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refactoring, initialization

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This commit is contained in:
StefanoPetrilli
2022-06-25 10:16:30 -05:00
parent bf0532867d
commit a54f084ffb
3 changed files with 307 additions and 197 deletions
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amgprec/impl/aggregator/MatchBoxPC.h
+24 -1
View File
@@ -59,7 +59,7 @@
#include <assert.h>
#include <map>
#include <vector>
// #include "matchboxp.h"
#include "omp.h"
#include "primitiveDataTypeDefinitions.h"
#include "dataStrStaticQueue.h"
@@ -175,6 +175,29 @@ inline MilanLongInt computeCandidateMate(MilanLongInt adj1,
MilanLongInt* Mate,
map <MilanLongInt, MilanLongInt> &Ghost2LocalMap);
inline void initialize(MilanLongInt NLVer, MilanLongInt NLEdge,
MilanLongInt StartIndex, MilanLongInt EndIndex,
MilanLongInt* numGhostEdgesPtr,
MilanLongInt* numGhostVerticesPtr,
MilanLongInt* insertMePtr,
MilanLongInt* verLocInd,
MilanLongInt* verLocPtr,
omp_lock_t* MateLock,
map <MilanLongInt, MilanLongInt> &Ghost2LocalMap,
vector <MilanLongInt>& Counter,
vector <MilanLongInt>& verGhostPtr,
vector <MilanLongInt>& verGhostInd,
vector <MilanLongInt>& tempCounter,
vector <MilanLongInt>& GMate,
vector<MilanLongInt>& Message,
vector<MilanLongInt>& QLocalVtx,
vector<MilanLongInt>& QGhostVtx,
vector<MilanLongInt>& QMsgType,
vector<MilanInt>& QOwner,
MilanLongInt* candidateMate,
staticQueue& U
);
void dalgoDistEdgeApproxDomEdgesLinearSearchMesgBndlSmallMateCMP
(
MilanLongInt NLVer, MilanLongInt NLEdge,
amgprec/impl/aggregator/algoDistEdgeApproxDomEdgesLinearSearchMesgBndlSmallMateCMP.cpp
+44 -196
View File
@@ -4,6 +4,7 @@
#include "isAlreadyMatched.cpp"
#include "findOwnerOfGhost.cpp"
#include "computeCandidateMate.cpp"
#include "initialize.cpp"
// ***********************************************************************
//
@@ -146,10 +147,6 @@ void dalgoDistEdgeApproxDomEdgesLinearSearchMesgBndlSmallMateCMP(
MilanReal startTime, finishTime;
//MilanReal Precision = MPI_Wtick(); //Get the precision of the MPI Timer
startTime = MPI_Wtime();
//Get the iterators for the graph:
//vector<MilanLongInt>::iterator verLocPtr = inputSubGraph.getVerPtr_b();
//vector<MilanLongInt>::iterator verLocInd = inputSubGraph.getVerInd_b();
//vector<MilanReal>::iterator edgeLocWeight = inputSubGraph.getEdgeWt_b();
//Data structures for sending and receiving messages:
vector<MilanLongInt> Message; // [ u, v, message_type ]
@@ -171,9 +168,8 @@ void dalgoDistEdgeApproxDomEdgesLinearSearchMesgBndlSmallMateCMP(
PCounter[i] = 0;
MilanLongInt NumMessagesBundled;
MilanInt ghostOwner; // Changed by Fabio to be an integer, addresses needs to be integers!
//vector<MilanLongInt> candidateMate;
MilanLongInt NumMessagesBundled = 0;
MilanInt ghostOwner = 0; // Changed by Fabio to be an integer, addresses needs to be integers!
