graph.adjwgt, &nparts, minsize, maxsize, options, part, &comm);
MPI_Barrier(comm);
stoptimer(tmr);
printf("Total Time = %lf\n", gettimer(tmr));
WriteParallelPartition(filename, part, graph.vtxdist, nparts, mype, npes);
IMfree(&graph.vtxdist, &graph.xadj, &graph.vvol, &graph.vsurf, &graph.vwgt,
&graph.adjncy, &graph.adjwgt, &part, LTERM);
}
int main(int argc, char *argv[])
{
int i, npart;
idxtype *part;
float ncut=0;
GraphType graph;
char filename[256],outputFile[256];
int wgtflag = 0, addSelfLoop=1, outputFileGiven=0, txtFormat=0 ;
int randomInit = 0;
idxtype minEdgeWeight = 0;
Options opt;
timer TOTALTmr, METISTmr, IOTmr;
initOptions(&opt);
if (argc < 2) {
print_help(argv[0]);
exit(0);
}
for (argv++; *argv != NULL; argv++){
if ((*argv)[0] == '-')
{
int temp;
switch ((*argv)[1])
{
case 'b':
case 'B':
opt.penalty_power=atof(*(++argv));
break;
case 'i':
case 'I':
opt.gamma=atof(*(++argv));
break;
case 'o':
case 'O':
strcpy(outputFile,*(++argv));
outputFileGiven=1;
break;
case 'D'://quality threshold. This is a post-processing step proposed in SR-MCL. If you dont want post-processing (this is what original MLR-MCL, R-MCL, MCL do, please set "-d 0"
case 'd':
opt.quality_threshold = atof(*(++argv));
break;
case 'w':
case 'W':
opt.weighted_density = true;
break;
case 'c':
case 'C':
opt.coarsenTo= atoi(*(++argv));
break;
default:
printf("Invalid option %s\n", *argv);
print_help(argv[0]);
exit(0);
}
}
else
{
strcpy(filename, *argv);
}
}
if ( randomInit > 0 )
InitRandom(time(NULL));
else
InitRandom(-1);
cleartimer(TOTALTmr);
cleartimer(METISTmr);
cleartimer(IOTmr);
starttimer(TOTALTmr);
starttimer(IOTmr);
ReadGraph(&graph, filename, &wgtflag, addSelfLoop, txtFormat);
if ( opt.matchType == MATCH_UNSPECIFIED )
{
// opt.matchType = (graph.nvtxs>50000) ? MATCH_POWERLAW_FC :
// MATCH_SHEMN;
opt.matchType = MATCH_SHEMN;
}
stoptimer(IOTmr);
if (graph.nvtxs <= 0) {
printf("Empty graph. Nothing to do.\n");
exit(0);
}
int noOfSingletons = 0;
GraphType *noSingletonGraph ;
idxtype* nodeMap = lookForSingletons(&graph, &noOfSingletons);
if ( noOfSingletons > 0 )
{
getSubgraph(&graph, nodeMap, graph.nvtxs-noOfSingletons,
wgtflag, &noSingletonGraph);
GKfree((void**)&(graph.xadj), (void**)&(graph.adjncy), LTERM);
if ( wgtflag&1 > 0 )
GKfree( (void**)&(graph.adjwgt), LTERM);
// free(graph.gdata);
printf("Found %d singleton nodes in the", noOfSingletons);
printf(" input graph. Removing them.\n");
}
if ( !outputFileGiven )
{
strcpy(outputFile, filename);
sprintf(outputFile,"%s.c%d.i%1.1f.b%1.1f",outputFile,opt.coarsenTo,opt.gamma,opt.penalty_power);
}
printf("Input graph information ---------------------------------------------------\n");
printf(" Name: %s, #Vertices: %d, #Edges: %d\n", filename, graph.nvtxs, graph.nedges/2);
printf("Output shall be placed in the file %s\n",
outputFile);
fflush(stdout);
part = idxmalloc(graph.nvtxs, "main: part");
printf("------------------------------------------------\n");
printf("Clustering....\n");
fflush(stdout);
starttimer(METISTmr); //YK: main algorithm starts here!
