refactor lbpm_serial_decomp
This commit is contained in:
James E McClure
parent
9663b13ffb
commit
ed6853345c
@ -231,7 +231,8 @@ void Domain::Decomp(std::shared_ptr<Database> domain_db )
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//.......................................................................
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//.......................................................................
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// Reading the domain information file
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// Reading the domain information file
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//.......................................................................
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//.......................................................................
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int rank_offset = 0;
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int rank_offset = 0;
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int rank = 0;
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int nprocs, nprocx, nprocy, nprocz, nx, ny, nz;
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int nprocs, nprocx, nprocy, nprocz, nx, ny, nz;
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int64_t global_Nx,global_Ny,global_Nz;
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int64_t global_Nx,global_Ny,global_Nz;
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int64_t i,j,k,n;
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int64_t i,j,k,n;
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@ -249,300 +250,297 @@ void Domain::Decomp(std::shared_ptr<Database> domain_db )
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outlet_layers_z = 0;
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outlet_layers_z = 0;
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checkerSize = 32;
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checkerSize = 32;
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// read the input database
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if (rank() == rank){
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//auto db = std::make_shared<Database>( filename );
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// Read domain parameters
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//auto domain_db = db->getDatabase( "Domain" );
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auto Filename = domain_db->getScalar<std::string>( "Filename" );
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//auto L = domain_db->getVector<double>( "L" );
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// Read domain parameters
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auto size = domain_db->getVector<int>( "n" );
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auto Filename = domain_db->getScalar<std::string>( "Filename" );
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auto SIZE = domain_db->getVector<int>( "N" );
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//auto L = domain_db->getVector<double>( "L" );
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auto nproc = domain_db->getVector<int>( "nproc" );
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auto size = domain_db->getVector<int>( "n" );
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if (domain_db->keyExists( "offset" )){
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auto SIZE = domain_db->getVector<int>( "N" );
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auto offset = domain_db->getVector<int>( "offset" );
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auto nproc = domain_db->getVector<int>( "nproc" );
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xStart = offset[0];
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if (domain_db->keyExists( "offset" )){
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yStart = offset[1];
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auto offset = domain_db->getVector<int>( "offset" );
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zStart = offset[2];
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xStart = offset[0];
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}
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yStart = offset[1];
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if (domain_db->keyExists( "InletLayers" )){
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zStart = offset[2];
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auto InletCount = domain_db->getVector<int>( "InletLayers" );
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}
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inlet_layers_x = InletCount[0];
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if (domain_db->keyExists( "InletLayers" )){
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inlet_layers_y = InletCount[1];
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auto InletCount = domain_db->getVector<int>( "InletLayers" );
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inlet_layers_z = InletCount[2];
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inlet_layers_x = InletCount[0];
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}
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inlet_layers_y = InletCount[1];
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if (domain_db->keyExists( "OutletLayers" )){
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inlet_layers_z = InletCount[2];
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auto OutletCount = domain_db->getVector<int>( "OutletLayers" );
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}
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outlet_layers_x = OutletCount[0];
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if (domain_db->keyExists( "OutletLayers" )){
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outlet_layers_y = OutletCount[1];
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auto OutletCount = domain_db->getVector<int>( "OutletLayers" );
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outlet_layers_z = OutletCount[2];
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outlet_layers_x = OutletCount[0];
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}
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outlet_layers_y = OutletCount[1];
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if (domain_db->keyExists( "checkerSize" )){
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outlet_layers_z = OutletCount[2];
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checkerSize = domain_db->getScalar<int>( "checkerSize" );
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}
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}
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if (domain_db->keyExists( "checkerSize" )){
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else {
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checkerSize = domain_db->getScalar<int>( "checkerSize" );
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checkerSize = SIZE[0];
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}
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}
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else {
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auto ReadValues = domain_db->getVector<int>( "ReadValues" );
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checkerSize = SIZE[0];
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auto WriteValues = domain_db->getVector<int>( "WriteValues" );
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}
