// closes the read archive
void CReadWriter::Close(void) {
// prevent the archive from being updated elsewhere
mIsOpen = false;
// flush the buffer
if(mPartitionMembers > 0) WritePartition();
// =================
// update the header
// =================
// update the number of reads in the archive
fseek64(mOutStream, UPDATE_HEADER_OFFSET, SEEK_SET);
fwrite((char*)&mNumReads, SIZEOF_UINT64, 1, mOutStream);
// update the number of bases in the archive
fwrite((char*)&mNumBases, SIZEOF_UINT64, 1, mOutStream);
// close the file stream
fclose(mOutStream);
}
/*************************************************************************
* 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);
}
sparse_matrix* graph_partition(LIST *list , partition_t* partition_info)
{
graph_t* graph;
params_t *params;
idx_t options[METIS_NOPTIONS], status;
idx_t objval;
sparse_matrix* matrix = (sparse_matrix*)malloc(sizeof(sparse_matrix));
graph = ReadGraph(list);
params = bmalloc(sizeof(*params), "Allocating memory for params");
METIS_SetDefaultOptions(options);
METIS_init_params(params, graph->ncon);
options[METIS_OPTION_OBJTYPE] = params->objtype;
options[METIS_OPTION_CTYPE] = params->ctype;
options[METIS_OPTION_IPTYPE] = params->iptype;
options[METIS_OPTION_RTYPE] = params->rtype;
options[METIS_OPTION_NO2HOP] = params->no2hop;
options[METIS_OPTION_MINCONN] = params->minconn;
options[METIS_OPTION_CONTIG] = params->contig;
options[METIS_OPTION_SEED] = params->seed;
options[METIS_OPTION_NITER] = params->niter;
options[METIS_OPTION_NCUTS] = params->ncuts;
options[METIS_OPTION_UFACTOR] = params->ufactor;
options[METIS_OPTION_DBGLVL] = params->dbglvl;
//print_input_data(graph,params);
params->tpwgts = NULL;
params->ubvec = NULL;
partition_info->partion_table = imalloc(graph->nvtxs, "Allocate memory for part");
switch (params->ptype) {
case METIS_PTYPE_RB:
status = METIS_PartGraphRecursive(&graph->nvtxs, &graph->ncon, graph->xadj,
graph->adjncy, graph->vwgt, graph->vsize, graph->adjwgt,
¶ms->nparts, params->tpwgts, params->ubvec, options,
&objval, partition_info->partion_table);
break;
case METIS_PTYPE_KWAY:
status = METIS_PartGraphKway(&graph->nvtxs, &graph->ncon, graph->xadj,
graph->adjncy, graph->vwgt, graph->vsize, graph->adjwgt,
¶ms->nparts, params->tpwgts, params->ubvec, options,
&objval, partition_info->partion_table);
break;
}
if (status != METIS_OK) {
fprintf(stderr,"\n***Metis returned with an error.***\n");
return NULL;
}
partition_info->size = graph->nvtxs;
partition_info->noOfParts = params->nparts;
WritePartition(params->filename, partition_info->partion_table, graph->nvtxs, params->nparts);
printf("Objval: %d\n",objval);
matrix->nz = -1;
matrix->n = graph->nvtxs;
matrix->p = graph->xadj;
matrix->i = graph->adjncy;
matrix->x = NULL;
return matrix;
}
// saves the read to the read archive
void CReadWriter::SaveRead(const Mosaik::Read& mr) {
// initialize
unsigned char readNameLen = (unsigned char)mr.Name.Length();
unsigned short numMate1Bases = (unsigned short)mr.Mate1.Bases.Length();
unsigned short numMate2Bases = (unsigned short)mr.Mate2.Bases.Length();
// return if both mates are empty
if((numMate1Bases == 0) && (numMate2Bases == 0)) return;
mNumBases += numMate1Bases + numMate2Bases;
