/usr/include/trilinos/Zoltan2_MatcherHelper.hpp is in libtrilinos-zoltan2-dev 12.10.1-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#define _ZOLTAN2_MatcherHelper_hpp_
#ifdef ZOLTAN2ND_HAVE_OMP
#include <omp.h>
#endif
#include <iostream>
#include <fstream>
#include <string>
#include <vector>
#include <algorithm>
#include <cstdlib>
#include <set>
#include <queue>
#include <cassert>
// PPF Matching code copied from Isorropia. Siva has reservations about algorithm
// robustness. It uses recursion, which can cause problems on the stack.
// Probably should rewrite at least some of these algorithms, eventually.
namespace Zoltan2 {
/** @ingroup matching_grp
An implementation of the Matcher interface that operates on Epetra matrices
and Graphs.
matching algorithms provides an interface to solve the Bipartite Matching
problem.
*/
////////////////////////////////////////////////////////////////////////////////
class Matcher
{
private:
int *mCRS_rowPtrs;
int *mCRS_cols;
// Number of vertices in u set (num row vertices)
int numU;
// Number of vertices in v set (num col vertices)
int numV;
// For each u vertex, the matching v vertex
std::vector<int> matchedVertexForU;
// For each v vertex, the matching u vertex
std::vector<int> matchedVertexForV;
std::vector<int> queue;
int* LV_;
int* LU_;
int* unmatchedU_;
int *parent_;
int *lookahead_;
bool finish_;
int numE,avgDegU_,k_star_,icm_,BFSInd_,numThread_,Qst_,Qend_,numMatched;
int *visitedV_;
void delete_matched_v();
int SGM();
int match_dfs();
int match_hk();
int construct_layered_graph();
int find_set_del_M();
int recursive_path_finder(int, int);
int dfs_path_finder(int);
int dfs_augment();
int augment_matching(int);
int DW_phase();
public:
/** @ingroup matching_grp
Constructor
\param[in] row pointer for CRS matrix for of bipartite graph
\param[in] cols for CRS matrix for of bipartite graph
\param[in] Number of vertices in u set (num row vertices)
\param[in] Number of vertices in v set (num col vertices)
*/
Matcher(int *_rowPtr, int *_cols, int _numU, int _numV, int _numE);
/** @ingroup matching_grp
Destructor
*/
virtual ~Matcher();
/* @ingroup matching_grp
Returns the number of matched vertices from Maximum Cardinality
Matching set
*/
int getNumberOfMatchedVertices()
{
int count=0;
for(unsigned int i=0;i<matchedVertexForU.size(); i++)
{
if(matchedVertexForU[i]!=-1)
{
count++;
}
}
return count;
}
const std::vector<int> &getVertexUMatches() {return matchedVertexForU;};
const std::vector<int> &getVertexVMatches() {return matchedVertexForV;};
/** @ingroup matching_grp
Computes the maximum cardinality matching.
*/
int match();
};
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
Matcher::Matcher(int *_rowPtr, int *_cols, int _numU, int _numV, int _numE)
:mCRS_rowPtrs(_rowPtr),mCRS_cols(_cols),numU(_numU),numV(_numV),numE(_numE)
{
finish_=false;
avgDegU_=numE/numU+1;
matchedVertexForU.resize(numU);
matchedVertexForV.resize(numV);
lookahead_=new int[numU];
unmatchedU_=new int[numU];
for(int i=0;i<numU;i++)
{
matchedVertexForU[i]=-1;
lookahead_[i]=mCRS_rowPtrs[i];
unmatchedU_[i]=i;
}
visitedV_=new int[numV];
parent_=new int[numV];
for(int i=0;i<numV;i++)
{
visitedV_[i]=0;
matchedVertexForV[i]=-1;
parent_[i]=-1;
}
numThread_=1;
}
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
Matcher::~Matcher()
{
delete [] lookahead_;
delete [] unmatchedU_;
if (parent_) delete [] parent_; parent_ = NULL;
if(visitedV_)
{
delete [] visitedV_;
}
}
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
// This function increases the matching size by one with the help of a
// augmenting path. The input is an integer which is the id of the last
// columns vertex of the augmenting path. We trace the whole path by
// backtraking using parent array. while tracing back we flip the unmatched
// edges to matched edges.
