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Over-wrote common/ with version from ScaLBL (AA model refactor)

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This commit is contained in:
James E McClure 2018-01-24 10:05:48 -05:00
parent 282c296935
commit db8a1bfba9
9 changed files with 4568 additions and 2762 deletions
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10
common/Communication.hpp
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@ -4,7 +4,7 @@
#include "common/Communication.h" #include "common/Communication.h"
#include "common/MPI_Helpers.h" #include "common/MPI_Helpers.h"
#include "common/Utilities.h" #include "common/Utilities.h"
#include "ProfilerApp.h" //#include "ProfilerApp.h"
/******************************************************** /********************************************************
@ -104,7 +104,7 @@ fillHalo<TYPE>::~fillHalo( )
template<class TYPE> template<class TYPE>
void fillHalo<TYPE>::fill( Array<TYPE>& data ) void fillHalo<TYPE>::fill( Array<TYPE>& data )
{ {
PROFILE_START("fillHalo::fill",1); //PROFILE_START("fillHalo::fill",1);
int depth2 = data.size(3); int depth2 = data.size(3);
ASSERT((int)data.size(0)==nx+2*ngx); ASSERT((int)data.size(0)==nx+2*ngx);
ASSERT((int)data.size(1)==ny+2*ngy); ASSERT((int)data.size(1)==ny+2*ngy);
@ -156,7 +156,7 @@ void fillHalo<TYPE>::fill( Array<TYPE>& data )
} }
} }
} }
PROFILE_STOP("fillHalo::fill",1); //PROFILE_STOP("fillHalo::fill",1);
} }
template<class TYPE> template<class TYPE>
void fillHalo<TYPE>::pack( const Array<TYPE>& data, int i0, int j0, int k0, TYPE *buffer ) void fillHalo<TYPE>::pack( const Array<TYPE>& data, int i0, int j0, int k0, TYPE *buffer )
@ -207,7 +207,7 @@ template<class TYPE>
template<class TYPE1, class TYPE2> template<class TYPE1, class TYPE2>
void fillHalo<TYPE>::copy( const Array<TYPE1>& src, Array<TYPE2>& dst ) void fillHalo<TYPE>::copy( const Array<TYPE1>& src, Array<TYPE2>& dst )
{ {
PROFILE_START("fillHalo::copy",1); //PROFILE_START("fillHalo::copy",1);
ASSERT( (int)src.size(0)==nx || (int)src.size(0)==nx+2*ngx ); ASSERT( (int)src.size(0)==nx || (int)src.size(0)==nx+2*ngx );
ASSERT( (int)dst.size(0)==nx || (int)dst.size(0)==nx+2*ngx ); ASSERT( (int)dst.size(0)==nx || (int)dst.size(0)==nx+2*ngx );
bool src_halo = (int)src.size(0)==nx+2*ngx; bool src_halo = (int)src.size(0)==nx+2*ngx;
@ -254,7 +254,7 @@ void fillHalo<TYPE>::copy( const Array<TYPE1>& src, Array<TYPE2>& dst )
} }
fill(dst); fill(dst);
} }
PROFILE_STOP("fillHalo::copy",1); //PROFILE_STOP("fillHalo::copy",1);
} }

1814
common/Domain.cpp
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File diff suppressed because it is too large Load Diff

187
common/Domain.h
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@ -24,6 +24,7 @@ void read_domain( int rank, int nprocs, MPI_Comm comm,
int& nprocx, int& nprocy, int& nprocz, int& nx, int& ny, int& nz, int& nprocx, int& nprocy, int& nprocz, int& nx, int& ny, int& nz,
int& nspheres, double& Lx, double& Ly, double& Lz ); int& nspheres, double& Lx, double& Ly, double& Lz );
//! Class to hold domain info //! Class to hold domain info
struct Domain{ struct Domain{
// Default constructor // Default constructor
@ -89,16 +90,15 @@ struct Domain{
// Solid indicator function // Solid indicator function
char *id; char *id;
// Blob information
IntArray BlobLabel;
IntArray BlobGraph;
void InitializeRanks(); void InitializeRanks();
void CommInit(MPI_Comm comm); void CommInit(MPI_Comm comm);
