Reply To: Segmentation fault for OpenLB 1.5

[Fany]

Hi Adrian,
Many thanks for your recommendation. I changed it, but there was a problem (MPI mode) as following:
[prepareGeometry] Prepare Geometry …
mlx5: csk060.cluster: got completion with error:
00000000 00000000 00000000 00000000
00000000 00000000 00000000 00000000
00000000 00000000 00000000 00000000
00000000 1f006802 0a009a4b 002ffcd2

What’s more, when I ran it by serial mode (MPI mode off), there was still a problem:
[prepareLattice] Prepare Lattice …
————————————————————————–
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
————————————————————————–
————————————————————————–
mpiexec noticed that process rank 0 with PID 26350 on node csk060 exited on signal 11 (Segmentation fault).
————————————————————————–

Here is my code of prepareGeometry, prepareLattice and setboundary:

void prepareGeometry( ThermalUnitConverter<T, NSDESCRIPTOR, TDESCRIPTOR> &converter, IndicatorF3D<T>& indicator,
STLreader<T>& stlReader, SuperGeometry<T,3>& superGeometry )
{

OstreamManager clout( std::cout,”prepareGeometry” );
clout << “Prepare Geometry …” << std::endl;

superGeometry.rename( 0,2,indicator );

superGeometry.rename( 2,1,stlReader );
superGeometry.clean();

// Set material number for inflow
IndicatorCircle3D<T> inflow( 0.218125,0.249987,0.0234818, 0., 1.,0., 0.0112342 );
IndicatorCylinder3D<T> layerInflow( inflow, 2.*converter.getConversionFactorLength() );
superGeometry.rename( 2,3,1,layerInflow );

// Set material number for outflow0
//IndicatorCircle3D<T> outflow0(0.2053696,0.0900099,0.0346537, 2.5522,5.0294,-1.5237, 0.0054686 );
IndicatorCircle3D<T> outflow0( 0.2053696,0.0900099,0.0346537, 0.,-1.,0., 0.0054686 );
IndicatorCylinder3D<T> layerOutflow0( outflow0, 2.*converter.getConversionFactorLength() );
superGeometry.rename( 2,4,1,layerOutflow0 );

// Set material number for outflow1
//IndicatorCircle3D<T> outflow1(0.2388403,0.0900099,0.0343228, -1.5129,5.1039,-2.8431, 0.0058006 );
IndicatorCircle3D<T> outflow1( 0.2388403,0.0900099,0.0343228, 0.,-1.,0., 0.0058006 );
IndicatorCylinder3D<T> layerOutflow1( outflow1, 2.*converter.getConversionFactorLength() );
superGeometry.rename( 2,5,1,layerOutflow1 );

// Removes all not needed boundary voxels outside the surface
superGeometry.clean();
// Removes all not needed boundary voxels inside the surface
superGeometry.innerClean( 3 );

superGeometry.checkForErrors();

superGeometry.print();
clout << “Prepare Geometry … OK” << std::endl;
}

// Set up the geometry of the simulation
void prepareLattice( ThermalUnitConverter<T, NSDESCRIPTOR, TDESCRIPTOR> &converter,
SuperLattice<T, NSDESCRIPTOR>& NSlattice,
SuperLattice<T, TDESCRIPTOR>& ADlattice,

STLreader<T>& stlReader,
SuperGeometry<T,3>& superGeometry )
{
OstreamManager clout( std::cout,”prepareLattice” );
clout << “Prepare Lattice …” << std::endl;

T omega = converter.getLatticeRelaxationFrequency();
T Tomega = converter.getLatticeThermalRelaxationFrequency();

// material=0 –> do nothing
ADlattice.defineDynamics<NoDynamics>(superGeometry, 0);
NSlattice.defineDynamics<NoDynamics>(superGeometry, 0);

// material=1 –> bulk dynamics
//lattice.defineDynamics( superGeometry,1,&bulkDynamics );
ADlattice.defineDynamics<AdvectionDiffusionBGKdynamics>(superGeometry, 1);
NSlattice.defineDynamics<ForcedBGKdynamics>(superGeometry, 1);

if ( bouzidiOn ) {
// // material=2 –> no dynamics + bouzidi zero velocity
ADlattice.defineDynamics<AdvectionDiffusionBGKdynamics>(superGeometry, 2);
setAdvectionDiffusionTemperatureBoundary<T,TDESCRIPTOR>(ADlattice, Tomega, superGeometry, 2);

NSlattice.defineDynamics<NoDynamics>(superGeometry, 2);
setBouzidiZeroVelocityBoundary<T,NSDESCRIPTOR>(NSlattice, superGeometry, 2, stlReader);