MilanLongInt* candidateMate = new MilanLongInt[1];
#ifdef PRINT_DEBUG_INFO_
cout<<"\n("<<myRank<<")NV: "<<NLVer<<" Edges: "<<NLEdge; fflush(stdout);
@@ -188,8 +184,6 @@ void dalgoDistEdgeApproxDomEdgesLinearSearchMesgBndlSmallMateCMP(
//Build the Ghost Vertex Set: Vg
map <MilanLongInt, MilanLongInt> Ghost2LocalMap; //Map each ghost vertex to a local vertex
// index that starts with zero to |Vg| - 1
map<MilanLongInt, MilanLongInt>::iterator storedAlready;
vector <MilanLongInt> Counter; //Store the edge count for each ghost vertex
MilanLongInt numGhostVertices = 0, numGhostEdges = 0, insertMe = 0; //Number of Ghost vertices
@@ -200,17 +194,6 @@ void dalgoDistEdgeApproxDomEdgesLinearSearchMesgBndlSmallMateCMP(
if (myRank == 0) cout<<"\n("<<myRank<<")About to compute Ghost Vertices..."; fflush(stdout);
#endif
/*
* OMP Ghost2LocalInitialization
* The cycle analyzes all the edges and when finds a ghost edge
* puts it in the Ghost2LocalMap.
* A critical region is needed when inserting data in the map.
*
* Despite the critical region it is still productive to
* parallelize this for because the critical region is exeuted
* only when a ghost edge is found and ghost edges are a minority.
*/
//Define Adjacency Lists for Ghost Vertices:
//cout<<"Building Ghost data structures ... \n\n";
vector <MilanLongInt> verGhostPtr, verGhostInd, tempCounter;
@@ -232,182 +215,37 @@ void dalgoDistEdgeApproxDomEdgesLinearSearchMesgBndlSmallMateCMP(
//Declare the locks
omp_lock_t MateLock[NLVer];
#ifdef TIME_TRACKER
double Ghost2LocalInitialization = MPI_Wtime();
#endif
initialize(NLVer, NLEdge, StartIndex,
EndIndex, &numGhostEdges,
&numGhostVertices, &insertMe,
verLocInd, verLocPtr,
MateLock,
Ghost2LocalMap, Counter,
verGhostPtr, verGhostInd,
tempCounter, GMate,
Message, QLocalVtx,
QGhostVtx, QMsgType, QOwner,
candidateMate, U);
finishTime = MPI_Wtime();
*ph0_time = finishTime - startTime; //Time taken for Phase-0: Initialization
startTime = MPI_Wtime();
/////////////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////// INITIALIZATION /////////////////////////////////////
/////////////////////////////////////////////////////////////////////////////////////////
//Compute the Initial Matching Set:
#pragma omp parallel private(insertMe, k, u, w, v, k1, adj1, adj2, adj11, adj12, heaviestEdgeWt, ghostOwner, privateU, privateMyCard, isEmpty, privateQLocalVtx, privateQGhostVtx, privateQMsgType, privateQOwner) firstprivate(StartIndex, EndIndex) default(shared) num_threads(4)
{
//Initialize the locks
//TODO this can be executed as task in parallel with other unparallelizable tasks
//TODO destroy the locks
//#pragma omp for schedule(static)
// for(int i = 0; i < NLVer; i++)
// omp_init_lock(&MateLock[i]);
// TODO comments about the reduction
#pragma omp for reduction(+ : numGhostEdges)
for (i = 0; i < NLEdge; i++) { //O(m) - Each edge stored twice
insertMe = verLocInd[i];
//cout<<"InsertMe on Process "<<myRank<<" is: "<<insertMe<<endl;
if ((insertMe < StartIndex) || (insertMe > EndIndex)) { //Find a ghost
numGhostEdges++;
#pragma omp critical
{
storedAlready = Ghost2LocalMap.find(insertMe);
if (storedAlready != Ghost2LocalMap.end()) { //Has already been added