if ( noOfSingletons > 0 )
{
mlmcl(&(noSingletonGraph->nvtxs), noSingletonGraph->xadj, noSingletonGraph->adjncy,
noSingletonGraph->vwgt,noSingletonGraph->adjwgt, &wgtflag, part, opt );
}
else
{
mlmcl(&graph.nvtxs, graph.xadj, graph.adjncy,graph.vwgt,
graph.adjwgt, &wgtflag, part, opt );
}
stoptimer(METISTmr);
printf("------------------------------------------------\n");
if ( noOfSingletons > 0 )
{
npart=mapPartition(part,noSingletonGraph->nvtxs);
ncut=ComputeNCut(noSingletonGraph, part,npart);
// printf("In graph that does not include singletons,");
// printf("No. of Clusters: %d, N-Cut value: %.2f\n",npart,ncut);
idxtype *clusterSizes = histogram(part,
graph.nvtxs-noOfSingletons, npart);
int maxSize = clusterSizes[idxamax(npart, clusterSizes)];
float avgClusterSize =
(graph.nvtxs-noOfSingletons)*1.0/(npart);
float balance = (maxSize*1.0) /
((graph.nvtxs-noOfSingletons)*1.0/npart);
float stdDevn = stdDeviation(clusterSizes, npart);
float avgNcut = ncut * 1.0/npart;
float normStdDevn = stdDevn/avgClusterSize;
// Warning: This computation only works if the singletons
// have been placed in their own clusters. This works for
// MLR-MCL, in other words, because it is guaranteed to
// place singletons in their own clusters.
printf("Output statistics for graph without singletons\n");
printf("Clusters: %d N-Cut: %.3f",
npart, ncut);
printf(" AvgN-Cut: %.3f Balance in cluster sizes: %.2f ",avgNcut,
balance);
printf("Std_Deviation in cluster sizes: %.2f ", stdDevn);
printf("Coefficient_of_Variation: %.2f\n", normStdDevn);
free( clusterSizes );
npart += noOfSingletons;
// ncut += noOfSingletons;
printf("Output statistics for original graph\n");
mapIndices(part, nodeMap, graph.nvtxs, npart-noOfSingletons);
}
else
{
npart=mapPartition(part,graph.nvtxs);
ncut=ComputeNCut(&graph, part,npart);
}
idxtype* clusterSizes = histogram(part, graph.nvtxs, npart);
int maxSize = clusterSizes[idxamax(npart, clusterSizes)];
float avgClusterSize = (graph.nvtxs)*1.0/(npart);
float balance = (maxSize*1.0)/(graph.nvtxs*1.0/npart);
float stdDevn = stdDeviation(clusterSizes, npart);
float avgNcut = ncut * 1.0/npart;
float normStdDevn = stdDevn/avgClusterSize;
printf("Clusters: %d N-Cut: %.3f AvgN-Cut: %.3f", npart,
ncut, avgNcut );
printf(" Balance in cluster sizes: %.2f Std.Deviation in cluster sizes: %.2f ",
balance, stdDevn);
printf("Coefficient_of_Variation: %.2f\n", normStdDevn);
starttimer(IOTmr);
my_WritePartition(outputFile, part, graph.nvtxs, opt.gamma);
if ( noOfSingletons > 0 )
{
free(nodeMap);
nodeMap = NULL;
}
printf("\nOutput is written to file: %s\n", outputFile);
stoptimer(IOTmr);
stoptimer(TOTALTmr);
printf("\nTiming Information --------------------------------------------------\n");
printf(" I/O: \t\t %7.3f\n", gettimer(IOTmr));
printf(" Partitioning: \t\t %7.3f (MLR-MCL time)\n", gettimer(METISTmr));
printf(" Total: \t\t %7.3f\n", gettimer(TOTALTmr));
printf("**********************************************************************\n");
GKfree((void**)&graph.xadj, (void**)&graph.adjncy, (void**)&graph.vwgt,
(void**)&graph.adjwgt, (void**)&part, LTERM);
}
void MLKKMRefine(CtrlType *ctrl, GraphType *orggraph, GraphType *graph, int nparts, int chain_length, float *tpwgts, float ubfactor)
{
int i, nlevels, mustfree=0, temp_cl;
GraphType *ptr;
IFSET(ctrl->dbglvl, DBG_TIME, starttimer(ctrl->UncoarsenTmr));