// // material=3 –> no dynamics + bouzidi velocity (inflow)
ADlattice.defineDynamics<AdvectionDiffusionBGKdynamics>( superGeometry, 3);
NSlattice.defineDynamics<NoDynamics>( superGeometry, 3);
setBouzidiVelocityBoundary<T,NSDESCRIPTOR>(NSlattice, superGeometry, 3, stlReader);

}
else {
// material=2 –> bounceBack dynamics
ADlattice.defineDynamics<AdvectionDiffusionBGKdynamics>(superGeometry, 2);
setAdvectionDiffusionTemperatureBoundary<T,TDESCRIPTOR>(ADlattice, Tomega, superGeometry, 2);
NSlattice.defineDynamics<BounceBack>(superGeometry, 2);
// setLocalVelocityBoundary<T,NSDESCRIPTOR>(NSlattice, omega, superGeometry, 2);

// material=3 –> bulk dynamics + velocity (inflow)
ADlattice.defineDynamics<AdvectionDiffusionBGKdynamics>( superGeometry, 3);
NSlattice.defineDynamics<ForcedBGKdynamics>( superGeometry, 3);
setLocalVelocityBoundary<T,NSDESCRIPTOR>(NSlattice, omega, superGeometry, 3);

}

// material=4,5 –> bulk dynamics + pressure (outflow)
ADlattice.defineDynamics<AdvectionDiffusionBGKdynamics>( superGeometry.getMaterialIndicator({4, 5}));
NSlattice.defineDynamics<ForcedBGKdynamics>( superGeometry.getMaterialIndicator({4, 5}));

setInterpolatedPressureBoundary<T,NSDESCRIPTOR>(NSlattice, omega, superGeometry.getMaterialIndicator({4, 5}));

// AnalyticalConst3D<T,T> rhoF( 1 );
// std::vector<T> velocity( 3,T() );
// AnalyticalConst3D<T,T> uF( velocity );

ADlattice.setParameter<descriptors::OMEGA>(converter.getLatticeThermalRelaxationFrequency());
NSlattice.setParameter<descriptors::OMEGA>(converter.getLatticeRelaxationFrequency());

clout << “Prepare Lattice … OK” << std::endl;
}

void setBoundaryValues(ThermalUnitConverter<T, NSDESCRIPTOR, TDESCRIPTOR> &converter,
SuperLattice<T, NSDESCRIPTOR>& NSlattice,
SuperLattice<T, TDESCRIPTOR>& ADlattice,
int iT, SuperGeometry<T,3>& superGeometry)
{

if (iT == 0) {

// T u_Re = converter.getLatticeVelocity( Re * converter.getPhysViscosity() / converter.getCharPhysLength() );

AnalyticalConst3D<T,T> rhoF(1.);
AnalyticalConst3D<T,T> uF( 0.0, converter.getLatticeVelocity(Re * converter.getPhysViscosity() / converter.getCharPhysLength()), 0.0);
AnalyticalConst3D<T,T> u0(0.0, 0.0, 0.0);
AnalyticalConst3D<T,T> T_cold(converter.getLatticeTemperature(Tcold));
AnalyticalConst3D<T,T> T_hot(converter.getLatticeTemperature(Thot));

// Initialize all values of distribution functions to their local equilibrium
NSlattice.defineRhoU(superGeometry, 3, rhoF, uF);
NSlattice.iniEquilibrium(superGeometry, 3, rhoF, uF);
NSlattice.defineRhoU( superGeometry.getMaterialIndicator({1, 4, 5}),rhoF, u0 );
NSlattice.iniEquilibrium( superGeometry.getMaterialIndicator({1, 4, 5}),rhoF, u0 );

ADlattice.defineRho(superGeometry, 1, T_cold);
ADlattice.iniEquilibrium(superGeometry, 1, T_cold, u0);
ADlattice.defineRho(superGeometry, 2, T_hot);
ADlattice.iniEquilibrium(superGeometry, 2, T_hot, u0);
ADlattice.defineRho(superGeometry.getMaterialIndicator({ 4, 5}), T_cold);
ADlattice.iniEquilibrium(superGeometry.getMaterialIndicator({ 4, 5}), T_cold, u0);
ADlattice.defineRho(superGeometry, 3, T_cold);
ADlattice.iniEquilibrium(superGeometry, 3, T_cold, u0);

NSlattice.defineU( superGeometry, 3, uF );

// Lattice initialize
NSlattice.initialize();
ADlattice.initialize();

}

}