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Merge branch 'morphLBM' of github.com:JamesEMcClure/LBPM-WIA into morphLBM

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JamesEMcclure
2019-08-07 16:38:12 -04:00
parent 04648451d0 6001b6a440
commit e049fa4482
12 changed files with 906 additions and 111 deletions
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434
common/Domain.cpp
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@@ -128,6 +128,59 @@ Domain::Domain( std::shared_ptr<Database> db, MPI_Comm Communicator):
rank_info = RankInfoStruct( myrank, rank_info.nx, rank_info.ny, rank_info.nz );
MPI_Barrier(Comm);
}
Domain::~Domain()
{
// Free sendList
delete [] sendList_x; delete [] sendList_y; delete [] sendList_z;
delete [] sendList_X; delete [] sendList_Y; delete [] sendList_Z;
delete [] sendList_xy; delete [] sendList_yz; delete [] sendList_xz;
delete [] sendList_Xy; delete [] sendList_Yz; delete [] sendList_xZ;
delete [] sendList_xY; delete [] sendList_yZ; delete [] sendList_Xz;
delete [] sendList_XY; delete [] sendList_YZ; delete [] sendList_XZ;
// Free sendBuf
delete [] sendBuf_x; delete [] sendBuf_y; delete [] sendBuf_z;
delete [] sendBuf_X; delete [] sendBuf_Y; delete [] sendBuf_Z;
delete [] sendBuf_xy; delete [] sendBuf_yz; delete [] sendBuf_xz;
delete [] sendBuf_Xy; delete [] sendBuf_Yz; delete [] sendBuf_xZ;
delete [] sendBuf_xY; delete [] sendBuf_yZ; delete [] sendBuf_Xz;
delete [] sendBuf_XY; delete [] sendBuf_YZ; delete [] sendBuf_XZ;
// Free recvList
delete [] recvList_x; delete [] recvList_y; delete [] recvList_z;
delete [] recvList_X; delete [] recvList_Y; delete [] recvList_Z;
delete [] recvList_xy; delete [] recvList_yz; delete [] recvList_xz;
delete [] recvList_Xy; delete [] recvList_Yz; delete [] recvList_xZ;
delete [] recvList_xY; delete [] recvList_yZ; delete [] recvList_Xz;
delete [] recvList_XY; delete [] recvList_YZ; delete [] recvList_XZ;
// Free recvBuf
delete [] recvBuf_x; delete [] recvBuf_y; delete [] recvBuf_z;
delete [] recvBuf_X; delete [] recvBuf_Y; delete [] recvBuf_Z;
delete [] recvBuf_xy; delete [] recvBuf_yz; delete [] recvBuf_xz;
delete [] recvBuf_Xy; delete [] recvBuf_Yz; delete [] recvBuf_xZ;
delete [] recvBuf_xY; delete [] recvBuf_yZ; delete [] recvBuf_Xz;
delete [] recvBuf_XY; delete [] recvBuf_YZ; delete [] recvBuf_XZ;
// Free sendData
delete [] sendData_x; delete [] sendData_y; delete [] sendData_z;
delete [] sendData_X; delete [] sendData_Y; delete [] sendData_Z;
delete [] sendData_xy; delete [] sendData_xY; delete [] sendData_Xy;
delete [] sendData_XY; delete [] sendData_xz; delete [] sendData_xZ;
delete [] sendData_Xz; delete [] sendData_XZ; delete [] sendData_yz;
delete [] sendData_yZ; delete [] sendData_Yz; delete [] sendData_YZ;
// Free recvData
delete [] recvData_x; delete [] recvData_y; delete [] recvData_z;
delete [] recvData_X; delete [] recvData_Y; delete [] recvData_Z;
delete [] recvData_xy; delete [] recvData_xY; delete [] recvData_Xy;
delete [] recvData_XY; delete [] recvData_xz; delete [] recvData_xZ;
delete [] recvData_Xz; delete [] recvData_XZ; delete [] recvData_yz;
delete [] recvData_yZ; delete [] recvData_Yz; delete [] recvData_YZ;
// Free id
delete [] id;
// Free the communicator
