Adding new code to reverted lbpm_uCT_pp since I somehow introduced a memory error that I didn't feel like debuggin
This commit is contained in:
James E McClure
parent
a4be801a70
commit
7eb030bca7
@ -11,338 +11,10 @@
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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 "common/Communication.h"
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#include "common/MPI_Helpers.h"
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#include "IO/MeshDatabase.h"
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#include "IO/netcdf.h"
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#include "IO/Writer.h"
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#include "ProfilerApp.h"
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inline void Med3D(Array<float> &Input, Array<float> &Output){
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// Perform a 3D Median filter on Input array with specified width
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int i,j,k,ii,jj,kk;
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int imin,jmin,kmin,imax,jmax,kmax;
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float *List;
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List=new float[9];
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int Nx = int(Input.size(0));
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int Ny = int(Input.size(1));
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int Nz = int(Input.size(2));
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for (k=1; k<Nz-1; k++){
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for (j=1; Ny-1; j++){
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for (i=1; Nz-1; i++){
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// Just use a 3x3x3 window (hit recursively if needed)
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imin = i-1;
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jmin = j-1;
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kmin = k-1;
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imax = i+1;
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jmax = j+1;
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kmax = k+1;
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// Populate the list with values in the window
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int Number=0;
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for (kk=kmin; kk<kmax; kk++){
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for (jj=jmin; jj<jmax; jj++){
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for (ii=imin; ii<imax; ii++){
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List[Number++] = Input(ii,jj,kk);
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}
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}
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}
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// Sort the first 5 entries and return the median
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for (ii=0; ii<5; ii++){
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for (jj=ii+1; jj<9; jj++){
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if (List[jj] < List[ii]){
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float tmp = List[ii];
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List[ii] = List[jj];
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List[jj] = tmp;
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}
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}
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}
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// Return the median
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Output(i,j,k) = List[4];
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}
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}
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}
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}
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inline void Sparsify(Array<float> &Fine, Array<float> &Coarse){
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// Create sparse version of Fine mesh to reduce filtering costs
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int i,j,k,ii,jj,kk;
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float x,y,z;
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// Fine mesh
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int Nx = int(Fine.size(0));
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int Ny = int(Fine.size(1));
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int Nz = int(Fine.size(2));
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// Coarse mesh
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int nx = int(Coarse.size(0));
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int ny = int(Coarse.size(1));
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int nz = int(Coarse.size(2));
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// compute the stride
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float hx = float(Nx-1) / float (nx-1);
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float hy = float(Ny-1) / float (ny-1);
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float hz = float(Nz-1) / float (nz-1);
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// Fill in the coarse mesh
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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; nz; i++){
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x = i*hx;
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y = j*hy;
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z = k*hz;
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ii = floor(x);
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jj = floor(y);
