Added support for multi-input domains in lbpm_segmented_decomp
This commit is contained in:
James E McClure
parent
9f046c9638
commit
7dc8f33d44
@ -18,294 +18,308 @@ int main(int argc, char **argv)
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// Initialize MPI
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int rank, nprocs;
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MPI_Init(&argc,&argv);
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MPI_Comm comm = MPI_COMM_WORLD;
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MPI_Comm_rank(comm,&rank);
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MPI_Comm_size(comm,&nprocs);
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{
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int SOLID=atoi(argv[1]);
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int NWP=atoi(argv[2]);
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//char NWP,SOLID;
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//SOLID=argv[1][0];
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//NWP=argv[2][0];
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if (rank==0){
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printf("Solid Label: %i \n",SOLID);
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printf("NWP Label: %i \n",NWP);
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}
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//.......................................................................
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// Reading the domain information file
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//.......................................................................
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int nprocx, nprocy, nprocz, nx, ny, nz, nspheres;
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double Lx, Ly, Lz;
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int Nx,Ny,Nz;
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int i,j,k,n;
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int BC=0;
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char Filename[40];
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int xStart,yStart,zStart;
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// char fluidValue,solidValue;
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std::vector<char> solidValues;
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std::vector<char> nwpValues;
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std::string line;
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if (rank==0){
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ifstream domain("Domain.in");
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domain >> nprocx;
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domain >> nprocy;
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domain >> nprocz;
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domain >> nx;
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domain >> ny;
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domain >> nz;
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domain >> nspheres;
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domain >> Lx;
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domain >> Ly;
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domain >> Lz;
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bool MULTINPUT=false;
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ifstream image("Segmented.in");
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image >> Filename; // Name of data file containing segmented data
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image >> Nx; // size of the binary file
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image >> Ny;
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image >> Nz;
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image >> xStart; // offset for the starting voxel
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image >> yStart;
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image >> zStart;
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int NWP,SOLID,rank_offset;
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SOLID=atoi(argv[1]);
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NWP=atoi(argv[2]);
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//char NWP,SOLID;
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//SOLID=argv[1][0];
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//NWP=argv[2][0];
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if (rank==0){
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printf("Solid Label: %i \n",SOLID);
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printf("NWP Label: %i \n",NWP);
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}
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if (argc > 3){
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rank_offset = atoi(argv[3]);
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}
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else{
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MULTINPUT=true;
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rank_offset=0;
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}
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}
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MPI_Barrier(comm);
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// Computational domain
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//.................................................
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MPI_Bcast(&nx,1,MPI_INT,0,comm);
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MPI_Bcast(&ny,1,MPI_INT,0,comm);
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MPI_Bcast(&nz,1,MPI_INT,0,comm);
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MPI_Bcast(&nprocx,1,MPI_INT,0,comm);
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MPI_Bcast(&nprocy,1,MPI_INT,0,comm);
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MPI_Bcast(&nprocz,1,MPI_INT,0,comm);
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MPI_Bcast(&nspheres,1,MPI_INT,0,comm);
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MPI_Bcast(&Lx,1,MPI_DOUBLE,0,comm);
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MPI_Bcast(&Ly,1,MPI_DOUBLE,0,comm);
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MPI_Bcast(&Lz,1,MPI_DOUBLE,0,comm);
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//.................................................
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MPI_Bcast(&Ny,1,MPI_INT,0,comm);
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MPI_Bcast(&Ny,1,MPI_INT,0,comm);
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MPI_Bcast(&Nz,1,MPI_INT,0,comm);
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MPI_Bcast(&xStart,1,MPI_INT,0,comm);
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MPI_Bcast(&yStart,1,MPI_INT,0,comm);
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MPI_Bcast(&zStart,1,MPI_INT,0,comm);
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//.................................................
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MPI_Barrier(comm);
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//.......................................................................
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// Reading the domain information file
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//.......................................................................