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auto ReadType = domain_db->getScalar<std::string>( "ReadType" );
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auto ReadValues = domain_db->getVector<int>( "ReadValues" );
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auto WriteValues = domain_db->getVector<int>( "WriteValues" );
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auto ReadType = domain_db->getScalar<std::string>( "ReadType" );
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if (ReadType == "8bit"){
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}
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else if (ReadType == "16bit"){
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}
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else{
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printf("INPUT ERROR: Valid ReadType are 8bit, 16bit \n");
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ReadType = "8bit";
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}
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nx = size[0];
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ny = size[1];
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nz = size[2];
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nprocx = nproc[0];
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nprocy = nproc[1];
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nprocz = nproc[2];
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global_Nx = SIZE[0];
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global_Ny = SIZE[1];
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global_Nz = SIZE[2];
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printf("Input media: %s\n",Filename.c_str());
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printf("Relabeling %lu values\n",ReadValues.size());
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for (int idx=0; idx<ReadValues.size(); idx++){
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int oldvalue=ReadValues[idx];
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int newvalue=WriteValues[idx];
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printf("oldvalue=%d, newvalue =%d \n",oldvalue,newvalue);
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}
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nprocs=nprocx*nprocy*nprocz;
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char *SegData = NULL;
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// Rank=0 reads the entire segmented data and distributes to worker processes
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if (rank()==0){
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printf("Dimensions of segmented image: %ld x %ld x %ld \n",global_Nx,global_Ny,global_Nz);
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int64_t SIZE = global_Nx*global_Ny*global_Nz;
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SegData = new char[SIZE];
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if (ReadType == "8bit"){
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if (ReadType == "8bit"){
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printf("Reading 8-bit input data \n");
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FILE *SEGDAT = fopen(Filename.c_str(),"rb");
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if (SEGDAT==NULL) ERROR("Domain.cpp: Error reading segmented data");
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size_t ReadSeg;
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ReadSeg=fread(SegData,1,SIZE,SEGDAT);
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if (ReadSeg != size_t(SIZE)) printf("Domain.cpp: Error reading segmented data \n");
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fclose(SEGDAT);
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}
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}
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else if (ReadType == "16bit"){
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else if (ReadType == "16bit"){
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printf("Reading 16-bit input data \n");
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short int *InputData;
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InputData = new short int[SIZE];
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FILE *SEGDAT = fopen(Filename.c_str(),"rb");
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if (SEGDAT==NULL) ERROR("Domain.cpp: Error reading segmented data");
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size_t ReadSeg;
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ReadSeg=fread(InputData,2,SIZE,SEGDAT);
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if (ReadSeg != size_t(SIZE)) printf("Domain.cpp: Error reading segmented data \n");
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fclose(SEGDAT);
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for (int n=0; n<SIZE; n++){
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SegData[n] = char(InputData[n]);
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}
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}
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}
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printf("Read segmented data from %s \n",Filename.c_str());
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else{
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}
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printf("INPUT ERROR: Valid ReadType are 8bit, 16bit \n");
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ReadType = "8bit";
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}
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if (inlet_layers_x > 0){
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nx = size[0];
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// use checkerboard pattern
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ny = size[1];
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printf("Checkerboard pattern at x inlet for %i layers \n",inlet_layers_x);
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nz = size[2];
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for (int k = 0; k<global_Nz; k++){
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nprocx = nproc[0];
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for (int j = 0; j<global_Ny; j++){
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nprocy = nproc[1];
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for (int i = xStart; i < xStart+inlet_layers_x; i++){
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nprocz = nproc[2];
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if ( (j/checkerSize + k/checkerSize)%2 == 0){
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global_Nx = SIZE[0];
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// void checkers
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global_Ny = SIZE[1];
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SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
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global_Nz = SIZE[2];
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}
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else{
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printf("Input media: %s\n",Filename.c_str());
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// solid checkers
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printf("Relabeling %lu values\n",ReadValues.size());
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SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
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for (int idx=0; idx<ReadValues.size(); idx++){