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kk = floor(z);
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// get the eight values in the cell
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float v1 = Fine(ii,jj,kk);
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float v2 = Fine(ii+1,jj,kk);
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float v3 = Fine(ii,jj+1,kk);
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float v4 = Fine(ii+1,jj+1,kk);
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float v5 = Fine(ii,jj,kk+1);
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float v6 = Fine(ii+1,jj,kk+1);
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float v7 = Fine(ii,jj+1,kk+1);
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float v8 = Fine(ii+1,jj+1,kk+1);
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Coarse(i,j,k)=0.125*(v1+v2+v3+v4+v5+v6+v7+v8);
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}
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}
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}
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}
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inline float minmod(float &a, float &b){
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float value;
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value = a;
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if ( a*b < 0.0) value=0.0;
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else if (fabs(a) > fabs(b)) value = b;
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return value;
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}
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inline float Eikonal3D(Array<float> &Distance, Array<char> &ID, Domain &Dm, int timesteps){
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/*
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* This routine converts the data in the Distance array to a signed distance
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* by solving the equation df/dt = sign(1-|grad f|), where Distance provides
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* the values of f on the mesh associated with domain Dm
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* It has been tested with segmented data initialized to values [-1,1]
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* and will converge toward the signed distance to the surface bounding the associated phases
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*
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* Reference:
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* Min C (2010) On reinitializing level set functions, Journal of Computational Physics 229
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*/
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int i,j,k;
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float dt=0.1;
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float Dx,Dy,Dz;
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float Dxp,Dxm,Dyp,Dym,Dzp,Dzm;
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float Dxxp,Dxxm,Dyyp,Dyym,Dzzp,Dzzm;
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float sign,norm;
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float LocalVar,GlobalVar,LocalMax,GlobalMax;
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int xdim,ydim,zdim;
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xdim=Dm.Nx-2;
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ydim=Dm.Ny-2;
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zdim=Dm.Nz-2;
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fillHalo<float> fillData(Dm.Comm, Dm.rank_info,xdim,ydim,zdim,1,1,1,0,1);
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// Arrays to store the second derivatives
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Array<float> Dxx(Dm.Nx,Dm.Ny,Dm.Nz);
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Array<float> Dyy(Dm.Nx,Dm.Ny,Dm.Nz);
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Array<float> Dzz(Dm.Nx,Dm.Ny,Dm.Nz);
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int count = 0;
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while (count < timesteps){
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// Communicate the halo of values
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fillData.fill(Distance);
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// Compute second order derivatives
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for (k=1;k<Dm.Nz-1;k++){
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for (j=1;j<Dm.Ny-1;j++){
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for (i=1;i<Dm.Nx-1;i++){
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Dxx(i,j,k) = Distance(i+1,j,k) + Distance(i-1,j,k) - 2*Distance(i,j,k);
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Dyy(i,j,k) = Distance(i,j+1,k) + Distance(i,j-1,k) - 2*Distance(i,j,k);
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Dzz(i,j,k) = Distance(i,j,k+1) + Distance(i,j,k-1) - 2*Distance(i,j,k);
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}
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}
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}
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fillData.fill(Dxx);
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fillData.fill(Dyy);
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fillData.fill(Dzz);
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LocalMax=LocalVar=0.0;
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// Execute the next timestep
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for (k=1;k<Dm.Nz-1;k++){
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for (j=1;j<Dm.Ny-1;j++){