////////////////////////////////////////////////////////////////////////////////
int Matcher::augment_matching(int tv)
{
int u,v,t,lnt=1;
v=tv;
while(true)
{
u=parent_[v];
t=matchedVertexForU[u];
matchedVertexForV[v]=u;
matchedVertexForU[u]=v;
if(t==-1)
break;
lnt+=2;
v=t;
}
return lnt;
}
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
// This function is almost similar to the previous function which is to find
// a vertex disjoint path. It is used for the algorithm DFS, PPF and in HKDW. The
// difference is that this function operates on the original graph not on the
// layerd subgraph. It also does the incorporates the lookahead mechanism and
// scanning adjacency list alternately from backward and from forward in
// alternate iterations for PPF and HKDW.
////////////////////////////////////////////////////////////////////////////////
int Matcher::dfs_path_finder(int u)
{
int i,ind=-1,res=0;
for(i=lookahead_[u];i<mCRS_rowPtrs[u+1];i++) // the lookahead scheme
{
ind=mCRS_cols[i];
assert(ind>=0 && ind<numV);
if(matchedVertexForV[ind]==-1)
{
int lock2=0;
if (visitedV_[ind]==0)
{
visitedV_[ind]=1;
lock2=1;
}
if(lock2>0)
{
parent_[ind]=u;
lookahead_[u]=i+1;
return ind;
}
}
}
if(icm_%2==1) // odd number iteration so scan the adj list forward dir
{
for(i=mCRS_rowPtrs[u];i<mCRS_rowPtrs[u+1];i++)
{
ind=mCRS_cols[i];
assert(ind>=0 && ind<numV);
int lock2=0;
if (visitedV_[ind]==0)
{
visitedV_[ind]=1;
lock2=1;
}
if(lock2>0)
{
parent_[ind]=u;
res=dfs_path_finder(matchedVertexForV[ind]);
if(res!=-1)
return res;
}
}
}
else // even number iteration so scan from backward
{
for(i=mCRS_rowPtrs[u+1]-1;i>=mCRS_rowPtrs[u];i--)
{
ind=mCRS_cols[i];
assert(ind>=0 && ind<numV);
int lock2=0;
if (visitedV_[ind]==0)
{
visitedV_[ind]=1;
lock2=1;
}
if(lock2>0)
{
parent_[ind]=u;
res=dfs_path_finder(matchedVertexForV[ind]);
if(res!=-1)
return res;
}
}
}
return -1;
}
////////////////////////////////////////////////////////////////////////////////
// ////////////////////////////////////////////////////////////////////////////////
// // This function starts the BFS phase for the HK and HKDW. It starts from the
// // layer 0 vertices and tries to find a vertex disjoint path from each of
// // these vertices.
// ////////////////////////////////////////////////////////////////////////////////
// int Matcher::find_set_del_M()
// {
// int i,j,count=0;
// delete_matched_v();
// #ifdef ZOLTAN2ND_HAVE_OMP
// #pragma omp parallel for private(j)
// #endif
// for(i=0;i<BFSInd_;i++)
// {
// j=recursive_path_finder(0,queue[i]);
// if(j!=-1)
// {
// augment_matching(j);
// //MMW: Not 100% this is necessary, let this in just in case bug in original code
// #ifdef ZOLTAN2ND_HAVE_OMP
// #pragma omp atomic
// #endif
// count++;
// }
// }
// return count;
// }
// ////////////////////////////////////////////////////////////////////////////////
// ////////////////////////////////////////////////////////////////////////////////
// // This is the additional Duff and Wiberg phase for the HKDW. This function
// // does nothing but first unset the locks and then runs PPF from the
// // remaining unmatched row vertices after the BFS phase of HK.