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}
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int oldvalue=ReadValues[idx];
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int newvalue=WriteValues[idx];
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printf("oldvalue=%d, newvalue =%d \n",oldvalue,newvalue);
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}
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nprocs=nprocx*nprocy*nprocz;
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char *SegData = NULL;
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// Rank=0 reads the entire segmented data and distributes to worker processes
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if (rank==0){
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printf("Dimensions of segmented image: %ld x %ld x %ld \n",global_Nx,global_Ny,global_Nz);
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int64_t SIZE = global_Nx*global_Ny*global_Nz;
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SegData = new char[SIZE];
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if (ReadType == "8bit"){
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printf("Reading 8-bit input data \n");
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FILE *SEGDAT = fopen(Filename.c_str(),"rb");
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if (SEGDAT==NULL) ERROR("Domain.cpp: Error reading segmented data");
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size_t ReadSeg;
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ReadSeg=fread(SegData,1,SIZE,SEGDAT);
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if (ReadSeg != size_t(SIZE)) printf("Domain.cpp: Error reading segmented data \n");
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fclose(SEGDAT);
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}
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else if (ReadType == "16bit"){
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printf("Reading 16-bit input data \n");
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short int *InputData;
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InputData = new short int[SIZE];
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FILE *SEGDAT = fopen(Filename.c_str(),"rb");
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if (SEGDAT==NULL) ERROR("Domain.cpp: Error reading segmented data");
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size_t ReadSeg;
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ReadSeg=fread(InputData,2,SIZE,SEGDAT);
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if (ReadSeg != size_t(SIZE)) printf("Domain.cpp: Error reading segmented data \n");
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fclose(SEGDAT);
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for (int n=0; n<SIZE; n++){
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SegData[n] = char(InputData[n]);
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}
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}
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}
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}
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printf("Read segmented data from %s \n",Filename.c_str());
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}
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}
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}
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if (inlet_layers_y > 0){
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if (inlet_layers_x > 0){
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printf("Checkerboard pattern at y inlet for %i layers \n",inlet_layers_y);
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// use checkerboard pattern
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// use checkerboard pattern
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printf("Checkerboard pattern at x inlet for %i layers \n",inlet_layers_x);
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for (int k = 0; k<global_Nz; k++){
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for (int k = 0; k<global_Nz; k++){
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for (int j = yStart; i < yStart+inlet_layers_y; j++){
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for (int j = 0; j<global_Ny; j++){
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for (int i = 0; i<global_Nx; i++){
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for (int i = xStart; i < xStart+inlet_layers_x; i++){
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if ( (i/checkerSize + k/checkerSize)%2 == 0){
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if ( (j/checkerSize + k/checkerSize)%2 == 0){
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// void checkers
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// void checkers
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SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
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SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
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}
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}
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else{
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else{
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// solid checkers
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// solid checkers
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SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
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SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
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}
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}
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}
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}
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}
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if (inlet_layers_z > 0){
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printf("Checkerboard pattern at z inlet for %i layers \n",inlet_layers_z);
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// use checkerboard pattern
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for (int k = zStart; k < zStart+inlet_layers_z; k++){
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for (int j = 0; j<global_Ny; j++){
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for (int i = 0; i<global_Nx; i++){
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if ( (i/checkerSize+j/checkerSize)%2 == 0){
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// void checkers
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SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
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}
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else{
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// solid checkers
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SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
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}
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}
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}
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}
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}
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if (outlet_layers_x > 0){
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// use checkerboard pattern
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printf("Checkerboard pattern at x outlet for %i layers \n",outlet_layers_x);
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for (int k = 0; k<global_Nz; k++){