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for (i=1;i<Dm.Nx-1;i++){
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int n = k*Dm.Nx*Dm.Ny + j*Dm.Nx + i;
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sign = -1;
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if (ID(i,j,k) == 1) sign = 1;
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// local second derivative terms
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Dxxp = minmod(Dxx(i,j,k),Dxx(i+1,j,k));
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Dyyp = minmod(Dyy(i,j,k),Dyy(i,j+1,k));
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Dzzp = minmod(Dzz(i,j,k),Dzz(i,j,k+1));
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Dxxm = minmod(Dxx(i,j,k),Dxx(i-1,j,k));
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Dyym = minmod(Dyy(i,j,k),Dyy(i,j-1,k));
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Dzzm = minmod(Dzz(i,j,k),Dzz(i,j,k-1));
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/* //............Compute upwind derivatives ...................
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Dxp = Distance(i+1,j,k) - Distance(i,j,k) + 0.5*Dxxp;
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Dyp = Distance(i,j+1,k) - Distance(i,j,k) + 0.5*Dyyp;
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Dzp = Distance(i,j,k+1) - Distance(i,j,k) + 0.5*Dzzp;
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Dxm = Distance(i,j,k) - Distance(i-1,j,k) + 0.5*Dxxm;
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Dym = Distance(i,j,k) - Distance(i,j-1,k) + 0.5*Dyym;
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Dzm = Distance(i,j,k) - Distance(i,j,k-1) + 0.5*Dzzm;
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*/
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Dxp = Distance(i+1,j,k);
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Dyp = Distance(i,j+1,k);
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Dzp = Distance(i,j,k+1);
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Dxm = Distance(i-1,j,k);
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Dym = Distance(i,j-1,k);
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Dzm = Distance(i,j,k-1);
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// Compute upwind derivatives for Godunov Hamiltonian
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if (sign < 0.0){
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if (Dxp > Dxm) Dx = Dxp - Distance(i,j,k) + 0.5*Dxxp;
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else Dx = Distance(i,j,k) - Dxm + 0.5*Dxxm;
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if (Dyp > Dym) Dy = Dyp - Distance(i,j,k) + 0.5*Dyyp;
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else Dy = Distance(i,j,k) - Dym + 0.5*Dyym;
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if (Dzp > Dzm) Dz = Dzp - Distance(i,j,k) + 0.5*Dzzp;
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else Dz = Distance(i,j,k) - Dzm + 0.5*Dzzm;
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}
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else{
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if (Dxp < Dxm) Dx = Dxp - Distance(i,j,k) + 0.5*Dxxp;
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else Dx = Distance(i,j,k) - Dxm + 0.5*Dxxm;
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if (Dyp < Dym) Dy = Dyp - Distance(i,j,k) + 0.5*Dyyp;
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else Dy = Distance(i,j,k) - Dym + 0.5*Dyym;
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if (Dzp < Dzm) Dz = Dzp - Distance(i,j,k) + 0.5*Dzzp;
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else Dz = Distance(i,j,k) - Dzm + 0.5*Dzzm;
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}
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norm=sqrt(Dx*Dx+Dy*Dy+Dz*Dz);
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if (norm > 1.0) norm=1.0;
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Distance(i,j,k) += dt*sign*(1.0 - norm);
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LocalVar += dt*sign*(1.0 - norm);
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if (fabs(dt*sign*(1.0 - norm)) > LocalMax)
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LocalMax = fabs(dt*sign*(1.0 - norm));
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}
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}
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}
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MPI_Allreduce(&LocalVar,&GlobalVar,1,MPI_FLOAT,MPI_SUM,Dm.Comm);
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MPI_Allreduce(&LocalMax,&GlobalMax,1,MPI_FLOAT,MPI_MAX,Dm.Comm);
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GlobalVar /= (Dm.Nx-2)*(Dm.Ny-2)*(Dm.Nz-2)*Dm.nprocx*Dm.nprocy*Dm.nprocz;
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count++;
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if (count%50 == 0 && Dm.rank==0 )
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printf("Time=%i, Max variation=%f, Global variation=%f \n",count,GlobalMax,GlobalVar);
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if (fabs(GlobalMax) < 1e-5){
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if (Dm.rank==0) printf("Exiting with max tolerance of 1e-5 \n");
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count=timesteps;
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}
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}
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return GlobalVar;
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}
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inline void NLM3D(Array<float> &Input, Array<float> &Mean, Array<float> &Output,
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const int d, const float h){