// ////////////////////////////////////////////////////////////////////////////////
// int Matcher::DW_phase()
// {
// int i,count=0;
// #ifdef ZOLTAN2ND_HAVE_OMP
// #pragma omp parallel for
// #endif
// for(i=0;i<numV;i++)
// {
// #ifdef ZOLTAN2ND_HAVE_OMP
// omp_unset_lock(&scannedV_[i]); // unsetting the locks
// #endif
// }
// #ifdef ZOLTAN2ND_HAVE_OMP
// #pragma omp parallel for
// #endif
// for(i=0;i<BFSInd_;i++) // calling the PPF
// {
// int u=queue[i];
// if(matchedVertexForU[u]==-1)
// {
// int ind=dfs_path_finder(u);
// if(ind!=-1)
// {
// augment_matching(ind);
// //MMW: Not 100% this is necessary, let this in just in case bug in original code
// #ifdef ISORROPIA_HAVE_OMP
// #pragma omp atomic
// #endif
// count++;
// }
// }
// }
// return count;
// }
// ////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
//This function is the starter function for PPF and DFS. It unsets the locks
//the call dfs_path_finder and then call the augment_matching.
////////////////////////////////////////////////////////////////////////////////
int Matcher::dfs_augment()
{
int i,flag=0,flag1=0,count=0,totc=0,index=numU,cur=0;
icm_=0;
while(true)
{
icm_++;
for(i=0;i<numV;i++)
{
visitedV_[i]=0;
}
cur=0;
for(i=0;i<numU;i++)
{
if(matchedVertexForU[i]==-1)
unmatchedU_[cur++]=i;
}
index=cur;
flag=flag1=count=0;
for(i=0;i<index;i++)
{
flag=1;
int u=unmatchedU_[i];
int ind=dfs_path_finder(u);
if(ind!=-1)
{
flag1=1;
augment_matching(ind);
}
}
if(flag==0 || flag1==0)
break;
else
{
cur=0;
for(i=0;i<index;i++)
{
if(matchedVertexForU[unmatchedU_[i]]==-1)
unmatchedU_[cur++]=unmatchedU_[i];
}
index=cur;
}
}
return totc;
}
////////////////////////////////////////////////////////////////////////////////
// ////////////////////////////////////////////////////////////////////////////////
// ////////////////////////////////////////////////////////////////////////////////
// int Matcher::SGM()
// {
// int i,j,lock,ind,count=0;
// #ifdef ZOLTAN2ND_HAVE_OMP
// #pragma omp parallel for private(j,ind,lock)
// #endif
// for(i=0;i<numU;i++)
// {
// for(j=mCRS_rowPtrs[i];j<mCRS_rowPtrs[i+1];j++)
// {
// ind=mCRS_cols[j];
// #ifdef ZOLTAN2ND_HAVE_OMP
// lock=omp_test_lock(&scannedV_[ind]);
// #else
// // mfh 07 Feb 2013: lock wasn't getting initialized if
// // ZOLTAN2ND_HAVE_OMP was not defined. omp_test_lock()
// // returns nonzero if the thread successfully acquired the
// // lock. If there's only one thread, that thread will
// // always be successful, so the default value of lock
// // should be nonzero.
// lock = 1;
// #endif
// if(lock>0)
// {
// matchedVertexForU[i]=ind;
// matchedVertexForV[ind]=i;
// break;
// }
// }
// }
// return count;
// }
// ////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
int Matcher::SGM()
{
int i,j,ind,count=0;
for(i=0;i<numU;i++)
{
for(j=mCRS_rowPtrs[i];j<mCRS_rowPtrs[i+1];j++)
{
ind=mCRS_cols[j];
int lock2=0;
if (visitedV_[ind]==0)
{
visitedV_[ind]=1;
lock2=1;
}
if(lock2>0)
{
matchedVertexForU[i]=ind;
matchedVertexForV[ind]=i;
break;
}
}
}
return count;
}
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
// Forking function for DFS based algorithm
////////////////////////////////////////////////////////////////////////////////
int Matcher::match_dfs()
{
int totc=0;
icm_=0;
totc=dfs_augment();
return totc;
}
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
int Matcher::match()
{
// User interface function for the matching..