if ( Comm != MPI_COMM_WORLD && Comm != MPI_COMM_NULL ) {
MPI_Comm_free(&Comm);
}
}
void Domain::initialize( std::shared_ptr<Database> db )
{
d_db = db;
@@ -187,58 +240,337 @@ void Domain::initialize( std::shared_ptr<Database> db )
MPI_Comm_size( Comm, &nprocs );
INSIST(nprocs == nproc[0]*nproc[1]*nproc[2],"Fatal error in processor count!");
}
Domain::~Domain()
{
// Free sendList
delete [] sendList_x; delete [] sendList_y; delete [] sendList_z;
delete [] sendList_X; delete [] sendList_Y; delete [] sendList_Z;
delete [] sendList_xy; delete [] sendList_yz; delete [] sendList_xz;
delete [] sendList_Xy; delete [] sendList_Yz; delete [] sendList_xZ;
delete [] sendList_xY; delete [] sendList_yZ; delete [] sendList_Xz;
delete [] sendList_XY; delete [] sendList_YZ; delete [] sendList_XZ;
// Free sendBuf
delete [] sendBuf_x; delete [] sendBuf_y; delete [] sendBuf_z;
delete [] sendBuf_X; delete [] sendBuf_Y; delete [] sendBuf_Z;
delete [] sendBuf_xy; delete [] sendBuf_yz; delete [] sendBuf_xz;
delete [] sendBuf_Xy; delete [] sendBuf_Yz; delete [] sendBuf_xZ;
delete [] sendBuf_xY; delete [] sendBuf_yZ; delete [] sendBuf_Xz;
delete [] sendBuf_XY; delete [] sendBuf_YZ; delete [] sendBuf_XZ;
// Free recvList
delete [] recvList_x; delete [] recvList_y; delete [] recvList_z;
delete [] recvList_X; delete [] recvList_Y; delete [] recvList_Z;
delete [] recvList_xy; delete [] recvList_yz; delete [] recvList_xz;
delete [] recvList_Xy; delete [] recvList_Yz; delete [] recvList_xZ;
delete [] recvList_xY; delete [] recvList_yZ; delete [] recvList_Xz;
delete [] recvList_XY; delete [] recvList_YZ; delete [] recvList_XZ;
// Free recvBuf
delete [] recvBuf_x; delete [] recvBuf_y; delete [] recvBuf_z;
delete [] recvBuf_X; delete [] recvBuf_Y; delete [] recvBuf_Z;
delete [] recvBuf_xy; delete [] recvBuf_yz; delete [] recvBuf_xz;
delete [] recvBuf_Xy; delete [] recvBuf_Yz; delete [] recvBuf_xZ;
delete [] recvBuf_xY; delete [] recvBuf_yZ; delete [] recvBuf_Xz;
delete [] recvBuf_XY; delete [] recvBuf_YZ; delete [] recvBuf_XZ;
// Free sendData
delete [] sendData_x; delete [] sendData_y; delete [] sendData_z;
delete [] sendData_X; delete [] sendData_Y; delete [] sendData_Z;
delete [] sendData_xy; delete [] sendData_xY; delete [] sendData_Xy;
delete [] sendData_XY; delete [] sendData_xz; delete [] sendData_xZ;
delete [] sendData_Xz; delete [] sendData_XZ; delete [] sendData_yz;
delete [] sendData_yZ; delete [] sendData_Yz; delete [] sendData_YZ;
// Free recvData
delete [] recvData_x; delete [] recvData_y; delete [] recvData_z;
delete [] recvData_X; delete [] recvData_Y; delete [] recvData_Z;
delete [] recvData_xy; delete [] recvData_xY; delete [] recvData_Xy;
delete [] recvData_XY; delete [] recvData_xz; delete [] recvData_xZ;
delete [] recvData_Xz; delete [] recvData_XZ; delete [] recvData_yz;
delete [] recvData_yZ; delete [] recvData_Yz; delete [] recvData_YZ;
// Free id
delete [] id;
// Free the communicator
if ( Comm != MPI_COMM_WORLD && Comm != MPI_COMM_NULL ) {
MPI_Comm_free(&Comm);
}
}
void Domain::Decomp(std::shared_ptr<Database> domain_db )
{
//.......................................................................
// Reading the domain information file
//.......................................................................