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int nprocx, nprocy, nprocz, nx, ny, nz, nspheres;
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double Lx, Ly, Lz;
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int Nx,Ny,Nz;
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int i,j,k,n;
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int BC=0;
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char Filename[40];
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int xStart,yStart,zStart;
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// char fluidValue,solidValue;
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// Check that the number of processors >= the number of ranks
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if ( rank==0 ) {
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printf("Number of MPI ranks required: %i \n", nprocx*nprocy*nprocz);
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printf("Number of MPI ranks used: %i \n", nprocs);
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printf("Full domain size: %i x %i x %i \n",nx*nprocx,ny*nprocy,nz*nprocz);
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}
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if ( nprocs < nprocx*nprocy*nprocz ){
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ERROR("Insufficient number of processors");
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}
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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: %i x %i x %i \n",Nx,Ny,Nz);
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SegData = new char[Nx*Ny*Nz];
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FILE *SEGDAT = fopen(Filename,"rb");
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if (SEGDAT==NULL) ERROR("Error reading segmented data");
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size_t ReadSeg;
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ReadSeg=fread(SegData,1,Nx*Ny*Nz,SEGDAT);
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if (ReadSeg != size_t(Nx*Ny*Nz)) printf("lbpm_segmented_decomp: Error reading segmented data (rank=%i)\n",rank);
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fclose(SEGDAT);
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printf("Read segmented data from %s \n",Filename);
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}
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MPI_Barrier(comm);
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std::vector<char> solidValues;
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std::vector<char> nwpValues;
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std::string line;
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// Get the rank info
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int N = (nx+2)*(ny+2)*(nz+2);
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Domain Dm(nx,ny,nz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,BC);
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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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n = k*(nx+2)*(ny+2)+j*(nx+2)+i;
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Dm.id[n] = 1;
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if (rank==0){
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ifstream domain("Domain.in");
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domain >> nprocx;
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domain >> nprocy;
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domain >> nprocz;
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domain >> nx;
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domain >> ny;
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domain >> nz;
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domain >> nspheres;
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domain >> Lx;
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domain >> Ly;
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domain >> Lz;
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ifstream image("Segmented.in");
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image >> Filename; // Name of data file containing segmented data
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image >> Nx; // size of the binary file
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image >> Ny;
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image >> Nz;
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image >> xStart; // offset for the starting voxel
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image >> yStart;
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image >> zStart;
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}
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MPI_Barrier(comm);
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// Computational domain
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//.................................................
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MPI_Bcast(&nx,1,MPI_INT,0,comm);
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MPI_Bcast(&ny,1,MPI_INT,0,comm);
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MPI_Bcast(&nz,1,MPI_INT,0,comm);
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MPI_Bcast(&nprocx,1,MPI_INT,0,comm);
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MPI_Bcast(&nprocy,1,MPI_INT,0,comm);
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MPI_Bcast(&nprocz,1,MPI_INT,0,comm);
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MPI_Bcast(&nspheres,1,MPI_INT,0,comm);
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MPI_Bcast(&Lx,1,MPI_DOUBLE,0,comm);
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MPI_Bcast(&Ly,1,MPI_DOUBLE,0,comm);
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MPI_Bcast(&Lz,1,MPI_DOUBLE,0,comm);
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//.................................................
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MPI_Bcast(&Ny,1,MPI_INT,0,comm);
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MPI_Bcast(&Ny,1,MPI_INT,0,comm);
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MPI_Bcast(&Nz,1,MPI_INT,0,comm);
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MPI_Bcast(&xStart,1,MPI_INT,0,comm);
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MPI_Bcast(&yStart,1,MPI_INT,0,comm);
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MPI_Bcast(&zStart,1,MPI_INT,0,comm);
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//.................................................
