OilfieldToolsNet/LBPM
4
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

refactor analysis to take color model as argument

Browse Source
This commit is contained in:
James McClure 2021-03-24 21:19:53 -04:00
parent aba4ca8455
commit 1ddf5e709e
6 changed files with 297 additions and 11 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

133
analysis/runAnalysis.cpp
View File

@ -706,6 +706,139 @@ runAnalysis::runAnalysis( std::shared_ptr<Database> input_db, const RankInfoStru
}
// Initialize the comms
for ( int i = 0; i < 1024; i++ )
d_comm_used[i] = false;
// Initialize the threads
int N_threads = db->getWithDefault<int>( "N_threads", 4 );
auto method = db->getWithDefault<std::string>( "load_balance", "default" );
createThreads( method, N_threads );
}
runAnalysis::runAnalysis( ScaLBL_ColorModel &ColorModel)
/* std::shared_ptr<Database> input_db, const RankInfoStruct &rank_info,
std::shared_ptr<ScaLBL_Communicator> ScaLBL_Comm, std::shared_ptr<Domain> Dm, int Np,
bool Regular, IntArray Map )
: d_Np( Np ),
d_regular( Regular ),
d_rank_info( rank_info ),
d_Map( Map ),
d_comm( Dm->Comm.dup() ),
d_ScaLBL_Comm( ScaLBL_Comm )*/
{
d_comm = ColorModel.Dm->Comm.dup();
d_Np = ColorModel.Np;
bool Regular = false;
auto input_db = ColorModel.db;
auto db = input_db->getDatabase( "Analysis" );
auto vis_db = input_db->getDatabase( "Visualization" );
// Ids of work items to use for dependencies
ThreadPool::thread_id_t d_wait_blobID;
ThreadPool::thread_id_t d_wait_analysis;
ThreadPool::thread_id_t d_wait_vis;
ThreadPool::thread_id_t d_wait_restart;
ThreadPool::thread_id_t d_wait_subphase;
char rankString[20];
sprintf( rankString, "%05d", ColorModel.Dm->rank() );
d_n[0] = ColorModel.Dm->Nx - 2;
d_n[1] = ColorModel.Dm->Ny - 2;
d_n[2] = ColorModel.Dm->Nz - 2;
d_N[0] = ColorModel.Dm->Nx;
d_N[1] = ColorModel.Dm->Ny;
d_N[2] = ColorModel.Dm->Nz;
d_restart_interval = db->getScalar<int>( "restart_interval" );
d_analysis_interval = db->getScalar<int>( "analysis_interval" );
d_subphase_analysis_interval = INT_MAX;
d_visualization_interval = INT_MAX;
d_blobid_interval = INT_MAX;
if ( db->keyExists( "blobid_interval" ) ) {
d_blobid_interval = db->getScalar<int>( "blobid_interval" );
}
if ( db->keyExists( "visualization_interval" ) ) {
d_visualization_interval = db->getScalar<int>( "visualization_interval" );
}
if ( db->keyExists( "subphase_analysis_interval" ) ) {
d_subphase_analysis_interval = db->getScalar<int>( "subphase_analysis_interval" );
}
auto restart_file = db->getScalar<std::string>( "restart_file" );