//cout<<"Process "<<myRank<<" found: "<<storedAlready->first<<" - "<<storedAlready->second<<endl;
Counter[storedAlready->second]++; //Increment the counter
} else { //Insert an entry for the ghost:
//cout<<"Process "<<myRank<<" * New insert: Key="<<insertMe<< " : Value="<<numGhostVertices<<endl;
Ghost2LocalMap[insertMe] = numGhostVertices; //Add a map entry
Counter.push_back(1); //Initialize the counter
numGhostVertices++; //Increment the number of ghost vertices
} //End of else()
}
} //End of if ( (insertMe < StartIndex) || (insertMe > EndIndex) )
} //End of for(ghost vertices)
#pragma omp single
{
//numGhostEdges = atomicNumGhostEdges;
#ifdef TIME_TRACKER
Ghost2LocalInitialization = MPI_Wtime() - Ghost2LocalInitialization;
fprintf(stderr, "Ghost2LocalInitialization time: %f\n", Ghost2LocalInitialization);
#endif
#ifdef PRINT_DEBUG_INFO_
cout<<"\n("<<myRank<<")NGhosts:" << numGhostVertices << " GhostEdges: "<<numGhostEdges;
if (!Ghost2LocalMap.empty()) {
cout<<"\n("<<myRank<<")Final Map : on process ";
cout<<"\n("<<myRank<<")Key \t Value \t Counter \n"; fflush(stdout);
storedAlready = Ghost2LocalMap.begin();
do {
cout<<storedAlready->second<<" - "<<storedAlready->first<<" : "<<Counter[storedAlready->second]<<endl;
fflush(stdout);
storedAlready++;
} while ( storedAlready != Ghost2LocalMap.end() );
}
#endif
//Initialize adjacency Lists for Ghost Vertices:
try {
verGhostPtr.reserve(numGhostVertices + 1); //Pointer Vector
tempCounter.reserve(numGhostVertices); //Pointer Vector
verGhostInd.reserve(numGhostEdges); //Index Vector
GMate.reserve(numGhostVertices); //Ghost Mate Vector
} catch (length_error) {
cout << "Error in function algoDistEdgeApproxDominatingEdgesLinearSearch: \n";
cout << "Not enough memory to allocate the internal variables \n";
exit(1);
}
//Initialize the Vectors:
verGhostPtr.resize(numGhostVertices + 1, 0); //Pointer Vector
tempCounter.resize(numGhostVertices, 0); //Temporary Counter
verGhostInd.resize(numGhostEdges, -1); //Index Vector
GMate.resize(numGhostVertices, -1); //Temporary Counter
verGhostPtr[0] = 0; //The first value
#ifdef PRINT_DEBUG_INFO_
cout<<"\n("<<myRank<<")Ghost Vertex Pointer: "; fflush(stdout);
#endif
#ifdef TIME_TRACKER
double verGhostPtrInitialization = MPI_Wtime();
#endif
/*
* Not parallelizable
*/
for (i = 0; i < numGhostVertices; i++) { //O(|Ghost Vertices|)
verGhostPtr[i + 1] = verGhostPtr[i] + Counter[i];
#ifdef PRINT_DEBUG_INFO_
cout<<verGhostPtr[i]<<"\t"; fflush(stdout);
#endif
}
} // End of single region
#ifdef TIME_TRACKER
verGhostPtrInitialization = MPI_Wtime() - verGhostPtrInitialization;
fprintf(stderr, "verGhostPtrInitialization time: %f\n", verGhostPtrInitialization);
#endif
#ifdef PRINT_DEBUG_INFO_
if ( numGhostVertices > 0 )
cout<<verGhostPtr[numGhostVertices]<<"\n";
fflush(stdout);
#endif
/*
* OMP verGhostIndInitialization
*
* In this cycle the verGhostInd is initialized
* with the datas related to ghost edges.
* The check to see if a node is a ghost node is
* executed in paralle and when a ghost node
* is found a critical region is started.
*
* Despite the critical region it's still useful to
* parallelize the for cause the ghost nodes
* are a minority hence the critical region is executed
* few times.