int rank_offset = 0;
int RANK = rank();
int nprocs, nprocx, nprocy, nprocz, nx, ny, nz;
int64_t global_Nx,global_Ny,global_Nz;
int64_t i,j,k,n;
int BC=0;
int64_t xStart,yStart,zStart;
int checkerSize;
//int inlet_layers_x, inlet_layers_y, inlet_layers_z;
//int outlet_layers_x, outlet_layers_y, outlet_layers_z;
xStart=yStart=zStart=0;
inlet_layers_x = 0;
inlet_layers_y = 0;
inlet_layers_z = 0;
outlet_layers_x = 0;
outlet_layers_y = 0;
outlet_layers_z = 0;
checkerSize = 32;
// Read domain parameters
auto Filename = domain_db->getScalar<std::string>( "Filename" );
//auto L = domain_db->getVector<double>( "L" );
auto size = domain_db->getVector<int>( "n" );
auto SIZE = domain_db->getVector<int>( "N" );
auto nproc = domain_db->getVector<int>( "nproc" );
if (domain_db->keyExists( "offset" )){
auto offset = domain_db->getVector<int>( "offset" );
xStart = offset[0];
yStart = offset[1];
zStart = offset[2];
}
if (domain_db->keyExists( "InletLayers" )){
auto InletCount = domain_db->getVector<int>( "InletLayers" );
inlet_layers_x = InletCount[0];
inlet_layers_y = InletCount[1];
inlet_layers_z = InletCount[2];
}
if (domain_db->keyExists( "OutletLayers" )){
auto OutletCount = domain_db->getVector<int>( "OutletLayers" );
outlet_layers_x = OutletCount[0];
outlet_layers_y = OutletCount[1];
outlet_layers_z = OutletCount[2];
}
if (domain_db->keyExists( "checkerSize" )){
checkerSize = domain_db->getScalar<int>( "checkerSize" );
}
else {
checkerSize = SIZE[0];
}
auto ReadValues = domain_db->getVector<int>( "ReadValues" );
auto WriteValues = domain_db->getVector<int>( "WriteValues" );
auto ReadType = domain_db->getScalar<std::string>( "ReadType" );
if (ReadType == "8bit"){
}
else if (ReadType == "16bit"){
}
else{
//printf("INPUT ERROR: Valid ReadType are 8bit, 16bit \n");
ReadType = "8bit";
}
nx = size[0];
ny = size[1];
nz = size[2];
nprocx = nproc[0];
nprocy = nproc[1];
nprocz = nproc[2];
global_Nx = SIZE[0];
global_Ny = SIZE[1];
global_Nz = SIZE[2];
nprocs=nprocx*nprocy*nprocz;
char *SegData = NULL;
if (RANK==0){
printf("Input media: %s\n",Filename.c_str());
printf("Relabeling %lu values\n",ReadValues.size());
for (int idx=0; idx<ReadValues.size(); idx++){
int oldvalue=ReadValues[idx];
int newvalue=WriteValues[idx];
printf("oldvalue=%d, newvalue =%d \n",oldvalue,newvalue);
}
// Rank=0 reads the entire segmented data and distributes to worker processes
printf("Dimensions of segmented image: %ld x %ld x %ld \n",global_Nx,global_Ny,global_Nz);
int64_t SIZE = global_Nx*global_Ny*global_Nz;
SegData = new char[SIZE];
if (ReadType == "8bit"){
printf("Reading 8-bit input data \n");
FILE *SEGDAT = fopen(Filename.c_str(),"rb");
if (SEGDAT==NULL) ERROR("Domain.cpp: Error reading segmented data");
size_t ReadSeg;
ReadSeg=fread(SegData,1,SIZE,SEGDAT);
if (ReadSeg != size_t(SIZE)) printf("Domain.cpp: Error reading segmented data \n");
fclose(SEGDAT);
}
else if (ReadType == "16bit"){
printf("Reading 16-bit input data \n");
short int *InputData;
InputData = new short int[SIZE];
FILE *SEGDAT = fopen(Filename.c_str(),"rb");
if (SEGDAT==NULL) ERROR("Domain.cpp: Error reading segmented data");
size_t ReadSeg;
ReadSeg=fread(InputData,2,SIZE,SEGDAT);
if (ReadSeg != size_t(SIZE)) printf("Domain.cpp: Error reading segmented data \n");
fclose(SEGDAT);
for (int n=0; n<SIZE; n++){
SegData[n] = char(InputData[n]);
}
}
printf("Read segmented data from %s \n",Filename.c_str());
if (inlet_layers_x > 0){
// use checkerboard pattern
printf("Checkerboard pattern at x inlet for %i layers \n",inlet_layers_x);
for (int k = 0; k<global_Nz; k++){
for (int j = 0; j<global_Ny; j++){
for (int i = xStart; i < xStart+inlet_layers_x; i++){
if ( (j/checkerSize + k/checkerSize)%2 == 0){
// void checkers
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
}
else{
// solid checkers
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
}
}
}
}
}
if (inlet_layers_y > 0){
printf("Checkerboard pattern at y inlet for %i layers \n",inlet_layers_y);
// use checkerboard pattern
for (int k = 0; k<global_Nz; k++){
for (int j = yStart; i < yStart+inlet_layers_y; j++){
for (int i = 0; i<global_Nx; i++){
if ( (i/checkerSize + k/checkerSize)%2 == 0){
// void checkers
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
}
else{
// solid checkers
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
}
}
}
}
}
if (inlet_layers_z > 0){
