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fix the build

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This commit is contained in:
James McClure 2021-01-05 18:43:44 -05:00
parent 345b43d9f8
commit 7f4f74779c
40 changed files with 242 additions and 710 deletions
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25
models/DFHModel.cpp
View File

@ -3,7 +3,7 @@ color lattice boltzmann model
*/
#include "models/DFHModel.h"
ScaLBL_DFHModel::ScaLBL_DFHModel(int RANK, int NP, MPI_Comm COMM):
ScaLBL_DFHModel::ScaLBL_DFHModel(int RANK, int NP, const Utilities::MPI& COMM):
rank(RANK), nprocs(NP), Restart(0),timestep(0),timestepMax(0),tauA(0),tauB(0),rhoA(0),rhoB(0),alpha(0),beta(0),
Fx(0),Fy(0),Fz(0),flux(0),din(0),dout(0),inletA(0),inletB(0),outletA(0),outletB(0),
Nx(0),Ny(0),Nz(0),N(0),Np(0),nprocx(0),nprocy(0),nprocz(0),BoundaryCondition(0),Lx(0),Ly(0),Lz(0),comm(COMM)
@ -114,9 +114,9 @@ void ScaLBL_DFHModel::SetDomain(){
id = new char [N];
for (int i=0; i<Nx*Ny*Nz; i++) Dm->id[i] = 1; // initialize this way
Averages = std::shared_ptr<TwoPhase> ( new TwoPhase(Dm) ); // TwoPhase analysis object
MPI_Barrier(comm);
comm.barrier();
Dm->CommInit();
MPI_Barrier(comm);
comm.barrier();
rank = Dm->rank();
}
@ -138,7 +138,7 @@ void ScaLBL_DFHModel::ReadInput(){
sprintf(LocalRankString,"%05d",rank);
sprintf(LocalRankFilename,"%s%s","SignDist.",LocalRankString);
ReadBinaryFile(LocalRankFilename, Averages->SDs.data(), N);
MPI_Barrier(comm);
comm.barrier();
if (rank == 0) cout << "Domain set." << endl;
}
@ -430,7 +430,8 @@ void ScaLBL_DFHModel::Initialize(){
}
}
}
MPI_Allreduce(&count_wet,&count_wet_global,1,MPI_DOUBLE,MPI_SUM,comm);
count_wet_global=Dm->Comm.sumReduce( count_wet);
if (rank==0) printf("Wetting phase volume fraction =%f \n",count_wet_global/double(Nx*Ny*Nz*nprocs));
// initialize phi based on PhaseLabel (include solid component labels)
ScaLBL_CopyToDevice(Phi, PhaseLabel, Np*sizeof(double));
@ -452,7 +453,7 @@ void ScaLBL_DFHModel::Initialize(){
timestep=0;
}
}
MPI_Bcast(&timestep,1,MPI_INT,0,comm);
//MPI_Bcast(&timestep,1,MPI_INT,0,comm);
// Read in the restart file to CPU buffers
double *cPhi = new double[Np];
double *cDist = new double[19*Np];
@ -474,7 +475,7 @@ void ScaLBL_DFHModel::Initialize(){
ScaLBL_DeviceBarrier();
delete [] cPhi;
delete [] cDist;
MPI_Barrier(comm);
comm.barrier();
}
if (rank==0) printf ("Initializing phase field \n");
@ -492,7 +493,7 @@ void ScaLBL_DFHModel::Run(){
//.......create and start timer............
double starttime,stoptime,cputime;
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
comm.barrier();
starttime = MPI_Wtime();
//.........................................
//************ MAIN ITERATION LOOP ***************************************/
@ -538,7 +539,7 @@ void ScaLBL_DFHModel::Run(){
}
ScaLBL_D3Q19_AAodd_DFH(NeighborList, fq, Aq, Bq, Den, Phi, Gradient, SolidPotential, rhoA, rhoB, tauA, tauB,
alpha, beta, Fx, Fy, Fz, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
ScaLBL_DeviceBarrier(); comm.barrier();
// *************EVEN TIMESTEP*************
timestep++;
@ -574,9 +575,9 @@ void ScaLBL_DFHModel::Run(){
}
ScaLBL_D3Q19_AAeven_DFH(NeighborList, fq, Aq, Bq, Den, Phi, Gradient, SolidPotential, rhoA, rhoB, tauA, tauB,
alpha, beta, Fx, Fy, Fz, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
ScaLBL_DeviceBarrier(); comm.barrier();
//************************************************************************
MPI_Barrier(comm);
comm.barrier();
PROFILE_STOP("Update");
// Run the analysis
@ -587,7 +588,7 @@ void ScaLBL_DFHModel::Run(){
PROFILE_SAVE("lbpm_color_simulator",1);
//************************************************************************
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
comm.barrier();
stoptime = MPI_Wtime();
if (rank==0) printf("-------------------------------------------------------------------\n");
// Compute the walltime per timestep

4
models/DFHModel.h
View File

@ -18,7 +18,7 @@ Implementation of color lattice boltzmann model
class ScaLBL_DFHModel{
public:
ScaLBL_DFHModel(int RANK, int NP, MPI_Comm COMM);
ScaLBL_DFHModel(int RANK, int NP, const Utilities::MPI& COMM);
~ScaLBL_DFHModel();
// functions in they should be run
@ -66,7 +66,7 @@ public:
double *Pressure;
private:
MPI_Comm comm;
Utilities::MPI comm;
int dist_mem_size;
int neighborSize;

14
models/GreyscaleColorModel.cpp
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@ -15,7 +15,7 @@ void DeleteArray( const TYPE *p )
delete [] p;
}
ScaLBL_GreyscaleColorModel::ScaLBL_GreyscaleColorModel(int RANK, int NP, MPI_Comm COMM):
ScaLBL_GreyscaleColorModel::ScaLBL_GreyscaleColorModel(int RANK, int NP, const Utilities::MPI& COMM):
rank(RANK), nprocs(NP), Restart(0),timestep(0),timestepMax(0),tauA(0),tauB(0),tauA_eff(0),tauB_eff(0),rhoA(0),rhoB(0),alpha(0),beta(0),
Fx(0),Fy(0),Fz(0),flux(0),din(0),dout(0),inletA(0),inletB(0),outletA(0),outletB(0),GreyPorosity(0),
Nx(0),Ny(0),Nz(0),N(0),Np(0),nprocx(0),nprocy(0),nprocz(0),BoundaryCondition(0),Lx(0),Ly(0),Lz(0),comm(COMM)
@ -135,9 +135,9 @@ void ScaLBL_GreyscaleColorModel::SetDomain(){
id = new signed char [N];
for (int i=0; i<Nx*Ny*Nz; i++) Dm->id[i] = 1; // initialize this way
Averages = std::shared_ptr<GreyPhaseAnalysis> ( new GreyPhaseAnalysis(Dm) ); // TwoPhase analysis object
MPI_Barrier(comm);
comm.barrier();
Dm->CommInit();
MPI_Barrier(comm);
comm.barrier();
// Read domain parameters
rank = Dm->rank();
nprocx = Dm->nprocx();
@ -601,7 +601,7 @@ void ScaLBL_GreyscaleColorModel::Create(){
Map.resize(Nx,Ny,Nz); Map.fill(-2);
auto neighborList= new int[18*Npad];
Np = ScaLBL_Comm->MemoryOptimizedLayoutAA(Map,neighborList,Mask->id.data(),Np);
MPI_Barrier(comm);
comm.barrier();
//...........................................................................
// MAIN VARIABLES ALLOCATED HERE
@ -740,7 +740,7 @@ void ScaLBL_GreyscaleColorModel::Initialize(){
ScaLBL_CopyToDevice(Phi,cPhi,N*sizeof(double));
ScaLBL_Comm->Barrier();
MPI_Barrier(comm);
comm.barrier();
if (rank==0) printf ("Initializing phase field from Restart\n");
ScaLBL_PhaseField_InitFromRestart(Den, Aq, Bq, 0, ScaLBL_Comm->LastExterior(), Np);
@ -912,7 +912,7 @@ void ScaLBL_GreyscaleColorModel::Run(){
//.......create and start timer............
double starttime,stoptime,cputime;
ScaLBL_Comm->Barrier();
MPI_Barrier(comm);
comm.barrier();
starttime = MPI_Wtime();
//.........................................
@ -1071,7 +1071,7 @@ void ScaLBL_GreyscaleColorModel::Run(){
}
}
RESTARTFILE.close();
MPI_Barrier(comm);
comm.barrier();
}
if (timestep%visualization_interval==0){
WriteVisFiles();