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for (int j = 0; j<global_Ny; j++){
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for (int i = xStart + nx*nprocx - outlet_layers_x; i < xStart + nx*nprocx; i++){
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if ( (j/checkerSize + k/checkerSize)%2 == 0){
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// void checkers
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SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
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}
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else{
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// solid checkers
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SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
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}
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}
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}
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}
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}
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if (outlet_layers_y > 0){
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printf("Checkerboard pattern at y outlet for %i layers \n",outlet_layers_y);
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// use checkerboard pattern
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for (int k = 0; k<global_Nz; k++){
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for (int j = yStart + ny*nprocy - outlet_layers_y; i < yStart + ny*nprocy; j++){
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for (int i = 0; i<global_Nx; i++){
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if ( (i/checkerSize + k/checkerSize)%2 == 0){
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// void checkers
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SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
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}
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else{
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// solid checkers
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SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
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}
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}
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}
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}
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}
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if (outlet_layers_z > 0){
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printf("Checkerboard pattern at z outlet for %i layers \n",outlet_layers_z);
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// use checkerboard pattern
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for (int k = zStart + nz*nprocz - outlet_layers_z; k < zStart + nz*nprocz; k++){
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for (int j = 0; j<global_Ny; j++){
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for (int i = 0; i<global_Nx; i++){
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if ( (i/checkerSize+j/checkerSize)%2 == 0){
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// void checkers
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SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
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}
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else{
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// solid checkers
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SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
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}
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}
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}
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}
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}
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// Get the rank info
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int64_t N = (nx+2)*(ny+2)*(nz+2);
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// number of sites to use for periodic boundary condition transition zone
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int64_t z_transition_size = (nprocz*nz - (global_Nz - zStart))/2;
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if (z_transition_size < 0) z_transition_size=0;
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char LocalRankFilename[40];
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char *loc_id;
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loc_id = new char [(nx+2)*(ny+2)*(nz+2)];
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std::vector<int> LabelCount(ReadValues.size(),0);
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// Set up the sub-domains
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if (rank()==0){
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printf("Distributing subdomains across %i processors \n",nprocs);
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printf("Process grid: %i x %i x %i \n",nprocx,nprocy,nprocz);
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printf("Subdomain size: %i x %i x %i \n",nx,ny,nz);
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printf("Size of transition region: %ld \n", z_transition_size);
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for (int kp=0; kp<nprocz; kp++){
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for (int jp=0; jp<nprocy; jp++){
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for (int ip=0; ip<nprocx; ip++){
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// rank of the process that gets this subdomain
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int rnk = kp*nprocx*nprocy + jp*nprocx + ip;
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// Pack and send the subdomain for rnk
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for (k=0;k<nz+2;k++){
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for (j=0;j<ny+2;j++){
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for (i=0;i<nx+2;i++){
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int64_t x = xStart + ip*nx + i-1;
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int64_t y = yStart + jp*ny + j-1;
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// int64_t z = zStart + kp*nz + k-1;
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int64_t z = zStart + kp*nz + k-1 - z_transition_size;
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if (x<xStart) x=xStart;
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if (!(x<global_Nx)) x=global_Nx-1;
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if (y<yStart) y=yStart;
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if (!(y<global_Ny)) y=global_Ny-1;
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if (z<zStart) z=zStart;
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if (!(z<global_Nz)) z=global_Nz-1;
|
|
||||||
int64_t nlocal = k*(nx+2)*(ny+2) + j*(nx+2) + i;
|
|
||||||
int64_t nglobal = z*global_Nx*global_Ny+y*global_Nx+x;
|
|
||||||
loc_id[nlocal] = SegData[nglobal];
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
// relabel the data
|
}
|
||||||
for (k=0;k<nz+2;k++){
|
}
|
||||||
for (j=0;j<ny+2;j++){
|
}
|
||||||
for (i=0;i<nx+2;i++){
|
|
||||||
n = k*(nx+2)*(ny+2) + j*(nx+2) + i;;
|
if (inlet_layers_y > 0){
|
||||||
char locval = loc_id[n];
|
printf("Checkerboard pattern at y inlet for %i layers \n",inlet_layers_y);
|
||||||
for (int idx=0; idx<ReadValues.size(); idx++){
|
// use checkerboard pattern
|
||||||
signed char oldvalue=ReadValues[idx];
|
for (int k = 0; k<global_Nz; k++){
|
||||||
signed char newvalue=WriteValues[idx];
|
for (int j = yStart; i < yStart+inlet_layers_y; j++){