/* Compute the parameters of the coarsest graph */
ComputeKWayPartitionParams(ctrl, graph, nparts);
temp_cl = chain_length;
/* Determine how many levels are there */
for (ptr=graph, nlevels=0; ptr!=orggraph; ptr=ptr->finer, nlevels++);
//printf("Number of levels is %d\n", nlevels);
for (i=0; ;i++) {
timer tmr;
float result;
cleartimer(tmr);
starttimer(tmr);
//pingpong(ctrl, graph, nparts, chain_length, tpwgts, ubfactor);
//chain_length /= 1.5;
//printf("Level: %d\n", i+1);
if (graph == orggraph){
//chain_length = chain_length>0 ? chain_length : 1;
pingpong(ctrl, graph, nparts, chain_length, tpwgts, ubfactor, 1);
break;
}
else{
//pingpong(ctrl, graph, nparts, 0, tpwgts, ubfactor, 0);
pingpong(ctrl, graph, nparts, chain_length, tpwgts, ubfactor, 0);
//chain_length /= 2;
}
//pingpong(ctrl, graph, nparts, chain_length, tpwgts, ubfactor);
// /* for time and quality each level
stoptimer(tmr);
//printf("Level %d: %7.3f", i+1, tmr);
if (cutType == NCUT){
result = ComputeNCut(graph, graph->where, nparts);
//printf(" %7f", result);
}
else{
result = ComputeRAsso(graph, graph->where, nparts);
//printf(" %7f", result);
}
//printf(" (%d)\n\n", graph->nvtxs);
//ends here*/
if (graph == orggraph)
break;
/*
if(i>1)
chain_length /= 10;
*/
GKfree((void **) &graph->gdata, LTERM); /* Deallocate the graph related arrays */
graph = graph->finer;
IFSET(ctrl->dbglvl, DBG_TIME, starttimer(ctrl->ProjectTmr));
if (graph->vwgt == NULL) {
graph->vwgt = idxsmalloc(graph->nvtxs, 1, "RefineKWay: graph->vwgt");
graph->adjwgt = idxsmalloc(graph->nedges, 1, "RefineKWay: graph->adjwgt");
mustfree = 1;
}
ProjectKWayPartition(ctrl, graph, nparts);
IFSET(ctrl->dbglvl, DBG_TIME, stoptimer(ctrl->ProjectTmr));
}
if (mustfree)
GKfree((void **) &graph->vwgt, (void **) &graph->adjwgt, LTERM);
IFSET(ctrl->dbglvl, DBG_TIME, stoptimer(ctrl->UncoarsenTmr));
}
/*************************************************************************
* Let the game begin
**************************************************************************/
main(int argc, char *argv[])
{
int i, options[10];
idxtype *perm, *iperm;
GraphType graph;
char filename[256];
int numflag = 0, wgtflag;
timer TOTALTmr, METISTmr, IOTmr, SMBTmr;
if (argc != 2) {
printf("Usage: %s <GraphFile>\n",argv[0]);
exit(0);
}
strcpy(filename, argv[1]);
cleartimer(TOTALTmr);
cleartimer(METISTmr);
cleartimer(IOTmr);
cleartimer(SMBTmr);
starttimer(TOTALTmr);
starttimer(IOTmr);
ReadGraph(&graph, filename, &wgtflag);
if (graph.nvtxs <= 0) {
printf("Empty graph. Nothing to do.\n");
exit(0);
}
if (graph.ncon != 1) {
printf("Ordering can only be applied to graphs with one constraint.\n");
exit(0);
}
stoptimer(IOTmr);
/* Ordering does not use weights! */
GKfree(&graph.vwgt, &graph.adjwgt, LTERM);
printf("**********************************************************************\n");
printf("%s", METISTITLE);
printf("Graph Information ---------------------------------------------------\n");
printf(" Name: %s, #Vertices: %d, #Edges: %d\n\n", filename, graph.nvtxs, graph.nedges/2);
printf("Node-Based Ordering... ----------------------------------------------\n");
perm = idxmalloc(graph.nvtxs, "main: perm");
iperm = idxmalloc(graph.nvtxs, "main: iperm");
options[0] = 0;
starttimer(METISTmr);
METIS_NodeND(&graph.nvtxs, graph.xadj, graph.adjncy, &numflag, options, perm, iperm);
stoptimer(METISTmr);
starttimer(IOTmr);