4
models/GreyscaleColorModel.h
View File

@ -17,7 +17,7 @@ Implementation of two-fluid greyscale color lattice boltzmann model
class ScaLBL_GreyscaleColorModel{
public:
ScaLBL_GreyscaleColorModel(int RANK, int NP, MPI_Comm COMM);
ScaLBL_GreyscaleColorModel(int RANK, int NP, const Utilities::MPI& COMM);
~ScaLBL_GreyscaleColorModel();
// functions in they should be run
@ -72,7 +72,7 @@ public:
double *Permeability_dvc;
private:
MPI_Comm comm;
Utilities::MPI comm;
int dist_mem_size;
int neighborSize;

22
models/GreyscaleModel.cpp
View File

@ -13,7 +13,7 @@ void DeleteArray( const TYPE *p )
delete [] p;
}
ScaLBL_GreyscaleModel::ScaLBL_GreyscaleModel(int RANK, int NP, MPI_Comm COMM):
ScaLBL_GreyscaleModel::ScaLBL_GreyscaleModel(int RANK, int NP, const Utilities::MPI& COMM):
rank(RANK), nprocs(NP), Restart(0),timestep(0),timestepMax(0),tau(0),tau_eff(0),Den(0),Fx(0),Fy(0),Fz(0),flux(0),din(0),dout(0),GreyPorosity(0),
Nx(0),Ny(0),Nz(0),N(0),Np(0),nprocx(0),nprocy(0),nprocz(0),BoundaryCondition(0),Lx(0),Ly(0),Lz(0),comm(COMM)
{
@ -121,9 +121,9 @@ void ScaLBL_GreyscaleModel::SetDomain(){
id = new signed char [N];
for (int i=0; i<Nx*Ny*Nz; i++) Dm->id[i] = 1; // initialize this way
MPI_Barrier(comm);
comm.barrier();
Dm->CommInit();
MPI_Barrier(comm);
comm.barrier();
// Read domain parameters
rank = Dm->rank();
nprocx = Dm->nprocx();
@ -367,7 +367,7 @@ void ScaLBL_GreyscaleModel::Create(){
Map.resize(Nx,Ny,Nz); Map.fill(-2);
auto neighborList= new int[18*Npad];
Np = ScaLBL_Comm->MemoryOptimizedLayoutAA(Map,neighborList,Mask->id.data(),Np);
MPI_Barrier(comm);
comm.barrier();
//...........................................................................
// MAIN VARIABLES ALLOCATED HERE
@ -454,7 +454,7 @@ void ScaLBL_GreyscaleModel::Initialize(){
ScaLBL_CopyToDevice(fq,cfq.get(),19*Np*sizeof(double));
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
comm.barrier();
}
}
@ -487,7 +487,7 @@ void ScaLBL_GreyscaleModel::Run(){
//.......create and start timer............
double starttime,stoptime,cputime;
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
comm.barrier();
starttime = MPI_Wtime();
//.........................................
@ -540,7 +540,7 @@ void ScaLBL_GreyscaleModel::Run(){
ScaLBL_D3Q19_AAodd_Greyscale_IMRT(NeighborList, fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Den,Pressure_dvc);
break;
}
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
ScaLBL_DeviceBarrier(); comm.barrier();
// *************EVEN TIMESTEP*************//
timestep++;
@ -580,7 +580,7 @@ void ScaLBL_GreyscaleModel::Run(){
ScaLBL_D3Q19_AAeven_Greyscale_IMRT(fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Den,Pressure_dvc);
break;
}
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
ScaLBL_DeviceBarrier(); comm.barrier();
//************************************************************************/
if (timestep%analysis_interval==0){
@ -735,7 +735,7 @@ void ScaLBL_GreyscaleModel::Run(){
RESTARTFILE=fopen(LocalRestartFile,"wb");
fwrite(cfq.get(),sizeof(double),19*Np,RESTARTFILE);
fclose(RESTARTFILE);
MPI_Barrier(comm);
comm.barrier();
}
}
@ -743,7 +743,7 @@ void ScaLBL_GreyscaleModel::Run(){
PROFILE_SAVE("lbpm_greyscale_simulator",1);
//************************************************************************
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
comm.barrier();
stoptime = MPI_Wtime();
if (rank==0) printf("-------------------------------------------------------------------\n");
// Compute the walltime per timestep
@ -766,7 +766,7 @@ void ScaLBL_GreyscaleModel::VelocityField(){
/* Minkowski Morphology(Mask);
int SIZE=Np*sizeof(double);
ScaLBL_D3Q19_Momentum(fq,Velocity, Np);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
ScaLBL_DeviceBarrier(); comm.barrier();
ScaLBL_CopyToHost(&VELOCITY[0],&Velocity[0],3*SIZE);
memcpy(Morphology.SDn.data(), Distance.data(), Nx*Ny*Nz*sizeof(double));

4
models/GreyscaleModel.h
View File

@ -18,7 +18,7 @@ Implementation of color lattice boltzmann model
class ScaLBL_GreyscaleModel{
public:
ScaLBL_GreyscaleModel(int RANK, int NP, MPI_Comm COMM);
ScaLBL_GreyscaleModel(int RANK, int NP, const Utilities::MPI& COMM);
~ScaLBL_GreyscaleModel();
// functions in they should be run
@ -76,7 +76,7 @@ public:
DoubleArray Pressure;
private:
MPI_Comm comm;
Utilities::MPI comm;
int dist_mem_size;
int neighborSize;

2
models/IonModel.cpp
View File

@ -6,7 +6,7 @@
#include "analysis/distance.h"
#include "common/ReadMicroCT.h"
ScaLBL_IonModel::ScaLBL_IonModel(int RANK, int NP, MPI_Comm COMM):
ScaLBL_IonModel::ScaLBL_IonModel(int RANK, int NP, const Utilities::MPI& COMM):
rank(RANK),nprocs(NP),timestep(0),timestepMax(0),time_conv(0),kb(0),electron_charge(0),T(0),Vt(0),k2_inv(0),h(0),
tolerance(0),number_ion_species(0),Nx(0),Ny(0),Nz(0),N(0),Np(0),nprocx(0),nprocy(0),nprocz(0),
fluidVelx_dummy(0),fluidVely_dummy(0),fluidVelz_dummy(0),

2
models/IonModel.h
View File

@ -22,7 +22,7 @@
class ScaLBL_IonModel{
public:
ScaLBL_IonModel(int RANK, int NP, MPI_Comm COMM);
ScaLBL_IonModel(int RANK, int NP, const Utilities::MPI& COMM);
~ScaLBL_IonModel();
// functions in they should be run

3
models/MRTModel.cpp
View File

@ -4,8 +4,7 @@
#include "models/MRTModel.h"
#include "analysis/distance.h"
#include "common/ReadMicroCT.h"
ScaLBL_MRTModel::ScaLBL_MRTModel(int RANK, int NP, MPI_Comm COMM):
ScaLBL_MRTModel::ScaLBL_MRTModel(int RANK, int NP, const Utilities::MPI& COMM):
rank(RANK), nprocs(NP), Restart(0),timestep(0),timestepMax(0),tau(0),
Fx(0),Fy(0),Fz(0),flux(0),din(0),dout(0),mu(0),
Nx(0),Ny(0),Nz(0),N(0),Np(0),nprocx(0),nprocy(0),nprocz(0),BoundaryCondition(0),Lx(0),Ly(0),Lz(0),comm(COMM)

4
models/MRTModel.h
View File

@ -17,7 +17,7 @@
class ScaLBL_MRTModel{
public:
ScaLBL_MRTModel(int RANK, int NP, MPI_Comm COMM);
ScaLBL_MRTModel(int RANK, int NP, const Utilities::MPI& COMM);
~ScaLBL_MRTModel();
// functions in they should be run
@ -63,7 +63,7 @@ public:
DoubleArray Velocity_y;
DoubleArray Velocity_z;
private:
Utilities::MPI comm;
Utilities::MPI comm;
// filenames
char LocalRankString[8];

2
models/MultiPhysController.cpp
View File

@ -1,6 +1,6 @@
#include "models/MultiPhysController.h"
ScaLBL_Multiphys_Controller::ScaLBL_Multiphys_Controller(int RANK, int NP, MPI_Comm COMM):
ScaLBL_Multiphys_Controller::ScaLBL_Multiphys_Controller(int RANK, int NP, const Utilities::MPI& COMM):
rank(RANK),nprocs(NP),Restart(0),timestepMax(0),num_iter_Stokes(0),num_iter_Ion(0),
analysis_interval(0),visualization_interval(0),tolerance(0),comm(COMM)
{

4
models/MultiPhysController.h
View File

@ -19,7 +19,7 @@
class ScaLBL_Multiphys_Controller{
public:
ScaLBL_Multiphys_Controller(int RANK, int NP, MPI_Comm COMM);
ScaLBL_Multiphys_Controller(int RANK, int NP, const Utilities::MPI& COMM);
~ScaLBL_Multiphys_Controller();
void ReadParams(string filename);
@ -44,7 +44,7 @@ public:
std::shared_ptr<Database> study_db;
private:
MPI_Comm comm;
Utilities::MPI comm;
// filenames
char LocalRankString[8];

