Updating I/O pattern for lbpm_refine_pp
This commit is contained in:
James E McClure
@@ -18,144 +18,254 @@ int main(int argc, char **argv)
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// Initialize MPI
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// Initialize MPI
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int rank, nprocs;
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int rank, nprocs;
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MPI_Init(&argc,&argv);
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MPI_Init(&argc,&argv);
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MPI_Comm comm = MPI_COMM_WORLD;
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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_rank(comm,&rank);
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MPI_Comm_size(comm,&nprocs);
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MPI_Comm_size(comm,&nprocs);
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{
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{
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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 nprocx, nprocy, nprocz, nx, ny, nz, nspheres;
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int nprocx, nprocy, nprocz, nx, ny, nz, nspheres;
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double Lx, Ly, Lz;
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double Lx, Ly, Lz;
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int i,j,k,n;
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int i,j,k,n;
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int BC=0;
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int BC=0;
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if ( rank==0 ) {
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if ( rank==0 ) {
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printf("lbpm_refine_pp: Refining signed distance mesh (x2) \n");
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printf("lbpm_refine_pp: Refining signed distance mesh (x2) \n");
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}
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}
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if (rank==0){
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if (rank==0){
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ifstream domain("Domain.in");
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ifstream domain("Domain.in");
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domain >> nprocx;
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domain >> nprocx;
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domain >> nprocy;
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domain >> nprocy;
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domain >> nprocz;
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domain >> nprocz;
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domain >> nx;
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domain >> nx;
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domain >> ny;
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domain >> ny;
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domain >> nz;
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domain >> nz;
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domain >> nspheres;
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domain >> nspheres;
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domain >> Lx;
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domain >> Lx;
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domain >> Ly;
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domain >> Ly;
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domain >> Lz;
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domain >> Lz;
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}
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}
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MPI_Barrier(comm);
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MPI_Barrier(comm);
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// Computational domain
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// Computational domain
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MPI_Bcast(&nx,1,MPI_INT,0,comm);
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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(&ny,1,MPI_INT,0,comm);
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MPI_Bcast(&nz,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(&nprocx,1,MPI_INT,0,comm);
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MPI_Bcast(&nprocy,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(&nprocz,1,MPI_INT,0,comm);
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MPI_Bcast(&nspheres,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(&Lx,1,MPI_DOUBLE,0,comm);
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MPI_Bcast(&Ly,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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MPI_Bcast(&Lz,1,MPI_DOUBLE,0,comm);
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//.................................................
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//.................................................
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MPI_Barrier(comm);
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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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// Check that the number of processors >= the number of ranks
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if ( rank==0 ) {
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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 required: %i \n", nprocx*nprocy*nprocz);
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printf("Number of MPI ranks used: %i \n", nprocs);
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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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printf("Full domain size: %i x %i x %i \n",nx*nprocx,ny*nprocy,nz*nprocz);
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}
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}
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if ( nprocs < nprocx*nprocy*nprocz ){
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if ( nprocs < nprocx*nprocy*nprocz ){
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ERROR("Insufficient number of processors");
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ERROR("Insufficient number of processors");
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}
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}
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char LocalRankFilename[40];
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char LocalRankFilename[40];
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int rnx,rny,rnz;
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int rnx,rny,rnz;
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rnx=2*(nx-1)+1;
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rnx=2*(nx-1)+1;
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rny=2*(ny-1)+1;
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rny=2*(ny-1)+1;
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rnz=2*(nz-1)+1;
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rnz=2*(nz-1)+1;
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rnx=2*nx;
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rny=2*ny;
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rnz=2*nz;
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if (rank==0) printf("Refining mesh to %i x %i x %i \n",rnx,rny,rnz);
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int BoundaryCondition=0;
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rnx=2*nx;
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Domain Dm(rnx,rny,rnz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,BoundaryCondition);
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rny=2*ny;
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rnz=2*nz;
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// Communication the halos
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if (rank==0) printf("Refining mesh to %i x %i x %i \n",rnx,rny,rnz);
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const RankInfoStruct rank_info(rank,nprocx,nprocy,nprocz);
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fillHalo<double> fillData(comm,rank_info,rnx,rny,rnz,1,1,1,0,1);
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nx+=2; ny+=2; nz+=2;
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int BoundaryCondition=0;
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rnx+=2; rny+=2; rnz+=2;
