1 | #include "mpi.hpp" |
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2 | #include <map> |
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3 | #include "cputime.hpp" /* time */ |
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4 | #include "meshutil.hpp" |
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5 | #include "polyg.hpp" |
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6 | #include "circle.hpp" |
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7 | #include "intersect.hpp" |
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8 | #include "intersection_ym.hpp" |
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9 | #include "errhandle.hpp" |
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10 | #include "mpi_routing.hpp" |
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11 | #include "gridRemap.hpp" |
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12 | |
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13 | #include "mapper.hpp" |
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14 | |
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15 | namespace sphereRemap { |
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16 | |
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17 | extern CRemapGrid srcGrid; |
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18 | #pragma omp threadprivate(srcGrid) |
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19 | |
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20 | extern CRemapGrid tgtGrid; |
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21 | #pragma omp threadprivate(tgtGrid) |
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22 | |
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23 | /* A subdivition of an array into N sub-arays |
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24 | can be represented by the length of the N arrays |
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25 | or by the offsets when each of the N arrays starts. |
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26 | This function convertes from the former to the latter. */ |
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27 | void cptOffsetsFromLengths(const int *lengths, int *offsets, int sz) |
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28 | { |
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29 | offsets[0] = 0; |
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30 | for (int i = 1; i < sz; i++) |
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31 | offsets[i] = offsets[i-1] + lengths[i-1]; |
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32 | } |
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33 | |
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34 | |
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35 | void Mapper::setSourceMesh(const double* boundsLon, const double* boundsLat, int nVertex, int nbCells, const double* pole, const long int* globalId) |
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36 | { |
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37 | srcGrid.pole = Coord(pole[0], pole[1], pole[2]); |
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38 | |
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39 | int mpiRank, mpiSize; |
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40 | MPI_Comm_rank(communicator, &mpiRank); |
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41 | MPI_Comm_size(communicator, &mpiSize); |
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42 | |
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43 | sourceElements.reserve(nbCells); |
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44 | sourceMesh.reserve(nbCells); |
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45 | sourceGlobalId.resize(nbCells) ; |
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46 | |
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47 | if (globalId==NULL) |
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48 | { |
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49 | long int offset ; |
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50 | long int nb=nbCells ; |
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51 | MPI_Scan(&nb,&offset,1,MPI_LONG,MPI_SUM,communicator) ; |
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52 | offset=offset-nb ; |
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53 | for(int i=0;i<nbCells;i++) sourceGlobalId[i]=offset+i ; |
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54 | } |
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55 | else sourceGlobalId.assign(globalId,globalId+nbCells); |
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56 | |
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57 | for (int i = 0; i < nbCells; i++) |
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58 | { |
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59 | int offs = i*nVertex; |
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60 | Elt elt(boundsLon + offs, boundsLat + offs, nVertex); |
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61 | elt.src_id.rank = mpiRank; |
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62 | elt.src_id.ind = i; |
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63 | elt.src_id.globalId = sourceGlobalId[i]; |
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64 | sourceElements.push_back(elt); |
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65 | sourceMesh.push_back(Node(elt.x, cptRadius(elt), &sourceElements.back())); |
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66 | cptEltGeom(sourceElements[i], Coord(pole[0], pole[1], pole[2])); |
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67 | } |
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68 | |
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69 | } |
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70 | |
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71 | void Mapper::setTargetMesh(const double* boundsLon, const double* boundsLat, int nVertex, int nbCells, const double* pole, const long int* globalId) |
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72 | { |
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73 | tgtGrid.pole = Coord(pole[0], pole[1], pole[2]); |
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74 | |
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75 | int mpiRank, mpiSize; |
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76 | MPI_Comm_rank(communicator, &mpiRank); |
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77 | MPI_Comm_size(communicator, &mpiSize); |
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78 | |
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79 | targetElements.reserve(nbCells); |
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80 | targetMesh.reserve(nbCells); |
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81 | |
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82 | targetGlobalId.resize(nbCells) ; |
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83 | if (globalId==NULL) |
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84 | { |
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85 | long int offset ; |
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86 | long int nb=nbCells ; |
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87 | MPI_Scan(&nb,&offset,1,MPI_LONG,MPI_SUM,communicator) ; |
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88 | offset=offset-nb ; |
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89 | for(int i=0;i<nbCells;i++) targetGlobalId[i]=offset+i ; |