void CommunicateMeshHalo(DoubleArray &Mesh); void CommunicateMeshHalo(DoubleArray &Mesh);
void BlobComm(MPI_Comm comm); void AssignComponentLabels(double *phase);
void AssignBlobConnections(); void TestCommInit(MPI_Comm comm);
//void MemoryOptimizedLayout(IntArray &Map, int *neighborList, int Np);
private: private:
@ -109,28 +109,6 @@ private:
int k2 = (k+nprocz)%nprocz; int k2 = (k+nprocz)%nprocz;
return i2 + j2*nprocx + k2*nprocx*nprocy; return i2 + j2*nprocx + k2*nprocx*nprocy;
} }
inline void PackBlobData(int *list, int count, int *sendbuf, int *data){
// Fill in the phase ID values from neighboring processors
// This packs up the values that need to be sent from one processor to another
int idx,n;
for (idx=0; idx<count; idx++){
n = list[idx];
sendbuf[idx] = data[n];
}
}
inline void UnpackBlobData(int *list, int count, int *recvbuf, int *data){
// Fill in the phase ID values from neighboring processors
// This unpacks the values once they have been recieved from neighbors
int idx,n;
for (idx=0; idx<count; idx++){
n = list[idx];
data[n] = recvbuf[idx];
}
}
int VoxelConnection(int n);
void getBlobConnections(int * List, int count, int neighbor, int direction);
}; };
@ -596,161 +574,6 @@ inline void ReadBinaryFile(char *FILENAME, double *Data, int N)
File.close(); File.close();
} }
inline double minmod(double &a, double &b){
double value;
value = a;
if ( a*b < 0.0) value=0.0;
else if (fabs(a) > fabs(b)) value = b;
return value;
}
inline double Eikonal(DoubleArray &Distance, char *ID, Domain &Dm, int timesteps){
/*
* This routine converts the data in the Distance array to a signed distance
* by solving the equation df/dt = sign(1-|grad f|), where Distance provides
* the values of f on the mesh associated with domain Dm
* It has been tested with segmented data initialized to values [-1,1]
* and will converge toward the signed distance to the surface bounding the associated phases
*
* Reference:
* Min C (2010) On reinitializing level set functions, Journal of Computational Physics 229
*/
int i,j,k;
double dt=0.1;
double Dx,Dy,Dz;
double Dxp,Dxm,Dyp,Dym,Dzp,Dzm;
double Dxxp,Dxxm,Dyyp,Dyym,Dzzp,Dzzm;
double sign,norm;
double LocalVar,GlobalVar,LocalMax,GlobalMax;
int xdim,ydim,zdim;
xdim=Dm.Nx-2;
ydim=Dm.Ny-2;
zdim=Dm.Nz-2;
fillHalo<double> fillData(Dm.Comm, Dm.rank_info,xdim,ydim,zdim,1,1,1,0,1);
// Arrays to store the second derivatives
DoubleArray Dxx(Dm.Nx,Dm.Ny,Dm.Nz);
DoubleArray Dyy(Dm.Nx,Dm.Ny,Dm.Nz);
DoubleArray Dzz(Dm.Nx,Dm.Ny,Dm.Nz);
int count = 0;
while (count < timesteps){
// Communicate the halo of values
fillData.fill(Distance);
// Compute second order derivatives
for (k=1;k<Dm.Nz-1;k++){
for (j=1;j<Dm.Ny-1;j++){
for (i=1;i<Dm.Nx-1;i++){
Dxx(i,j,k) = Distance(i+1,j,k) + Distance(i-1,j,k) - 2*Distance(i,j,k);
Dyy(i,j,k) = Distance(i,j+1,k) + Distance(i,j-1,k) - 2*Distance(i,j,k);
Dzz(i,j,k) = Distance(i,j,k+1) + Distance(i,j,k-1) - 2*Distance(i,j,k);
}
}
}
fillData.fill(Dxx);
fillData.fill(Dyy);
fillData.fill(Dzz);
LocalMax=LocalVar=0.0;
// Execute the next timestep
for (k=1;k<Dm.Nz-1;k++){
for (j=1;j<Dm.Ny-1;j++){
for (i=1;i<Dm.Nx-1;i++){
int n = k*Dm.Nx*Dm.Ny + j*Dm.Nx + i;
sign = 1;
if (ID[n] == 0) sign = -1;
// local second derivative terms
Dxxp = minmod(Dxx(i,j,k),Dxx(i+1,j,k));
Dyyp = minmod(Dyy(i,j,k),Dyy(i,j+1,k));
Dzzp = minmod(Dzz(i,j,k),Dzz(i,j,k+1));
Dxxm = minmod(Dxx(i,j,k),Dxx(i-1,j,k));
Dyym = minmod(Dyy(i,j,k),Dyy(i,j-1,k));
Dzzm = minmod(Dzz(i,j,k),Dzz(i,j,k-1));
/* //............Compute upwind derivatives ...................