d_restartFile = restart_file + "." + rankString;
d_rank = d_comm.getRank();
writeIDMap( ID_map_struct(), 0, id_map_filename );
// Initialize IO for silo
IO::initialize( "", "silo", "false" );
// Create the MeshDataStruct
d_meshData.resize( 1 );
d_meshData[0].meshName = "domain";
d_meshData[0].mesh = std::make_shared<IO::DomainMesh>(
d_rank_info, d_n[0], d_n[1], d_n[2], ColorModel.Dm->Lx, ColorModel.Dm->Ly, ColorModel.Dm->Lz );
auto PhaseVar = std::make_shared<IO::Variable>();
auto PressVar = std::make_shared<IO::Variable>();
auto VxVar = std::make_shared<IO::Variable>();
auto VyVar = std::make_shared<IO::Variable>();
auto VzVar = std::make_shared<IO::Variable>();
auto SignDistVar = std::make_shared<IO::Variable>();
auto BlobIDVar = std::make_shared<IO::Variable>();
if ( vis_db->getWithDefault<bool>( "save_phase_field", true ) ) {
PhaseVar->name = "phase";
PhaseVar->type = IO::VariableType::VolumeVariable;
PhaseVar->dim = 1;
PhaseVar->data.resize( d_n[0], d_n[1], d_n[2] );
d_meshData[0].vars.push_back( PhaseVar );
}
if ( vis_db->getWithDefault<bool>( "save_pressure", false ) ) {
PressVar->name = "Pressure";
PressVar->type = IO::VariableType::VolumeVariable;
PressVar->dim = 1;
PressVar->data.resize( d_n[0], d_n[1], d_n[2] );
d_meshData[0].vars.push_back( PressVar );
}
if ( vis_db->getWithDefault<bool>( "save_velocity", false ) ) {
VxVar->name = "Velocity_x";
VxVar->type = IO::VariableType::VolumeVariable;
VxVar->dim = 1;
VxVar->data.resize( d_n[0], d_n[1], d_n[2] );
d_meshData[0].vars.push_back( VxVar );
VyVar->name = "Velocity_y";
VyVar->type = IO::VariableType::VolumeVariable;
VyVar->dim = 1;
VyVar->data.resize( d_n[0], d_n[1], d_n[2] );
d_meshData[0].vars.push_back( VyVar );
VzVar->name = "Velocity_z";
VzVar->type = IO::VariableType::VolumeVariable;
VzVar->dim = 1;
VzVar->data.resize( d_n[0], d_n[1], d_n[2] );
d_meshData[0].vars.push_back( VzVar );
}
if ( vis_db->getWithDefault<bool>( "save_distance", false ) ) {
SignDistVar->name = "SignDist";
SignDistVar->type = IO::VariableType::VolumeVariable;
SignDistVar->dim = 1;
SignDistVar->data.resize( d_n[0], d_n[1], d_n[2] );
d_meshData[0].vars.push_back( SignDistVar );
}
if ( vis_db->getWithDefault<bool>( "save_connected_components", false ) ) {
BlobIDVar->name = "BlobID";
BlobIDVar->type = IO::VariableType::VolumeVariable;
BlobIDVar->dim = 1;
BlobIDVar->data.resize( d_n[0], d_n[1], d_n[2] );
d_meshData[0].vars.push_back( BlobIDVar );
}
// Initialize the comms
for ( int i = 0; i < 1024; i++ )
d_comm_used[i] = false;

