Adding domain decomposition to lbpm_uCT_pp (in progress)
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James E McClure committed
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43f1d53fa7
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@@ -23,7 +23,7 @@ int main(int argc, char **argv)
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MPI_Comm_size(comm,&nprocs);
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int SOLID=atoi(argv[1]);
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int SOLID=atoi(argv[1]);
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int NWP=atoi(argv[2]);
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if (rank==0){
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printf("Solid Label %i \n",SOLID);
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+197
-63
@@ -3,81 +3,215 @@
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// and averaging on a blob-by-blob basis
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// James E. McClure 2014
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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 "common/Array.h"
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#include "common/Domain.h"
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#include "IO/netcdf.h"
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#include "ProfilerApp.h"
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void load( const std::string filename )
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{
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int fid = netcdf::open( filename );
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std::vector<std::string> vars = netcdf::getVarNames( fid );
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for (size_t i=0; i<vars.size(); i++) {
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printf("Reading variable %s\n",vars[i].c_str());
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netcdf::VariableType type = netcdf::getVarType( fid, vars[i] );
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if ( type == netcdf::STRING )
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Array<std::string> tmp = netcdf::getVar<std::string>( fid, vars[i] );
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else if ( type == netcdf::SHORT )
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Array<short> tmp = netcdf::getVar<short>( fid, vars[i] );
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else
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Array<double> tmp = netcdf::getVar<double>( fid, vars[i] );
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}
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std::vector<std::string> attr = netcdf::getAttNames( fid );
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for (size_t i=0; i<attr.size(); i++) {
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printf("Reading attribute %s\n",attr[i].c_str());
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netcdf::VariableType type = netcdf::getAttType( fid, attr[i] );
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if ( type == netcdf::STRING )
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Array<std::string> tmp = netcdf::getAtt<std::string>( fid, attr[i] );
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else
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Array<double> tmp = netcdf::getAtt<double>( fid, attr[i] );
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}
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netcdf::close( fid );
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}
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int main(int argc, char **argv)
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{
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PROFILE_START("Main");
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//std::vector<std::string> filenames;
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std::string filename;
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if ( argc==0 ) {
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printf("At least one filename must be specified\n");
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return 1;
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}
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else {
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filename=std::string(argv[1]);
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printf("Reading file: %s\n",filename.c_str());
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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 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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int fid = netcdf::open(filename);
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// Read all of the attributes
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std::vector<std::string> attr = netcdf::getAttNames( fid );
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for (size_t i=0; i<attr.size(); i++) {
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printf("Reading attribute %s\n",attr[i].c_str());
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netcdf::VariableType type = netcdf::getAttType( fid, attr[i] );
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if ( type == netcdf::STRING ){
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Array<std::string> tmp = netcdf::getAtt<std::string>( fid, attr[i] );
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//std::vector<std::string> filenames;
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std::string filename;
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if ( argc==0 ) {
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printf("At least one filename must be specified\n");
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return 1;
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}
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else{
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//Array<double> tmp = netcdf::getAtt<double>( fid, attr[i] );
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else {
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filename=std::string(argv[1]);
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printf("Input data file: %s\n",filename.c_str());
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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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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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}
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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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// Read the data array
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std::string varname("VOLUME");
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printf("Reading %s\n",varname.c_str());
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Array<float> VOLUME = netcdf::getVar<float>( fid, varname);
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//printf("VOLUME size = %zu \n",VOLUME.length());
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printf("VOLUME dims = %zu x %zu x %zu \n",VOLUME.size(0),VOLUME.size(1),VOLUME.size(2));
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printf("Sucess!! \n");
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netcdf::close( fid );
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PROFILE_SAVE("TestNetcdf");
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return 0;
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PROFILE_START("ReadVolume");
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// Read the input volume to rank 0 only, then distribute pieces to workers
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if (rank==0){
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// Open the netcdf file
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int fid = netcdf::open(filename);
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// Read all of the attributes
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std::vector<std::string> attr = netcdf::getAttNames( fid );
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for (size_t i=0; i<attr.size(); i++) {
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printf("Reading attribute %s\n",attr[i].c_str());
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netcdf::VariableType type = netcdf::getAttType( fid, attr[i] );
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if ( type == netcdf::STRING ){
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Array<std::string> tmp = netcdf::getAtt<std::string>( fid, attr[i] );
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}
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else{
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//Array<double> tmp = netcdf::getAtt<double>( fid, attr[i] );
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}
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}
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// Read the VOLUME data array
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std::string varname("VOLUME");
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printf("Reading %s\n",varname.c_str());
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Array<float> VOLUME = netcdf::getVar<float>( fid, varname);
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printf("VOLUME dims = %zu x %zu x %zu \n",VOLUME.size(0),VOLUME.size(1),VOLUME.size(2));
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printf("Sucess!! \n");
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netcdf::close( fid );
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}
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PROFILE_SAVE("ReadVolume");
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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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Dm.CommInit(comm);
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/*
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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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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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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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*/
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MPI_Barrier(comm);
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MPI_Finalize();
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return 0;
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}
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