*/
#ifdef TIME_TRACKER
double verGhostIndInitialization = MPI_Wtime();
#endif
#pragma omp for nowait schedule(static)
for (v = 0; v < NLVer; v++) {
adj1 = verLocPtr[v]; //Vertex Pointer
adj2 = verLocPtr[v + 1];
for (k = adj1; k < adj2; k++) {
w = verLocInd[k]; //Get the adjacent vertex
if ((w < StartIndex) || (w > EndIndex)) { //Find a ghost
#pragma omp critical
{
insertMe = verGhostPtr[Ghost2LocalMap[w]] + tempCounter[Ghost2LocalMap[w]]; //Where to insert
verGhostInd[insertMe] = v + StartIndex; //Add the adjacency
tempCounter[Ghost2LocalMap[w]]++; //Increment the counter
}
} //End of if((w < StartIndex) || (w > EndIndex))
} //End of for(k)
} //End of for (v)
#pragma omp single
{
#ifdef TIME_TRACKER
verGhostIndInitialization = MPI_Wtime() - verGhostIndInitialization;
fprintf(stderr, "verGhostIndInitialization time: %f\n", verGhostIndInitialization);
#endif
#ifdef PRINT_DEBUG_INFO_
cout<<"\n("<<myRank<<")Ghost Vertex Index: ";
for ( v=0; v < numGhostEdges; v++ )
cout<<verGhostInd[v]<<"\t";
cout<<endl; fflush(stdout);
#endif
Message.resize(3, -1);
message_type = 0;
NumMessagesBundled = 0;
ghostOwner = 0;
try {
QLocalVtx.reserve(numGhostEdges); //Local Vertex
QGhostVtx.reserve(numGhostEdges); //Ghost Vertex
QMsgType.reserve(numGhostEdges); //Message Type (Request/Failure)
QOwner.reserve(numGhostEdges); //Owner of the ghost: COmpute once and use later
} catch (length_error) {
cout << "Error in function algoDistEdgeApproxDominatingEdgesMessageBundling: \n";
cout << "Not enough memory to allocate the internal variables \n";
exit(1);
}
#ifdef PRINT_DEBUG_INFO_
{
#ifdef PRINT_DEBUG_INFO_
cout<<"\n("<<myRank<<")Allocating CandidateMate.. "; fflush(stdout);
#endif
//Allocate Data Structures:
@@ -434,9 +272,7 @@ void dalgoDistEdgeApproxDomEdgesLinearSearchMesgBndlSmallMateCMP(
cout<<"\n("<<myRank<<"=========================************==============================="<<endl; fflush(stdout);
fflush(stdout);
#endif
//MPI_Barrier(comm);
finishTime = MPI_Wtime();
*ph0_time = finishTime - startTime; //Time taken for Phase-0: Initialization
#ifdef PRINT_DEBUG_INFO_
cout<<"\n("<<myRank<<") Setup Time :"<< *ph0_time <<endl; fflush(stdout);
fflush(stdout);
@@ -444,15 +280,27 @@ void dalgoDistEdgeApproxDomEdgesLinearSearchMesgBndlSmallMateCMP(
#ifdef DEBUG_HANG_
if (myRank == 0) cout<<"\n("<<myRank<<") Setup Time :"<< *ph0_time <<endl; fflush(stdout);
#endif
startTime = MPI_Wtime();
/////////////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////// INITIALIZATION /////////////////////////////////////
/////////////////////////////////////////////////////////////////////////////////////////
//Compute the Initial Matching Set:
S = numGhostVertices; //Initialize S with number of Ghost Vertices
} // end of single region
/*
* Create the Queue Data Structure for the Dominating Set
*
* I had to declare the staticuQueue U before the parallel region
* to have it in the correct scope. Since we can't change the dimension
* of a staticQueue I had to destroy the previous object and instantiate
* a new one of the correct size.
*/
U.~staticQueue();
new(&U) staticQueue(NLVer + numGhostVertices);
S = numGhostVertices; //Initialize S with number of Ghost Vertices
}
/*
* OMP PARALLEL_COMPUTE_CANDIDATE_MATE_B has been splitted from
* PARALLEL_PROCESS_EXPOSED_VERTEX_B in order to better parallelize
amgprec/impl/aggregator/initialize.cpp
+239
View File
@@ -0,0 +1,239 @@
#include "MatchBoxPC.h"
#include <stdio.h>
#include <iostream>
#include <assert.h>
#include <map>
#include <vector>
#include "primitiveDataTypeDefinitions.h"
