verGhostIndInitialization and Ghost2LocalInitialization cycles parallelization

amgprec/impl/aggregator/Makefile

@@ -4,7 +4,7 @@ INCDIR=../../../include
 MODDIR=../../../modules
 HERE=../..
 
-FINCLUDES=$(FMFLAG)$(HERE) $(FMFLAG)$(MODDIR) $(FMFLAG)$(INCDIR) $(PSBLAS_INCLUDES)
+FINCLUDES=$(FMFLAG)$(HERE) $(FMFLAG)$(MODDIR) $(FMFLAG)$(INCDIR) $(PSBLAS_INCLUDES) -fopenmp
 CXXINCLUDES=$(FMFLAG)$(HERE) $(FMFLAG)$(INCDIR) $(FMFLAG)/.
 
 #CINCLUDES= -I${SUPERLU_INCDIR} -I${HSL_INCDIR}  -I${SPRAL_INCDIR} -I/home/users/pasqua/Ambra/BootCMatch/include -lBCM -L/home/users/pasqua/Ambra/BootCMatch/lib  -lm

amgprec/impl/aggregator/MatchBoxPC.cpp

@@ -60,13 +60,12 @@ void dMatchBoxPC(MilanLongInt NLVer, MilanLongInt NLEdge,
 		MilanLongInt* ph1_card, MilanLongInt* ph2_card ) {
 #if !defined(SERIAL_MPI)
   MPI_Comm C_comm=MPI_Comm_f2c(icomm);
+
 #ifdef DEBUG
   fprintf(stderr,"MatchBoxPC: rank %d nlver %ld nledge %ld [ %ld %ld ]\n",
 	  myRank,NLVer, NLEdge,verDistance[0],verDistance[1]);
 #endif
 
-#ifdef #IE
-
     #ifdef TIME_TRACKER
         double tmr = MPI_Wtime();
     #endif

amgprec/impl/aggregator/algoDistEdgeApproxDomEdgesLinearSearchMesgBndlSmallMateC.cpp

@@ -1,4 +1,6 @@
 #include "MatchBoxPC.h"
+#include <omp.h>
+#include <stdio.h>
 // ***********************************************************************
 //
 //        MatchboxP: A C++ library for approximate weighted matching
@@ -167,25 +169,40 @@ void dalgoDistEdgeApproxDomEdgesLinearSearchMesgBndlSmallMateC(
     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.
+     */
+
 #ifdef TIME_TRACKER
     double Ghost2LocalInitialization = MPI_Wtime();
 #endif
+
+#pragma omp parallel for private(insertMe) firstprivate(StartIndex, EndIndex) default(shared)
     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
-            storedAlready = Ghost2LocalMap.find( insertMe );
+#pragma omp critical
-            if ( storedAlready != Ghost2LocalMap.end() ) { //Has already been added
+            {
-                //cout<<"Process "<<myRank<<" found: "<<storedAlready->first<<" - "<<storedAlready->second<<endl;
-                Counter[storedAlready->second]++; //Increment the counter
-                numGhostEdges++;
-            } 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
                 numGhostEdges++;
-                numGhostVertices++;  //Increment the number of ghost vertices
+                storedAlready = Ghost2LocalMap.find(insertMe);
-            } //End of else()
+                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)
 
@@ -243,19 +260,37 @@ void dalgoDistEdgeApproxDomEdgesLinearSearchMesgBndlSmallMateC(
     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 parallel for private(insertMe, k, adj1, adj2) firstprivate(StartIndex, EndIndex) default(shared)
     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
-                insertMe = verGhostPtr[Ghost2LocalMap[w]] + tempCounter[Ghost2LocalMap[w]]; //Where to insert
+#pragma omp critical
-                verGhostInd[insertMe] = v+StartIndex; //Add the adjacency
+                {
-                tempCounter[Ghost2LocalMap[w]]++; //Increment the counter
+                    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)

exec.sh

@@ -0,0 +1,7 @@
+make all
+cd samples/advanced/pdegen
+make amg_d_pde3d
+cd runs
+mpirun -np 8 amg_d_pde3d amg_pde3d.inp
+
+

samples/advanced/pdegen/Makefile

@@ -3,7 +3,7 @@ AMGINCDIR=$(AMGDIR)/include
 include $(AMGINCDIR)/Make.inc.amg4psblas
 AMGMODDIR=$(AMGDIR)/modules
 AMGLIBDIR=$(AMGDIR)/lib
-AMG_LIBS=-L$(AMGLIBDIR) -lpsb_krylov -lamg_prec -lpsb_prec
+AMG_LIBS=-L$(AMGLIBDIR) -lpsb_krylov -lamg_prec -lpsb_prec -llapack -lblas
 FINCLUDES=$(FMFLAG). $(FMFLAG)$(AMGMODDIR) $(FMFLAG)$(AMGINCDIR) $(PSBLAS_INCLUDES) $(FIFLAG).
 
 LINKOPT=