2
models/PoissonSolver.cpp
View File

@ -5,7 +5,7 @@
#include "analysis/distance.h"
#include "common/ReadMicroCT.h"
ScaLBL_Poisson::ScaLBL_Poisson(int RANK, int NP, MPI_Comm COMM):
ScaLBL_Poisson::ScaLBL_Poisson(int RANK, int NP, const Utilities::MPI& COMM):
rank(RANK), nprocs(NP),timestep(0),timestepMax(0),tau(0),k2_inv(0),tolerance(0),h(0),
epsilon0(0),epsilon0_LB(0),epsilonR(0),epsilon_LB(0),Vin(0),Vout(0),Nx(0),Ny(0),Nz(0),N(0),Np(0),analysis_interval(0),
chargeDen_dummy(0),WriteLog(0),

2
models/PoissonSolver.h
View File

@ -21,7 +21,7 @@
class ScaLBL_Poisson{
public:
ScaLBL_Poisson(int RANK, int NP, MPI_Comm COMM);
ScaLBL_Poisson(int RANK, int NP, const Utilities::MPI& COMM);
~ScaLBL_Poisson();
// functions in they should be run

2
models/StokesModel.cpp
View File

@ -5,7 +5,7 @@
#include "analysis/distance.h"
#include "common/ReadMicroCT.h"
ScaLBL_StokesModel::ScaLBL_StokesModel(int RANK, int NP, MPI_Comm COMM):
ScaLBL_StokesModel::ScaLBL_StokesModel(int RANK, int NP, const Utilities::MPI& COMM):
rank(RANK), nprocs(NP), Restart(0),timestep(0),timestepMax(0),tau(0),
Fx(0),Fy(0),Fz(0),flux(0),din(0),dout(0),mu(0),h(0),nu_phys(0),rho_phys(0),rho0(0),den_scale(0),time_conv(0),tolerance(0),
Nx(0),Ny(0),Nz(0),N(0),Np(0),nprocx(0),nprocy(0),nprocz(0),BoundaryCondition(0),Lx(0),Ly(0),Lz(0),comm(COMM)

4
models/StokesModel.h
View File

@ -20,7 +20,7 @@
class ScaLBL_StokesModel{
public:
ScaLBL_StokesModel(int RANK, int NP, MPI_Comm COMM);
ScaLBL_StokesModel(int RANK, int NP, const Utilities::MPI& COMM);
~ScaLBL_StokesModel();
// functions in they should be run
@ -89,4 +89,4 @@ private:
void Velocity_LB_to_Phys(DoubleArray &Vel_reg);
vector<double> computeElectricForceAvg(double *ChargeDensity, double *ElectricField);
};
#endif
#endif

390
tests/GenerateSphereTest.cpp
View File

@ -9,7 +9,7 @@
//#include "common/pmmc.h"
#include "common/Domain.h"
#include "common/SpherePack.h"
#include "common/MPI_Helpers.h"
#include "common/MPI.h"
#include "common/Communication.h"
/*
@ -70,8 +70,8 @@ inline void MorphOpen(DoubleArray SignDist, char *id, Domain &Dm, int nx, int ny
}
}
// total Global is the number of nodes in the pore-space
MPI_Allreduce(&count,&totalGlobal,1,MPI_DOUBLE,MPI_SUM,Dm.Comm);
MPI_Allreduce(&maxdist,&maxdistGlobal,1,MPI_DOUBLE,MPI_MAX,Dm.Comm);
totalGlobal = Dm.Comm.sumReduce( count );
maxdistGlobal = Dm.Comm.sumReduce( maxdist );
double volume=double(nprocx*nprocy*nprocz)*double(nx-2)*double(ny-2)*double(nz-2);
double porosity=totalGlobal/volume;
if (rank==0) printf("Media Porosity: %f \n",porosity);
@ -145,10 +145,9 @@ inline void MorphOpen(DoubleArray SignDist, char *id, Domain &Dm, int nx, int ny
// Increase the critical radius until the target saturation is met
double deltaR=0.05; // amount to change the radius in voxel units
double Rcrit_old=0.0;
double Rcrit_new=0.0;
double Rcrit_old;
double Rcrit_new;
double GlobalNumber = 1.f;
int imin,jmin,kmin,imax,jmax,kmax;
Rcrit_new = maxdistGlobal;
@ -253,7 +252,7 @@ inline void MorphOpen(DoubleArray SignDist, char *id, Domain &Dm, int nx, int ny
UnpackID(Dm.recvList("YZ"), Dm.recvCount("YZ") ,recvID_YZ, id);
//......................................................................................
MPI_Allreduce(&LocalNumber,&GlobalNumber,1,MPI_DOUBLE,MPI_SUM,Dm.Comm);
//double GlobalNumber = Dm.Comm.sumReduce( LocalNumber );
count = 0.f;
for (int k=1; k<Nz-1; k++){
@ -266,7 +265,7 @@ inline void MorphOpen(DoubleArray SignDist, char *id, Domain &Dm, int nx, int ny
}
}
}
MPI_Allreduce(&count,&countGlobal,1,MPI_DOUBLE,MPI_SUM,Dm.Comm);
countGlobal = Dm.Comm.sumReduce( count );
sw_new = countGlobal/totalGlobal;
sw_diff_new = abs(sw_new-SW);
// for test only
@ -296,364 +295,11 @@ inline void MorphOpen(DoubleArray SignDist, char *id, Domain &Dm, int nx, int ny
int main(int argc, char **argv)
{
//*****************************************
// ***** MPI STUFF ****************
//*****************************************
// Initialize MPI
Auto-merging tests/test_dcel_tri_normal.cpp
CONFLICT (content): Merge conflict in tests/test_dcel_tri_normal.cpp
Auto-merging tests/test_dcel_minkowski.cpp
CONFLICT (content): Merge conflict in tests/test_dcel_minkowski.cpp
Auto-merging tests/testCommunication.cpp
CONFLICT (content): Merge conflict in tests/testCommunication.cpp
Auto-merging tests/lbpm_uCT_pp.cpp
CONFLICT (content): Merge conflict in tests/lbpm_uCT_pp.cpp
Auto-merging tests/lbpm_uCT_maskfilter.cpp
CONFLICT (content): Merge conflict in tests/lbpm_uCT_maskfilter.cpp
Auto-merging tests/lbpm_squaretube_pp.cpp
CONFLICT (content): Merge conflict in tests/lbpm_squaretube_pp.cpp
Auto-merging tests/lbpm_sphere_pp.cpp
CONFLICT (content): Merge conflict in tests/lbpm_sphere_pp.cpp
Auto-merging tests/lbpm_segmented_pp.cpp
CONFLICT (content): Merge conflict in tests/lbpm_segmented_pp.cpp
Auto-merging tests/lbpm_segmented_decomp.cpp
CONFLICT (content): Merge conflict in tests/lbpm_segmented_decomp.cpp
Auto-merging tests/lbpm_refine_pp.cpp
CONFLICT (content): Merge conflict in tests/lbpm_refine_pp.cpp
Auto-merging tests/lbpm_random_pp.cpp
CONFLICT (content): Merge conflict in tests/lbpm_random_pp.cpp
Auto-merging tests/lbpm_porenetwork_pp.cpp
CONFLICT (content): Merge conflict in tests/lbpm_porenetwork_pp.cpp
Auto-merging tests/lbpm_plates_pp.cpp
CONFLICT (content): Merge conflict in tests/lbpm_plates_pp.cpp
Auto-merging tests/lbpm_permeability_simulator.cpp
CONFLICT (content): Merge conflict in tests/lbpm_permeability_simulator.cpp
Auto-merging tests/lbpm_nonnewtonian_simulator.cpp
CONFLICT (content): Merge conflict in tests/lbpm_nonnewtonian_simulator.cpp
Auto-merging tests/lbpm_nondarcy_simulator.cpp
CONFLICT (content): Merge conflict in tests/lbpm_nondarcy_simulator.cpp
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Utilities::startup( argc, argv );
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
int nprocs = comm.getSize();
int rank = comm.getRank();
int nprocs = comm.getSize();
{
// parallel domain size (# of sub-domains)
int nprocx,nprocy,nprocz;
@ -743,14 +389,14 @@ Automatic merge failed; fix conflicts and then commit the result.
//.......................................................................
if (rank == 0) printf("Reading the sphere packing \n");
if (rank == 0) ReadSpherePacking(nspheres,cx,cy,cz,rad);
MPI_Barrier(comm);
comm.barrier();
// Broadcast the sphere packing to all processes
MPI_Bcast(cx,nspheres,MPI_DOUBLE,0,comm);
MPI_Bcast(cy,nspheres,MPI_DOUBLE,0,comm);
MPI_Bcast(cz,nspheres,MPI_DOUBLE,0,comm);
MPI_Bcast(rad,nspheres,MPI_DOUBLE,0,comm);
comm.bcast(cx,nspheres,0);
comm.bcast(cy,nspheres,0);
comm.bcast(cz,nspheres,0);
comm.bcast(rad,nspheres,0);
//...........................................................................
MPI_Barrier(comm);
comm.barrier();
if (rank == 0) cout << "Domain set." << endl;
if (rank == 0){
// Compute the Sauter mean diameter
@ -764,7 +410,7 @@ Automatic merge failed; fix conflicts and then commit the result.
D = 6.0*(Nx-2)*nprocx*totVol / totArea / Lx;
printf("Sauter Mean Diameter (computed from sphere packing) = %f \n",D);
}
MPI_Bcast(&D,1,MPI_DOUBLE,0,comm);
comm.bcast(&D,1,0);
//.......................................................................
SignedDistance(SignDist.data(),nspheres,cx,cy,cz,rad,Lx,Ly,Lz,Nx,Ny,Nz,
@ -796,7 +442,7 @@ Automatic merge failed; fix conflicts and then commit the result.
}
}
sum_local = 1.0*sum;
MPI_Allreduce(&sum_local,&porosity,1,MPI_DOUBLE,MPI_SUM,comm);
porosity = comm.sumReduce(sum_local);
porosity = porosity*iVol_global;
if (rank==0) printf("Media porosity = %f \n",porosity);