Dxp = Distance(i+1,j,k) - Distance(i,j,k) + 0.5*Dxxp;
Dyp = Distance(i,j+1,k) - Distance(i,j,k) + 0.5*Dyyp;
Dzp = Distance(i,j,k+1) - Distance(i,j,k) + 0.5*Dzzp;
Dxm = Distance(i,j,k) - Distance(i-1,j,k) + 0.5*Dxxm;
Dym = Distance(i,j,k) - Distance(i,j-1,k) + 0.5*Dyym;
Dzm = Distance(i,j,k) - Distance(i,j,k-1) + 0.5*Dzzm;
*/
Dxp = Distance(i+1,j,k)- Distance(i,j,k) - 0.5*Dxxp;
Dyp = Distance(i,j+1,k)- Distance(i,j,k) - 0.5*Dyyp;
Dzp = Distance(i,j,k+1)- Distance(i,j,k) - 0.5*Dzzp;
Dxm = Distance(i,j,k) - Distance(i-1,j,k) + 0.5*Dxxm;
Dym = Distance(i,j,k) - Distance(i,j-1,k) + 0.5*Dyym;
Dzm = Distance(i,j,k) - Distance(i,j,k-1) + 0.5*Dzzm;
// Compute upwind derivatives for Godunov Hamiltonian
if (sign < 0.0){
if (Dxp + Dxm > 0.f) Dx = Dxp*Dxp;
else Dx = Dxm*Dxm;
if (Dyp + Dym > 0.f) Dy = Dyp*Dyp;
else Dy = Dym*Dym;
if (Dzp + Dzm > 0.f) Dz = Dzp*Dzp;
else Dz = Dzm*Dzm;
}
else{
if (Dxp + Dxm < 0.f) Dx = Dxp*Dxp;
else Dx = Dxm*Dxm;
if (Dyp + Dym < 0.f) Dy = Dyp*Dyp;
else Dy = Dym*Dym;
if (Dzp + Dzm < 0.f) Dz = Dzp*Dzp;
else Dz = Dzm*Dzm;
}
//Dx = max(Dxp*Dxp,Dxm*Dxm);
//Dy = max(Dyp*Dyp,Dym*Dym);
//Dz = max(Dzp*Dzp,Dzm*Dzm);
norm=sqrt(Dx + Dy + Dz);
if (norm > 1.0) norm=1.0;
Distance(i,j,k) += dt*sign*(1.0 - norm);
LocalVar += dt*sign*(1.0 - norm);
if (fabs(dt*sign*(1.0 - norm)) > LocalMax)
LocalMax = fabs(dt*sign*(1.0 - norm));
}
}
}
MPI_Allreduce(&LocalVar,&GlobalVar,1,MPI_DOUBLE,MPI_SUM,Dm.Comm);
MPI_Allreduce(&LocalMax,&GlobalMax,1,MPI_DOUBLE,MPI_MAX,Dm.Comm);
GlobalVar /= (Dm.Nx-2)*(Dm.Ny-2)*(Dm.Nz-2)*Dm.nprocx*Dm.nprocy*Dm.nprocz;
count++;
if (count%50 == 0 && Dm.rank==0 )
printf("Time=%i, Max variation=%f, Global variation=%f \n",count,GlobalMax,GlobalVar);
if (fabs(GlobalMax) < 1e-5){
if (Dm.rank==0) printf("Exiting with max tolerance of 1e-5 \n");
count=timesteps;
}
}
return GlobalVar;
}
#endif #endif

4
common/MPI_Helpers.hpp
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@ -27,7 +27,7 @@ void pack( const std::vector<TYPE>& rhs, char *buffer )
size_t size = rhs.size(); size_t size = rhs.size();
memcpy(buffer,&size,sizeof(size_t)); memcpy(buffer,&size,sizeof(size_t));
size_t pos = sizeof(size_t); size_t pos = sizeof(size_t);
for (size_t i=0; i<rhs.size(); i++) { for (int i=0; i<rhs.size(); i++) {
pack(rhs[i],&buffer[pos]); pack(rhs[i],&buffer[pos]);
pos += packsize(rhs[i]); pos += packsize(rhs[i]);
} }
@ -40,7 +40,7 @@ void unpack( std::vector<TYPE>& data, const char *buffer )
data.clear(); data.clear();
data.resize(size); data.resize(size);
size_t pos = sizeof(size_t); size_t pos = sizeof(size_t);
for (size_t i=0; i<data.size(); i++) { for (int i=0; i<data.size(); i++) {
unpack(data[i],&buffer[pos]); unpack(data[i],&buffer[pos]);
pos += packsize(data[i]); pos += packsize(data[i]);