WritePermutation(filename, iperm, graph.nvtxs);
stoptimer(IOTmr);
starttimer(SMBTmr);
ComputeFillIn(&graph, iperm);
stoptimer(SMBTmr);
stoptimer(TOTALTmr);
printf("\nTiming Information --------------------------------------------------\n");
printf(" I/O: \t %7.3f\n", gettimer(IOTmr));
printf(" Ordering: \t %7.3f (ONMETIS time)\n", gettimer(METISTmr));
printf(" Symbolic Factorization: \t %7.3f\n", gettimer(SMBTmr));
printf(" Total: \t %7.3f\n", gettimer(TOTALTmr));
printf("**********************************************************************\n");
GKfree(&graph.xadj, &graph.adjncy, &perm, &iperm, LTERM);
}
/*************************************************************************
* Let the game begin
**************************************************************************/
main(int argc, char *argv[])
{
int i, j, ne, nn, etype, numflag=0, nparts, edgecut;
idxtype *elmnts, *epart, *npart;
timer IOTmr, DUALTmr;
char etypestr[4][5] = {"TRI", "TET", "HEX", "QUAD"};
GraphType graph;
if (argc != 3) {
printf("Usage: %s <meshfile> <nparts>\n",argv[0]);
exit(0);
}
nparts = atoi(argv[2]);
if (nparts < 2) {
printf("nparts must be greater than one.\n");
exit(0);
}
cleartimer(IOTmr);
cleartimer(DUALTmr);
starttimer(IOTmr);
elmnts = ReadMesh(argv[1], &ne, &nn, &etype);
stoptimer(IOTmr);
epart = idxmalloc(ne, "main: epart");
npart = idxmalloc(nn, "main: npart");
printf("**********************************************************************\n");
printf("%s", METISTITLE);
printf("Mesh Information ----------------------------------------------------\n");
printf(" Name: %s, #Elements: %d, #Nodes: %d, Etype: %s\n\n", argv[1], ne, nn, etypestr[etype-1]);
printf("Partitioning Nodal Graph... -----------------------------------------\n");
starttimer(DUALTmr);
METIS_PartMeshNodal(&ne, &nn, elmnts, &etype, &numflag, &nparts, &edgecut, epart, npart);
stoptimer(DUALTmr);
printf(" %d-way Edge-Cut: %7d, Balance: %5.2f\n", nparts, edgecut, ComputeElementBalance(ne, nparts, epart));
starttimer(IOTmr);
WriteMeshPartition(argv[1], nparts, ne, epart, nn, npart);
stoptimer(IOTmr);
printf("\nTiming Information --------------------------------------------------\n");
printf(" I/O: \t\t %7.3f\n", gettimer(IOTmr));
printf(" Partitioning: \t\t %7.3f\n", gettimer(DUALTmr));
printf("**********************************************************************\n");
/*
graph.nvtxs = ne;
graph.xadj = idxmalloc(ne+1, "xadj");
graph.vwgt = idxsmalloc(ne, 1, "vwgt");
graph.adjncy = idxmalloc(10*ne, "adjncy");
graph.adjwgt = idxsmalloc(10*ne, 1, "adjncy");
METIS_MeshToDual(&ne, &nn, elmnts, &etype, &numflag, graph.xadj, graph.adjncy);
ComputePartitionInfo(&graph, nparts, epart);
GKfree(&graph.xadj, &graph.adjncy, &graph.vwgt, &graph.adjwgt, LTERM);
*/
GKfree(&elmnts, &epart, &npart, LTERM);
}
/*************************************************************************
* Let the game begin
**************************************************************************/
main(int argc, char *argv[])
{
int i, nparts, options[10];
idxtype *part;
float rubvec[MAXNCON], lbvec[MAXNCON];
GraphType graph;
char filename[256];
int numflag = 0, wgtflag = 0, edgecut;
timer TOTALTmr, METISTmr, IOTmr;
if (argc != 3) {
printf("Usage: %s <GraphFile> <Nparts>\n",argv[0]);
exit(0);
}
strcpy(filename, argv[1]);
nparts = atoi(argv[2]);
if (nparts < 2) {
printf("The number of partitions should be greater than 1!\n");