28
tests/TestBlobIdentify.cpp
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@ -23,21 +23,19 @@ inline double rand2()
// Test if all ranks agree on a value
bool allAgree( int x, MPI_Comm comm ) {
bool allAgree( int x, const Utilities::MPI& comm ) {
int x2 = x;
MPI_Bcast(&x2,1,MPI_INT,0,comm);
comm.bcast(&x2,1,0);
int diff = x==x2 ? 0:1;
int diff2 = 0;
MPI_Allreduce(&diff,&diff2,1,MPI_INT,MPI_SUM,comm);
int diff2 = comm.sumReduce( diff );
return diff2==0;
}
template<class T>
bool allAgree( const std::vector<T>& x, MPI_Comm comm ) {
bool allAgree( const std::vector<T>& x, const Utilities::MPI& comm ) {
std::vector<T> x2 = x;
MPI_Bcast(&x2[0],x.size()*sizeof(T)/sizeof(int),MPI_INT,0,comm);
comm.bcast(&x2[0],x.size()*sizeof(T)/sizeof(int),0);
int diff = x==x2 ? 0:1;
int diff2 = 0;
MPI_Allreduce(&diff,&diff2,1,MPI_INT,MPI_SUM,comm);
int diff2 = comm.sumReduce( diff );
return diff2==0;
}
@ -74,9 +72,9 @@ struct bubble_struct {
// Create a random set of bubles
std::vector<bubble_struct> create_bubbles( int N_bubbles, double Lx, double Ly, double Lz, MPI_Comm comm )
std::vector<bubble_struct> create_bubbles( int N_bubbles, double Lx, double Ly, double Lz, const Utilities::MPI& comm )
{
int rank = comm_rank(comm);
int rank = comm.getRank();
std::vector<bubble_struct> bubbles(N_bubbles);
if ( rank == 0 ) {
double R0 = 0.2*Lx*Ly*Lz/pow((double)N_bubbles,0.333);
@ -91,7 +89,7 @@ std::vector<bubble_struct> create_bubbles( int N_bubbles, double Lx, double Ly,
}
}
size_t N_bytes = N_bubbles*sizeof(bubble_struct);
MPI_Bcast((char*)&bubbles[0],N_bytes,MPI_CHAR,0,comm);
comm.bcast((char*)&bubbles[0],N_bytes,0);
return bubbles;
}
@ -124,7 +122,7 @@ void fillBubbleData( const std::vector<bubble_struct>& bubbles, DoubleArray& Pha
// Shift all of the data by the given number of cells
void shift_data( DoubleArray& data, int sx, int sy, int sz, const RankInfoStruct& rank_info, MPI_Comm comm )
void shift_data( DoubleArray& data, int sx, int sy, int sz, const RankInfoStruct& rank_info, const Utilities::MPI& comm )
{
int nx = data.size(0)-2;
int ny = data.size(1)-2;
@ -296,7 +294,7 @@ int main(int argc, char **argv)
velocity[i].z = bubbles[i].radius*(2*rand2()-1);
}
}
MPI_Bcast((char*)&velocity[0],bubbles.size()*sizeof(Point),MPI_CHAR,0,comm);
comm.bcast((char*)&velocity[0],bubbles.size()*sizeof(Point),0);
fillBubbleData( bubbles, Phase, SignDist, Lx, Ly, Lz, rank_info );
fillData.fill(Phase);
fillData.fill(SignDist);
@ -390,8 +388,8 @@ int main(int argc, char **argv)
printf("\n");
}
}
MPI_Bcast(&N1,1,MPI_INT,0,comm);
MPI_Bcast(&N2,1,MPI_INT,0,comm);
comm.bcast(&N1,1,0);
comm.bcast(&N2,1,0);
if ( N1!=nblobs || N2!=nblobs2 ) {
if ( rank==0 )
printf("Error, blob ids do not map in moving bubble test (%i,%i,%i,%i)\n",

29
tests/TestBubbleDFH.cpp
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@ -9,7 +9,7 @@
#include "common/Communication.h"
#include "analysis/TwoPhase.h"
#include "analysis/runAnalysis.h"
#include "common/MPI_Helpers.h"
#include "common/MPI.h"
#include "ProfilerApp.h"
#include "threadpool/thread_pool.h"
@ -43,7 +43,7 @@ int main(int argc, char **argv)
int device=ScaLBL_SetDevice(rank);
printf("Using GPU ID %i for rank %i \n",device,rank);
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
comm.barrier();
PROFILE_ENABLE(1);
//PROFILE_ENABLE_TRACE();
@ -70,7 +70,7 @@ int main(int argc, char **argv)
// Initialize compute device
// int device=ScaLBL_SetDevice(rank);
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
comm.barrier();
Utilities::setErrorHandlers();
@ -116,7 +116,7 @@ int main(int argc, char **argv)
// Get the rank info
const RankInfoStruct rank_info(rank,nprocx,nprocy,nprocz);
MPI_Barrier(comm);
comm.barrier();
if (nprocs != nprocx*nprocy*nprocz){
printf("nprocx = %i \n",nprocx);
@ -165,7 +165,7 @@ int main(int argc, char **argv)
// Mask that excludes the solid phase
auto Mask = std::make_shared<Domain>(domain_db,comm);
MPI_Barrier(comm);
comm.barrier();
Nx+=2; Ny+=2; Nz += 2;
int N = Nx*Ny*Nz;
@ -249,6 +249,7 @@ int main(int argc, char **argv)
auto neighborList= new int[18*Npad];
Np = ScaLBL_Comm->MemoryOptimizedLayoutAA(Map,neighborList,Mask->id.data(),Np);
comm.barrier();
//...........................................................................
// MAIN VARIABLES ALLOCATED HERE
//...........................................................................
@ -384,8 +385,8 @@ int main(int argc, char **argv)
//.......create and start timer............
double starttime,stoptime,cputime;
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
starttime = MPI_Wtime();
comm.barrier();
starttime = Utilities::MPI::time();
//.........................................
err = 1.0;
@ -434,7 +435,7 @@ int main(int argc, char **argv)
}
ScaLBL_D3Q19_AAodd_DFH(NeighborList, fq, Aq, Bq, Den, Phi, Gradient, SolidPotential, rhoA, rhoB, tauA, tauB,
alpha, beta, Fx, Fy, Fz, 0, ScaLBL_Comm->next, Np);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
ScaLBL_DeviceBarrier(); comm.barrier();
// *************EVEN TIMESTEP*************
timestep++;
@ -470,9 +471,9 @@ int main(int argc, char **argv)
}
ScaLBL_D3Q19_AAeven_DFH(NeighborList, fq, Aq, Bq, Den, Phi, Gradient, SolidPotential, rhoA, rhoB, tauA, tauB,
alpha, beta, Fx, Fy, Fz, 0, ScaLBL_Comm->next, Np);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
ScaLBL_DeviceBarrier(); comm.barrier();
//************************************************************************
MPI_Barrier(comm);
comm.barrier();
PROFILE_STOP("Update");
// Run the analysis
@ -484,8 +485,8 @@ int main(int argc, char **argv)
PROFILE_SAVE("lbpm_color_simulator",1);
//************************************************************************
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
stoptime = MPI_Wtime();
comm.barrier();
stoptime = Utilities::MPI::time();
if (rank==0) printf("-------------------------------------------------------------------\n");
// Compute the walltime per timestep
cputime = (stoptime - starttime)/timestep;
@ -544,9 +545,9 @@ int main(int argc, char **argv)
PROFILE_STOP("Main");
PROFILE_SAVE("lbpm_color_simulator",1);
// ****************************************************
MPI_Barrier(comm);
comm.barrier();
} // Limit scope so variables that contain communicators will free before MPI_Finialize
Utilities::shutdown();
Utilities::shutdown();
return check;
}