} }

3425
common/ScaLBL.h
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File diff suppressed because it is too large Load Diff

1686
common/StackTrace.cpp
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File diff suppressed because it is too large Load Diff

187
common/StackTrace.h
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@ -1,31 +1,12 @@
#ifndef included_AtomicStackTrace #ifndef included_StackTrace
#define included_AtomicStackTrace #define included_StackTrace
#include <functional>
#include <iostream>
#include <stdio.h> #include <stdio.h>
#include <stdlib.h> #include <stdlib.h>
#include <iostream>
#include <vector> #include <vector>
#include <thread>
#include <memory>
#include <set>
// Check for and include MPI
// clang-format off
#if defined(USE_MPI) || defined(USE_EXT_MPI)
#include "mpi.h"
#elif defined(__has_include)
#if __has_include("mpi.h")
#include "mpi.h"
#else
typedef int MPI_Comm;
#endif
#else
typedef int MPI_Comm;
#endif
// clang-format on
namespace StackTrace { namespace StackTrace {
@ -38,179 +19,29 @@ struct stack_info {
std::string filename; std::string filename;
int line; int line;
//! Default constructor //! Default constructor
stack_info() : address( nullptr ), address2( nullptr ), line( 0 ) {} stack_info(): address(NULL), address2(NULL), line(0) {}
//! Operator==
bool operator==( const stack_info& rhs ) const;
//! Operator!=
bool operator!=( const stack_info& rhs ) const;
//! Print the stack info //! Print the stack info
std::string print() const; std::string print() const;
//! Compute the number of bytes needed to store the object
size_t size() const;
//! Pack the data to a byte array, returning a pointer to the end of the data
char* pack( char* ptr ) const;
//! Unpack the data from a byte array, returning a pointer to the end of the data
const char* unpack( const char* ptr );
//! Pack a vector of data to a memory block
static std::vector<char> packArray( const std::vector<stack_info>& data );
//! Unpack a vector of data from a memory block
static std::vector<stack_info> unpackArray( const char* data );
}; };
struct multi_stack_info { //! Function to return the current call stack
int N;
stack_info stack;
std::vector<multi_stack_info> children;
//! Default constructor
multi_stack_info() : N( 0 ) {}
//! Add the given stack to the multistack
void add( size_t N, const stack_info *stack );
//! Print the stack info
std::vector<std::string> print( const std::string& prefix=std::string() ) const;
};
/*!
* @brief Get the current call stack
* @details This function returns the current call stack for the current thread
* @return Returns vector containing the stack
*/
std::vector<stack_info> getCallStack(); std::vector<stack_info> getCallStack();
/*!