bool isPairedEnd = false;
if(numMate2Bases > 0) isPairedEnd = true;
// calculate the entry size
unsigned short entrySize = 2 * numMate1Bases + readNameLen + SIZEOF_SHORT + 2;
if(isPairedEnd) entrySize += 2 * numMate2Bases + SIZEOF_SHORT;
if(mIsSOLiD) {
entrySize += SOLID_PREFIX_LENGTH;
if(isPairedEnd) entrySize += SOLID_PREFIX_LENGTH;
}
// check the memory buffer
if(mBufferPosition >= (mBufferLen - entrySize)) AdjustBuffer();
// ============================
// serialize data to our buffer
// ============================
// no need to leave space for entry size
unsigned int bufferOffset = mBufferPosition;
// store the read type
mBuffer[bufferOffset++] = (isPairedEnd ? 1 : 0);
// store the read name
mBuffer[bufferOffset++] = readNameLen;
memcpy(mBuffer + bufferOffset, mr.Name.CData(), readNameLen);
bufferOffset += readNameLen;
// ============
// store mate 1
// ============
// sanity check
if ( mr.Mate1.Bases.Length() != mr.Mate1.Qualities.Length() ) {
printf("ERROR: The lengths of bases(%u) and qualities(%u) of Read (%s) didn't match.\n", mr.Mate1.Bases.Length(), mr.Mate1.Qualities.Length(), mr.Name.CData());
exit(1);
}
// store the read length
memcpy(mBuffer + bufferOffset, (char*)&numMate1Bases, SIZEOF_SHORT);
bufferOffset += SIZEOF_SHORT;
// store the bases
memcpy(mBuffer + bufferOffset, mr.Mate1.Bases.CData(), numMate1Bases);
bufferOffset += numMate1Bases;
if(mIsSOLiD) {
memcpy(mBuffer + bufferOffset, mr.Mate1.SolidPrefixTransition, SOLID_PREFIX_LENGTH);
bufferOffset += SOLID_PREFIX_LENGTH;
}
// store the qualities
memcpy(mBuffer + bufferOffset, mr.Mate1.Qualities.CData(), numMate1Bases);
bufferOffset += numMate1Bases;
// ============
// store mate 2
// ============
if(isPairedEnd) {
// sanity check
if ( mr.Mate2.Bases.Length() != mr.Mate2.Qualities.Length() ) {
printf("ERROR: The lengths of bases(%u) and qualities(%u) of Read (%s) didn't match.\n", mr.Mate2.Bases.Length(), mr.Mate2.Qualities.Length(), mr.Name.CData());
exit(1);
}
// store the read length
memcpy(mBuffer + bufferOffset, (char*)&numMate2Bases, SIZEOF_SHORT);
bufferOffset += SIZEOF_SHORT;
// store the bases
memcpy(mBuffer + bufferOffset, mr.Mate2.Bases.CData(), numMate2Bases);
bufferOffset += numMate2Bases;
if(mIsSOLiD) {
memcpy(mBuffer + bufferOffset, mr.Mate2.SolidPrefixTransition, SOLID_PREFIX_LENGTH);
bufferOffset += SOLID_PREFIX_LENGTH;
}
// store the qualities
memcpy(mBuffer + bufferOffset, mr.Mate2.Qualities.CData(), numMate2Bases);
bufferOffset += numMate2Bases;
}
// check the buffer
if(bufferOffset >= mBufferLen) {
cout << endl << "ERROR: Buffer overrun detected when saving read. Used " << bufferOffset << " bytes, but allocated " << mBufferLen << " bytes." << endl;
exit(1);
}
// update the partition variables and buffer position
mPartitionMembers++;
mBufferPosition = bufferOffset;
// flush the buffer
if(mPartitionMembers >= mPartitionSize) WritePartition();
// increment the read counter
mNumReads++;
}
idx_t* gpmetis( int argc, char **argv )
/*************************************************************************/
/*! Let the game begin! */
/*************************************************************************/
//int main(int argc, char *argv[])
{
idx_t i;
char *curptr, *newptr;
idx_t options[METIS_NOPTIONS];