14
tests/TestColorBubble.cpp
View File

@ -7,7 +7,7 @@
#include <iostream>
#include <fstream>
#include "common/ScaLBL.h"
#include "common/MPI_Helpers.h"
#include "common/MPI.h"
#include "models/ColorModel.h"
using namespace std;
@ -64,14 +64,11 @@ inline void InitializeBubble(ScaLBL_ColorModel &ColorModel, double BubbleRadius)
//***************************************************************************************
int main(int argc, char **argv)
{
//*****************************************
// ***** MPI STUFF ****************
//*****************************************
// Initialize MPI
Utilities::startup( argc, argv );
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
int nprocs = comm.getSize();
int rank = comm.getRank();
int nprocs = comm.getSize();
int check=0;
{
if (rank == 0){
@ -95,7 +92,8 @@ int main(int argc, char **argv)
ColorModel.Run();
ColorModel.WriteDebug();
}
Utilities::shutdown();
Utilities::shutdown();
return check;
}

19
tests/TestColorGradDFH.cpp
View File

@ -7,7 +7,7 @@
#include <iostream>
#include <fstream>
#include "common/ScaLBL.h"
#include "common/MPI_Helpers.h"
#include "common/MPI.h"
using namespace std;
@ -25,14 +25,11 @@ std::shared_ptr<Database> loadInputs( int nprocs )
//***************************************************************************************
int main(int argc, char **argv)
{
//*****************************************
// ***** MPI STUFF ****************
//*****************************************
// Initialize MPI
Utilities::startup( argc, argv );
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
int nprocs = comm.getSize();
int rank = comm.getRank();
int nprocs = comm.getSize();
int check=0;
{
// parallel domain size (# of sub-domains)
@ -81,7 +78,7 @@ int main(int argc, char **argv)
}
}
Dm->CommInit();
MPI_Barrier(comm);
comm.barrier();
if (rank == 0) cout << "Domain set." << endl;
if (rank==0) printf ("Create ScaLBL_Communicator \n");
@ -208,7 +205,9 @@ int main(int argc, char **argv)
}
}
Utilities::shutdown();
return check;
}
Utilities::shutdown();
return check;
}

9
tests/TestFluxBC.cpp
View File

@ -90,7 +90,7 @@ int main (int argc, char **argv)
Np = ScaLBL_Comm->MemoryOptimizedLayoutAA(Map,neighborList,Dm->id.data(),Np);
comm.barrier();
 //......................device distributions.................................
//......................device distributions.................................
int dist_mem_size = Np*sizeof(double);
if (rank==0) printf ("Allocating distributions \n");
@ -148,7 +148,7 @@ int main (int argc, char **argv)
double *VEL;
VEL= new double [3*Np];
int SIZE=3*Np*sizeof(double);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
ScaLBL_Comm->Barrier();
ScaLBL_CopyToHost(&VEL[0],&dvc_vel[0],SIZE);
double Q = 0.f;
@ -191,7 +191,8 @@ int main (int argc, char **argv)
din = ScaLBL_Comm->D3Q19_Flux_BC_z(NeighborList, fq, flux, timestep);
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
ScaLBL_D3Q19_AAodd_MRT(NeighborList, fq, 0, ScaLBL_Comm->next, Np, rlx_setA, rlx_setB, Fx, Fy, Fz);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
ScaLBL_Comm->Barrier();
timestep++;
ScaLBL_Comm->SendD3Q19AA(fq); //READ FORM NORMAL
@ -200,7 +201,7 @@ int main (int argc, char **argv)
din = ScaLBL_Comm->D3Q19_Flux_BC_z(NeighborList, fq, flux, timestep);
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
ScaLBL_D3Q19_AAeven_MRT(fq, 0, ScaLBL_Comm->next, Np, rlx_setA, rlx_setB, Fx, Fy, Fz);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
ScaLBL_Comm->Barrier();
timestep++;
//************************************************************************/

6
tests/TestForceD3Q19.cpp
View File

@ -1,5 +1,5 @@
#include <iostream>
#include "common/MPI_Helpers.h"
#include "common/MPI.h"
#include "common/Utilities.h"
#include <math.h>
@ -443,14 +443,14 @@ inline void MRT_Transform(double *dist, int Np, double Fx, double Fy, double Fz)
int main (int argc, char **argv)
{
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
int nprocs = comm.getSize();
for (int i=0; i<nprocs; i++) {
if ( rank==i )
printf("%i of %i: Testing force term \n",rank,nprocs);
MPI_Barrier(MPI_COMM_WORLD);
comm.barrier();
}
// Create a memory leak for valgrind to find

34
tests/TestForceMoments.cpp
View File

@ -7,7 +7,7 @@
#include <iostream>
#include <fstream>
#include "common/ScaLBL.h"
#include "common/MPI_Helpers.h"
#include "common/MPI.h"
using namespace std;
@ -46,14 +46,11 @@ std::shared_ptr<Database> loadInputs( int nprocs )
//***************************************************************************************
int main(int argc, char **argv)
{
//*****************************************
// ***** MPI STUFF ****************
//*****************************************
// Initialize MPI
Utilities::startup( argc, argv );
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
int nprocs = comm.getSize();
int rank = comm.getRank();
int nprocs = comm.getSize();
int check=0;
{
// parallel domain size (# of sub-domains)
@ -97,7 +94,7 @@ int main(int argc, char **argv)
printf("********************************************************\n");
}
MPI_Barrier(comm);
comm.barrier();
kproc = rank/(nprocx*nprocy);
jproc = (rank-nprocx*nprocy*kproc)/nprocx;
iproc = rank-nprocx*nprocy*kproc-nprocz*jproc;
@ -105,7 +102,7 @@ int main(int argc, char **argv)
if (rank == 0) {
printf("i,j,k proc=%d %d %d \n",iproc,jproc,kproc);
}
MPI_Barrier(comm);
comm.barrier();
if (rank == 1){
printf("i,j,k proc=%d %d %d \n",iproc,jproc,kproc);
printf("\n\n");
@ -142,7 +139,7 @@ int main(int argc, char **argv)
}
}
Dm->CommInit();
MPI_Barrier(comm);
comm.barrier();
if (rank == 0) cout << "Domain set." << endl;
int Np=0; // number of local pore nodes
@ -187,7 +184,7 @@ int main(int argc, char **argv)
if (rank == 0) PrintNeighborList(neighborList,Np, rank);
MPI_Barrier(comm);
comm.barrier();
//......................device distributions.................................
int dist_mem_size = Np*sizeof(double);
@ -212,13 +209,13 @@ int main(int argc, char **argv)
//.......create and start timer............
double starttime,stoptime,cputime;
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
starttime = MPI_Wtime();
ScaLBL_DeviceBarrier(); comm.barrier();
starttime = Utilities::MPI::time();
/************ MAIN ITERATION LOOP (timing communications)***************************************/
//ScaLBL_Comm->SendD3Q19(dist, &dist[10*Np]);
//ScaLBL_Comm->RecvD3Q19(dist, &dist[10*Np]);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
ScaLBL_DeviceBarrier(); comm.barrier();
if (rank==0) printf("Beginning AA timesteps...\n");
if (rank==0) printf("********************************************************\n");
@ -230,14 +227,14 @@ int main(int argc, char **argv)
ScaLBL_D3Q19_AAodd_MRT(NeighborList, dist, ScaLBL_Comm->first_interior, ScaLBL_Comm->last_interior, Np, rlx_setA, rlx_setB, Fx, Fy, Fz);
ScaLBL_Comm->RecvD3Q19AA(dist); //WRITE INTO OPPOSITE
ScaLBL_D3Q19_AAodd_MRT(NeighborList, dist, 0, ScaLBL_Comm->next, Np, rlx_setA, rlx_setB, Fx, Fy, Fz);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
ScaLBL_DeviceBarrier(); comm.barrier();
timestep++;
ScaLBL_Comm->SendD3Q19AA(dist); //READ FORM NORMAL
ScaLBL_D3Q19_AAeven_MRT(dist, ScaLBL_Comm->first_interior, ScaLBL_Comm->last_interior, Np, rlx_setA, rlx_setB, Fx, Fy, Fz);
ScaLBL_Comm->RecvD3Q19AA(dist); //WRITE INTO OPPOSITE
ScaLBL_D3Q19_AAeven_MRT(dist, 0, ScaLBL_Comm->next, Np, rlx_setA, rlx_setB, Fx, Fy, Fz);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
ScaLBL_DeviceBarrier(); comm.barrier();
timestep++;
//************************************************************************/
@ -247,7 +244,7 @@ int main(int argc, char **argv)
//************************************************************************/
stoptime = MPI_Wtime();
stoptime = Utilities::MPI::time();
// cout << "CPU time: " << (stoptime - starttime) << " seconds" << endl;
cputime = stoptime - starttime;
// cout << "Lattice update rate: "<< double(Nx*Ny*Nz*timestep)/cputime/1000000 << " MLUPS" << endl;
@ -329,6 +326,7 @@ int main(int argc, char **argv)
}
Utilities::shutdown();
Utilities::shutdown();
return check;
}

