Added pre-processor and domain decomposition tool for segmented data
This commit is contained in:
James E McClure
237
tests/lbpm_segmented_decomp.cpp
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237
tests/lbpm_segmented_decomp.cpp
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/*
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* Pre-processor to generate signed distance function from segmented data
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* segmented data should be stored in a raw binary file as 1-byte integer (type char)
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* will output distance functions for phases
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*/
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#include <stdio.h>
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#include <stdlib.h>
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#include <math.h>
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#include <iostream>
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#include <fstream>
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#include <sstream>
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#include <Array.h>
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#include <Domain.h>
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int main(int argc, char **argv)
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{
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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_rank(MPI_COMM_WORLD,&rank);
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MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
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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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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(MPI_COMM_WORLD);
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// Computational domain
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MPI_Bcast(&nx,1,MPI_INT,0,MPI_COMM_WORLD);
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MPI_Bcast(&ny,1,MPI_INT,0,MPI_COMM_WORLD);
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MPI_Bcast(&nz,1,MPI_INT,0,MPI_COMM_WORLD);
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MPI_Bcast(&nprocx,1,MPI_INT,0,MPI_COMM_WORLD);
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MPI_Bcast(&nprocy,1,MPI_INT,0,MPI_COMM_WORLD);
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MPI_Bcast(&nprocz,1,MPI_INT,0,MPI_COMM_WORLD);
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MPI_Bcast(&nspheres,1,MPI_INT,0,MPI_COMM_WORLD);
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MPI_Bcast(&Lx,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
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MPI_Bcast(&Ly,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
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MPI_Bcast(&Lz,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
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//.................................................
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MPI_Barrier(MPI_COMM_WORLD);
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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;
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SegData = new char[Nx*Ny*Nz];
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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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FILE *SEGDAT = fopen(Filename,"rb");
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if (SEGDAT==NULL) ERROR("Error reading segmented data");
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fread(SegData,1,Nx*Ny*Nz,SEGDAT);
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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(MPI_COMM_WORLD);
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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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Dm.CommInit(MPI_COMM_WORLD);
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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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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 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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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,MPI_COMM_WORLD);
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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,MPI_COMM_WORLD,MPI_STATUS_IGNORE);
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}
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MPI_Barrier(MPI_COMM_WORLD);
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nx+=2; ny+=2; nz+=2;
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int count = 0;
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N=nx*ny*nz;
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/* char *id;
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id = new char [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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// Initialize the solid phase
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// if (Dm.id[n] == 0) id[n] = 0;
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// else id[n] = 1;
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}
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}
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}
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DoubleArray Distance(nx,ny,nz);
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// Initialize the signed distance function
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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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// Initialize distance to +/- 1
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Distance(i,j,k) = 1.0*id[n]-0.5;
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}
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}
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}
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*/
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// if (rank==0) printf("Nx = %i \n",(int)Distance.size(0));
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// if (rank==0) printf("Ny = %i \n",(int)Distance.size(1));
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// if (rank==0) printf("Nz = %i \n",(int)Distance.size(2));
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// printf("Initialized! Converting to Signed Distance function \n");
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// SSO(Distance,id,Dm,10);
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char LocalRankFilename[40];
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sprintf(LocalRankFilename,"ID.%05i",rank);
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FILE *ID = fopen(LocalRankFilename,"wb");
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fwrite(Dm.id,1,N,ID);
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// fwrite(Distance.get(),8,Distance.length(),ID);
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fclose(ID);
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int symrank,sympz;
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sympz = 2*nprocz - Dm.kproc -1;
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symrank = sympz*nprocx*nprocy + Dm.jproc*nprocx + Dm.iproc;
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// DoubleArray SymDist(nx,ny,nz);
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char *symid;
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symid = new char [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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int nsym=(nz-k-1)*nx*ny+j*nx+i;
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symid[nsym] = Dm.id[n];
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//SymDist(i,j,nz-k-1)=Distance(i,j,k);
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}
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}
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}
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sprintf(LocalRankFilename,"ID.%05i",symrank);
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FILE *SYMID = fopen(LocalRankFilename,"wb");
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// fwrite(SymDist.get(),8,SymDist.length(),SYMDIST);
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fwrite(symid,1,N,SYMID);
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fclose(SYMID);
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MPI_Barrier(MPI_COMM_WORLD);
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MPI_Finalize();
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return 0;
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}
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