#include "dataStrStaticQueue.h"
#include "omp.h"
inline void initialize(MilanLongInt NLVer, MilanLongInt NLEdge,
MilanLongInt StartIndex, MilanLongInt EndIndex,
MilanLongInt* numGhostEdgesPtr,
MilanLongInt* numGhostVerticesPtr,
MilanLongInt* insertMePtr,
MilanLongInt* verLocInd,
MilanLongInt* verLocPtr,
omp_lock_t* MateLock,
map <MilanLongInt, MilanLongInt> &Ghost2LocalMap,
vector <MilanLongInt>& Counter,
vector <MilanLongInt>& verGhostPtr,
vector <MilanLongInt>& verGhostInd,
vector <MilanLongInt>& tempCounter,
vector <MilanLongInt>& GMate,
vector<MilanLongInt>& Message,
vector<MilanLongInt>& QLocalVtx,
vector<MilanLongInt>& QGhostVtx,
vector<MilanLongInt>& QMsgType,
vector<MilanInt>& QOwner,
MilanLongInt* candidateMate,
staticQueue& U
)
{
MilanLongInt insertMe = 0, numGhostEdges = 0, numGhostVertices = 0;
MilanLongInt adj1, adj2;
int i, v, k, w;
// index that starts with zero to |Vg| - 1
map<MilanLongInt, MilanLongInt>::iterator storedAlready;
#pragma omp parallel private(insertMe, k, w, v, adj1, adj2) firstprivate(StartIndex, EndIndex) default(shared) num_threads(4)
{
//Initialize the locks
//TODO this can be executed as task in parallel with other unparallelizable tasks
//TODO destroy the locks
#pragma omp for schedule(static)
for(i = 0; i < NLVer; i++)
omp_init_lock(&MateLock[i]);
#ifdef TIME_TRACKER
double Ghost2LocalInitialization = MPI_Wtime();
#endif
/*
* OMP Ghost2LocalInitialization
* The cycle analyzes all the edges and when finds a ghost edge
* puts it in the Ghost2LocalMap.
* A critical region is needed when inserting data in the map.
*
* Despite the critical region it is still productive to
* parallelize this for because the critical region is exeuted
* only when a ghost edge is found and ghost edges are a minority.
*/
// TODO comments about the reduction
#pragma omp for reduction(+ : numGhostEdges)
for (i = 0; i < NLEdge; i++) { //O(m) - Each edge stored twice
insertMe = verLocInd[i];
//cout<<"InsertMe on Process "<<myRank<<" is: "<<insertMe<<endl;
if ((insertMe < StartIndex) || (insertMe > EndIndex)) { //Find a ghost
numGhostEdges++;
#pragma omp critical
{
storedAlready = Ghost2LocalMap.find(insertMe);
if (storedAlready != Ghost2LocalMap.end()) { //Has already been added
//cout<<"Process "<<myRank<<" found: "<<storedAlready->first<<" - "<<storedAlready->second<<endl;
Counter[storedAlready->second]++; //Increment the counter
} else { //Insert an entry for the ghost:
//cout<<"Process "<<myRank<<" * New insert: Key="<<insertMe<< " : Value="<<numGhostVertices<<endl;
Ghost2LocalMap[insertMe] = numGhostVertices; //Add a map entry
Counter.push_back(1); //Initialize the counter
numGhostVertices++; //Increment the number of ghost vertices
} //End of else()
}
} //End of if ( (insertMe < StartIndex) || (insertMe > EndIndex) )
} //End of for(ghost vertices)
#pragma omp single
{
//numGhostEdges = atomicNumGhostEdges;
#ifdef TIME_TRACKER
Ghost2LocalInitialization = MPI_Wtime() - Ghost2LocalInitialization;
fprintf(stderr, "Ghost2LocalInitialization time: %f\n", Ghost2LocalInitialization);
#endif
#ifdef PRINT_DEBUG_INFO_
cout<<"\n("<<myRank<<")NGhosts:" << numGhostVertices << " GhostEdges: "<<numGhostEdges;
if (!Ghost2LocalMap.empty()) {
cout<<"\n("<<myRank<<")Final Map : on process ";
cout<<"\n("<<myRank<<")Key \t Value \t Counter \n"; fflush(stdout);
storedAlready = Ghost2LocalMap.begin();
do {
cout<<storedAlready->second<<" - "<<storedAlready->first<<" : "<<Counter[storedAlready->second]<<endl;
fflush(stdout);
storedAlready++;
} while ( storedAlready != Ghost2LocalMap.end() );
}
#endif