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MPI_Barrier(comm);
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// Check that the number of processors >= the number of ranks
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if ( rank==0 ) {
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printf("Number of MPI ranks required: %i \n", nprocx*nprocy*nprocz);
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printf("Number of MPI ranks used: %i \n", nprocs);
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printf("Full domain size: %i x %i x %i \n",nx*nprocx,ny*nprocy,nz*nprocz);
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}
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if ( nprocs < nprocx*nprocy*nprocz ){
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ERROR("Insufficient number of processors");
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}
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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: %i x %i x %i \n",Nx,Ny,Nz);
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SegData = new char[Nx*Ny*Nz];
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FILE *SEGDAT = fopen(Filename,"rb");
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if (SEGDAT==NULL) ERROR("Error reading segmented data");
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size_t ReadSeg;
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ReadSeg=fread(SegData,1,Nx*Ny*Nz,SEGDAT);
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if (ReadSeg != size_t(Nx*Ny*Nz)) printf("lbpm_segmented_decomp: Error reading segmented data (rank=%i)\n",rank);
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fclose(SEGDAT);
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printf("Read segmented data from %s \n",Filename);
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}
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MPI_Barrier(comm);
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// Get the rank info
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int N = (nx+2)*(ny+2)*(nz+2);
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Domain Dm(nx,ny,nz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,BC);
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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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n = k*(nx+2)*(ny+2)+j*(nx+2)+i;
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Dm.id[n] = 1;
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}
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}
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}
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}
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Dm.CommInit(comm);
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Dm.CommInit(comm);
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// number of sites to use for periodic boundary condition transition zone
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int z_transition_size = (nprocz*nz - (Nz - zStart))/2;
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if (z_transition_size < 0) z_transition_size=0;
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// number of sites to use for periodic boundary condition transition zone
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int z_transition_size = (nprocz*nz - (Nz - zStart))/2;
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if (z_transition_size < 0) z_transition_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",Dm.nprocx,Dm.nprocy,Dm.nprocz);
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printf("Subdomain size: %i \n",N);
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printf("Size of transition region: %i \n", z_transition_size);
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char *tmp;
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tmp = new char[N];
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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*Dm.nprocx*Dm.nprocy + jp*Dm.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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int x = xStart + ip*nx + i-1;
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int y = yStart + jp*ny + j-1;
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// int z = zStart + kp*nz + k-1;
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int z = zStart + kp*nz + k-1 - z_transition_size;
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if (z<zStart) z=zStart;
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if (!(z<Nz)) z=Nz-1;
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int nlocal = k*(nx+2)*(ny+2) + j*(nx+2) + i;
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int nglobal = z*Nx*Ny+y*Nx+x;
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tmp[nlocal] = SegData[nglobal];
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}
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}
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}
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if (rnk==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",Dm.nprocx,Dm.nprocy,Dm.nprocz);
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printf("Subdomain size: %i \n",N);
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printf("Size of transition region: %i \n", z_transition_size);
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char *tmp;
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tmp = new char[N];
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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*Dm.nprocx*Dm.nprocy + jp*Dm.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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int x = xStart + ip*nx + i-1;
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int y = yStart + jp*ny + j-1;
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// int z = zStart + kp*nz + k-1;
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int z = zStart + kp*nz + k-1 - z_transition_size;
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if (z<zStart) z=zStart;
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if (!(z<Nz)) z=Nz-1;
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int nlocal = k*(nx+2)*(ny+2) + j*(nx+2) + i;
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Dm.id[nlocal] = tmp[nlocal];
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int nglobal = z*Nx*Ny+y*Nx+x;
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tmp[nlocal] = SegData[nglobal];
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}
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}
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}
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}
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else{
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printf("Sending data to process %i \n", rnk);
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MPI_Send(tmp,N,MPI_CHAR,rnk,15,comm);
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if (rnk==0){
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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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int nlocal = k*(nx+2)*(ny+2) + j*(nx+2) + i;
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Dm.id[nlocal] = tmp[nlocal];
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}
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}
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}
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}
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else{
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printf("Sending data to process %i \n", rnk);
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MPI_Send(tmp,N,MPI_CHAR,rnk,15,comm);
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}
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}
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}
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}
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}
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}
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else{
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// Recieve the subdomain from rank = 0
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printf("Ready to recieve data %i at process %i \n", N,rank);
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MPI_Recv(Dm.id,N,MPI_CHAR,0,15,comm,MPI_STATUS_IGNORE);
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else{
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// Recieve the subdomain from rank = 0
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printf("Ready to recieve data %i at process %i \n", N,rank);
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MPI_Recv(Dm.id,N,MPI_CHAR,0,15,comm,MPI_STATUS_IGNORE);
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}
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MPI_Barrier(comm);
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nx+=2; ny+=2; nz+=2;
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N=nx*ny*nz;
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if (rank==0) printf("All sub-domains recieved \n");
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for (k=0;k<nz;k++){
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for (j=0;j<ny;j++){
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for (i=0;i<nx;i++){
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n = k*nx*ny+j*nx+i;
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if (Dm.id[n]==char(SOLID)) Dm.id[n] = 0;
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else if (Dm.id[n]==char(NWP)) Dm.id[n] = 1;
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else Dm.id[n] = 2;
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}
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}
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}
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if (rank==0) printf("Domain set \n");
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int count = 0;
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int total = 0;
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int countGlobal = 0;
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int totalGlobal = 0;
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for (k=1;k<nz-1;k++){
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for (j=1;j<ny-1;j++){
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for (i=1;i<nx-1;i++){
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n=k*nx*ny+j*nx+i;
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total++;
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if (Dm.id[n] == 0){
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count++;
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}
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}
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}
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}
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MPI_Allreduce(&count,&countGlobal,1,MPI_INT,MPI_SUM,comm);
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MPI_Allreduce(&total,&totalGlobal,1,MPI_INT,MPI_SUM,comm);
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float porosity = float(totalGlobal-countGlobal)/totalGlobal;
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if (rank==0) printf("Porosity=%f\n",porosity);
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if (rank==0){
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int xstart = xStart; // Is this correct?