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Domain Dm(rnx,rny,rnz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,BoundaryCondition);
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int N = nx*ny*nz;
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// Define communication sub-domain -- everywhere
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// Communication the halos
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for (int k=0; k<rnz; k++){
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const RankInfoStruct rank_info(rank,nprocx,nprocy,nprocz);
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for (int j=0; j<rny; j++){
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fillHalo<double> fillData(comm,rank_info,rnx,rny,rnz,1,1,1,0,1);
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for (int i=0; i<rnx; i++){
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n = k*rnx*rny+j*rnx+i;
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nx+=2; ny+=2; nz+=2;
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Dm.id[n] = 1;
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rnx+=2; rny+=2; rnz+=2;
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int N = nx*ny*nz;
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// Define communication sub-domain -- everywhere
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for (int k=0; k<rnz; k++){
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for (int j=0; j<rny; j++){
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for (int i=0; i<rnx; i++){
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n = k*rnx*rny+j*rnx+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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}
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}
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Dm.CommInit(comm);
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Dm.CommInit(comm);
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DoubleArray SignDist(nx,ny,nz);
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DoubleArray SignDist(nx,ny,nz);
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// Read the signed distance from file
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// Read the signed distance from file
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sprintf(LocalRankFilename,"SignDist.%05i",rank);
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sprintf(LocalRankFilename,"SignDist.%05i",rank);
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FILE *DIST = fopen(LocalRankFilename,"rb");
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FILE *DIST = fopen(LocalRankFilename,"rb");
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size_t ReadSignDist;
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size_t ReadSignDist;
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ReadSignDist=fread(SignDist.data(),8,N,DIST);
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ReadSignDist=fread(SignDist.data(),8,N,DIST);
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if (ReadSignDist != size_t(N)) printf("lbpm_refine_pp: Error reading signed distance function (rank=%i)\n",rank);
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if (ReadSignDist != size_t(N)) printf("lbpm_refine_pp: Error reading signed distance function (rank=%i)\n",rank);
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fclose(DIST);
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fclose(DIST);
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if ( rank==0 ) printf("Set up Domain, read input distance \n");
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if ( rank==0 ) printf("Set up Domain, read input distance \n");
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DoubleArray RefinedSignDist(rnx,rny,rnz);
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DoubleArray RefinedSignDist(rnx,rny,rnz);
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TriLinPoly LocalApprox;
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TriLinPoly LocalApprox;
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Point pt;
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Point pt;
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int ri,rj,rk,rn; //refined mesh indices
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int ri,rj,rk,rn; //refined mesh indices
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for (rk=1; rk<rnz-2; rk++){
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for (rk=1; rk<rnz-2; rk++){
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for (rj=1; rj<rny-2; rj++){
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for (rj=1; rj<rny-2; rj++){
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for (ri=1; ri<rnx-2; ri++){
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for (ri=1; ri<rnx-2; ri++){
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n = rk*rnx*rny+rj*rnx+ri;
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n = rk*rnx*rny+rj*rnx+ri;
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// starting node for each processor matches exactly
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// starting node for each processor matches exactly
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i = (ri-1)/2+1;
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i = (ri-1)/2+1;
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j = (rj-1)/2+1;
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j = (rj-1)/2+1;
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k = (rk-1)/2+1;
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k = (rk-1)/2+1;
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//printf("(%i,%i,%i -> %i,%i,%i) \n",ri,rj,rk,i,j,k);
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//printf("(%i,%i,%i -> %i,%i,%i) \n",ri,rj,rk,i,j,k);
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// Assign local tri-linear polynomial
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// Assign local tri-linear polynomial
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LocalApprox.assign(SignDist,i,j,k);
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LocalApprox.assign(SignDist,i,j,k);
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pt.x=0.5*(ri-1)+1.f;
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pt.x=0.5*(ri-1)+1.f;
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pt.y=0.5*(rj-1)+1.f;
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pt.y=0.5*(rj-1)+1.f;
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pt.z=0.5*(rk-1)+1.f;
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pt.z=0.5*(rk-1)+1.f;
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RefinedSignDist(ri,rj,rk) = LocalApprox.eval(pt);
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RefinedSignDist(ri,rj,rk) = LocalApprox.eval(pt);
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}
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}
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}
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}
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}
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fillData.fill(RefinedSignDist);
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// sprintf(LocalRankFilename,"ID.%05i",rank);
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//FILE *ID = fopen(LocalRankFilename,"wb");
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//fwrite(id,1,N,ID);
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//fclose(ID);
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sprintf(LocalRankFilename,"RefineDist.%05i",rank);
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FILE *REFINEDIST = fopen(LocalRankFilename,"wb");
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fwrite(RefinedSignDist.data(),8,rnx*rny*rnz,REFINEDIST);
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fclose(REFINEDIST);
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DoubleArray BlockDist(nx,ny,nz);
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int writerank;
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// Write output blocks with the same sub-domain size as origina
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// refinement increases the size of the process grid
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writerank = 8*kproc*nprocx*nprocy + 4*jproc*nprocx + 2*iproc;
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for (int k=0; k<nz; k++){
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for (int j=0; j<ny; j++){
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for (int i=0; i<nx; i++){
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BlockDist(i,j,k) = RefinedSignDist(i,j,k);
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}
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}