printf("Checkerboard pattern at z inlet for %i layers \n",inlet_layers_z);
// use checkerboard pattern
for (int k = zStart; k < zStart+inlet_layers_z; k++){
for (int j = 0; j<global_Ny; j++){
for (int i = 0; i<global_Nx; i++){
if ( (i/checkerSize+j/checkerSize)%2 == 0){
// void checkers
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
}
else{
// solid checkers
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
}
}
}
}
}
if (outlet_layers_x > 0){
// use checkerboard pattern
printf("Checkerboard pattern at x outlet for %i layers \n",outlet_layers_x);
for (int k = 0; k<global_Nz; k++){
for (int j = 0; j<global_Ny; j++){
for (int i = xStart + nx*nprocx - outlet_layers_x; i < xStart + nx*nprocx; i++){
if ( (j/checkerSize + k/checkerSize)%2 == 0){
// void checkers
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
}
else{
// solid checkers
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
}
}
}
}
}
if (outlet_layers_y > 0){
printf("Checkerboard pattern at y outlet for %i layers \n",outlet_layers_y);
// use checkerboard pattern
for (int k = 0; k<global_Nz; k++){
for (int j = yStart + ny*nprocy - outlet_layers_y; i < yStart + ny*nprocy; j++){
for (int i = 0; i<global_Nx; i++){
if ( (i/checkerSize + k/checkerSize)%2 == 0){
// void checkers
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
}
else{
// solid checkers
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
}
}
}
}
}
if (outlet_layers_z > 0){
printf("Checkerboard pattern at z outlet for %i layers \n",outlet_layers_z);
// use checkerboard pattern
for (int k = zStart + nz*nprocz - outlet_layers_z; k < zStart + nz*nprocz; k++){
for (int j = 0; j<global_Ny; j++){
for (int i = 0; i<global_Nx; i++){
if ( (i/checkerSize+j/checkerSize)%2 == 0){
// void checkers
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
}
else{
// solid checkers
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
}
}
}
}
}
}
// Get the rank info
int64_t N = (nx+2)*(ny+2)*(nz+2);
// number of sites to use for periodic boundary condition transition zone
int64_t z_transition_size = (nprocz*nz - (global_Nz - zStart))/2;
if (z_transition_size < 0) z_transition_size=0;
char LocalRankFilename[40];
char *loc_id;
loc_id = new char [(nx+2)*(ny+2)*(nz+2)];
std::vector<int> LabelCount(ReadValues.size(),0);
// 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",nprocx,nprocy,nprocz);
printf("Subdomain size: %i x %i x %i \n",nx,ny,nz);
printf("Size of transition region: %ld \n", z_transition_size);
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*nprocx*nprocy + jp*nprocx + ip;
// Pack and send the subdomain for rnk
for (k=0;k<nz+2;k++){
for (j=0;j<ny+2;j++){
for (i=0;i<nx+2;i++){
int64_t x = xStart + ip*nx + i-1;
int64_t y = yStart + jp*ny + j-1;
// int64_t z = zStart + kp*nz + k-1;
int64_t z = zStart + kp*nz + k-1 - z_transition_size;
if (x<xStart) x=xStart;
if (!(x<global_Nx)) x=global_Nx-1;
if (y<yStart) y=yStart;
if (!(y<global_Ny)) y=global_Ny-1;
if (z<zStart) z=zStart;
if (!(z<global_Nz)) z=global_Nz-1;
int64_t nlocal = k*(nx+2)*(ny+2) + j*(nx+2) + i;
int64_t nglobal = z*global_Nx*global_Ny+y*global_Nx+x;
loc_id[nlocal] = SegData[nglobal];
}
}
}
// relabel the data
for (k=0;k<nz+2;k++){
for (j=0;j<ny+2;j++){
for (i=0;i<nx+2;i++){
n = k*(nx+2)*(ny+2) + j*(nx+2) + i;;
char locval = loc_id[n];
for (int idx=0; idx<ReadValues.size(); idx++){
signed char oldvalue=ReadValues[idx];
signed char newvalue=WriteValues[idx];
if (locval == oldvalue){
loc_id[n] = newvalue;
LabelCount[idx]++;
idx = ReadValues.size();
}
}
}
}
}
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;
id[nlocal] = loc_id[nlocal];
}
}
}
}
else{
//printf("Sending data to process %i \n", rnk);
MPI_Send(loc_id,N,MPI_CHAR,rnk,15,Comm);
}
// Write the data for this rank data
sprintf(LocalRankFilename,"ID.%05i",rnk+rank_offset);
FILE *ID = fopen(LocalRankFilename,"wb");
fwrite(loc_id,1,(nx+2)*(ny+2)*(nz+2),ID);
fclose(ID);
}
}
}
for (int idx=0; idx<ReadValues.size(); idx++){
int label=ReadValues[idx];
int count=LabelCount[idx];
printf("Label=%d, Count=%d \n",label,count);
}
}
else{
// Recieve the subdomain from rank = 0
//printf("Ready to recieve data %i at process %i \n", N,rank);
MPI_Recv(id,N,MPI_CHAR,0,15,Comm,MPI_STATUS_IGNORE);
}
MPI_Barrier(Comm);
}
/********************************************************
* Initialize communication *