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// Implemenation of 3D non-local means filter
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// d determines the width of the search volume
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// h is a free parameter for non-local means (i.e. 1/sigma^2)
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float weight, sum;
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int i,j,k,ii,jj,kk;
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int imin,jmin,kmin,imax,jmax,kmax;
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int Nx = int(Input.size(0));
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int Ny = int(Input.size(1));
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int Nz = int(Input.size(2));
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// Compute the local means
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for (k=1; k<Nz-1; k++){
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for (j=1; Ny-1; j++){
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for (i=1; Nz-1; i++){
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imin = max(0,i-d);
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jmin = max(0,j-d);
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kmin = max(0,k-d);
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imax = max(Nx-1,i+d);
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jmax = max(Ny-1,j+d);
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kmax = max(Nz-1,k+d);
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// Populate the list with values in the window
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sum = 0; weight=0;
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for (kk=kmin; kk<kmax; kk++){
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for (jj=jmin; jj<jmax; jj++){
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for (ii=imin; ii<imax; ii++){
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sum += Input(ii,jj,kk);
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weight++;
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}
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}
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}
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Mean(i,j,k) = sum / weight;
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}
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}
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}
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// Compute the non-local means
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for (k=1; k<Nz-1; k++){
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for (j=1; Ny-1; j++){
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for (i=1; Nz-1; i++){
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imin = max(0,i-d);
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jmin = max(0,j-d);
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kmin = max(0,k-d);
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imax = max(Nx-1,i+d);
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jmax = max(Ny-1,j+d);
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kmax = max(Nz-1,k+d);
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// compute the expensive non-local means
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sum = 0; weight=0;
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for (kk=kmin; kk<kmax; kk++){
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for (jj=jmin; jj<jmax; jj++){
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for (ii=imin; ii<imax; ii++){
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float tmp = Mean(i,j,k) - Mean(ii,jj,kk);
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sum += exp(-tmp*tmp*h)*Input(ii,jj,kk);
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weight += exp(-tmp*tmp*h);
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}
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}
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}
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Output(i,j,k) = sum / weight;
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}
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}
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}
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}
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int main(int argc, char **argv)
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{
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@ -420,6 +92,48 @@ int main(int argc, char **argv)
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ERROR("Insufficient number of processors");
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}
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PROFILE_START("ReadVolume");
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Array<float> VOLUME;
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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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VOLUME = netcdf::getVar<float>( fid, varname);
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Nx = int(VOLUME.size(0));
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Ny = int(VOLUME.size(1));
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Nz = int(VOLUME.size(2));
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printf("VOLUME dims = %i x %i x %i \n",Nx,Ny,Nz);
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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_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_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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@ -434,115 +148,68 @@ int main(int argc, char **argv)
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Dm.CommInit(comm);
