void Compute(graph<vertex>& GA, commandLine P) {
t10.start();
char* oFile = P.getOptionValue("-out"); //file to write eccentricites
srand (time(NULL));
uintT seed = rand();
cout << "seed = " << seed << endl;
t0.start();
long n = GA.n;
uintE* ecc = newA(uintE,n);
{parallel_for(long i=0;i<n;i++) ecc[i] = UINT_E_MAX;}
t0.stop();
//BEGIN COMPUTE CONNECTED COMPONENTS
t1.start();
intE* Labels = newA(intE,n);
{parallel_for(long i=0;i<n;i++) {
if(GA.V[i].getOutDegree() == 0) Labels[i] = -i-1; //singletons
else Labels[i] = INT_E_MAX;
}}
//get max degree vertex
uintE maxV = sequence::reduce<uintE>((intE)0,(intE)n,maxF<intE>(),getDegree<vertex>(GA.V));
//visit large component with BFS
CCBFS(maxV,GA,Labels);
//visit small components with label propagation
Components(GA, Labels);
//sort by component ID
intPair* CCpairs = newA(intPair,n);
{parallel_for(long i=0;i<n;i++)
if(Labels[i] < 0)
CCpairs[i] = make_pair(-Labels[i]-1,i);
else CCpairs[i] = make_pair(Labels[i],i);
}
free(Labels);
intSort::iSort(CCpairs, n, n+1, firstF<uintE,uintE>());
uintE* changes = newA(uintE,n);
changes[0] = 0;
{parallel_for(long i=1;i<n;i++)
changes[i] = (CCpairs[i].first != CCpairs[i-1].first) ? i : UINT_E_MAX;}
uintE* CCoffsets = newA(uintE,n);
uintE numCC = sequence::filter(changes, CCoffsets, n, nonMaxF());
CCoffsets[numCC] = n;
free(changes);
t1.stop();
//END COMPUTE CONNECTED COMPONENTS
uintE maxS = min((uintE)n,(uintE)sqrt(n*log2(n)));
uintE maxSampleSize = max((uintE)10,max((uintE)((n/maxS)*log2(n)),maxS));
//data structures to be shared by all components
uintE** Dists = newA(uintE*,maxSampleSize);
uintE* Dist = newA(uintE,maxSampleSize*n);
{parallel_for(long i=0;i<maxSampleSize;i++) Dists[i] = Dist+i*n;}
{parallel_for(long i=0;i<n*maxSampleSize;i++) Dist[i] = UINT_E_MAX;}
intPair* wDist = newA(intPair,n);
{parallel_for(long i=0;i<n;i++)
wDist[i] = make_pair(UINT_E_MAX,UINT_E_MAX);}
intPair* minDists = newA(intPair,n);
uintE* starts = newA(uintE,n);
uintE* starts2 = newA(uintE,n);
uintE* maxDists = newA(uintE,n);
//BEGIN COMPUTE ECCENTRICITES PER COMPONENT
t4.start();
for(long k = 0; k < numCC; k++) {
uintE o = CCoffsets[k];
uintE CCsize = CCoffsets[k+1] - o;
if(CCsize == 1) ecc[CCpairs[o].second] = 0; //singletons have ecc of 0
if(CCsize == 2) { //size 2 CC's have ecc of 1
ecc[CCpairs[o].second] = ecc[CCpairs[o+1].second] = 1;
} else if(CCsize > 1) {
//do main computation
t2.start();
uintE s = min(CCsize,(uintE)sqrt(CCsize*log2(CCsize)));
//pick sample of about \sqrt{n\log n} vertices
long sampleSize = min(CCsize,max((uintE)10,(uintE)((CCsize/s)*log2(CCsize))));
//pick random vertices
{parallel_for(ulong i=0;i<CCsize;i++) {
//pick with probability sampleSize/CCsize
uintT index = hash(i+seed) % CCsize;
if(index < sampleSize) starts[i] = CCpairs[o+i].second;
else starts[i] = UINT_E_MAX;
}}
//pack down
uintE numUnique = sequence::filter(starts,starts2,CCsize,nonMaxF());
//sample cannot be empty!