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90 | } |
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91 | else targetGlobalId.assign(globalId,globalId+nbCells); |
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92 | |
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93 | for (int i = 0; i < nbCells; i++) |
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94 | { |
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95 | int offs = i*nVertex; |
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96 | Elt elt(boundsLon + offs, boundsLat + offs, nVertex); |
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97 | targetElements.push_back(elt); |
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98 | targetMesh.push_back(Node(elt.x, cptRadius(elt), &sourceElements.back())); |
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99 | cptEltGeom(targetElements[i], Coord(pole[0], pole[1], pole[2])); |
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100 | } |
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101 | |
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102 | |
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103 | } |
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104 | |
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105 | void Mapper::setSourceValue(const double* val) |
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106 | { |
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107 | int size=sourceElements.size() ; |
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108 | for(int i=0;i<size;++i) sourceElements[i].val=val[i] ; |
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109 | } |
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110 | |
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111 | void Mapper::getTargetValue(double* val) |
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112 | { |
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113 | int size=targetElements.size() ; |
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114 | for(int i=0;i<size;++i) val[i]=targetElements[i].val ; |
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115 | } |
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116 | |
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117 | vector<double> Mapper::computeWeights(int interpOrder, bool renormalize, bool quantity) |
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118 | { |
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119 | vector<double> timings; |
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120 | int mpiSize, mpiRank; |
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121 | MPI_Comm_size(communicator, &mpiSize); |
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122 | MPI_Comm_rank(communicator, &mpiRank); |
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123 | |
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124 | this->buildSSTree(sourceMesh, targetMesh); |
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125 | |
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126 | if (mpiRank == 0 && verbose) cout << "Computing intersections ..." << endl; |
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127 | double tic = cputime(); |
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128 | computeIntersection(&targetElements[0], targetElements.size()); |
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129 | timings.push_back(cputime() - tic); |
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130 | |
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131 | tic = cputime(); |
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132 | if (interpOrder == 2) { |
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133 | if (mpiRank == 0 && verbose) cout << "Computing grads ..." << endl; |
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134 | buildMeshTopology(); |
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135 | computeGrads(); |
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136 | } |
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137 | timings.push_back(cputime() - tic); |
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138 | |
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139 | /* Prepare computation of weights */ |
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140 | /* compute number of intersections which for the first order case |
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141 | corresponds to the number of edges in the remap matrix */ |
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142 | int nIntersections = 0; |
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143 | for (int j = 0; j < targetElements.size(); j++) |
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144 | { |
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145 | Elt &elt = targetElements[j]; |
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146 | for (list<Polyg*>::iterator it = elt.is.begin(); it != elt.is.end(); it++) |
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147 | nIntersections++; |
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148 | } |
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149 | /* overallocate for NMAX neighbours for each elements */ |
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150 | remapMatrix = new double[nIntersections*NMAX]; |
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151 | srcAddress = new int[nIntersections*NMAX]; |
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152 | srcRank = new int[nIntersections*NMAX]; |
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153 | dstAddress = new int[nIntersections*NMAX]; |
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154 | sourceWeightId =new long[nIntersections*NMAX]; |
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155 | targetWeightId =new long[nIntersections*NMAX]; |
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156 | |
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157 | |
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158 | if (mpiRank == 0 && verbose) cout << "Remapping..." << endl; |
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159 | tic = cputime(); |
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160 | nWeights = remap(&targetElements[0], targetElements.size(), interpOrder, renormalize, quantity); |
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161 | timings.push_back(cputime() - tic); |
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162 | |
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163 | for (int i = 0; i < targetElements.size(); i++) targetElements[i].delete_intersections(); |
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164 | |
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165 | return timings; |
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166 | } |
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167 | |
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168 | /** |
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169 | @param elements are cells of the target grid that are distributed over CPUs |
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170 | indepentently of the distribution of the SS-tree. |
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171 | @param nbElements is the size of the elements array. |
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172 | @param order is the order of interpolaton (must be 1 or 2). |
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173 | */ |
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174 | int Mapper::remap(Elt *elements, int nbElements, int order, bool renormalize, bool quantity) |