//Initialize adjacency Lists for Ghost Vertices:
try {
verGhostPtr.reserve(numGhostVertices + 1); //Pointer Vector
tempCounter.reserve(numGhostVertices); //Pointer Vector
verGhostInd.reserve(numGhostEdges); //Index Vector
GMate.reserve(numGhostVertices); //Ghost Mate Vector
} catch (length_error) {
cout << "Error in function algoDistEdgeApproxDominatingEdgesLinearSearch: \n";
cout << "Not enough memory to allocate the internal variables \n";
exit(1);
}
//Initialize the Vectors:
verGhostPtr.resize(numGhostVertices + 1, 0); //Pointer Vector
tempCounter.resize(numGhostVertices, 0); //Temporary Counter
verGhostInd.resize(numGhostEdges, -1); //Index Vector
GMate.resize(numGhostVertices, -1); //Temporary Counter
verGhostPtr[0] = 0; //The first value
#ifdef PRINT_DEBUG_INFO_
cout<<"\n("<<myRank<<")Ghost Vertex Pointer: "; fflush(stdout);
#endif
#ifdef TIME_TRACKER
double verGhostPtrInitialization = MPI_Wtime();
#endif
/*
* Not parallelizable
*/
for (i = 0; i < numGhostVertices; i++) { //O(|Ghost Vertices|)
verGhostPtr[i + 1] = verGhostPtr[i] + Counter[i];
#ifdef PRINT_DEBUG_INFO_
cout<<verGhostPtr[i]<<"\t"; fflush(stdout);
#endif
}
} // End of single region
#ifdef TIME_TRACKER
verGhostPtrInitialization = MPI_Wtime() - verGhostPtrInitialization;
fprintf(stderr, "verGhostPtrInitialization time: %f\n", verGhostPtrInitialization);
#endif
#ifdef PRINT_DEBUG_INFO_
if ( numGhostVertices > 0 )
cout<<verGhostPtr[numGhostVertices]<<"\n";
fflush(stdout);
#endif
/*
* OMP verGhostIndInitialization
*
* In this cycle the verGhostInd is initialized
* with the datas related to ghost edges.
* The check to see if a node is a ghost node is
* executed in paralle and when a ghost node
* is found a critical region is started.
*
* Despite the critical region it's still useful to
* parallelize the for cause the ghost nodes
* are a minority hence the critical region is executed
* few times.
*/
#ifdef TIME_TRACKER
double verGhostIndInitialization = MPI_Wtime();
#endif
#pragma omp for nowait schedule(static)
for (v = 0; v < NLVer; v++) {
adj1 = verLocPtr[v]; //Vertex Pointer
adj2 = verLocPtr[v + 1];
for (k = adj1; k < adj2; k++) {
w = verLocInd[k]; //Get the adjacent vertex
if ((w < StartIndex) || (w > EndIndex)) { //Find a ghost
#pragma omp critical
{
insertMe = verGhostPtr[Ghost2LocalMap[w]] + tempCounter[Ghost2LocalMap[w]]; //Where to insert
verGhostInd[insertMe] = v + StartIndex; //Add the adjacency
tempCounter[Ghost2LocalMap[w]]++; //Increment the counter
}
} //End of if((w < StartIndex) || (w > EndIndex))
} //End of for(k)
} //End of for (v)
}
#pragma omp single
{
#ifdef TIME_TRACKER
verGhostIndInitialization = MPI_Wtime() - verGhostIndInitialization;
fprintf(stderr, "verGhostIndInitialization time: %f\n", verGhostIndInitialization);
#endif
#ifdef PRINT_DEBUG_INFO_
cout<<"\n("<<myRank<<")Ghost Vertex Index: ";
for ( v=0; v < numGhostEdges; v++ )
cout<<verGhostInd[v]<<"\t";
cout<<endl; fflush(stdout);
#endif
Message.resize(3, -1);
//message_type = 0;
//NumMessagesBundled = 0;
//ghostOwner = 0;
try {
QLocalVtx.reserve(numGhostEdges); //Local Vertex
QGhostVtx.reserve(numGhostEdges); //Ghost Vertex
QMsgType.reserve(numGhostEdges); //Message Type (Request/Failure)
QOwner.reserve(numGhostEdges); //Owner of the ghost: COmpute once and use later
} catch (length_error) {
cout << "Error in function algoDistEdgeApproxDominatingEdgesMessageBundling: \n";
cout << "Not enough memory to allocate the internal variables \n";
exit(1);
}
} // end of single region
*numGhostEdgesPtr = numGhostEdges;
*numGhostVerticesPtr = numGhostVertices;
*insertMePtr = insertMe;
}