exit(0);
}
cleartimer(TOTALTmr);
cleartimer(METISTmr);
cleartimer(IOTmr);
starttimer(TOTALTmr);
starttimer(IOTmr);
ReadGraph(&graph, filename, &wgtflag);
if (graph.nvtxs <= 0) {
printf("Empty graph. Nothing to do.\n");
exit(0);
}
stoptimer(IOTmr);
printf("**********************************************************************\n");
printf("%s", METISTITLE);
printf("Graph Information ---------------------------------------------------\n");
printf(" Name: %s, #Vertices: %d, #Edges: %d, #Parts: %d\n", filename, graph.nvtxs, graph.nedges/2, nparts);
if (graph.ncon > 1)
printf(" Balancing Constraints: %d\n", graph.ncon);
printf("\nK-way Partitioning... -----------------------------------------------\n");
part = idxmalloc(graph.nvtxs, "main: part");
options[0] = 0;
starttimer(METISTmr);
if (graph.ncon == 1) {
METIS_PartGraphKway(&graph.nvtxs, graph.xadj, graph.adjncy, graph.vwgt, graph.adjwgt,
&wgtflag, &numflag, &nparts, options, &edgecut, part);
}
else {
for (i=0; i<graph.ncon; i++)
rubvec[i] = HORIZONTAL_IMBALANCE;
METIS_mCPartGraphKway(&graph.nvtxs, &graph.ncon, graph.xadj, graph.adjncy, graph.vwgt,
graph.adjwgt, &wgtflag, &numflag, &nparts, rubvec, options, &edgecut, part);
}
stoptimer(METISTmr);
ComputePartitionBalance(&graph, nparts, part, lbvec);
printf(" %d-way Edge-Cut: %7d, Balance: ", nparts, edgecut);
for (i=0; i<graph.ncon; i++)
printf("%5.2f ", lbvec[i]);
printf("\n");
starttimer(IOTmr);
WritePartition(filename, part, graph.nvtxs, nparts);
stoptimer(IOTmr);
stoptimer(TOTALTmr);
printf("\nTiming Information --------------------------------------------------\n");
printf(" I/O: \t\t %7.3f\n", gettimer(IOTmr));
printf(" Partitioning: \t\t %7.3f (KMETIS time)\n", gettimer(METISTmr));
printf(" Total: \t\t %7.3f\n", gettimer(TOTALTmr));
printf("**********************************************************************\n");
GKfree(&graph.xadj, &graph.adjncy, &graph.vwgt, &graph.adjwgt, &part, LTERM);
}
/*************************************************************************
* This function clears the timers
**************************************************************************/
void InitTimers(CtrlType *ctrl)
{
cleartimer(ctrl->TotalTmr);
cleartimer(ctrl->InitPartTmr);
cleartimer(ctrl->MatchTmr);
cleartimer(ctrl->ContractTmr);
cleartimer(ctrl->CoarsenTmr);
cleartimer(ctrl->UncoarsenTmr);
cleartimer(ctrl->RefTmr);
cleartimer(ctrl->ProjectTmr);
cleartimer(ctrl->SplitTmr);
cleartimer(ctrl->SepTmr);
cleartimer(ctrl->AuxTmr1);
cleartimer(ctrl->AuxTmr2);
cleartimer(ctrl->AuxTmr3);
cleartimer(ctrl->AuxTmr4);
cleartimer(ctrl->AuxTmr5);
cleartimer(ctrl->AuxTmr6);
}
/*************************************************************************
* This function initializes the various timers
**************************************************************************/
void InitTimers(CtrlType *ctrl)
{
cleartimer(ctrl->TotalTmr);
cleartimer(ctrl->InitPartTmr);
cleartimer(ctrl->MatchTmr);
cleartimer(ctrl->ContractTmr);
cleartimer(ctrl->CoarsenTmr);
cleartimer(ctrl->RefTmr);
cleartimer(ctrl->SetupTmr);
cleartimer(ctrl->ProjectTmr);
cleartimer(ctrl->KWayInitTmr);
cleartimer(ctrl->KWayTmr);
cleartimer(ctrl->MoveTmr);
cleartimer(ctrl->RemapTmr);
cleartimer(ctrl->AuxTmr1);
cleartimer(ctrl->AuxTmr2);
cleartimer(ctrl->AuxTmr3);
cleartimer(ctrl->AuxTmr4);
cleartimer(ctrl->AuxTmr5);
cleartimer(ctrl->AuxTmr6);
}