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175 | { |
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176 | int mpiSize, mpiRank; |
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177 | MPI_Comm_size(communicator, &mpiSize); |
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178 | MPI_Comm_rank(communicator, &mpiRank); |
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179 | |
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180 | /* create list of intersections (super mesh elements) for each rank */ |
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181 | multimap<int, Polyg *> *elementList = new multimap<int, Polyg *>[mpiSize]; |
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182 | for (int j = 0; j < nbElements; j++) |
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183 | { |
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184 | Elt& e = elements[j]; |
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185 | for (list<Polyg *>::iterator it = e.is.begin(); it != e.is.end(); it++) |
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186 | elementList[(*it)->id.rank].insert(pair<int, Polyg *>((*it)->id.ind, *it)); |
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187 | } |
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188 | |
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189 | int *nbSendElement = new int[mpiSize]; |
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190 | int **sendElement = new int*[mpiSize]; /* indices of elements required from other rank */ |
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191 | double **recvValue = new double*[mpiSize]; |
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192 | double **recvArea = new double*[mpiSize]; |
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193 | Coord **recvGrad = new Coord*[mpiSize]; |
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194 | GloId **recvNeighIds = new GloId*[mpiSize]; /* ids of the of the source neighbours which also contribute through gradient */ |
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195 | for (int rank = 0; rank < mpiSize; rank++) |
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196 | { |
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197 | /* get size for allocation */ |
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198 | int last = -1; /* compares unequal to any index */ |
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199 | int index = -1; /* increased to starting index 0 in first iteration */ |
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200 | for (multimap<int, Polyg *>::iterator it = elementList[rank].begin(); it != elementList[rank].end(); ++it) |
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201 | { |
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202 | if (last != it->first) |
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203 | index++; |
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204 | (it->second)->id.ind = index; |
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205 | last = it->first; |
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206 | } |
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207 | nbSendElement[rank] = index + 1; |
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208 | |
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209 | /* if size is non-zero allocate and collect indices of elements on other ranks that we intersect */ |
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210 | if (nbSendElement[rank] > 0) |
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211 | { |
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212 | sendElement[rank] = new int[nbSendElement[rank]]; |
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213 | recvValue[rank] = new double[nbSendElement[rank]]; |
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214 | recvArea[rank] = new double[nbSendElement[rank]]; |
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215 | if (order == 2) |
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216 | { |
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217 | recvNeighIds[rank] = new GloId[nbSendElement[rank]*(NMAX+1)]; |
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218 | recvGrad[rank] = new Coord[nbSendElement[rank]*(NMAX+1)]; |
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219 | } |
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220 | else |
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221 | recvNeighIds[rank] = new GloId[nbSendElement[rank]]; |
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222 | |
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223 | last = -1; |
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224 | index = -1; |
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225 | for (multimap<int, Polyg *>::iterator it = elementList[rank].begin(); it != elementList[rank].end(); ++it) |
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226 | { |
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227 | if (last != it->first) |
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228 | index++; |
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229 | sendElement[rank][index] = it->first; |
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230 | last = it->first; |
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231 | } |
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232 | } |
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233 | } |
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234 | |
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235 | /* communicate sizes of source elements to be sent (index lists and later values and gradients) */ |
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236 | int *nbRecvElement = new int[mpiSize]; |
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237 | MPI_Alltoall(nbSendElement, 1, MPI_INT, nbRecvElement, 1, MPI_INT, communicator); |
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238 | |
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239 | /* communicate indices of source elements on other ranks whoes value and gradient we need (since intersection) */ |
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240 | int nbSendRequest = 0; |
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241 | int nbRecvRequest = 0; |
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242 | int **recvElement = new int*[mpiSize]; |
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243 | double **sendValue = new double*[mpiSize]; |
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244 | double **sendArea = new double*[mpiSize]; |
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245 | Coord **sendGrad = new Coord*[mpiSize]; |
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246 | GloId **sendNeighIds = new GloId*[mpiSize]; |
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247 | MPI_Request *sendRequest = new MPI_Request[4*mpiSize]; |
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248 | MPI_Request *recvRequest = new MPI_Request[4*mpiSize]; |
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249 | for (int rank = 0; rank < mpiSize; rank++) |
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250 | { |
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251 | if (nbSendElement[rank] > 0) |
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252 | { |
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253 | MPI_Issend(sendElement[rank], nbSendElement[rank], MPI_INT, rank, 0, communicator, &sendRequest[nbSendRequest]); |