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}
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sprintf(LocalRankFilename,"RefineDist.%05i",writerank);
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REFINEDIST = fopen(LocalRankFilename,"wb");
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fwrite(BlockDist.data(),8,nx*ny*nz,REFINEDIST);
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fclose(REFINEDIST);
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writerank = 8*kproc*nprocx*nprocy + 4*jproc*nprocx + 2*iproc+1;
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for (int k=0; k<nz; k++){
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for (int j=0; j<ny; j++){
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for (int i=0; i<nx; i++){
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BlockDist(i,j,k) = RefinedSignDist(i+nx,j,k);
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}
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}
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}
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sprintf(LocalRankFilename,"RefineDist.%05i",writerank);
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REFINEDIST = fopen(LocalRankFilename,"wb");
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fwrite(BlockDist.data(),8,nx*ny*nz,REFINEDIST);
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fclose(REFINEDIST);
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writerank = (2*kproc)*4*nprocx*nprocy + (2*jproc+1)*2*nprocx + 2*iproc+1;
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for (int k=0; k<nz; k++){
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for (int j=0; j<ny; j++){
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for (int i=0; i<nx; i++){
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BlockDist(i,j,k) = RefinedSignDist(i+nx,j+ny,k);
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}
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}
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}
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sprintf(LocalRankFilename,"RefineDist.%05i",writerank);
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REFINEDIST = fopen(LocalRankFilename,"wb");
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fwrite(BlockDist.data(),8,nx*ny*nz,REFINEDIST);
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fclose(REFINEDIST);
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writerank = (2*kproc)*4*nprocx*nprocy + (2*jproc+1)*2*nprocx + 2*iproc;
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for (int k=0; k<nz; k++){
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for (int j=0; j<ny; j++){
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for (int i=0; i<nx; i++){
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BlockDist(i,j,k) = RefinedSignDist(i,j+ny,k);
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}
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}
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}
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sprintf(LocalRankFilename,"RefineDist.%05i",writerank);
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REFINEDIST = fopen(LocalRankFilename,"wb");
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fwrite(BlockDist.data(),8,nx*ny*nz,REFINEDIST);
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fclose(REFINEDIST);
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writerank = (2*kproc+1)*4*nprocx*nprocy + (2*jproc)*2*nprocx + 2*iproc;
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for (int k=0; k<nz; k++){
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for (int j=0; j<ny; j++){
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for (int i=0; i<nx; i++){
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BlockDist(i,j,k) = RefinedSignDist(i,j,k+nz);
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}
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}
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}
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sprintf(LocalRankFilename,"RefineDist.%05i",writerank);
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REFINEDIST = fopen(LocalRankFilename,"wb");
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fwrite(BlockDist.data(),8,nx*ny*nz,REFINEDIST);
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fclose(REFINEDIST);
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writerank = (2*kproc+1)*4*nprocx*nprocy + (2*jproc)*2*nprocx + 2*iproc+1;
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for (int k=0; k<nz; k++){
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for (int j=0; j<ny; j++){
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for (int i=0; i<nx; i++){
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BlockDist(i,j,k) = RefinedSignDist(i+nx,j,k+nz);
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}
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}
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}
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sprintf(LocalRankFilename,"RefineDist.%05i",writerank);
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REFINEDIST = fopen(LocalRankFilename,"wb");
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fwrite(BlockDist.data(),8,nx*ny*nz,REFINEDIST);
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fclose(REFINEDIST);
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writerank = (2*kproc+1)*4*nprocx*nprocy + (2*jproc+1)*2*nprocx + 2*iproc;
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for (int k=0; k<nz; k++){
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for (int j=0; j<ny; j++){
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for (int i=0; i<nx; i++){
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BlockDist(i,j,k) = RefinedSignDist(i,j+ny,k+nz);
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}
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}
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}
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sprintf(LocalRankFilename,"RefineDist.%05i",writerank);
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REFINEDIST = fopen(LocalRankFilename,"wb");
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fwrite(BlockDist.data(),8,nx*ny*nz,REFINEDIST);
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fclose(REFINEDIST);
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writerank = (2*kproc+1)*4*nprocx*nprocy + (2*jproc+1)*2*nprocx + 2*iproc+1;
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for (int k=0; k<nz; k++){
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for (int j=0; j<ny; j++){
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for (int i=0; i<nx; i++){
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BlockDist(i,j,k) = RefinedSignDist(i+nx,j+ny,k+nz);
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}
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}
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}
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sprintf(LocalRankFilename,"RefineDist.%05i",writerank);
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REFINEDIST = fopen(LocalRankFilename,"wb");
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fwrite(BlockDist.data(),8,nx*ny*nz,REFINEDIST);
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fclose(REFINEDIST);
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}
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}
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fillData.fill(RefinedSignDist);
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// sprintf(LocalRankFilename,"ID.%05i",rank);
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//FILE *ID = fopen(LocalRankFilename,"wb");
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//fwrite(id,1,N,ID);
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//fclose(ID);
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sprintf(LocalRankFilename,"RefineDist.%05i",rank);
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FILE *REFINEDIST = fopen(LocalRankFilename,"wb");
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fwrite(RefinedSignDist.data(),8,rnx*rny*rnz,REFINEDIST);
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fclose(REFINEDIST);
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}
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MPI_Barrier(comm);
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MPI_Barrier(comm);
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MPI_Finalize();
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MPI_Finalize();
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return 0;
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return 0;
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Block a user