|
||||||
if (locval == oldvalue){
|
for (int i = 0; i<global_Nx; i++){
|
||||||
loc_id[n] = newvalue;
|
if ( (i/checkerSize + k/checkerSize)%2 == 0){
|
||||||
LabelCount[idx]++;
|
// void checkers
|
||||||
idx = ReadValues.size();
|
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
|
||||||
}
|
}
|
||||||
|
else{
|
||||||
|
// solid checkers
|
||||||
|
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (inlet_layers_z > 0){
|
||||||
|
printf("Checkerboard pattern at z inlet for %i layers \n",inlet_layers_z);
|
||||||
|
// use checkerboard pattern
|
||||||
|
for (int k = zStart; k < zStart+inlet_layers_z; k++){
|
||||||
|
for (int j = 0; j<global_Ny; j++){
|
||||||
|
for (int i = 0; i<global_Nx; i++){
|
||||||
|
if ( (i/checkerSize+j/checkerSize)%2 == 0){
|
||||||
|
// void checkers
|
||||||
|
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
|
||||||
|
}
|
||||||
|
else{
|
||||||
|
// solid checkers
|
||||||
|
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (outlet_layers_x > 0){
|
||||||
|
// use checkerboard pattern
|
||||||
|
printf("Checkerboard pattern at x outlet for %i layers \n",outlet_layers_x);
|
||||||
|
for (int k = 0; k<global_Nz; k++){
|
||||||
|
for (int j = 0; j<global_Ny; j++){
|
||||||
|
for (int i = xStart + nx*nprocx - outlet_layers_x; i < xStart + nx*nprocx; i++){
|
||||||
|
if ( (j/checkerSize + k/checkerSize)%2 == 0){
|
||||||
|
// void checkers
|
||||||
|
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
|
||||||
|
}
|
||||||
|
else{
|
||||||
|
// solid checkers
|
||||||
|
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (outlet_layers_y > 0){
|
||||||
|
printf("Checkerboard pattern at y outlet for %i layers \n",outlet_layers_y);
|
||||||
|
// use checkerboard pattern
|
||||||
|
for (int k = 0; k<global_Nz; k++){
|
||||||
|
for (int j = yStart + ny*nprocy - outlet_layers_y; i < yStart + ny*nprocy; j++){
|
||||||
|
for (int i = 0; i<global_Nx; i++){
|
||||||
|
if ( (i/checkerSize + k/checkerSize)%2 == 0){
|
||||||
|
// void checkers
|
||||||
|
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
|
||||||
|
}
|
||||||
|
else{
|
||||||
|
// solid checkers
|
||||||
|
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (outlet_layers_z > 0){
|
||||||
|
printf("Checkerboard pattern at z outlet for %i layers \n",outlet_layers_z);
|
||||||
|
// use checkerboard pattern
|
||||||
|
for (int k = zStart + nz*nprocz - outlet_layers_z; k < zStart + nz*nprocz; k++){
|
||||||
|
for (int j = 0; j<global_Ny; j++){
|
||||||
|
for (int i = 0; i<global_Nx; i++){
|
||||||
|
if ( (i/checkerSize+j/checkerSize)%2 == 0){
|
||||||
|
// void checkers
|
||||||
|
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
|
||||||
|
}
|
||||||
|
else{
|
||||||
|
// solid checkers
|
||||||
|
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// Get the rank info
|
||||||
|
int64_t N = (nx+2)*(ny+2)*(nz+2);
|
||||||
|
|
||||||
|
// number of sites to use for periodic boundary condition transition zone
|
||||||
|
int64_t z_transition_size = (nprocz*nz - (global_Nz - zStart))/2;
|
||||||
|
if (z_transition_size < 0) z_transition_size=0;
|
||||||
|
|
||||||
|
char LocalRankFilename[40];
|
||||||
|
char *loc_id;
|
||||||
|
loc_id = new char [(nx+2)*(ny+2)*(nz+2)];
|
||||||
|
|
||||||
|
std::vector<int> LabelCount(ReadValues.size(),0);
|
||||||
|
// Set up the sub-domains
|
||||||
|
if (rank==0){
|
||||||
|
printf("Distributing subdomains across %i processors \n",nprocs);
|
||||||
|
printf("Process grid: %i x %i x %i \n",nprocx,nprocy,nprocz);
|
||||||
|
printf("Subdomain size: %i x %i x %i \n",nx,ny,nz);
|
||||||
|
printf("Size of transition region: %ld \n", z_transition_size);
|
||||||
|
|
||||||
|
for (int kp=0; kp<nprocz; kp++){
|
||||||
|
for (int jp=0; jp<nprocy; jp++){
|
||||||
|
for (int ip=0; ip<nprocx; ip++){
|
||||||
|
// rank of the process that gets this subdomain
|
||||||
|
int rnk = kp*nprocx*nprocy + jp*nprocx + ip;
|
||||||
|
// Pack and send the subdomain for rnk
|
||||||
|
for (k=0;k<nz+2;k++){
|
||||||
|
for (j=0;j<ny+2;j++){
|
||||||
|
for (i=0;i<nx+2;i++){
|
||||||
|
int64_t x = xStart + ip*nx + i-1;
|
||||||
|
int64_t y = yStart + jp*ny + j-1;
|
||||||
|
// int64_t z = zStart + kp*nz + k-1;
|
||||||
|
int64_t z = zStart + kp*nz + k-1 - z_transition_size;
|
||||||
|
if (x<xStart) x=xStart;
|
||||||
|
if (!(x<global_Nx)) x=global_Nx-1;
|
||||||
|
if (y<yStart) y=yStart;
|
||||||
|
if (!(y<global_Ny)) y=global_Ny-1;
|
||||||
|
if (z<zStart) z=zStart;
|
||||||
|
if (!(z<global_Nz)) z=global_Nz-1;
|
||||||
|
int64_t nlocal = k*(nx+2)*(ny+2) + j*(nx+2) + i;
|
||||||
|
int64_t nglobal = z*global_Nx*global_Ny+y*global_Nx+x;
|
||||||
|
loc_id[nlocal] = SegData[nglobal];
|
||||||
}
|
}
|
||||||
//if (loc_id[n]==char(SOLID)) loc_id[n] = 0;
|
|
||||||
//else if (loc_id[n]==char(NWP)) loc_id[n] = 1;
|
|
||||||
//else loc_id[n] = 2;
|
|
||||||
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
// relabel the data
|
||||||
|
for (k=0;k<nz+2;k++){
|
||||||
|
for (j=0;j<ny+2;j++){
|
||||||
|
for (i=0;i<nx+2;i++){
|
||||||
|
n = k*(nx+2)*(ny+2) + j*(nx+2) + i;;
|
||||||
|
char locval = loc_id[n];
|
||||||
|
for (int idx=0; idx<ReadValues.size(); idx++){
|
||||||
|
signed char oldvalue=ReadValues[idx];
|
||||||
|
signed char newvalue=WriteValues[idx];
|
||||||
|
if (locval == oldvalue){
|
||||||
|
loc_id[n] = newvalue;
|
||||||
|
LabelCount[idx]++;
|
||||||
|
idx = ReadValues.size();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
//if (loc_id[n]==char(SOLID)) loc_id[n] = 0;
|
||||||
|
//else if (loc_id[n]==char(NWP)) loc_id[n] = 1;
|
||||||
|
//else loc_id[n] = 2;
|
||||||
|
|
||||||
// Write the data for this rank data
|
}
|
||||||
sprintf(LocalRankFilename,"ID.%05i",rnk+rank_offset);
|
}
|
||||||
FILE *ID = fopen(LocalRankFilename,"wb");
|
}
|
||||||
fwrite(loc_id,1,(nx+2)*(ny+2)*(nz+2),ID);
|
|
||||||
fclose(ID);
|
// Write the data for this rank data
|
||||||
|
sprintf(LocalRankFilename,"ID.%05i",rnk+rank_offset);
|
||||||
|
FILE *ID = fopen(LocalRankFilename,"wb");
|
||||||
|
fwrite(loc_id,1,(nx+2)*(ny+2)*(nz+2),ID);
|
||||||
|
fclose(ID);
|
||||||
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
for (int idx=0; idx<ReadValues.size(); idx++){
|
||||||
|
int label=ReadValues[idx];
|
||||||
|
int count=LabelCount[idx];
|
||||||
|
printf("Label=%d, Count=%d \n",label,count);
|
||||||
|
}
|
||||||
}
|
}
|
||||||
for (int idx=0; idx<ReadValues.size(); idx++){
|
|
||||||
int label=ReadValues[idx];
|
|
||||||
int count=LabelCount[idx];
|
|
||||||
printf("Label=%d, Count=%d \n",label,count);
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/********************************************************
|
/********************************************************
|
||||||
|
|||||||
@ -17,25 +17,6 @@ int main(int argc, char **argv)
|
|||||||
{
|
{
|
||||||
|
|
||||||
int rank=0;
|
int rank=0;
|
||||||
|
|
||||||
/* bool MULTINPUT=false;
|
|
||||||
|
|
||||||
int NWP,SOLID,rank_offset;
|
|
||||||
SOLID=atoi(argv[1]);
|
|
||||||
NWP=atoi(argv[2]);
|
|
||||||
|
|
||||||
if (rank==0){
|
|
||||||
printf("Solid Label: %i \n",SOLID);
|
|
||||||
printf("NWP Label: %i \n",NWP);
|
|
||||||
}
|
|
||||||
if (argc > 3){
|
|
||||||
rank_offset = atoi(argv[3]);
|
|
||||||
}
|
|
||||||
else{
|
|
||||||
MULTINPUT=true;
|
|
||||||
rank_offset=0;
|
|
||||||
}
|
|
||||||
*/
|
|
||||||
string filename;
|
string filename;
|
||||||
if (argc > 1)
|
if (argc > 1)
|
||||||
filename=argv[1];
|
filename=argv[1];
|
||||||
@ -44,320 +25,12 @@ int main(int argc, char **argv)
|
|||||||
}
|
}
|
||||||
int rank_offset=0;
|
int rank_offset=0;
|
||||||
|
|
||||||
//.......................................................................
|
|
||||||
// Reading the domain information file
|
|
||||||
//.......................................................................