if(numUnique == 0) { starts2[0] = CCpairs[o+(hash(seed)%CCsize)].second; numUnique++; }
if(numUnique > maxSampleSize) numUnique = maxSampleSize; //cap at maxSampleSize
t2.stop();
t3.start();
//execute BFS per sample
{for(long i=0;i<numUnique;i++) {
uintE v = starts2[i];
Dists[i][v] = 0; //set source dist to 0
vertexSubset Frontier(n,v);
uintE round = 0;
while(!Frontier.isEmpty()){
round++;
vertexSubset output =
edgeMap(GA, Frontier, BFS_F(Dists[i],round),GA.m/20);
Frontier.del();
Frontier = output;
}
Frontier.del();
ecc[v] = round-1; //set radius for sample vertex
}}
t3.stop();
t4.start();
//store max distance from sample for each vertex so that we can
//reuse Distance arrays
{parallel_for(long i=0;i<CCsize;i++) {
uintE v = CCpairs[o+i].second;
//if not one of the vertices we did BFS on
if(ecc[v] == UINT_E_MAX) {
uintE max_from_sample = 0;
//compute max distance from sampled vertex
for(long j=0;j<numUnique;j++) {
uintE d = Dists[j][v];
if(d > max_from_sample) max_from_sample = d;
}
maxDists[i] = max_from_sample;
}}}
t4.stop();
t5.start();
//find furthest vertex from sample set S
{parallel_for(long j=0;j<CCsize;j++) {
uintE v = CCpairs[o+j].second;
uintE m = UINT_E_MAX;
for(long i=0;i<numUnique;i++) {
uintE d = Dists[i][v];
if(d < m) m = d;
if(d == 0) break;
}
minDists[j] = make_pair(m,v);
}}
intPair furthest =
sequence::reduce<intPair>(minDists,(intE)CCsize,maxFirstF());
uintE w = furthest.second;
t5.stop();
t3.start();
//reset Dist array entries
{parallel_for(long i=0;i<numUnique;i++) {
parallel_for(long j=0;j<CCsize;j++) {
uintE v = CCpairs[o+j].second;
Dists[i][v] = UINT_E_MAX;
}
}}
t3.stop();
t6.start();
//execute BFS from w and find \sqrt{n log n} neighborhood of w
uintE nghSize = min(CCsize,max((uintE)10,s));
uintE* Ngh_s = starts; //reuse starts array
bool filled_Ngh = 0;
//stores distance from w and index of closest vertex in Ngh_s on
//path from w to v
wDist[w] = make_pair(0,0); //set source dist to 0
vertexSubset Frontier(n,w);
uintE round = 0;
uintE numVisited = 0;
while(!Frontier.isEmpty()){
round++;
if(!filled_Ngh) {
Frontier.toSparse();
//Note: if frontier size < nghSize - visited, there is non-determinism in which vertices
//get added to Ngh_s as the ordering of vertices on the frontier is non-deterministic
{parallel_for(long i=0;i<min(nghSize-numVisited,(uintE)Frontier.numNonzeros());i++) {
Ngh_s[numVisited+i] = Frontier.s[i];
wDist[Frontier.s[i]].second = numVisited+i;
}
numVisited += Frontier.numNonzeros();
if(numVisited >= nghSize) filled_Ngh = 1;
}}
vertexSubset output =
edgeMap(GA, Frontier, BFS_Pair_F(wDist,round),GA.m/20);
Frontier.del();
Frontier = output;
}
Frontier.del();
ecc[w] = round-1; //set radius for w
t6.stop();
t7.start();
//execute BFS from each vertex in neighborhood of w
uintE** Dists2 = Dists; //reuse distance array
uintE* Dist2 = Dist;
{for(long i=0;i<nghSize;i++) {
uintE v = Ngh_s[i];
Dists2[i][v] = 0; //set source dist to 0
vertexSubset Frontier(n,v);
uintE round = 0;
while(!Frontier.isEmpty()){
round++;
vertexSubset output =