26
tests/TestInterfaceSpeed.cpp
View File

@ -2,7 +2,7 @@
#include <math.h>
#include "analysis/TwoPhase.h"
#include "common/MPI_Helpers.h"
#include "common/MPI.h"
#include "common/Communication.h"
#include "IO/Mesh.h"
#include "IO/Writer.h"
@ -21,6 +21,7 @@ int main (int argc, char *argv[])
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
// Load inputs
string FILENAME = argv[1];
// Load inputs
@ -35,7 +36,7 @@ int main (int argc, char *argv[])
Nx+=2; Ny+=2; Nz+=2;
for (i=0; i<Nx*Ny*Nz; i++) Dm->id[i] = 1;
for (int i=0; i<Nx*Ny*Nz; i++) Dm->id[i] = 1;
Dm->CommInit();
@ -46,9 +47,9 @@ int main (int argc, char *argv[])
double dist1,dist2;
Cx = Cy = Cz = N*0.5;
for (k=0; k<Nz; k++){
for (j=0; j<Ny; j++){
for (i=0; i<Nx; i++){
for (int k=0; k<Nz; k++){
for (int j=0; j<Ny; j++){
for (int i=0; i<Nx; i++){
dist2 = sqrt((i-Cx)*(i-Cx)+(j-Cy)*(j-Cy)+(k-Cz)*(k-Cz)) - CAPRAD;
dist2 = fabs(Cz-k)-HEIGHT;
@ -57,9 +58,9 @@ int main (int argc, char *argv[])
}
}
Cz += SPEED;
for (k=0; k<Nz; k++){
for (j=0; j<Ny; j++){
for (i=0; i<Nx; i++){
for (int k=0; k<Nz; k++){
for (int j=0; j<Ny; j++){
for (int i=0; i<Nx; i++){
dist1 = sqrt((i-Cx)*(i-Cx)+(j-Cy)*(j-Cy)) - RADIUS;
dist2 = sqrt((i-Cx)*(i-Cx)+(j-Cy)*(j-Cy)+(k-Cz)*(k-Cz)) - CAPRAD;
@ -72,9 +73,9 @@ int main (int argc, char *argv[])
}
}
Cz += SPEED;
for (k=0; k<Nz; k++){
for (j=0; j<Ny; j++){
for (i=0; i<Nx; i++){
for (int k=0; k<Nz; k++){
for (int j=0; j<Ny; j++){
for (int i=0; i<Nx; i++){
dist2 = sqrt((i-Cx)*(i-Cx)+(j-Cy)*(j-Cy)+(k-Cz)*(k-Cz)) - CAPRAD;
dist2 = fabs(Cz-k)-HEIGHT;
@ -144,7 +145,8 @@ int main (int argc, char *argv[])
}
return toReturn;
comm.barrier();
Utilities::shutdown();
return 0;
Utilities::shutdown();
}

14
tests/TestMap.cpp
View File

@ -7,7 +7,7 @@
#include <iostream>
#include <fstream>
#include "common/ScaLBL.h"
#include "common/MPI_Helpers.h"
#include "common/MPI.h"
using namespace std;
@ -26,11 +26,8 @@ std::shared_ptr<Database> loadInputs( int nprocs )
//***************************************************************************************
int main(int argc, char **argv)
{
//*****************************************
// ***** MPI STUFF ****************
//*****************************************
// Initialize MPI
Utilities::startup( argc, argv );
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
int check=0;
{
@ -42,6 +39,7 @@ int main(int argc, char **argv)
{1,0,1},{-1,0,-1},{1,0,-1},{-1,0,1},
{0,1,1},{0,-1,-1},{0,1,-1},{0,-1,1}};
int rank = comm.getRank();
if (rank == 0){
printf("********************************************************\n");
printf("Running unit test: TestMap \n");
@ -49,7 +47,7 @@ int main(int argc, char **argv)
}
// Load inputs
auto db = loadInputs( nprocs );
auto db = loadInputs( comm.getSize() );
int Nx = db->getVector<int>( "n" )[0];
int Ny = db->getVector<int>( "n" )[1];
int Nz = db->getVector<int>( "n" )[2];
@ -92,7 +90,7 @@ int main(int argc, char **argv)
Np = ScaLBL_Comm->MemoryOptimizedLayoutAA(Map,neighborList,Dm->id.data(),Np);
comm.barrier();
// Check the neighborlist
printf("Check neighborlist: exterior %i, first interior %i last interior %i \n",ScaLBL_Comm->LastExterior(),ScaLBL_Comm->FirstInterior(),ScaLBL_Comm->LastInterior());
for (int idx=0; idx<ScaLBL_Comm->LastExterior(); idx++){
@ -193,7 +191,7 @@ int main(int argc, char **argv)
delete [] TmpMap;
}
Utilities::shutdown();
Utilities::shutdown();
return check;
}

4
tests/TestMomentsD3Q19.cpp
View File

@ -1,5 +1,5 @@
#include <iostream>
#include "common/MPI_Helpers.h"
#include "common/MPI.h"
#include "common/Utilities.h"
#include <math.h>
@ -470,7 +470,7 @@ int main (int argc, char **argv)
for (int i=0; i<nprocs; i++) {
if ( rank==i )
printf("%i of %i: TestMoments\n",rank,nprocs);
MPI_Barrier(MPI_COMM_WORLD);
comm.barrier();
}
// Create a memory leak for valgrind to find

24
tests/TestNernstPlanck.cpp
View File

@ -20,26 +20,23 @@ using namespace std;
int main(int argc, char **argv)
{
// Initialize MPI
// Initialize MPI
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
int nprocs = comm.getSize();
{ // Limit scope so variables that contain communicators will free before MPI_Finialize
MPI_Comm comm;
MPI_Comm_dup(MPI_COMM_WORLD,&comm);
int rank = comm_rank(comm);
int nprocs = comm_size(comm);
if (rank == 0){
printf("********************************************************\n");
printf("Running Test for LB-Poisson-Ion Coupling \n");
printf("********************************************************\n");
}
// Initialize compute device
ScaLBL_SetDevice(rank);
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
// Initialize compute device
int device=ScaLBL_SetDevice(rank);
NULL_USE( device );
ScaLBL_DeviceBarrier();
comm.barrier();
PROFILE_ENABLE(1);
//PROFILE_ENABLE_TRACE();
@ -97,9 +94,6 @@ int main(int argc, char **argv)
PROFILE_STOP("Main");
PROFILE_SAVE("TestNernstPlanck",1);
// ****************************************************
//
MPI_Barrier(comm);
MPI_Comm_free(&comm);
} // Limit scope so variables that contain communicators will free before MPI_Finialize
Utilities::shutdown();

22
tests/TestPNP_Stokes.cpp
View File

@ -21,25 +21,25 @@ using namespace std;
int main(int argc, char **argv)
{
// Initialize MPI and error handlers
// Initialize MPI
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
int nprocs = comm.getSize();
{ // Limit scope so variables that contain communicators will free before MPI_Finialize
MPI_Comm comm;
MPI_Comm_dup(MPI_COMM_WORLD,&comm);
int rank = comm_rank(comm);
int nprocs = comm_size(comm);
if (rank == 0){
printf("********************************************************\n");
printf("Running Test for LB-Poisson-Ion Coupling \n");
printf("********************************************************\n");
}
// Initialize compute device
ScaLBL_SetDevice(rank);
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
// Initialize compute device
int device=ScaLBL_SetDevice(rank);
NULL_USE( device );
ScaLBL_DeviceBarrier();
comm.barrier();
PROFILE_ENABLE(1);
//PROFILE_ENABLE_TRACE();
@ -118,9 +118,7 @@ int main(int argc, char **argv)
PROFILE_STOP("Main");
PROFILE_SAVE("TestPNP_Stokes",1);
// ****************************************************
MPI_Barrier(comm);
MPI_Comm_free(&comm);
} // Limit scope so variables that contain communicators will free before MPI_Finialize