|
|
||||||
int nprocs, nprocx, nprocy, nprocz, nx, ny, nz, nspheres;
|
|
||||||
double Lx, Ly, Lz;
|
|
||||||
int64_t Nx,Ny,Nz;
|
|
||||||
int64_t i,j,k,n;
|
|
||||||
int BC=0;
|
|
||||||
int64_t xStart,yStart,zStart;
|
|
||||||
int checkerSize;
|
|
||||||
int inlet_count_x, inlet_count_y, inlet_count_z;
|
|
||||||
int outlet_count_x, outlet_count_y, outlet_count_z;
|
|
||||||
// char fluidValue,solidValue;
|
|
||||||
|
|
||||||
xStart=yStart=zStart=0;
|
|
||||||
inlet_count_x = 0;
|
|
||||||
inlet_count_y = 0;
|
|
||||||
inlet_count_z = 0;
|
|
||||||
outlet_count_x = 0;
|
|
||||||
outlet_count_y = 0;
|
|
||||||
outlet_count_z = 0;
|
|
||||||
checkerSize = 32;
|
|
||||||
// read the input database
|
// read the input database
|
||||||
auto db = std::make_shared<Database>( filename );
|
auto db = std::make_shared<Database>( filename );
|
||||||
auto domain_db = db->getDatabase( "Domain" );
|
auto domain_db = db->getDatabase( "Domain" );
|
||||||
|
|
||||||
// Read domain parameters
|
std::shared_ptr<Domain> Dm (new Domain(domain_db,comm));
|
||||||
auto Filename = domain_db->getScalar<std::string>( "Filename" );
|
|
||||||
//auto L = domain_db->getVector<double>( "L" );
|
|
||||||
auto size = domain_db->getVector<int>( "n" );
|
|
||||||
auto SIZE = domain_db->getVector<int>( "N" );
|
|
||||||
auto nproc = domain_db->getVector<int>( "nproc" );
|
|
||||||
if (domain_db->keyExists( "offset" )){
|
|
||||||
auto offset = domain_db->getVector<int>( "offset" );
|
|
||||||
xStart = offset[0];
|
|
||||||
yStart = offset[1];
|
|
||||||
zStart = offset[2];
|
|
||||||
}
|
|
||||||
if (domain_db->keyExists( "InletLayers" )){
|
|
||||||
auto InletCount = domain_db->getVector<int>( "InletLayers" );
|
|
||||||
inlet_count_x = InletCount[0];
|
|
||||||
inlet_count_y = InletCount[1];
|
|
||||||
inlet_count_z = InletCount[2];
|
|
||||||
}
|
|
||||||
if (domain_db->keyExists( "OutletLayers" )){
|
|
||||||
auto OutletCount = domain_db->getVector<int>( "OutletLayers" );
|
|
||||||
outlet_count_x = OutletCount[0];
|
|
||||||
outlet_count_y = OutletCount[1];
|
|
||||||
outlet_count_z = OutletCount[2];
|
|
||||||
}
|
|
||||||
if (domain_db->keyExists( "checkerSize" )){
|
|
||||||
checkerSize = domain_db->getScalar<int>( "checkerSize" );
|
|
||||||
}
|
|
||||||
else {
|
|
||||||
checkerSize = SIZE[0];
|
|
||||||
}
|
|
||||||
auto ReadValues = domain_db->getVector<int>( "ReadValues" );
|
|
||||||
auto WriteValues = domain_db->getVector<int>( "WriteValues" );
|
|
||||||
auto ReadType = domain_db->getScalar<std::string>( "ReadType" );
|
|
||||||
if (ReadType == "8bit"){
|
|
||||||
}
|
|
||||||
else if (ReadType == "16bit"){
|
|
||||||
}
|
|
||||||
else{
|
|
||||||
printf("INPUT ERROR: Valid ReadType are 8bit, 16bit \n");
|
|
||||||
ReadType = "8bit";
|
|
||||||
}
|
|
||||||
|
|
||||||
nx = size[0];
|
Dm->Decomp(domain_db);
|
||||||
ny = size[1];
|
|
||||||
nz = size[2];
|
|
||||||
nprocx = nproc[0];
|
|
||||||
nprocy = nproc[1];
|
|
||||||
nprocz = nproc[2];
|
|
||||||
Nx = SIZE[0];
|
|
||||||
Ny = SIZE[1];
|
|
||||||
Nz = SIZE[2];
|
|
||||||
|
|
||||||
printf("Input media: %s\n",Filename.c_str());
|
|
||||||
printf("Relabeling %lu values\n",ReadValues.size());
|
|
||||||
for (int idx=0; idx<ReadValues.size(); idx++){
|
|
||||||
int oldvalue=ReadValues[idx];
|
|
||||||
int newvalue=WriteValues[idx];
|
|
||||||
printf("oldvalue=%d, newvalue =%d \n",oldvalue,newvalue);
|
|
||||||
}
|
|
||||||
|
|
||||||
nprocs=nprocx*nprocy*nprocz;
|
|
||||||
|
|
||||||
char *SegData = NULL;
|
|
||||||
// Rank=0 reads the entire segmented data and distributes to worker processes
|
|
||||||
if (rank==0){
|
|
||||||
printf("Dimensions of segmented image: %ld x %ld x %ld \n",Nx,Ny,Nz);
|
|
||||||
int64_t SIZE = Nx*Ny*Nz;
|
|
||||||
SegData = new char[SIZE];
|
|
||||||
if (ReadType == "8bit"){
|
|
||||||
printf("Reading 8-bit input data \n");
|
|
||||||