edgeMap(GA, Frontier, BFS_F(Dists2[i],round),GA.m/20);
Frontier.del();
Frontier = output;
}
Frontier.del();
ecc[v] = round-1; //set radius of vertex in Ngh_s
}}
t7.stop();
t8.start();
//min radius of sample
parallel_for(long i=0;i<numUnique;i++) starts2[i] = ecc[starts2[i]];
uintE min_r_sample =
sequence::reduce<uintE>(starts2,numUnique,minF<uintE>());
//compute ecc values
{parallel_for(long i=0;i<CCsize;i++) {
uintE v = CCpairs[o+i].second;
//if not one of the vertices we did BFS on
if(ecc[v] == UINT_E_MAX) {
uintE d_vw = wDist[v].first;
uintE rv = max(maxDists[i],d_vw);
//index in Ngh_s of closest vertex in Ngh_s on path from w to v
uintE index_vt = wDist[v].second;
uintE vt = Ngh_s[index_vt];
uintE d_vt_v = Dists2[index_vt][v];
uintE d_vt_w = Dists2[index_vt][w];
if(d_vt_v <= d_vt_w) ecc[v] = max(rv,ecc[vt]);
else ecc[v] = max(rv,min_r_sample);
}
}}
t8.stop();
t7.start();
//reset Dist array entries
{parallel_for(long i=0;i<nghSize;i++) {
parallel_for(long j=0;j<CCsize;j++) {
uintE v = CCpairs[o+j].second;
Dists2[i][v] = UINT_E_MAX;
}
}}
t7.stop();
t6.start();
//reset wDist array entries
{parallel_for(long i=0;i<CCsize;i++) {
uintE v = CCpairs[o+i].second;
wDist[v] = make_pair(UINT_E_MAX,UINT_E_MAX);
}}
t6.stop();
}
void Compute(graph<vertex>& GA, commandLine P) {
t5.start();
long length = P.getOptionLongValue("-r",0); //number of words per vertex
char* oFile = P.getOptionValue("-out"); //file to write eccentricites
srand (time(NULL));
uintT seed = rand();
cout << "seed = " << seed << endl;
t0.start();
long n = GA.n;
uintE* ecc = newA(uintE,n);
uintE* ecc2 = newA(uintE,n);
{parallel_for(long i=0;i<n;i++) {
ecc[i] = ecc2[i] = 0;
}}
t0.stop();
//BEGIN COMPUTE CONNECTED COMPONENTS
t1.start();
intE* Labels = newA(intE,n);
{parallel_for(long i=0;i<n;i++) {
if(GA.V[i].getOutDegree() == 0) Labels[i] = -i-1; //singletons
else Labels[i] = INT_E_MAX;
}}
//get max degree vertex
uintE maxV = sequence::reduce<uintE>((intE)0,(intE)n,maxF<intE>(),getDegree<vertex>(GA.V));
//visit large component with BFS
CCBFS(maxV,GA,Labels);
//visit small components with label propagation
Components(GA, Labels);
//sort by component ID
intPair* CCpairs = newA(intPair,n);
{parallel_for(long i=0;i<n;i++)
if(Labels[i] < 0)
CCpairs[i] = make_pair(-Labels[i]-1,i);
else CCpairs[i] = make_pair(Labels[i],i);
}
free(Labels);
intSort::iSort(CCpairs, n, n+1,firstF<uintE,uintE>());
uintE* changes = newA(uintE,n);
changes[0] = 0;
{parallel_for(long i=1;i<n;i++)
changes[i] = (CCpairs[i].first != CCpairs[i-1].first) ? i : UINT_E_MAX;}
uintE* CCoffsets = newA(uintE,n);
uintE numCC = sequence::filter(changes, CCoffsets, n, nonMaxF());
CCoffsets[numCC] = n;
free(changes);
t1.stop();
//END COMPUTE CONNECTED COMPONENTS
//init data structures
t0.start();
length = max((long)1,min((n+63)/64,(long)length));
long* VisitedArray = newA(long,n*length);
long* NextVisitedArray = newA(long,n*length);
int* flags = newA(int,n);
{parallel_for(long i=0;i<n;i++) flags[i] = -1;}
uintE* starts = newA(uintE,n);
intPair* pairs = newA(intPair,n);