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254 | nbSendRequest++; |
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255 | } |
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256 | |
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257 | if (nbRecvElement[rank] > 0) |
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258 | { |
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259 | recvElement[rank] = new int[nbRecvElement[rank]]; |
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260 | sendValue[rank] = new double[nbRecvElement[rank]]; |
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261 | sendArea[rank] = new double[nbRecvElement[rank]]; |
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262 | if (order == 2) |
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263 | { |
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264 | sendNeighIds[rank] = new GloId[nbRecvElement[rank]*(NMAX+1)]; |
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265 | sendGrad[rank] = new Coord[nbRecvElement[rank]*(NMAX+1)]; |
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266 | } |
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267 | else |
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268 | { |
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269 | sendNeighIds[rank] = new GloId[nbRecvElement[rank]]; |
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270 | } |
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271 | MPI_Irecv(recvElement[rank], nbRecvElement[rank], MPI_INT, rank, 0, communicator, &recvRequest[nbRecvRequest]); |
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272 | nbRecvRequest++; |
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273 | } |
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274 | } |
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275 | |
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276 | MPI_Status *status = new MPI_Status[4*mpiSize]; |
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277 | |
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278 | MPI_Waitall(nbRecvRequest, recvRequest, status); |
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279 | MPI_Waitall(nbSendRequest, sendRequest, status); |
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280 | |
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281 | |
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282 | /* for all indices that have been received from requesting ranks: pack values and gradients, then send */ |
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283 | nbSendRequest = 0; |
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284 | nbRecvRequest = 0; |
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285 | for (int rank = 0; rank < mpiSize; rank++) |
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286 | { |
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287 | if (nbRecvElement[rank] > 0) |
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288 | { |
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289 | int jj = 0; // jj == j if no weight writing |
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290 | for (int j = 0; j < nbRecvElement[rank]; j++) |
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291 | { |
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292 | sendValue[rank][j] = sstree.localElements[recvElement[rank][j]].val; |
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293 | sendArea[rank][j] = sstree.localElements[recvElement[rank][j]].area; |
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294 | if (order == 2) |
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295 | { |
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296 | sendGrad[rank][jj] = sstree.localElements[recvElement[rank][j]].grad; |
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297 | sendNeighIds[rank][jj] = sstree.localElements[recvElement[rank][j]].src_id; |
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298 | jj++; |
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299 | for (int i = 0; i < NMAX; i++) |
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300 | { |
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301 | sendGrad[rank][jj] = sstree.localElements[recvElement[rank][j]].gradNeigh[i]; |
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302 | sendNeighIds[rank][jj] = sstree.localElements[recvElement[rank][j]].neighId[i]; |
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303 | jj++; |
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304 | } |
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305 | } |
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306 | else |
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307 | sendNeighIds[rank][j] = sstree.localElements[recvElement[rank][j]].src_id; |
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308 | } |
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309 | MPI_Issend(sendValue[rank], nbRecvElement[rank], MPI_DOUBLE, rank, 0, communicator, &sendRequest[nbSendRequest]); |
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310 | nbSendRequest++; |
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311 | MPI_Issend(sendArea[rank], nbRecvElement[rank], MPI_DOUBLE, rank, 1, communicator, &sendRequest[nbSendRequest]); |
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312 | nbSendRequest++; |
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313 | if (order == 2) |
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314 | { |
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315 | MPI_Issend(sendGrad[rank], 3*nbRecvElement[rank]*(NMAX+1), |
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316 | MPI_DOUBLE, rank, 2, communicator, &sendRequest[nbSendRequest]); |
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317 | nbSendRequest++; |
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318 | MPI_Issend(sendNeighIds[rank], 4*nbRecvElement[rank]*(NMAX+1), MPI_INT, rank, 3, communicator, &sendRequest[nbSendRequest]); |
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319 | //ym --> attention taille GloId |
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320 | nbSendRequest++; |
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321 | } |
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322 | else |
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323 | { |
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324 | MPI_Issend(sendNeighIds[rank], 4*nbRecvElement[rank], MPI_INT, rank, 4, communicator, &sendRequest[nbSendRequest]); |
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325 | //ym --> attention taille GloId |
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326 | nbSendRequest++; |
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327 | } |
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328 | } |
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329 | if (nbSendElement[rank] > 0) |
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330 | { |
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331 | MPI_Irecv(recvValue[rank], nbSendElement[rank], MPI_DOUBLE, rank, 0, communicator, &recvRequest[nbRecvRequest]); |
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332 | nbRecvRequest++; |
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333 | MPI_Irecv(recvArea[rank], nbSendElement[rank], MPI_DOUBLE, rank, 1, communicator, &recvRequest[nbRecvRequest]); |
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334 | nbRecvRequest++; |
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335 | if (order == 2) |