FILE *SEGDAT = fopen(Filename.c_str(),"rb");
|
|
||||||
if (SEGDAT==NULL) ERROR("Error reading segmented data");
|
|
||||||
size_t ReadSeg;
|
|
||||||
ReadSeg=fread(SegData,1,SIZE,SEGDAT);
|
|
||||||
if (ReadSeg != size_t(SIZE)) printf("lbpm_segmented_decomp: Error reading segmented data (rank=%i)\n",rank);
|
|
||||||
fclose(SEGDAT);
|
|
||||||
}
|
|
||||||
else if (ReadType == "16bit"){
|
|
||||||
printf("Reading 16-bit input data \n");
|
|
||||||
short int *InputData;
|
|
||||||
InputData = new short int[SIZE];
|
|
||||||
FILE *SEGDAT = fopen(Filename.c_str(),"rb");
|
|
||||||
if (SEGDAT==NULL) ERROR("Error reading segmented data");
|
|
||||||
size_t ReadSeg;
|
|
||||||
ReadSeg=fread(InputData,2,SIZE,SEGDAT);
|
|
||||||
if (ReadSeg != size_t(SIZE)) printf("lbpm_segmented_decomp: Error reading segmented data (rank=%i)\n",rank);
|
|
||||||
fclose(SEGDAT);
|
|
||||||
for (int n=0; n<SIZE; n++){
|
|
||||||
SegData[n] = char(InputData[n]);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
printf("Read segmented data from %s \n",Filename.c_str());
|
|
||||||
}
|
|
||||||
|
|
||||||
if (inlet_count_x > 0){
|
|
||||||
// use checkerboard pattern
|
|
||||||
printf("Checkerboard pattern at x inlet for %i layers \n",inlet_count_x);
|
|
||||||
for (int k = 0; k<Nz; k++){
|
|
||||||
for (int j = 0; j<Ny; j++){
|
|
||||||
for (int i = xStart; i < xStart+inlet_count_x; i++){
|
|
||||||
if ( (j/checkerSize + k/checkerSize)%2 == 0){
|
|
||||||
// void checkers
|
|
||||||
SegData[k*Nx*Ny+j*Nx+i] = 2;
|
|
||||||
}
|
|
||||||
else{
|
|
||||||
// solid checkers
|
|
||||||
SegData[k*Nx*Ny+j*Nx+i] = 0;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
if (inlet_count_y > 0){
|
|
||||||
printf("Checkerboard pattern at y inlet for %i layers \n",inlet_count_y);
|
|
||||||
// use checkerboard pattern
|
|
||||||
for (int k = 0; k<Nz; k++){
|
|
||||||
for (int j = yStart; i < yStart+inlet_count_y; j++){
|
|
||||||
for (int i = 0; i<Nx; i++){
|
|
||||||
if ( (i/checkerSize + k/checkerSize)%2 == 0){
|
|
||||||
// void checkers
|
|
||||||
SegData[k*Nx*Ny+j*Nx+i] = 2;
|
|
||||||
}
|
|
||||||
else{
|
|
||||||
// solid checkers
|
|
||||||
SegData[k*Nx*Ny+j*Nx+i] = 0;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
if (inlet_count_z > 0){
|
|
||||||
printf("Checkerboard pattern at z inlet for %i layers \n",inlet_count_z);
|
|
||||||
// use checkerboard pattern
|
|
||||||
for (int k = zStart; k < zStart+inlet_count_z; k++){
|
|
||||||
for (int j = 0; j<Ny; j++){
|
|
||||||
for (int i = 0; i<Nx; i++){
|
|
||||||
if ( (i/checkerSize+j/checkerSize)%2 == 0){
|
|
||||||
// void checkers
|
|
||||||
SegData[k*Nx*Ny+j*Nx+i] = 2;
|
|
||||||
}
|
|
||||||
else{
|
|
||||||
// solid checkers
|
|
||||||
SegData[k*Nx*Ny+j*Nx+i] = 0;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
if (outlet_count_x > 0){
|
|
||||||
// use checkerboard pattern
|
|
||||||
printf("Checkerboard pattern at x outlet for %i layers \n",outlet_count_x);
|
|
||||||
for (int k = 0; k<Nz; k++){
|
|
||||||
for (int j = 0; j<Ny; j++){
|
|
||||||
for (int i = xStart + nx*nprocx - outlet_count_x; i < xStart + nx*nprocx; i++){
|
|
||||||
if ( (j/checkerSize + k/checkerSize)%2 == 0){
|
|
||||||
// void checkers
|
|
||||||
SegData[k*Nx*Ny+j*Nx+i] = 2;
|
|
||||||
}
|
|
||||||
else{
|
|
||||||
// solid checkers
|
|
||||||
SegData[k*Nx*Ny+j*Nx+i] = 0;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
if (outlet_count_y > 0){
|
|
||||||
printf("Checkerboard pattern at y outlet for %i layers \n",outlet_count_y);
|
|
||||||
// use checkerboard pattern
|
|
||||||
for (int k = 0; k<Nz; k++){
|
|
||||||
for (int j = yStart + ny*nprocy - outlet_count_y; i < yStart + ny*nprocy; j++){
|
|
||||||
for (int i = 0; i<Nx; i++){
|
|
||||||
if ( (i/checkerSize + k/checkerSize)%2 == 0){
|
|
||||||
// void checkers
|
|
||||||
SegData[k*Nx*Ny+j*Nx+i] = 2;
|
|
||||||
}
|
|
||||||
else{
|
|