3
analysis/runAnalysis.h
View File

@ -7,6 +7,7 @@
#include "common/Communication.h"
#include "common/ScaLBL.h"
#include "threadpool/thread_pool.h"
#include "models/ColorModel.h"
#include <limits.h>
@ -31,6 +32,8 @@ public:
runAnalysis( std::shared_ptr<Database> db, const RankInfoStruct &rank_info,
std::shared_ptr<ScaLBL_Communicator> ScaLBL_Comm, std::shared_ptr<Domain> dm, int Np,
bool Regular, IntArray Map );
runAnalysis( ScaLBL_ColorModel &ColorModel);
//! Destructor
~runAnalysis();

126
models/ColorModel.cpp
View File

@ -531,6 +531,121 @@ void ScaLBL_ColorModel::Initialize(){
ScaLBL_CopyToHost(Averages->Phi.data(),Phi,N*sizeof(double));
}
double ScaLBL_ColorModel::Run(int returntime){
int nprocs=nprocx*nprocy*nprocz;
//************ MAIN ITERATION LOOP ***************************************/
comm.barrier();
PROFILE_START("Loop");
//std::shared_ptr<Database> analysis_db;
bool Regular = false;
auto current_db = db->cloneDatabase();
auto t1 = std::chrono::system_clock::now();
int START_TIMESTEP = timestep;
int EXIT_TIMESTEP = min(timestepMax,returntime);
while (timestep < EXIT_TIMESTEP ) {
//if ( rank==0 ) { printf("Running timestep %i (%i MB)\n",timestep+1,(int)(Utilities::getMemoryUsage()/1048576)); }
PROFILE_START("Update");
// *************ODD TIMESTEP*************
timestep++;
// Compute the Phase indicator field
// Read for Aq, Bq happens in this routine (requires communication)
ScaLBL_Comm->BiSendD3Q7AA(Aq,Bq); //READ FROM NORMAL
ScaLBL_D3Q7_AAodd_PhaseField(NeighborList, dvcMap, Aq, Bq, Den, Phi, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
ScaLBL_Comm->BiRecvD3Q7AA(Aq,Bq); //WRITE INTO OPPOSITE
ScaLBL_Comm->Barrier();
ScaLBL_D3Q7_AAodd_PhaseField(NeighborList, dvcMap, Aq, Bq, Den, Phi, 0, ScaLBL_Comm->LastExterior(), Np);
// Perform the collision operation
ScaLBL_Comm->SendD3Q19AA(fq); //READ FROM NORMAL
if (BoundaryCondition > 0 && BoundaryCondition < 5){
ScaLBL_Comm->Color_BC_z(dvcMap, Phi, Den, inletA, inletB);
ScaLBL_Comm->Color_BC_Z(dvcMap, Phi, Den, outletA, outletB);
}
// Halo exchange for phase field
ScaLBL_Comm_Regular->SendHalo(Phi);
ScaLBL_D3Q19_AAodd_Color(NeighborList, dvcMap, fq, Aq, Bq, Den, Phi, Velocity, rhoA, rhoB, tauA, tauB,
alpha, beta, Fx, Fy, Fz, Nx, Nx*Ny, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
ScaLBL_Comm_Regular->RecvHalo(Phi);
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
ScaLBL_Comm->Barrier();
// Set BCs
if (BoundaryCondition == 3){
ScaLBL_Comm->D3Q19_Pressure_BC_z(NeighborList, fq, din, timestep);
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
}
if (BoundaryCondition == 4){
din = ScaLBL_Comm->D3Q19_Flux_BC_z(NeighborList, fq, flux, timestep);
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
}
else if (BoundaryCondition == 5){
ScaLBL_Comm->D3Q19_Reflection_BC_z(fq);
ScaLBL_Comm->D3Q19_Reflection_BC_Z(fq);
}
ScaLBL_D3Q19_AAodd_Color(NeighborList, dvcMap, fq, Aq, Bq, Den, Phi, Velocity, rhoA, rhoB, tauA, tauB,
alpha, beta, Fx, Fy, Fz, Nx, Nx*Ny, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_Comm->Barrier();
// *************EVEN TIMESTEP*************
timestep++;
// Compute the Phase indicator field
ScaLBL_Comm->BiSendD3Q7AA(Aq,Bq); //READ FROM NORMAL
ScaLBL_D3Q7_AAeven_PhaseField(dvcMap, Aq, Bq, Den, Phi, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
ScaLBL_Comm->BiRecvD3Q7AA(Aq,Bq); //WRITE INTO OPPOSITE
ScaLBL_Comm->Barrier();
ScaLBL_D3Q7_AAeven_PhaseField(dvcMap, Aq, Bq, Den, Phi, 0, ScaLBL_Comm->LastExterior(), Np);
// Perform the collision operation
ScaLBL_Comm->SendD3Q19AA(fq); //READ FORM NORMAL
// Halo exchange for phase field
if (BoundaryCondition > 0 && BoundaryCondition < 5){