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// Allocate local arrays for every MPI rank
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Array<float> LOCVOL(nx+2,ny+2,nz+2);
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Array<float> LOCVOL(nx+2,ny+2,nz+2);
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// Set up the sub-domains
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int xStart,yStart,zStart;
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xStart=Nx/2;
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yStart=Ny/2;
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zStart=Nz/2;
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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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float *tmp;
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tmp = new float[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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// Read the volume file and distribute to all processes
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PROFILE_START("ReadVolume");
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//{
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Array<float> VOLUME;
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// Read the input volume to rank 0 only, then distribute pieces to workers
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if (rank==0){
|
||||
// Open the netcdf file
|
||||
int fid = netcdf::open(filename);
|
||||
|
||||
// Read all of the attributes
|
||||
std::vector<std::string> attr = netcdf::getAttNames( fid );
|
||||
for (size_t i=0; i<attr.size(); i++) {
|
||||
printf("Reading attribute %s\n",attr[i].c_str());
|
||||
netcdf::VariableType type = netcdf::getAttType( fid, attr[i] );
|
||||
if ( type == netcdf::STRING ){
|
||||
Array<std::string> tmp = netcdf::getAtt<std::string>( fid, attr[i] );
|
||||
}
|
||||
else{
|
||||
//Array<double> tmp = netcdf::getAtt<double>( fid, attr[i] );
|
||||
}
|
||||
}
|
||||
|
||||
// Read the VOLUME data array
|
||||
std::string varname("VOLUME");
|
||||
printf("Reading %s\n",varname.c_str());
|
||||
VOLUME = netcdf::getVar<float>( fid, varname);
|
||||
Nx = int(VOLUME.size(0));
|
||||
Ny = int(VOLUME.size(1));
|
||||
Nz = int(VOLUME.size(2));
|
||||
printf("VOLUME dims = %i x %i x %i \n",Nx,Ny,Nz);
|
||||
printf("Sucess!! \n");
|
||||
netcdf::close( fid );
|
||||
}
|
||||
PROFILE_SAVE("ReadVolume");
|
||||
|
||||
MPI_Bcast(&Ny,1,MPI_INT,0,comm);
|
||||
MPI_Bcast(&Ny,1,MPI_INT,0,comm);
|
||||
MPI_Bcast(&Nz,1,MPI_INT,0,comm);
|
||||
|
||||
MPI_Barrier(comm);
|
||||
|
||||
N=(nx+2)*(ny+2)*(nz+2);
|
||||
|
||||
// Set up the sub-domains
|
||||
if (rank==0){
|
||||
printf("Distributing subdomains across %i processors \n",nprocs);
|
||||
printf("Process grid: %i x %i x %i \n",Dm.nprocx,Dm.nprocy,Dm.nprocz);
|
||||
printf("Subdomain size: %i \n",N);
|
||||
// printf("Size of transition region: %i \n", z_transition_size);
|
||||
float *tmp;
|
||||
tmp = new float[N];
|
||||
for (int kp=0; kp<nprocz; kp++){
|
||||
for (int jp=0; jp<nprocy; jp++){
|
||||
for (int ip=0; ip<nprocx; ip++){
|
||||
// rank of the process that gets this subdomain
|
||||
int rnk = kp*Dm.nprocx*Dm.nprocy + jp*Dm.nprocx + ip;
|
||||
// Pack and send the subdomain for rnk
|
||||
int nlocal = k*(nx+2)*(ny+2) + j*(nx+2) + i;
|
||||
tmp[nlocal] = VOLUME(x,y,z);
|
||||
}
|
||||
}
|
||||
}
|
||||
if (rnk==0){
|
||||
for (k=0;k<nz+2;k++){
|
||||
for (j=0;j<ny+2;j++){
|
||||
for (i=0;i<nx+2;i++){
|
||||
int x = xStart + ip*nx + i-1;
|
||||
int y = yStart + jp*ny + j-1;
|
||||
int z = zStart + kp*nz + k-1;
|
||||
|
||||
int nlocal = k*(nx+2)*(ny+2) + j*(nx+2) + i;
|
||||
tmp[nlocal] = VOLUME(x,y,z);
|
||||
LOCVOL(i,j,k) = tmp[nlocal];
|
||||
}
|
||||
}
|
||||
}
|
||||
if (rnk==0){
|
||||
for (k=0;k<nz+2;k++){
|
||||
for (j=0;j<ny+2;j++){
|
||||
for (i=0;i<nx+2;i++){
|
||||
int nlocal = k*(nx+2)*(ny+2) + j*(nx+2) + i;
|
||||
LOCVOL(i,j,k) = tmp[nlocal];
|
||||
}
|
||||
}
|
||||
}
|
||||
printf("Copied local array at rank = 0 %i \n", rnk);
|
||||
}
|
||||
else{
|
||||
printf("Sending data to process %i \n", rnk);
|
||||
MPI_Send(tmp,N,MPI_FLOAT,rnk,15,comm);
|
||||
}
|
||||
}
|
||||
else{
|
||||
printf("Sending data to process %i \n", rnk);
|
||||
MPI_Send(tmp,N,MPI_FLOAT,rnk,15,comm);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
else{
|
||||
// Recieve the subdomain from rank = 0
|
||||
printf("Ready to recieve data %i at process %i \n", N,rank);
|
||||
MPI_Recv(LOCVOL.get(),N,MPI_FLOAT,0,15,comm,MPI_STATUS_IGNORE);
|
||||
}
|
||||
MPI_Barrier(comm);
|
||||
//}
|
||||
}
|
||||
else{
|
||||
// Recieve the subdomain from rank = 0
|
||||
printf("Ready to recieve data %i at process %i \n", N,rank);
|
||||
MPI_Recv(LOCVOL.get(),N,MPI_FLOAT,0,15,comm,MPI_STATUS_IGNORE);
|
||||
}
|
||||
MPI_Barrier(comm);
|
||||
|
||||
nx+=2; ny+=2; nz+=2;
|
||||
N=nx*ny*nz;
|
||||
|
||||
if (rank==0) printf("All sub-domains recieved \n");
|
||||
|
||||
// Filter the volume in distributed memory
|
||||
// Create sparse structures to make an initial guess, then refine
|
||||
|
||||
int nsx,nsy,nsz;
|
||||
nsx=nx/8; nsy=ny/8; nsz=nz/8;
|
||||
|
||||
@ -686,6 +353,28 @@ int main(int argc, char **argv)
|
||||
}
|
||||
|
||||
IO::writeData( 0, meshData, 2, comm );
|
||||
/* 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");
|
||||
*/
|
||||
// Write the local volume files
|
||||
char LocalRankString[8];
|
||||
char LocalRankFilename[40];
|
||||
sprintf(LocalRankString,"%05d",rank);
|
||||
sprintf(LocalRankFilename,"Seg.%s",LocalRankString);
|
||||
FILE * SEG;
|
||||
SEG=fopen(LocalRankFilename,"wb");
|
||||
fwrite(LOCVOL.get(),4,N,SEG);
|
||||
fclose(SEG);
|
||||
|
||||
MPI_Barrier(comm);
|
||||
MPI_Finalize();
|
||||
|
||||
Loading…
Reference in New Issue
Block a user