int totc=0;
totc=SGM();
totc+=match_dfs();
numMatched = totc;
return 0;
}
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
// Calculate vertex cover (which is vertex separator) from matching
// VC = (U-L) union (B intersection L)
//
// Let X be the exposed nodes in U (those without a match)
//
// E':
// Matched edges should be directed VtoU -- just use vertVMatches array
// All other edges should be directed UtoV -- use modified biGraphCRScols
//
// L is the set of vertices in (U union V, E') that can be reached from X
//
//
// Perhaps I should use internal class members in this function
// However, I decided not to do this for now since I'm changing some of these
// member variables in this function
////////////////////////////////////////////////////////////////////////////////
void getVCfromMatching(const std::vector<int> &bigraphCRSRowPtr,
std::vector<int> &bigraphCRSCols,
const std::vector<int> &vertUMatches,
const std::vector<int> &vertVMatches,
const std::vector<int> &bigraphVMapU,
const std::vector<int> &bigraphVMapV,
std::vector<int> &VC)
{
int numU = vertUMatches.size();
int numV = vertVMatches.size();
//////////////////////////////////////////////////////////////////////
// Build X
//////////////////////////////////////////////////////////////////////
std::set<int> X;
for(int i=0;i<numU; i++)
{
if(vertUMatches[i]==-1)
{
X.insert(i);
}
}
//////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////
// Non matched edges should be directed UtoV
// Removed matches edges from bipartite graph (set to -1)
// -- perhaps replace this with something more efficient/compact
//////////////////////////////////////////////////////////////////////
for (int uID=0;uID<numU;uID++)
{
for (int eIdx=bigraphCRSRowPtr[uID];eIdx<bigraphCRSRowPtr[uID+1];eIdx++)
{
int vID = bigraphCRSCols[eIdx];
if (vertUMatches[uID]==vID)
{
bigraphCRSCols[eIdx]=-1;
}
}
}
//////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////
// Calculate L - set of vertices in (U union V, E') that can be reached from X
//////////////////////////////////////////////////////////////////////
std::set<int> L;
std::queue<int> queue;
std::copy(X.begin(), X.end(), std::inserter( L, L.begin() ) );
for(std::set<int>::const_iterator iter = X.begin(); iter != X.end(); ++iter)
{
L.insert(bigraphVMapU[*iter]); // L contains all vertices in X
queue.push(*iter); // copy on to queue
}
int iteration=0;
while(queue.size()!=0)
{
//Number of active vertices on this side of bipartite graph
int nstarts=queue.size();
for (int i=0; i<nstarts; i++)
{
int start = queue.front();
queue.pop();
//Traverse from U to V
if(iteration%2==0)
{
//Traverse edges starting from vertex "start"
for (int eIdx=bigraphCRSRowPtr[start];eIdx<bigraphCRSRowPtr[start+1];eIdx++)
{
int newV = bigraphCRSCols[eIdx];
//Edge is in correct direction (U to V) => newV is valid
if (newV!=-1)
{
// If this vertex has not been reached
if(L.find(bigraphVMapV[newV])==L.end())
{
L.insert(bigraphVMapV[newV]);
queue.push(newV);
}
}
}
}
//Traverse from V to U
else
{
int newU = vertVMatches[start];
// If this vertex has not been reached
if(L.find(bigraphVMapU[newU])==L.end())
{
L.insert(bigraphVMapU[newU]);
queue.push(newU);
}
}
} // for
iteration++;
} //while
//////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////
// Calc VC = (U-L) union (B intersection L)
//////////////////////////////////////////////////////////////////////
for(int uID=0;uID<numU;uID++)
{
// if vertex not in L, it is in VC
if(L.find(bigraphVMapU[uID])==L.end())
{
VC.push_back(bigraphVMapU[uID]);
}
}
for(int vID=0;vID<numV;vID++)
{
// if vertex is in L, it is in VC
if(L.find(bigraphVMapV[vID])!=L.end())
{
VC.push_back(bigraphVMapV[vID]);
}
}
//////////////////////////////////////////////////////////////////////
}
////////////////////////////////////////////////////////////////////////////////
} //Zoltan2 namespace
#endif //ifdef
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