18
tests/TestPoiseuille.cpp
View File

@ -7,7 +7,7 @@
#include <iostream>
#include <fstream>
#include "common/ScaLBL.h"
#include "common/MPI_Helpers.h"
#include "common/MPI.h"
#include "models/MRTModel.h"
void ParallelPlates(ScaLBL_MRTModel &MRT){
@ -47,14 +47,11 @@ void ParallelPlates(ScaLBL_MRTModel &MRT){
//***************************************************************************************
int main(int argc, char **argv)
{
//*****************************************
// ***** MPI STUFF ****************
//*****************************************
// Initialize MPI
Utilities::startup( argc, argv );
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
int nprocs = comm.getSize();
int rank = comm.getRank();
int nprocs = comm.getSize();
int check=0;
{
if (rank == 0){
@ -76,7 +73,7 @@ int main(int argc, char **argv)
int SIZE=MRT.Np*sizeof(double);
ScaLBL_D3Q19_Momentum(MRT.fq,MRT.Velocity, MRT.Np);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
ScaLBL_DeviceBarrier(); comm.barrier();
ScaLBL_CopyToHost(&Vz[0],&MRT.Velocity[0],3*SIZE);
if (rank == 0) printf("Force: %f,%f,%f \n",MRT.Fx,MRT.Fy,MRT.Fz);
@ -90,7 +87,7 @@ int main(int argc, char **argv)
j=Ny/2; k=Nz/2;
if (rank == 0) printf("Channel width=%f \n",W);
if (rank == 0) printf("ID flag vz analytical\n");
MPI_Barrier(comm);
comm.barrier();
if (rank == 0) {
for (i=0;i<Nx;i++){
@ -128,6 +125,7 @@ int main(int argc, char **argv)
}
}
Utilities::shutdown();
Utilities::shutdown();
return check;
}

21
tests/TestPoissonSolver.cpp
View File

@ -20,23 +20,21 @@ int main(int argc, char **argv)
{
// Initialize MPI
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
int nprocs = comm.getSize();
{// Limit scope so variables that contain communicators will free before MPI_Finialize
MPI_Comm comm;
MPI_Comm_dup(MPI_COMM_WORLD,&comm);
int rank = comm_rank(comm);
int nprocs = comm_size(comm);
if (rank == 0){
printf("********************************************************\n");
printf("Running Test for LB-Poisson Solver \n");
printf("********************************************************\n");
}
// Initialize compute device
ScaLBL_SetDevice(rank);
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
// Initialize compute device
int device=ScaLBL_SetDevice(rank);
NULL_USE( device );
ScaLBL_DeviceBarrier();
comm.barrier();
PROFILE_ENABLE(1);
//PROFILE_ENABLE_TRACE();
@ -69,9 +67,6 @@ int main(int argc, char **argv)
PROFILE_SAVE("TestPoissonSolver",1);
// ****************************************************
MPI_Barrier(comm);
MPI_Comm_free(&comm);
} // Limit scope so variables that contain communicators will free before MPI_Finialize
Utilities::shutdown();

20
tests/TestPressVel.cpp
View File

@ -7,19 +7,16 @@
#include <iostream>
#include <fstream>
#include "common/ScaLBL.h"
#include "common/MPI_Helpers.h"
#include "common/MPI.h"
//***************************************************************************************
int main(int argc, char **argv)
{
//*****************************************
// ***** MPI STUFF ****************
//*****************************************
// Initialize MPI
Utilities::startup( argc, argv );
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
int rank = comm.getRank();
int check=0;
{
if (rank == 0){
@ -48,7 +45,7 @@ int main(int argc, char **argv)
printf("********************************************************\n");
}
MPI_Barrier(comm);
comm.barrier();
int kproc = rank/(nprocx*nprocy);
int jproc = (rank-nprocx*nprocy*kproc)/nprocx;
int iproc = rank-nprocx*nprocy*kproc-nprocz*jproc;
@ -56,7 +53,7 @@ int main(int argc, char **argv)
if (rank == 0) {
printf("i,j,k proc=%d %d %d \n",iproc,jproc,kproc);
}
MPI_Barrier(comm);
comm.barrier();
if (rank == 1){
printf("i,j,k proc=%d %d %d \n",iproc,jproc,kproc);
printf("\n\n");
@ -100,11 +97,11 @@ int main(int argc, char **argv)
}
}
}
MPI_Allreduce(&sum_local,&sum,1,MPI_DOUBLE,MPI_SUM,comm);
sum = comm.sumReduce( sum_local );
porosity = sum*iVol_global;
if (rank==0) printf("Media porosity = %f \n",porosity);
MPI_Barrier(comm);
comm.barrier();
if (rank == 0) cout << "Domain set." << endl;
if (rank==0) printf ("Create ScaLBL_Communicator \n");
@ -191,6 +188,7 @@ int main(int argc, char **argv)
}
}
}
Utilities::shutdown();
Utilities::shutdown();
return check;
}

4
tests/hello_world.cpp
View File

@ -1,5 +1,5 @@
#include <iostream>
#include "common/MPI_Helpers.h"
#include "common/MPI.h"
#include "common/Utilities.h"
@ -13,7 +13,7 @@ int main (int argc, char **argv)
for (int i=0; i<nprocs; i++) {
if ( rank==i )
printf("%i of %i: Hello world\n",rank,nprocs);
MPI_Barrier(MPI_COMM_WORLD);
comm.barrier();
}
// Create a memory leak for valgrind to find

2
tests/lbpm_dfh_simulator.cpp
View File

@ -58,7 +58,7 @@ int main(int argc, char **argv)
PROFILE_STOP("Main");
PROFILE_SAVE("lbpm_color_simulator",1);
// ****************************************************
MPI_Barrier(comm);
comm.barrier();
} // Limit scope so variables that contain communicators will free before MPI_Finialize
Utilities::shutdown();
}

99
tests/lbpm_minkowski_scalar.cpp
View File

@ -33,7 +33,7 @@ int main(int argc, char **argv)
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
int nprocs = comm.getSize();
//int nprocs = comm.getSize();
{
Utilities::setErrorHandlers();
PROFILE_START("Main");
@ -64,108 +64,21 @@ int main(int argc, char **argv)
auto nx = size[0];
auto ny = size[1];
auto nz = size[2];
auto nprocx = nproc[0];
/*auto nprocx = nproc[0];
auto nprocy = nproc[1];
auto nprocz = nproc[2];
auto Nx = SIZE[0];
auto Ny = SIZE[1];
auto Nz = SIZE[2];
*/
int i,j,k,n;
char *SegData = NULL;
// Rank=0 reads the entire segmented data and distributes to worker processes
if (rank==0){
printf("Dimensions of segmented image: %i x %i x %i \n",Nx,Ny,Nz);
SegData = new char[Nx*Ny*Nz];
FILE *SEGDAT = fopen(Filename.c_str(),"rb");
if (SEGDAT==NULL) ERROR("Error reading segmented data");
size_t ReadSeg;
ReadSeg=fread(SegData,1,Nx*Ny*Nz,SEGDAT);
if (ReadSeg != size_t(Nx*Ny*Nz)) printf("lbpm_segmented_decomp: Error reading segmented data (rank=%i)\n",rank);
fclose(SEGDAT);
printf("Read segmented data from %s \n",Filename.c_str());
}
MPI_Barrier(comm);
// Get the rank info
int N = (nx+2)*(ny+2)*(nz+2);
std::shared_ptr<Domain> Dm (new Domain(domain_db,comm));
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;
Dm->id[n] = 1;
}
}
}
std::shared_ptr<Domain> Dm = std::shared_ptr<Domain>(new Domain(domain_db,comm)); // full domain for analysis
comm.barrier();
Dm->CommInit();
int z_transition_size = 0;
int xStart = 0;
int yStart = 0;
int zStart = 0;
// Set up the sub-domains
if (rank==0){
printf("Distributing subdomain 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);
char *tmp;
tmp = new char[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
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 z = zStart + kp*nz + k-1 - z_transition_size;
if (x<xStart) x=xStart;
if (!(x<Nx)) x=Nx-1;
if (y<yStart) y=yStart;
if (!(y<Ny)) y=Ny-1;
if (z<zStart) z=zStart;
if (!(z<Nz)) z=Nz-1;
int nlocal = k*(nx+2)*(ny+2) + j*(nx+2) + i;
int nglobal = z*Nx*Ny+y*Nx+x;
tmp[nlocal] = SegData[nglobal];
}
}
}
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;
Dm->id[nlocal] = tmp[nlocal];
}
}
}
}
else{
printf("Sending data to process %i \n", rnk);
MPI_Send(tmp,N,MPI_CHAR,rnk,15,comm);
}
}
}
}
}
else{
// Recieve the subdomain from rank = 0
printf("Ready to recieve data %i at process %i \n", N,rank);
comm.recv(Dm->id.data(),N,0,15);
}
MPI_Barrier(comm);
// Compute the Minkowski functionals
MPI_Barrier(comm);
comm.barrier();
std::shared_ptr<Minkowski> Averages(new Minkowski(Dm));
// Calculate the distance