ScaLBL_Comm->Color_BC_z(dvcMap, Phi, Den, inletA, inletB);
ScaLBL_Comm->Color_BC_Z(dvcMap, Phi, Den, outletA, outletB);
}
ScaLBL_Comm_Regular->SendHalo(Phi);
ScaLBL_D3Q19_AAeven_Color(dvcMap, fq, Aq, Bq, Den, Phi, Velocity, rhoA, rhoB, tauA, tauB,
alpha, beta, Fx, Fy, Fz, Nx, Nx*Ny, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
ScaLBL_Comm_Regular->RecvHalo(Phi);
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
ScaLBL_Comm->Barrier();
// Set boundary conditions
if (BoundaryCondition == 3){
ScaLBL_Comm->D3Q19_Pressure_BC_z(NeighborList, fq, din, timestep);
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
}
else if (BoundaryCondition == 4){
din = ScaLBL_Comm->D3Q19_Flux_BC_z(NeighborList, fq, flux, timestep);
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
}
else if (BoundaryCondition == 5){
ScaLBL_Comm->D3Q19_Reflection_BC_z(fq);
ScaLBL_Comm->D3Q19_Reflection_BC_Z(fq);
}
ScaLBL_D3Q19_AAeven_Color(dvcMap, fq, Aq, Bq, Den, Phi, Velocity, rhoA, rhoB, tauA, tauB,
alpha, beta, Fx, Fy, Fz, Nx, Nx*Ny, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_Comm->Barrier();
//************************************************************************
}
PROFILE_STOP("Update");
PROFILE_STOP("Loop");
PROFILE_SAVE("lbpm_color_simulator",1);
//************************************************************************
// Compute the walltime per timestep
auto t2 = std::chrono::system_clock::now();
double cputime = std::chrono::duration<double>( t2 - t1 ).count() / (timestep - START_TIMESTEP);
// Performance obtained from each node
double MLUPS = double(Np)/cputime/1000000;
if (rank==0) printf("********************************************************\n");
if (rank==0) printf("CPU time = %f \n", cputime);
if (rank==0) printf("Lattice update rate (per core)= %f MLUPS \n", MLUPS);
return(MLUPS);
MLUPS *= nprocs;
}
void ScaLBL_ColorModel::Run(){
int nprocs=nprocx*nprocy*nprocz;
const RankInfoStruct rank_info(rank,nprocx,nprocy,nprocz);
@ -580,7 +695,6 @@ void ScaLBL_ColorModel::Run(){
if (color_db->keyExists( "krA_morph_factor" )){
KRA_MORPH_FACTOR = color_db->getScalar<double>( "krA_morph_factor" );
}
/* defaults for simulation protocols */
auto protocol = color_db->getWithDefault<std::string>( "protocol", "none" );
if (protocol == "image sequence"){
@ -625,7 +739,7 @@ void ScaLBL_ColorModel::Run(){
if (analysis_db->keyExists( "seed_water" )){
seed_water = analysis_db->getScalar<double>( "seed_water" );
if (rank == 0) printf("Seed water in oil %f (seed_water) \n",seed_water);
USE_SEED = true;
ASSERT(protocol == "seed water");
}
if (analysis_db->keyExists( "morph_delta" )){
morph_delta = analysis_db->getScalar<double>( "morph_delta" );
@ -656,7 +770,6 @@ void ScaLBL_ColorModel::Run(){
MAX_MORPH_TIMESTEPS = analysis_db->getScalar<int>( "max_morph_timesteps" );
}
if (rank==0){
printf("********************************************************\n");
if (protocol == "image sequence"){
@ -1320,7 +1433,7 @@ double ScaLBL_ColorModel::MorphInit(const double beta, const double target_delta
double vF = 0.f;
double vS = 0.f;
double delta_volume;
double WallFactor = 0.0;
double WallFactor = 1.0;
bool USE_CONNECTED_NWP = false;
DoubleArray phase(Nx,Ny,Nz);
@ -1343,6 +1456,11 @@ double ScaLBL_ColorModel::MorphInit(const double beta, const double target_delta
}
}
double volume_initial = Dm->Comm.sumReduce( count);
double PoreVolume = Dm->Volume*Dm->Porosity();
/*ensure target isn't an absurdly small fraction of pore volume */
if (volume_initial < target_delta_volume*PoreVolume){
volume_initial = target_delta_volume*PoreVolume;
}
/*
sprintf(LocalRankFilename,"phi_initial.%05i.raw",rank);
FILE *INPUT = fopen(LocalRankFilename,"wb");