||||||
// solid checkers
|
|
||||||
SegData[k*Nx*Ny+j*Nx+i] = 0;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
if (outlet_count_z > 0){
|
|
||||||
printf("Checkerboard pattern at z outlet for %i layers \n",outlet_count_z);
|
|
||||||
// use checkerboard pattern
|
|
||||||
for (int k = zStart + nz*nprocz - outlet_count_z; k < zStart + nz*nprocz; k++){
|
|
||||||
for (int j = 0; j<Ny; j++){
|
|
||||||
for (int i = 0; i<Nx; i++){
|
|
||||||
if ( (i/checkerSize+j/checkerSize)%2 == 0){
|
|
||||||
// void checkers
|
|
||||||
SegData[k*Nx*Ny+j*Nx+i] = 2;
|
|
||||||
}
|
|
||||||
else{
|
|
||||||
// solid checkers
|
|
||||||
SegData[k*Nx*Ny+j*Nx+i] = 0;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
// Get the rank info
|
|
||||||
int64_t N = (nx+2)*(ny+2)*(nz+2);
|
|
||||||
|
|
||||||
// number of sites to use for periodic boundary condition transition zone
|
|
||||||
int64_t z_transition_size = (nprocz*nz - (Nz - zStart))/2;
|
|
||||||
if (z_transition_size < 0) z_transition_size=0;
|
|
||||||
|
|
||||||
char LocalRankFilename[40];
|
|
||||||
char *loc_id;
|
|
||||||
loc_id = new char [(nx+2)*(ny+2)*(nz+2)];
|
|
||||||
|
|
||||||
std::vector<int> LabelCount(ReadValues.size(),0);
|
|
||||||
// Set up the sub-domains
|
|
||||||
if (rank==0){
|
|
||||||
printf("Distributing subdomains across %i processors \n",nprocs);
|
|
||||||
printf("Process grid: %i x %i x %i \n",nprocx,nprocy,nprocz);
|
|
||||||
printf("Subdomain size: %i x %i x %i \n",nx,ny,nz);
|
|
||||||
printf("Size of transition region: %ld \n", z_transition_size);
|
|
||||||
|
|
||||||
for (int kp=0; kp<nprocz; kp++){
|
|
||||||
for (int jp=0; jp<nprocy; jp++){
|
|
||||||
for (int ip=0; ip<nprocx; ip++){
|
|
||||||
// rank of the process that gets this subdomain
|
|
||||||
int rnk = kp*nprocx*nprocy + jp*nprocx + ip;
|
|
||||||
// Pack and send the subdomain for rnk
|
|
||||||
for (k=0;k<nz+2;k++){
|
|
||||||
for (j=0;j<ny+2;j++){
|
|
||||||
for (i=0;i<nx+2;i++){
|
|
||||||
int64_t x = xStart + ip*nx + i-1;
|
|
||||||
int64_t y = yStart + jp*ny + j-1;
|
|
||||||
// int64_t z = zStart + kp*nz + k-1;
|
|
||||||
int64_t z = zStart + kp*nz + k-1 - z_transition_size;
|
|
||||||
if (x<xStart) x=xStart;
|
|
||||||
if (!(x<Nx)) x=Nx-1;
|
|
||||||
if (y<yStart) y=yStart;
|
|
||||||
if (!(y<Ny)) y=Ny-1;
|
|
||||||
if (z<zStart) z=zStart;
|
|
||||||
if (!(z<Nz)) z=Nz-1;
|
|
||||||
int64_t nlocal = k*(nx+2)*(ny+2) + j*(nx+2) + i;
|
|
||||||
int64_t nglobal = z*Nx*Ny+y*Nx+x;
|
|
||||||
loc_id[nlocal] = SegData[nglobal];
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
// relabel the data
|
|
||||||
for (k=0;k<nz+2;k++){
|
|
||||||
for (j=0;j<ny+2;j++){
|
|
||||||
for (i=0;i<nx+2;i++){
|
|
||||||
n = k*(nx+2)*(ny+2) + j*(nx+2) + i;;
|
|
||||||
char locval = loc_id[n];
|
|
||||||
for (int idx=0; idx<ReadValues.size(); idx++){
|
|
||||||
signed char oldvalue=ReadValues[idx];
|
|
||||||
signed char newvalue=WriteValues[idx];
|
|
||||||
if (locval == oldvalue){
|
|
||||||
loc_id[n] = newvalue;
|
|
||||||
LabelCount[idx]++;
|
|
||||||
idx = ReadValues.size();
|
|
||||||
}
|
|
||||||
}
|
|
||||||
//if (loc_id[n]==char(SOLID)) loc_id[n] = 0;
|
|
||||||
//else if (loc_id[n]==char(NWP)) loc_id[n] = 1;
|
|
||||||
//else loc_id[n] = 2;
|
|
||||||
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
// Write the data for this rank data
|
|
||||||
sprintf(LocalRankFilename,"ID.%05i",rnk+rank_offset);
|
|
||||||
FILE *ID = fopen(LocalRankFilename,"wb");
|
|
||||||
fwrite(loc_id,1,(nx+2)*(ny+2)*(nz+2),ID);
|
|
||||||
fclose(ID);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
for (int idx=0; idx<ReadValues.size(); idx++){
|
|
||||||
int label=ReadValues[idx];
|
|
||||||
int count=LabelCount[idx];
|
|
||||||
printf("Label=%d, Count=%d \n",label,count);
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|||||||
Loading…
Reference in New Issue
Block a user