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int ystart = yStart;
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int zstart = zStart;
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//totalGlobal=(Nx-xstart)*(Ny-ystart)*(Nz-zstart);
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countGlobal = 0;
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for (k=zstart; k<zstart+nprocz*(nz-2); k++){
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for (j=ystart; j<ystart+nprocy*(ny-2); j++){
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for (i=xstart; i<xstart+nprocx*(nx-2); i++){
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n=k*Nx*Ny+j*Nx+i;
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if (n < Nx*Ny*Nz){
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if (SegData[n] == char(SOLID)){
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countGlobal++;
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}
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}
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}
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}
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}
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float porosity = float(totalGlobal-countGlobal)/totalGlobal;
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printf("Original Porosity=%f\n",porosity);
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}
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count = 0;
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total = 0;
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countGlobal = 0;
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totalGlobal = 0;
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for (k=1;k<nz-1;k++){
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for (j=1;j<ny-1;j++){
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for (i=1;i<nx-1;i++){
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n=k*nx*ny+j*nx+i;
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if (Dm.id[n] != 0) total++;
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if (Dm.id[n] == 2) count++;
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}
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}
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}
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MPI_Allreduce(&count,&countGlobal,1,MPI_INT,MPI_SUM,comm);
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MPI_Allreduce(&total,&totalGlobal,1,MPI_INT,MPI_SUM,comm);
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float saturation = float(countGlobal)/totalGlobal;
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if (rank==0) printf("wetting phase saturation=%f\n",saturation);
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char LocalRankFilename[40];
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sprintf(LocalRankFilename,"ID.%05i",rank+rank_offset);
|
||||
FILE *ID = fopen(LocalRankFilename,"wb");
|
||||
fwrite(Dm.id,1,N,ID);
|
||||
// fwrite(Distance.get(),8,Distance.length(),ID);
|
||||
fclose(ID);
|
||||
|
||||
if (!MULTINPUT){
|
||||
|
||||
if (rank==0) printf("Writing symmetric domain reflection\n");
|
||||
MPI_Barrier(comm);
|
||||
int symrank,sympz;
|
||||
sympz = 2*nprocz - Dm.kproc -1;
|
||||
symrank = sympz*nprocx*nprocy + Dm.jproc*nprocx + Dm.iproc;
|
||||
|
||||
// DoubleArray SymDist(nx,ny,nz);
|
||||
char *symid;
|
||||
symid = new char [N];
|
||||
for (k=0;k<nz;k++){
|
||||
for (j=0;j<ny;j++){
|
||||
for (i=0;i<nx;i++){
|
||||
n=k*nx*ny+j*nx+i;
|
||||
int nsym=(nz-k-1)*nx*ny+j*nx+i;
|
||||
symid[nsym] = Dm.id[n];
|
||||
//SymDist(i,j,nz-k-1)=Distance(i,j,k);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
sprintf(LocalRankFilename,"ID.%05i",symrank);
|
||||
FILE *SYMID = fopen(LocalRankFilename,"wb");
|
||||
// fwrite(SymDist.get(),8,SymDist.length(),SYMDIST);
|
||||
fwrite(symid,1,N,SYMID);
|
||||
fclose(SYMID);
|
||||
}
|
||||
}
|
||||
MPI_Barrier(comm);
|
||||
|
||||
nx+=2; ny+=2; nz+=2;
|
||||
N=nx*ny*nz;
|
||||
|
||||
if (rank==0) printf("All sub-domains recieved \n");
|
||||
for (k=0;k<nz;k++){
|
||||
for (j=0;j<ny;j++){
|
||||
for (i=0;i<nx;i++){
|
||||
n = k*nx*ny+j*nx+i;
|
||||
if (Dm.id[n]==char(SOLID)) Dm.id[n] = 0;
|
||||
else if (Dm.id[n]==char(NWP)) Dm.id[n] = 1;
|
||||
else Dm.id[n] = 2;
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
if (rank==0) printf("Domain set \n");
|
||||
|
||||
int count = 0;
|
||||
int total = 0;
|
||||
int countGlobal = 0;
|
||||
int totalGlobal = 0;
|
||||
for (k=1;k<nz-1;k++){
|
||||
for (j=1;j<ny-1;j++){
|
||||
for (i=1;i<nx-1;i++){
|
||||
n=k*nx*ny+j*nx+i;
|
||||
total++;
|
||||
if (Dm.id[n] == 0){
|
||||
count++;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
MPI_Allreduce(&count,&countGlobal,1,MPI_INT,MPI_SUM,comm);
|
||||
MPI_Allreduce(&total,&totalGlobal,1,MPI_INT,MPI_SUM,comm);
|
||||
|
||||
|
||||
float porosity = float(totalGlobal-countGlobal)/totalGlobal;
|
||||
if (rank==0) printf("Porosity=%f\n",porosity);
|
||||
|
||||
if (rank==0){
|
||||
int xstart = xStart; // Is this correct?