t0.stop();
//BEGIN COMPUTE ECCENTRICITES PER COMPONENT
for(long k = 0; k < numCC; k++) {
t2.start();
uintE o = CCoffsets[k];
uintE CCsize = CCoffsets[k+1] - o;
if(CCsize == 2) { //size 2 CC's have ecc of 1
ecc[CCpairs[o].second] = ecc[CCpairs[o+1].second] = 1;
t2.stop();
} else if(CCsize > 1) { //size 1 CC's already have ecc of 0
//do main computation
long myLength = min((long)length,((long)CCsize+63)/64);
//initialize bit vectors for component vertices
{parallel_for(long i=0;i<CCsize;i++) {
uintT v = CCpairs[o+i].second;
parallel_for(long j=0;j<myLength;j++)
VisitedArray[v*myLength+j] = NextVisitedArray[v*myLength+j] = 0;
}}
long sampleSize = min((long)CCsize,(long)64*myLength);
uintE* starts2 = newA(uintE,sampleSize);
//pick random vertices (could have duplicates)
{parallel_for(ulong i=0;i<sampleSize;i++) {
uintT index = hashInt(i+seed) % CCsize;
if(flags[index] == -1 && CAS(&flags[index],-1,(int)i)) {
starts[i] = CCpairs[o+index].second;
NextVisitedArray[CCpairs[o+index].second*myLength + i/64] = (long) 1<<(i%64);
} else starts[i] = UINT_E_MAX;
}}
//remove duplicates
uintE numUnique = sequence::filter(starts,starts2,sampleSize,nonMaxF());
//reset flags
parallel_for(ulong i=0;i<sampleSize;i++) {
uintT index = hashInt(i+seed) % CCsize;
if(flags[index] == i) flags[index] = -1;
}
//first phase
vertexSubset Frontier(n,numUnique,starts2); //initial frontier
//note: starts2 will be freed inside the following loop
uintE round = 0;
while(!Frontier.isEmpty()){
round++;
vertexMap(Frontier, Ecc_Vertex_F(myLength,VisitedArray,NextVisitedArray));
vertexSubset output =
edgeMap(GA, Frontier,
Ecc_F(myLength,VisitedArray,NextVisitedArray,ecc,round),
GA.m/20);
Frontier.del();
Frontier = output;
}
Frontier.del();
t2.stop();
//second phase if size of CC > 64
if(CCsize > 1024) {
//sort by ecc
t3.start();
{parallel_for(long i=0;i<CCsize;i++) {
pairs[i] = make_pair(ecc[CCpairs[o+i].second],CCpairs[o+i].second);
}}
intPair maxR = sequence::reduce(pairs,CCsize,maxFirstF());
intSort::iSort(pairs, CCsize, 1+maxR.first, firstF<uintE,uintE>());
t3.stop();
t4.start();
//reset bit vectors for component vertices
{parallel_for(long i=0;i<CCsize;i++) {
uintT v = CCpairs[o+i].second;
parallel_for(long j=0;j<myLength;j++)
VisitedArray[v*myLength+j] = NextVisitedArray[v*myLength+j] = 0;
}}
starts2 = newA(uintE,sampleSize);
//pick starting points with highest ecc ("fringe" vertices)
{parallel_for(long i=0;i<sampleSize;i++) {
intE v = pairs[CCsize-i-1].second;
starts2[i] = v;
NextVisitedArray[v*myLength + i/64] = (long) 1<<(i%64);
}}
vertexSubset Frontier2(n,sampleSize,starts2); //initial frontier
//note: starts2 will be freed inside the following loop
round = 0;
while(!Frontier2.isEmpty()){
round++;
vertexMap(Frontier2, Ecc_Vertex_F(myLength,VisitedArray,NextVisitedArray));
vertexSubset output =
edgeMap(GA, Frontier2,Ecc_F(myLength,VisitedArray,NextVisitedArray,ecc2,round), GA.m/20);
Frontier2.del();
Frontier2 = output;
}
Frontier2.del();
{parallel_for(long i=0;i<n;i++) ecc[i] = max(ecc[i],ecc2[i]);}
t4.stop();
}
}