20
tests/lbpm_morph_pp.cpp
View File

@ -23,9 +23,9 @@
int main(int argc, char **argv)
{
// Initialize MPI
Utilities::startup( argc, argv );
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
int rank = comm.getRank();
{
//.......................................................................
// Reading the domain information file
@ -125,13 +125,13 @@ int main(int argc, char **argv)
if (rank==0) printf("Initialized solid phase -- Converting to Signed Distance function \n");
CalcDist(SignDist,id_solid,*Dm);
MPI_Barrier(comm);
comm.barrier();
// Extract only the connected part of NWP
BlobIDstruct new_index;
double vF=0.0; double vS=0.0;
ComputeGlobalBlobIDs(nx-2,ny-2,nz-2,Dm->rank_info,phase,SignDist,vF,vS,phase_label,Dm->Comm);
MPI_Barrier(Dm->Comm);
Dm->Comm.barrier();
int count_connected=0;
int count_porespace=0;
@ -153,9 +153,9 @@ int main(int argc, char **argv)
}
}
}
count_connected=sumReduce( Dm->Comm, count_connected);
count_porespace=sumReduce( Dm->Comm, count_porespace);
count_water=sumReduce( Dm->Comm, count_water);
count_connected = Dm->Comm.sumReduce( count_connected );
count_porespace = Dm->Comm.sumReduce( count_porespace );
count_water = Dm->Comm.sumReduce( count_water );
for (int k=0; k<nz; k++){
for (int j=0; j<ny; j++){
@ -213,7 +213,7 @@ int main(int argc, char **argv)
}
}
}
count_water=sumReduce( Dm->Comm, count_water);
count_water = Dm->Comm.sumReduce( count_water );
SW = double(count_water) / count_porespace;
if(rank==0) printf("Final saturation: %f \n", SW);
@ -234,12 +234,12 @@ int main(int argc, char **argv)
}
}
}
MPI_Barrier(comm);
comm.barrier();
auto filename2 = READFILE + ".morph.raw";
if (rank==0) printf("Writing file to: %s \n", filename2.c_str());
Mask->AggregateLabels(filename2);
}
Utilities::shutdown();
Utilities::shutdown();
}

8
tests/lbpm_morphdrain_pp.cpp
View File

@ -23,9 +23,9 @@
int main(int argc, char **argv)
{
// Initialize MPI
Utilities::startup( argc, argv );
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
int rank = comm.getRank();
{
//.......................................................................
// Reading the domain information file
@ -119,7 +119,7 @@ int main(int argc, char **argv)
if (rank==0) printf("Initialized solid phase -- Converting to Signed Distance function \n");
CalcDist(SignDist,id_solid,*Dm);
MPI_Barrier(comm);
comm.barrier();
// Run the morphological opening
MorphDrain(SignDist, id, Dm, SW);
@ -194,7 +194,7 @@ int main(int argc, char **argv)
}
}
}
MPI_Barrier(comm);
comm.barrier();
auto filename2 = READFILE + ".morphdrain.raw";
if (rank==0) printf("Writing file to: %s \n", filename2.data() );

8
tests/lbpm_morphopen_pp.cpp
View File

@ -23,9 +23,9 @@
int main(int argc, char **argv)
{
// Initialize MPI
Utilities::startup( argc, argv );
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
int rank = comm.getRank();
{
//.......................................................................
// Reading the domain information file
@ -121,7 +121,7 @@ int main(int argc, char **argv)
if (rank==0) printf("Initialized solid phase -- Converting to Signed Distance function \n");
CalcDist(SignDist,id_solid,*Dm);
MPI_Barrier(comm);
comm.barrier();
// Run the morphological opening
MorphOpen(SignDist, id, Dm, SW, ErodeLabel, OpenLabel);
@ -196,7 +196,7 @@ int main(int argc, char **argv)
}
}
}
MPI_Barrier(comm);
comm.barrier();
auto filename2 = READFILE + ".morphopen.raw";
if (rank==0) printf("Writing file to: %s \n", filename2.data());

12
tests/lbpm_permeability_simulator.cpp
View File

@ -9,7 +9,7 @@
#include "common/ScaLBL.h"
#include "common/Communication.h"
#include "analysis/TwoPhase.h"
#include "common/MPI_Helpers.h"
#include "common/MPI.h"
#include "models/MRTModel.h"
//#define WRITE_SURFACES
@ -24,10 +24,10 @@ using namespace std;
int main(int argc, char **argv)
{
// Initialize MPI
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
int nprocs = comm.getSize();
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
int nprocs = comm.getSize();
{
if (rank == 0){
printf("********************************************************\n");
@ -38,7 +38,7 @@ int main(int argc, char **argv)
int device=ScaLBL_SetDevice(rank);
NULL_USE( device );
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
comm.barrier();
ScaLBL_MRTModel MRT(rank,nprocs,comm);
auto filename = argv[1];

21
tests/testCommunication.cpp
View File

@ -6,7 +6,7 @@
#include <fstream>
#include "common/Communication.h"
#include "common/MPI_Helpers.h"
#include "common/MPI.h"
#include "common/Array.h"
using namespace std;
@ -15,11 +15,9 @@ using namespace std;
//***************************************************************************************
int test_communication( MPI_Comm comm, int nprocx, int nprocy, int nprocz )
int test_communication( const Utilities::MPI& comm, int nprocx, int nprocy, int nprocz )
{
int rank,nprocs;
MPI_Comm_rank(comm,&rank);
MPI_Comm_size(comm,&nprocs);
int rank = comm.getRank();
int iproc,jproc,kproc;
int sendtag,recvtag;
if (rank==0) printf("\nRunning test %i %i %i\n",nprocx,nprocy,nprocz);
@ -38,7 +36,7 @@ int test_communication( MPI_Comm comm, int nprocx, int nprocy, int nprocz )
rank_xy, rank_XY, rank_xY, rank_Xy,
rank_xz, rank_XZ, rank_xZ, rank_Xz,
rank_yz, rank_YZ, rank_yZ, rank_Yz );
MPI_Barrier(comm);
comm.barrier();
//**********************************
@ -85,7 +83,7 @@ int test_communication( MPI_Comm comm, int nprocx, int nprocy, int nprocz )
sendCount_xy = sendCount_yz = sendCount_xz = sendCount_Xy = sendCount_Yz = sendCount_xZ = 0;
sendCount_xY = sendCount_yZ = sendCount_Xz = sendCount_XY = sendCount_YZ = sendCount_XZ = 0;
MPI_Barrier(comm);
comm.barrier();
if (rank==0) printf ("SendLists are ready on host\n");
//......................................................................................
// Use MPI to fill in the recvCounts form the associated processes
@ -158,7 +156,7 @@ int test_communication( MPI_Comm comm, int nprocx, int nprocy, int nprocz )
recvCount_yz, recvCount_YZ, recvCount_yZ, recvCount_Yz,
rank_x, rank_y, rank_z, rank_X, rank_Y, rank_Z, rank_xy, rank_XY, rank_xY,
rank_Xy, rank_xz, rank_XZ, rank_xZ, rank_Xz, rank_yz, rank_YZ, rank_yZ, rank_Yz );
MPI_Barrier(comm);
comm.barrier();
if (rank==0) printf ("RecvLists finished\n");
// Free memory
@ -181,11 +179,9 @@ int test_communication( MPI_Comm comm, int nprocx, int nprocy, int nprocz )
template<class TYPE>
int testHalo( MPI_Comm comm, int nprocx, int nprocy, int nprocz, int depth )
int testHalo( const Utilities::MPI& comm, int nprocx, int nprocy, int nprocz, int depth )
{
int rank,nprocs;
MPI_Comm_rank(comm,&rank);
MPI_Comm_size(comm,&nprocs);
int rank = comm.getRank();
if ( rank==0 )
printf("\nRunning Halo test %i %i %i %i\n",nprocx,nprocy,nprocz,depth);
@ -292,7 +288,6 @@ int main(int argc, char **argv)
int N_errors_global = comm.sumReduce( N_errors );
comm.barrier();
Utilities::shutdown();
if ( rank==0 ) {
if ( N_errors_global==0 )
std::cout << "All tests passed\n";