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336 | { |
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337 | MPI_Irecv(recvGrad[rank], 3*nbSendElement[rank]*(NMAX+1), |
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338 | MPI_DOUBLE, rank, 2, communicator, &recvRequest[nbRecvRequest]); |
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339 | nbRecvRequest++; |
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340 | MPI_Irecv(recvNeighIds[rank], 4*nbSendElement[rank]*(NMAX+1), MPI_INT, rank, 3, communicator, &recvRequest[nbRecvRequest]); |
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341 | //ym --> attention taille GloId |
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342 | nbRecvRequest++; |
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343 | } |
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344 | else |
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345 | { |
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346 | MPI_Irecv(recvNeighIds[rank], 4*nbSendElement[rank], MPI_INT, rank, 4, communicator, &recvRequest[nbRecvRequest]); |
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347 | //ym --> attention taille GloId |
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348 | nbRecvRequest++; |
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349 | } |
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350 | } |
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351 | } |
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352 | |
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353 | MPI_Waitall(nbRecvRequest, recvRequest, status); |
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354 | MPI_Waitall(nbSendRequest, sendRequest, status); |
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355 | |
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356 | |
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357 | |
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358 | /* now that all values and gradients are available use them to computed interpolated values on target |
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359 | and also to compute weights */ |
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360 | int i = 0; |
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361 | for (int j = 0; j < nbElements; j++) |
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362 | { |
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363 | Elt& e = elements[j]; |
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364 | |
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365 | /* since for the 2nd order case source grid elements can contribute to a destination grid element over several "paths" |
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366 | (step1: gradient is computed using neighbours on same grid, step2: intersection uses several elements on other grid) |
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367 | accumulate them so that there is only one final weight between two elements */ |
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368 | map<GloId,double> wgt_map; |
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369 | |
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370 | /* for destination element `e` loop over all intersetions/the corresponding source elements */ |
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371 | for (list<Polyg *>::iterator it = e.is.begin(); it != e.is.end(); it++) |
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372 | { |
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373 | /* it is the intersection element, so it->x and it->area are barycentre and area of intersection element (super mesh) |
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374 | but it->id is id of the source element that it intersects */ |
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375 | int n1 = (*it)->id.ind; |
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376 | int rank = (*it)->id.rank; |
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377 | double fk = recvValue[rank][n1]; |
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378 | double srcArea = recvArea[rank][n1]; |
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379 | double w = (*it)->area; |
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380 | if (quantity) w/=srcArea ; |
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381 | |
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382 | /* first order: src value times weight (weight = supermesh area), later divide by target area */ |
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383 | int kk = (order == 2) ? n1 * (NMAX + 1) : n1; |
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384 | GloId neighID = recvNeighIds[rank][kk]; |
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385 | wgt_map[neighID] += w; |
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386 | |
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387 | if (order == 2) |
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388 | { |
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389 | for (int k = 0; k < NMAX+1; k++) |
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390 | { |
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391 | int kk = n1 * (NMAX + 1) + k; |
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392 | GloId neighID = recvNeighIds[rank][kk]; |
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393 | if (neighID.ind != -1) wgt_map[neighID] += w * scalarprod(recvGrad[rank][kk], (*it)->x); |
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394 | } |
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395 | |
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396 | } |
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397 | } |
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398 | |
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399 | double renorm=0; |
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400 | if (renormalize) |
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401 | for (map<GloId,double>::iterator it = wgt_map.begin(); it != wgt_map.end(); it++) renorm+=it->second / e.area; |
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402 | else renorm=1. ; |
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403 | |
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404 | for (map<GloId,double>::iterator it = wgt_map.begin(); it != wgt_map.end(); it++) |
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405 | { |
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406 | if (quantity) this->remapMatrix[i] = (it->second ) / renorm; |
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407 | else this->remapMatrix[i] = (it->second / e.area) / renorm; |
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408 | this->srcAddress[i] = it->first.ind; |
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409 | this->srcRank[i] = it->first.rank; |
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410 | this->dstAddress[i] = j; |
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411 | this->sourceWeightId[i]= it->first.globalId ; |
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412 | this->targetWeightId[i]= targetGlobalId[j] ; |
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413 | i++; |
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414 | } |
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415 | } |
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416 | |
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417 | /* free all memory allocated in this function */ |