|
||||
int ystart = yStart;
|
||||
int zstart = zStart;
|
||||
//totalGlobal=(Nx-xstart)*(Ny-ystart)*(Nz-zstart);
|
||||
countGlobal = 0;
|
||||
for (k=zstart; k<zstart+nprocz*(nz-2); k++){
|
||||
for (j=ystart; j<ystart+nprocy*(ny-2); j++){
|
||||
for (i=xstart; i<xstart+nprocx*(nx-2); i++){
|
||||
|
||||
n=k*Nx*Ny+j*Nx+i;
|
||||
if (n < Nx*Ny*Nz){
|
||||
if (SegData[n] == char(SOLID)){
|
||||
countGlobal++;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
float porosity = float(totalGlobal-countGlobal)/totalGlobal;
|
||||
printf("Original Porosity=%f\n",porosity);
|
||||
}
|
||||
|
||||
count = 0;
|
||||
total = 0;
|
||||
countGlobal = 0;
|
||||
totalGlobal = 0;
|
||||
for (k=1;k<nz-1;k++){
|
||||
for (j=1;j<ny-1;j++){
|
||||
for (i=1;i<nx-1;i++){
|
||||
n=k*nx*ny+j*nx+i;
|
||||
if (Dm.id[n] != 0) total++;
|
||||
if (Dm.id[n] == 2) count++;
|
||||
}
|
||||
}
|
||||
}
|
||||
MPI_Allreduce(&count,&countGlobal,1,MPI_INT,MPI_SUM,comm);
|
||||
MPI_Allreduce(&total,&totalGlobal,1,MPI_INT,MPI_SUM,comm);
|
||||
float saturation = float(countGlobal)/totalGlobal;
|
||||
if (rank==0) printf("wetting phase saturation=%f\n",saturation);
|
||||
|
||||
|
||||
char LocalRankFilename[40];
|
||||
|
||||
sprintf(LocalRankFilename,"ID.%05i",rank);
|
||||
FILE *ID = fopen(LocalRankFilename,"wb");
|
||||
fwrite(Dm.id,1,N,ID);
|
||||
// fwrite(Distance.get(),8,Distance.length(),ID);
|
||||
fclose(ID);
|
||||
|
||||
if (rank==0) printf("Writing symmetric domain reflection\n");
|
||||
MPI_Barrier(comm);
|
||||
int symrank,sympz;
|
||||
sympz = 2*nprocz - Dm.kproc -1;
|
||||
symrank = sympz*nprocx*nprocy + Dm.jproc*nprocx + Dm.iproc;
|
||||
|
||||
// DoubleArray SymDist(nx,ny,nz);
|
||||
char *symid;
|
||||
symid = new char [N];
|
||||
for (k=0;k<nz;k++){
|
||||
for (j=0;j<ny;j++){
|
||||
for (i=0;i<nx;i++){
|
||||
n=k*nx*ny+j*nx+i;
|
||||
int nsym=(nz-k-1)*nx*ny+j*nx+i;
|
||||
symid[nsym] = Dm.id[n];
|
||||
//SymDist(i,j,nz-k-1)=Distance(i,j,k);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
sprintf(LocalRankFilename,"ID.%05i",symrank);
|
||||
FILE *SYMID = fopen(LocalRankFilename,"wb");
|
||||
// fwrite(SymDist.get(),8,SymDist.length(),SYMDIST);
|
||||
fwrite(symid,1,N,SYMID);
|
||||
fclose(SYMID);
|
||||
}
|
||||
MPI_Barrier(comm);
|
||||
MPI_Finalize();
|
||||
MPI_Finalize();
|
||||
}
|
||||
|
||||
Loading…
Reference in New Issue
Block a user