6
models/ColorModel.h
View File

@ -16,6 +16,10 @@ Implementation of color lattice boltzmann model
#include "ProfilerApp.h"
#include "threadpool/thread_pool.h"
#ifndef ScaLBL_ColorModel_INC
#define ScaLBL_ColorModel_INC
class ScaLBL_ColorModel{
public:
ScaLBL_ColorModel(int RANK, int NP, const Utilities::MPI& COMM);
@ -29,6 +33,7 @@ public:
void Create();
void Initialize();
void Run();
double Run(int returntime);
void WriteDebug();
void getPhaseField(DoubleArray &f);
@ -99,4 +104,5 @@ private:
int timestep;
int timestep_previous;
};
#endif

36
tests/lbpm_color_simulator.cpp
View File

@ -27,19 +27,24 @@ int main( int argc, char **argv )
// Initialize
Utilities::startup( argc, argv );
// Load the input database
auto db = std::make_shared<Database>( argv[1] );
{ // Limit scope so variables that contain communicators will free before MPI_Finialize
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
int nprocs = comm.getSize();
std::string SimulationMode = "production";
// Load the input database
auto db = std::make_shared<Database>( argv[1] );
if (argc > 2) {
SimulationMode = "development";
}
if ( rank == 0 ) {
printf( "********************************************************\n" );
printf( "Running Color LBM \n" );
printf( "********************************************************\n" );
if (SimulationMode == "development")
printf("**** DEVELOPMENT MODE ENABLED *************\n");
}
// Initialize compute device
int device = ScaLBL_SetDevice( rank );
@ -62,8 +67,29 @@ int main( int argc, char **argv )
ColorModel.Create(); // creating the model will create data structure to match the pore
// structure and allocate variables
ColorModel.Initialize(); // initializing the model will set initial conditions for variables
ColorModel.Run();
// ColorModel.WriteDebug();
if (SimulationMode == "development"){
double MLUPS=0.0;
int timestep = 0;
int analysis_interval = ColorModel.timestepMax;
if (ColorModel.analysis_db->keyExists( "" )){
analysis_interval = ColorModel.analysis_db->getScalar<int>( "analysis_interval" );
}
FlowAdaptor Adapt(ColorModel);
runAnalysis analysis(ColorModel);
while (ColorModel.timestep < ColorModel.timestepMax){
timestep += analysis_interval;
MLUPS = ColorModel.Run(timestep);
if (rank==0) printf("Lattice update rate (per MPI process)= %f MLUPS \n", MLUPS);
Adapt.MoveInterface(ColorModel);
}
} //Analysis.WriteVis(LeeModel,LeeModel.db, timestep);
else
ColorModel.Run();
ColorModel.WriteDebug();
PROFILE_STOP( "Main" );
auto file = db->getWithDefault<std::string>( "TimerFile", "lbpm_color_simulator" );

4
tests/lbpm_freelee_simulator.cpp
View File

@ -62,8 +62,8 @@ int main( int argc, char **argv )
double MLUPS=0.0;
int timestep = 0;
int visualization_time = LeeModel.timestepMax;
if (LeeModel.vis_db->keyExists( "visualizataion_interval" )){
visualization_time = LeeModel.vis_db->getScalar<int>( "visualizataion_interval" );
if (LeeModel.vis_db->keyExists( "visualization_interval" )){
visualization_time = LeeModel.vis_db->getScalar<int>( "visualization_interval" );
timestep += visualization_time;
}
while (LeeModel.timestep < LeeModel.timestepMax){