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418 | for (int rank = 0; rank < mpiSize; rank++) |
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419 | { |
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420 | if (nbSendElement[rank] > 0) |
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421 | { |
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422 | delete[] sendElement[rank]; |
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423 | delete[] recvValue[rank]; |
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424 | delete[] recvArea[rank]; |
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425 | if (order == 2) |
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426 | { |
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427 | delete[] recvGrad[rank]; |
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428 | } |
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429 | delete[] recvNeighIds[rank]; |
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430 | } |
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431 | if (nbRecvElement[rank] > 0) |
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432 | { |
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433 | delete[] recvElement[rank]; |
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434 | delete[] sendValue[rank]; |
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435 | delete[] sendArea[rank]; |
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436 | if (order == 2) |
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437 | delete[] sendGrad[rank]; |
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438 | delete[] sendNeighIds[rank]; |
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439 | } |
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440 | } |
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441 | delete[] status; |
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442 | delete[] sendRequest; |
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443 | delete[] recvRequest; |
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444 | delete[] elementList; |
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445 | delete[] nbSendElement; |
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446 | delete[] nbRecvElement; |
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447 | delete[] sendElement; |
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448 | delete[] recvElement; |
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449 | delete[] sendValue; |
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450 | delete[] recvValue; |
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451 | delete[] sendGrad; |
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452 | delete[] recvGrad; |
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453 | delete[] sendNeighIds; |
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454 | delete[] recvNeighIds; |
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455 | |
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456 | return i; |
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457 | } |
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458 | |
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459 | void Mapper::computeGrads() |
---|
460 | { |
---|
461 | /* array of pointers to collect local elements and elements received from other cpu */ |
---|
462 | vector<Elt*> globalElements(sstree.nbLocalElements + nbNeighbourElements); |
---|
463 | int index = 0; |
---|
464 | for (int i = 0; i < sstree.nbLocalElements; i++, index++) |
---|
465 | globalElements[index] = &(sstree.localElements[i]); |
---|
466 | for (int i = 0; i < nbNeighbourElements; i++, index++) |
---|
467 | globalElements[index] = &neighbourElements[i]; |
---|
468 | |
---|
469 | update_baryc(sstree.localElements, sstree.nbLocalElements); |
---|
470 | computeGradients(&globalElements[0], sstree.nbLocalElements); |
---|
471 | } |
---|
472 | |
---|
473 | /** for each element of the source grid, finds all the neighbouring elements that share an edge |
---|
474 | (filling array neighbourElements). This is used later to compute gradients */ |
---|
475 | void Mapper::buildMeshTopology() |
---|
476 | { |
---|
477 | int mpiSize, mpiRank; |
---|
478 | MPI_Comm_size(communicator, &mpiSize); |
---|
479 | MPI_Comm_rank(communicator, &mpiRank); |
---|
480 | |
---|
481 | vector<Node> *routingList = new vector<Node>[mpiSize]; |
---|
482 | vector<vector<int> > routes(sstree.localTree.leafs.size()); |
---|
483 | |
---|
484 | sstree.routeIntersections(routes, sstree.localTree.leafs); |
---|
485 | |
---|
486 | for (int i = 0; i < routes.size(); ++i) |
---|
487 | for (int k = 0; k < routes[i].size(); ++k) |
---|
488 | routingList[routes[i][k]].push_back(sstree.localTree.leafs[i]); |
---|
489 | routingList[mpiRank].clear(); |
---|
490 | |
---|
491 | |
---|
492 | CMPIRouting mpiRoute(communicator); |
---|
493 | mpiRoute.init(routes); |
---|
494 | int nRecv = mpiRoute.getTotalSourceElement(); |
---|
495 | |
---|
496 | int *nbSendNode = new int[mpiSize]; |
---|
497 | int *nbRecvNode = new int[mpiSize]; |
---|
498 | int *sendMessageSize = new int[mpiSize]; |
---|
499 | int *recvMessageSize = new int[mpiSize]; |
---|
500 | |
---|
501 | for (int rank = 0; rank < mpiSize; rank++) |
---|
502 | { |
---|
503 | nbSendNode[rank] = routingList[rank].size(); |
---|
504 | sendMessageSize[rank] = 0; |
---|
505 | for (size_t j = 0; j < routingList[rank].size(); j++) |
---|
506 | { |
---|
507 | Elt *elt = (Elt *) (routingList[rank][j].data); |
---|
508 | sendMessageSize[rank] += packedPolygonSize(*elt); |
---|
509 | } |
---|
510 | } |
---|
511 | |
---|
512 | MPI_Alltoall(nbSendNode, 1, MPI_INT, nbRecvNode, 1, MPI_INT, communicator); |
---|
513 | MPI_Alltoall(sendMessageSize, 1, MPI_INT, recvMessageSize, 1, MPI_INT, communicator); |
---|
514 | |
---|
515 | char **sendBuffer = new char*[mpiSize]; |
---|
516 | char **recvBuffer = new char*[mpiSize]; |
---|
517 | int *pos = new int[mpiSize]; |
---|
518 | |
---|
519 | for (int rank = 0; rank < mpiSize; rank++) |
---|
520 | { |
---|
521 | if (nbSendNode[rank] > 0) sendBuffer[rank] = new char[sendMessageSize[rank]]; |
---|
522 | if (nbRecvNode[rank] > 0) recvBuffer[rank] = new char[recvMessageSize[rank]]; |
---|
523 | } |
---|
524 | |
---|
525 | for (int rank = 0; rank < mpiSize; rank++) |
---|
526 | { |
---|
527 | pos[rank] = 0; |
---|
528 | for (size_t j = 0; j < routingList[rank].size(); j++) |
---|
529 | { |
---|
530 | Elt *elt = (Elt *) (routingList[rank][j].data); |
---|
531 | packPolygon(*elt, sendBuffer[rank], pos[rank]); |
---|
532 | } |
---|
533 | } |
---|
534 | delete [] routingList; |
---|
535 | |
---|
536 | |
---|
537 | int nbSendRequest = 0; |
---|
538 | int nbRecvRequest = 0; |
---|
539 | MPI_Request *sendRequest = new MPI_Request[mpiSize]; |
---|
540 | MPI_Request *recvRequest = new MPI_Request[mpiSize]; |
---|
541 | MPI_Status *status = new MPI_Status[mpiSize]; |
---|
542 | |
---|
543 | for (int rank = 0; rank < mpiSize; rank++) |
---|
544 | { |
---|
545 | if (nbSendNode[rank] > 0) |
---|
546 | { |
---|
547 | MPI_Issend(sendBuffer[rank], sendMessageSize[rank], MPI_CHAR, rank, 0, communicator, &sendRequest[nbSendRequest]); |
---|
548 | nbSendRequest++; |
---|
549 | } |
---|
550 | if (nbRecvNode[rank] > 0) |
---|
551 | { |
---|
552 | MPI_Irecv(recvBuffer[rank], recvMessageSize[rank], MPI_CHAR, rank, 0, communicator, &recvRequest[nbRecvRequest]); |
---|
553 | nbRecvRequest++; |
---|
554 | } |
---|
555 | } |
---|
556 | |
---|
557 | MPI_Waitall(nbRecvRequest, recvRequest, status); |
---|
558 | MPI_Waitall(nbSendRequest, sendRequest, status); |
---|
559 | |
---|
560 | for (int rank = 0; rank < mpiSize; rank++) |