graph_t *graph;
idx_t *part;
idx_t objval;
params_t *params;
int status=0;
gk_optind = 0;
//printf( "argc: %d\n", argc );
//printf( "gk_optind %d\n", gk_optind );
fflush( stdout );
for( i = 0; i < argc; i++ )
{
//printf( "%s*\n", argv[ i ] );
}
params = parse_cmdline(argc, argv);
//printf( "gk_optind %d\n", gk_optind );
//fflush( stdout );
//return NULL;
gk_startcputimer(params->iotimer);
graph = ReadGraph(params);
ReadTPwgts(params, graph->ncon);
gk_stopcputimer(params->iotimer);
/* Check if the graph is contiguous */
if (params->contig && !IsConnected(graph, 0)) {
printf("***The input graph is not contiguous.\n"
"***The specified -contig option will be ignored.\n");
params->contig = 0;
}
/* Get ubvec if supplied */
if (params->ubvecstr) {
params->ubvec = rmalloc(graph->ncon, "main");
curptr = params->ubvecstr;
for (i=0; i<graph->ncon; i++) {
params->ubvec[i] = strtoreal(curptr, &newptr);
if (curptr == newptr)
errexit("Error parsing entry #%"PRIDX" of ubvec [%s] (possibly missing).\n",
i, params->ubvecstr);
curptr = newptr;
}
}
/* Setup iptype */
if (params->iptype == -1) {
if (params->ptype == METIS_PTYPE_RB) {
if (graph->ncon == 1)
params->iptype = METIS_IPTYPE_GROW;
else
params->iptype = METIS_IPTYPE_RANDOM;
}
}
GPPrintInfo(params, graph);
part = imalloc(graph->nvtxs, "main: part");
METIS_SetDefaultOptions(options);
options[METIS_OPTION_OBJTYPE] = params->objtype;
options[METIS_OPTION_CTYPE] = params->ctype;
options[METIS_OPTION_IPTYPE] = params->iptype;
options[METIS_OPTION_RTYPE] = params->rtype;
options[METIS_OPTION_MINCONN] = params->minconn;
options[METIS_OPTION_CONTIG] = params->contig;
options[METIS_OPTION_SEED] = params->seed;
options[METIS_OPTION_NITER] = params->niter;
options[METIS_OPTION_NCUTS] = params->ncuts;
options[METIS_OPTION_UFACTOR] = params->ufactor;
options[METIS_OPTION_DBGLVL] = params->dbglvl;
gk_malloc_init();
gk_startcputimer(params->parttimer);
switch (params->ptype) {
case METIS_PTYPE_RB:
status = METIS_PartGraphRecursive(&graph->nvtxs, &graph->ncon, graph->xadj,
graph->adjncy, graph->vwgt, graph->vsize, graph->adjwgt,
¶ms->nparts, params->tpwgts, params->ubvec, options,
&objval, part);
break;
case METIS_PTYPE_KWAY:
status = METIS_PartGraphKway(&graph->nvtxs, &graph->ncon, graph->xadj,
graph->adjncy, graph->vwgt, graph->vsize, graph->adjwgt,
¶ms->nparts, params->tpwgts, params->ubvec, options,
&objval, part);
break;
}
gk_stopcputimer(params->parttimer);
if (gk_GetCurMemoryUsed() != 0)
printf("***It seems that Metis did not free all of its memory! Report this.\n");
params->maxmemory = gk_GetMaxMemoryUsed();
gk_malloc_cleanup(0);
if (status != METIS_OK) {
printf("\n***Metis returned with an error.\n");
}
else {
if (!params->nooutput) {
/* Write the solution */
gk_startcputimer(params->iotimer);
WritePartition(params->filename, part, graph->nvtxs, params->nparts);
gk_stopcputimer(params->iotimer);
}
GPReportResults(params, graph, part, objval);
}
idx_t *r_part = ( idx_t* ) calloc( graph->nvtxs, sizeof( idx_t ) );
for( i = 0; i < graph->nvtxs; i++ )
{
r_part[ i ] = part[ i ];
}
FreeGraph(&graph);
gk_free((void **)&part, LTERM);
gk_free((void **)¶ms->filename, ¶ms->tpwgtsfile, ¶ms->tpwgts,
¶ms->ubvecstr, ¶ms->ubvec, ¶ms, LTERM);
return r_part;
}