---|
561 | if (nbSendNode[rank] > 0) delete [] sendBuffer[rank]; |
---|
562 | delete [] sendBuffer; |
---|
563 | |
---|
564 | char **sendBuffer2 = new char*[mpiSize]; |
---|
565 | char **recvBuffer2 = new char*[mpiSize]; |
---|
566 | |
---|
567 | for (int rank = 0; rank < mpiSize; rank++) |
---|
568 | { |
---|
569 | nbSendNode[rank] = 0; |
---|
570 | sendMessageSize[rank] = 0; |
---|
571 | |
---|
572 | if (nbRecvNode[rank] > 0) |
---|
573 | { |
---|
574 | set<NodePtr> neighbourList; |
---|
575 | pos[rank] = 0; |
---|
576 | for (int j = 0; j < nbRecvNode[rank]; j++) |
---|
577 | { |
---|
578 | Elt elt; |
---|
579 | unpackPolygon(elt, recvBuffer[rank], pos[rank]); |
---|
580 | Node node(elt.x, cptRadius(elt), &elt); |
---|
581 | findNeighbour(sstree.localTree.root, &node, neighbourList); |
---|
582 | } |
---|
583 | nbSendNode[rank] = neighbourList.size(); |
---|
584 | for (set<NodePtr>::iterator it = neighbourList.begin(); it != neighbourList.end(); it++) |
---|
585 | { |
---|
586 | Elt *elt = (Elt *) ((*it)->data); |
---|
587 | sendMessageSize[rank] += packedPolygonSize(*elt); |
---|
588 | } |
---|
589 | |
---|
590 | sendBuffer2[rank] = new char[sendMessageSize[rank]]; |
---|
591 | pos[rank] = 0; |
---|
592 | |
---|
593 | for (set<NodePtr>::iterator it = neighbourList.begin(); it != neighbourList.end(); it++) |
---|
594 | { |
---|
595 | Elt *elt = (Elt *) ((*it)->data); |
---|
596 | packPolygon(*elt, sendBuffer2[rank], pos[rank]); |
---|
597 | } |
---|
598 | } |
---|
599 | } |
---|
600 | for (int rank = 0; rank < mpiSize; rank++) |
---|
601 | if (nbRecvNode[rank] > 0) delete [] recvBuffer[rank]; |
---|
602 | delete [] recvBuffer; |
---|
603 | |
---|
604 | |
---|
605 | MPI_Barrier(communicator); |
---|
606 | MPI_Alltoall(nbSendNode, 1, MPI_INT, nbRecvNode, 1, MPI_INT, communicator); |
---|
607 | MPI_Alltoall(sendMessageSize, 1, MPI_INT, recvMessageSize, 1, MPI_INT, communicator); |
---|
608 | |
---|
609 | for (int rank = 0; rank < mpiSize; rank++) |
---|
610 | if (nbRecvNode[rank] > 0) recvBuffer2[rank] = new char[recvMessageSize[rank]]; |
---|
611 | |
---|
612 | nbSendRequest = 0; |
---|
613 | nbRecvRequest = 0; |
---|
614 | |
---|
615 | for (int rank = 0; rank < mpiSize; rank++) |
---|
616 | { |
---|
617 | if (nbSendNode[rank] > 0) |
---|
618 | { |
---|
619 | MPI_Issend(sendBuffer2[rank], sendMessageSize[rank], MPI_CHAR, rank, 0, communicator, &sendRequest[nbSendRequest]); |
---|
620 | nbSendRequest++; |
---|
621 | } |
---|
622 | if (nbRecvNode[rank] > 0) |
---|
623 | { |
---|
624 | MPI_Irecv(recvBuffer2[rank], recvMessageSize[rank], MPI_CHAR, rank, 0, communicator, &recvRequest[nbRecvRequest]); |
---|
625 | nbRecvRequest++; |
---|
626 | } |
---|
627 | } |
---|
628 | |
---|
629 | MPI_Waitall(nbRecvRequest, recvRequest, status); |
---|
630 | MPI_Waitall(nbSendRequest, sendRequest, status); |
---|
631 | |
---|
632 | int nbNeighbourNodes = 0; |
---|
633 | for (int rank = 0; rank < mpiSize; rank++) |
---|
634 | nbNeighbourNodes += nbRecvNode[rank]; |
---|
635 | |
---|
636 | neighbourElements = new Elt[nbNeighbourNodes]; |
---|
637 | nbNeighbourElements = nbNeighbourNodes; |
---|
638 | |
---|
639 | int index = 0; |
---|
640 | for (int rank = 0; rank < mpiSize; rank++) |
---|
641 | { |
---|
642 | pos[rank] = 0; |
---|
643 | for (int j = 0; j < nbRecvNode[rank]; j++) |
---|
644 | { |
---|
645 | unpackPolygon(neighbourElements[index], recvBuffer2[rank], pos[rank]); |
---|
646 | neighbourElements[index].id.ind = sstree.localTree.leafs.size() + index; |
---|
647 | index++; |
---|
648 | } |
---|
649 | } |
---|
650 | for (int rank = 0; rank < mpiSize; rank++) |
---|
651 | { |
---|
652 | if (nbRecvNode[rank] > 0) delete [] recvBuffer2[rank]; |
---|
653 | if (nbSendNode[rank] > 0) delete [] sendBuffer2[rank]; |
---|
654 | } |
---|
655 | delete [] recvBuffer2; |
---|
656 | delete [] sendBuffer2; |
---|
657 | delete [] sendMessageSize; |
---|
658 | delete [] recvMessageSize; |
---|
659 | delete [] nbSendNode; |
---|
660 | delete [] nbRecvNode; |
---|
661 | delete [] sendRequest; |
---|
662 | delete [] recvRequest; |
---|
663 | delete [] status; |
---|
664 | delete [] pos; |
---|
665 | |
---|
666 | /* re-compute on received elements to avoid having to send this information */ |
---|
667 | neighbourNodes.resize(nbNeighbourNodes); |
---|
668 | setCirclesAndLinks(neighbourElements, neighbourNodes); |
---|
669 | cptAllEltsGeom(neighbourElements, nbNeighbourNodes, srcGrid.pole); |
---|
670 | |
---|
671 | /* the local SS tree must include nodes from other cpus if they are potential |
---|
672 | intersector of a local node */ |
---|
673 | sstree.localTree.insertNodes(neighbourNodes); |
---|
674 | |
---|
675 | /* for every local element, |
---|
676 | use the SS-tree to find all elements (including neighbourElements) |
---|
677 | who are potential neighbours because their circles intersect, |
---|
678 | then check all canditates for common edges to build up connectivity information |
---|
679 | */ |
---|
680 | for (int j = 0; j < sstree.localTree.leafs.size(); j++) |
---|
681 | { |
---|
682 | Node& node = sstree.localTree.leafs[j]; |
---|
683 | |
---|
684 | /* find all leafs whoes circles that intersect node's circle and save into node->intersectors */ |
---|
685 | node.search(sstree.localTree.root); |
---|
686 | |
---|
687 | Elt *elt = (Elt *)(node.data); |
---|
688 | |
---|
689 | for (int i = 0; i < elt->n; i++) elt->neighbour[i] = NOT_FOUND; |
---|
690 | |
---|
691 | /* for element `elt` loop through all nodes in the SS-tree |
---|
692 | whoes circles intersect with the circle around `elt` (the SS intersectors) |
---|
693 | and check if they are neighbours in the sense that the two elements share an edge. |
---|
694 | If they do, save this information for elt */ |
---|
695 | for (list<NodePtr>::iterator it = (node.intersectors).begin(); it != (node.intersectors).end(); ++it) |
---|
696 | { |
---|
697 | Elt *elt2 = (Elt *)((*it)->data); |
---|
698 | set_neighbour(*elt, *elt2); |
---|
699 | } |
---|
700 | |
---|
701 | /* |
---|
702 | for (int i = 0; i < elt->n; i++) |
---|
703 | { |
---|
704 | if (elt->neighbour[i] == NOT_FOUND) |
---|
705 | error_exit("neighbour not found"); |
---|
706 | } |
---|
707 | */ |
---|
708 | } |
---|
709 | } |
---|
710 | |
---|
711 | /** @param elements are the target grid elements */ |
---|
712 | void Mapper::computeIntersection(Elt *elements, int nbElements) |
---|
713 | { |
---|
714 | int mpiSize, mpiRank; |
---|
715 | MPI_Comm_size(communicator, &mpiSize); |
---|
716 | MPI_Comm_rank(communicator, &mpiRank); |
---|
717 | |
---|
718 | MPI_Barrier(communicator); |
---|
719 | |
---|
720 | vector<Node> *routingList = new vector<Node>[mpiSize]; |
---|
721 | |
---|
722 | vector<Node> routeNodes; routeNodes.reserve(nbElements); |
---|
723 | for (int j = 0; j < nbElements; j++) |
---|
724 | { |
---|
725 | elements[j].id.ind = j; |
---|
726 | elements[j].id.rank = mpiRank; |
---|
727 | routeNodes.push_back(Node(elements[j].x, cptRadius(elements[j]), &elements[j])); |
---|
728 | } |
---|
729 | |
---|
730 | vector<vector<int> > routes(routeNodes.size()); |
---|
731 | sstree.routeIntersections(routes, routeNodes); |
---|
732 | for (int i = 0; i < routes.size(); ++i) |
---|
733 | for (int k = 0; k < routes[i].size(); ++k) |
---|
734 | routingList[routes[i][k]].push_back(routeNodes[i]); |
---|
735 | |
---|
736 | if (verbose >= 2) |
---|
737 | { |
---|
738 | cout << " --> rank " << mpiRank << " nbElements " << nbElements << " : "; |
---|
739 | for (int rank = 0; rank < mpiSize; rank++) |
---|
740 | cout << routingList[rank].size() << " "; |
---|
741 | cout << endl; |
---|
742 | } |
---|
743 | MPI_Barrier(communicator); |
---|
744 | |
---|
745 | int *nbSendNode = new int[mpiSize]; |
---|
746 | int *nbRecvNode = new int[mpiSize]; |
---|
747 | int *sentMessageSize = new int[mpiSize]; |
---|
748 | int *recvMessageSize = new int[mpiSize]; |
---|
749 | |
---|
750 | for (int rank = 0; rank < mpiSize; rank++) |
---|
751 | { |
---|
752 | nbSendNode[rank] = routingList[rank].size(); |
---|
753 | sentMessageSize[rank] = 0; |
---|
754 | for (size_t j = 0; j < routingList[rank].size(); j++) |
---|
755 | { |
---|
756 | Elt *elt = (Elt *) (routingList[rank][j].data); |
---|
757 | sentMessageSize[rank] += packedPolygonSize(*elt); |
---|
758 | } |
---|
759 | } |
---|
760 | |
---|
761 | MPI_Alltoall(nbSendNode, 1, MPI_INT, nbRecvNode, 1, MPI_INT, communicator); |
---|
762 | MPI_Alltoall(sentMessageSize, 1, MPI_INT, recvMessageSize, 1, MPI_INT, communicator); |
---|
763 | |
---|
764 | int total = 0; |
---|
765 | |
---|
766 | for (int rank = 0; rank < mpiSize; rank++) |
---|
767 | { |
---|
768 | total = total + nbRecvNode[rank]; |
---|
769 | } |
---|
770 | |
---|
771 | if (verbose >= 2) cout << "---> rank " << mpiRank << " : compute intersection : total received nodes " << total << endl; |
---|
772 | char **sendBuffer = new char*[mpiSize]; |
---|
773 | char **recvBuffer = new char*[mpiSize]; |
---|
774 | int *pos = new int[mpiSize]; |
---|
775 | |
---|
776 | for (int rank = 0; rank < mpiSize; rank++) |
---|
777 | { |
---|
778 | if (nbSendNode[rank] > 0) sendBuffer[rank] = new char[sentMessageSize[rank]]; |
---|
779 | if (nbRecvNode[rank] > 0) recvBuffer[rank] = new char[recvMessageSize[rank]]; |
---|
780 | } |
---|
781 | |
---|
782 | for (int rank = 0; rank < mpiSize; rank++) |
---|
783 | { |
---|
784 | pos[rank] = 0; |
---|
785 | for (size_t j = 0; j < routingList[rank].size(); j++) |
---|
786 | { |
---|
787 | Elt* elt = (Elt *) (routingList[rank][j].data); |
---|
788 | packPolygon(*elt, sendBuffer[rank], pos[rank]); |
---|
789 | } |
---|
790 | } |
---|
791 | delete [] routingList; |
---|
792 | |
---|
793 | int nbSendRequest = 0; |
---|
794 | int nbRecvRequest = 0; |
---|
795 | MPI_Request *sendRequest = new MPI_Request[mpiSize]; |
---|
796 | MPI_Request *recvRequest = new MPI_Request[mpiSize]; |
---|
797 | MPI_Status *status = new MPI_Status[mpiSize]; |
---|
798 | |
---|
799 | for (int rank = 0; rank < mpiSize; rank++) |
---|
800 | { |
---|
801 | if (nbSendNode[rank] > 0) |
---|
802 | { |
---|
803 | MPI_Issend(sendBuffer[rank], sentMessageSize[rank], MPI_CHAR, rank, 0, communicator, &sendRequest[nbSendRequest]); |
---|
804 | nbSendRequest++; |
---|
805 | } |
---|
806 | if (nbRecvNode[rank] > 0) |
---|
807 | { |
---|
808 | MPI_Irecv(recvBuffer[rank], recvMessageSize[rank], MPI_CHAR, rank, 0, communicator, &recvRequest[nbRecvRequest]); |
---|
809 | nbRecvRequest++; |
---|
810 | } |
---|
811 | } |
---|
812 | |
---|
813 | MPI_Waitall(nbRecvRequest, recvRequest, status); |
---|
814 | MPI_Waitall(nbSendRequest, sendRequest, status); |
---|
815 | |
---|
816 | |
---|
817 | char **sendBuffer2 = new char*[mpiSize]; |
---|
818 | char **recvBuffer2 = new char*[mpiSize]; |
---|
819 | |
---|
820 | double tic = cputime(); |
---|
821 | for (int rank = 0; rank < mpiSize; rank++) |
---|
822 | { |
---|
823 | sentMessageSize[rank] = 0; |
---|
824 | |
---|
825 | if (nbRecvNode[rank] > 0) |
---|
826 | { |
---|
827 | Elt *recvElt = new Elt[nbRecvNode[rank]]; |
---|
828 | pos[rank] = 0; |
---|
829 | for (int j = 0; j < nbRecvNode[rank]; j++) |
---|
830 | { |
---|
831 | unpackPolygon(recvElt[j], recvBuffer[rank], pos[rank]); |
---|
832 | cptEltGeom(recvElt[j], tgtGrid.pole); |
---|
833 | Node recvNode(recvElt[j].x, cptRadius(recvElt[j]), &recvElt[j]); |
---|
834 | recvNode.search(sstree.localTree.root); |
---|
835 | /* for a node holding an element of the target, loop throught candidates for intersecting source */ |
---|
836 | for (list<NodePtr>::iterator it = (recvNode.intersectors).begin(); it != (recvNode.intersectors).end(); ++it) |
---|
837 | { |
---|
838 | Elt *elt2 = (Elt *) ((*it)->data); |
---|
839 | /* recvElt is target, elt2 is source */ |
---|
840 | // intersect(&recvElt[j], elt2); |
---|
841 | intersect_ym(&recvElt[j], elt2); |
---|
842 | } |
---|
843 | |
---|
844 | if (recvElt[j].is.size() > 0) sentMessageSize[rank] += packIntersectionSize(recvElt[j]); |
---|
845 | |
---|
846 | // here recvNode goes out of scope |
---|
847 | } |
---|
848 | |
---|
849 | if (sentMessageSize[rank] > 0) |
---|
850 | { |
---|
851 | sentMessageSize[rank] += sizeof(int); |
---|
852 | sendBuffer2[rank] = new char[sentMessageSize[rank]]; |
---|
853 | *((int *) sendBuffer2[rank]) = 0; |
---|
854 | pos[rank] = sizeof(int); |
---|
855 | for (int j = 0; j < nbRecvNode[rank]; j++) |
---|
856 | { |
---|
857 | packIntersection(recvElt[j], sendBuffer2[rank], pos[rank]); |
---|
858 | //FIXME should be deleted: recvElt[j].delete_intersections(); // intersection areas have been packed to buffer and won't be used any more |
---|
859 | } |
---|
860 | } |
---|
861 | delete [] recvElt; |
---|
862 | |
---|
863 | } |
---|
864 | } |
---|
865 | delete [] pos; |
---|
866 | |
---|
867 | for (int rank = 0; rank < mpiSize; rank++) |
---|
868 | { |
---|
869 | if (nbSendNode[rank] > 0) delete [] sendBuffer[rank]; |
---|
870 | if (nbRecvNode[rank] > 0) delete [] recvBuffer[rank]; |
---|
871 | nbSendNode[rank] = 0; |
---|
872 | } |
---|
873 | |
---|
874 | if (verbose >= 2) cout << "Rank " << mpiRank << " Compute (internal) intersection " << cputime() - tic << " s" << endl; |
---|
875 | MPI_Alltoall(sentMessageSize, 1, MPI_INT, recvMessageSize, 1, MPI_INT, communicator); |
---|
876 | |
---|
877 | for (int rank = 0; rank < mpiSize; rank++) |
---|
878 | if (recvMessageSize[rank] > 0) |
---|
879 | recvBuffer2[rank] = new char[recvMessageSize[rank]]; |
---|
880 | |
---|
881 | nbSendRequest = 0; |
---|
882 | nbRecvRequest = 0; |
---|
883 | |
---|
884 | for (int rank = 0; rank < mpiSize; rank++) |
---|
885 | { |
---|
886 | if (sentMessageSize[rank] > 0) |
---|
887 | { |
---|
888 | MPI_Issend(sendBuffer2[rank], sentMessageSize[rank], MPI_CHAR, rank, 0, communicator, &sendRequest[nbSendRequest]); |
---|
889 | nbSendRequest++; |
---|
890 | } |
---|
891 | if (recvMessageSize[rank] > 0) |
---|
892 | { |
---|
893 | MPI_Irecv(recvBuffer2[rank], recvMessageSize[rank], MPI_CHAR, rank, 0, communicator, &recvRequest[nbRecvRequest]); |
---|
894 | nbRecvRequest++; |
---|
895 | } |
---|
896 | } |
---|
897 | |
---|
898 | MPI_Waitall(nbRecvRequest, recvRequest, status); |
---|
899 | MPI_Waitall(nbSendRequest, sendRequest, status); |
---|
900 | |
---|
901 | |
---|
902 | |
---|
903 | delete [] sendRequest; |
---|
904 | delete [] recvRequest; |
---|
905 | delete [] status; |
---|
906 | for (int rank = 0; rank < mpiSize; rank++) |
---|
907 | { |
---|
908 | if (nbRecvNode[rank] > 0) |
---|
909 | { |
---|
910 | if (sentMessageSize[rank] > 0) |
---|
911 | delete [] sendBuffer2[rank]; |
---|
912 | } |
---|
913 | |
---|
914 | if (recvMessageSize[rank] > 0) |
---|
915 | { |
---|
916 | unpackIntersection(elements, recvBuffer2[rank]); |
---|
917 | delete [] recvBuffer2[rank]; |
---|
918 | } |
---|
919 | } |
---|
920 | delete [] sendBuffer2; |
---|
921 | delete [] recvBuffer2; |
---|
922 | delete [] sendBuffer; |
---|
923 | delete [] recvBuffer; |
---|
924 | |
---|
925 | delete [] nbSendNode; |
---|
926 | delete [] nbRecvNode; |
---|
927 | delete [] sentMessageSize; |
---|
928 | delete [] recvMessageSize; |
---|
929 | } |
---|
930 | |
---|
931 | Mapper::~Mapper() |
---|
932 | { |
---|
933 | delete [] remapMatrix; |
---|
934 | delete [] srcAddress; |
---|
935 | delete [] srcRank; |
---|
936 | delete [] dstAddress; |
---|
937 | if (neighbourElements) delete [] neighbourElements; |
---|
938 | } |
---|
939 | |
---|
940 | } |
---|