* @brief Get the current call stack for a thread
* @details This function returns the current call stack for the given thread
* @param[in] id The thread id of the stack we want to return
* @return Returns vector containing the stack
*/
std::vector<stack_info> getCallStack( std::thread::native_handle_type id );
/*!
* @brief Get the current call stack for all threads
* @details This function returns the current call stack for all threads
* in the current process.
* Note: This functionality may not be availible on all platforms
* @return Returns vector containing the stack
*/
multi_stack_info getAllCallStacks( );
/*!
* @brief Get the current call stack for all threads/processes
* @details This function returns the current call stack for all threads
* for all processes in the current process. This function requires
* the user to call globalCallStackInitialize() before calling this
* routine, and globalCallStackFinalize() before exiting.
* Note: This functionality may not be availible on all platforms
* @return Returns vector containing the stack
*/
multi_stack_info getGlobalCallStacks( );
//! Function to return the current call stack for the current thread
std::vector<void *> backtrace();
//! Function to return the current call stack for the given thread
std::vector<void *> backtrace( std::thread::native_handle_type id );
//! Function to return the current call stack for all threads
std::vector<std::vector<void *>> backtraceAll();
//! Function to return the stack info for a given address //! Function to return the stack info for a given address
stack_info getStackInfo( void *address ); stack_info getStackInfo( void* address );
//! Function to return the stack info for a given address
std::vector<stack_info> getStackInfo( const std::vector<void *> &address );
//! Function to return the signal name
std::string signalName( int signal );
/*! /*!
* Return the symbols from the current executable (not availible for all platforms) * Return the symbols from the current executable (not availible for all platforms)
* @return Returns 0 if sucessful * @return Returns 0 if sucessful
*/ */
int getSymbols( int getSymbols( std::vector<void*>& address, std::vector<char>& type, std::vector<std::string>& obj );
std::vector<void *> &address, std::vector<char> &type, std::vector<std::string> &obj );
/*!
* Return the name of the executable
* @return Returns the name of the executable (usually the full path)
*/
std::string getExecutable();
/*!
* Return the search path for the symbols
* @return Returns the search path for the symbols
*/
std::string getSymPaths();
//!< Terminate type
enum class terminateType { signal, exception };
/*!
* Set the error handlers
* @param[in] Function to terminate the program: abort(msg,type)
*/
void setErrorHandlers( std::function<void( std::string, terminateType )> abort );
/*!
* Set the given signals to the handler
* @param[in] Function to terminate the program: abort(msg,type)
*/
void setSignals( const std::vector<int>& signals, void (*handler) (int) );
//! Clear a signal set by setSignals
void clearSignal( int signal );
//! Clear all signals set by setSignals
void clearSignals( );
//! Return a list of all signals that can be caught
std::vector<int> allSignalsToCatch( );
//! Return a default list of signals to catch
std::vector<int> defaultSignalsToCatch( );
//! Get a list of the active threads
std::set<std::thread::native_handle_type> activeThreads( );
//! Get a handle to this thread
std::thread::native_handle_type thisThread( );
//! Initialize globalCallStack functionallity
void globalCallStackInitialize( MPI_Comm comm );
//! Clean up globalCallStack functionallity
void globalCallStackFinalize( );
/*!
* @brief Call system command
* @details This function calls a system command, waits for the program
* to execute, captures and returns the output and exit code.
* @param[in] cmd Command to execute
* @param[out] exit_code Exit code returned from child process
* @return Returns string containing the output
*/
std::string exec( const std::string& cmd, int& exit_code );
} // namespace StackTrace } // namespace StackTrace
#endif #endif

14
common/Utilities.cpp
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@ -236,9 +236,9 @@ size_t Utilities::getMemoryUsage()
size_t N_bytes = 0; size_t N_bytes = 0;
#if defined(USE_LINUX) #if defined(USE_LINUX)
struct mallinfo meminfo = mallinfo(); struct mallinfo meminfo = mallinfo();
size_t size_hblkhd = static_cast<unsigned int>( meminfo.hblkhd ); size_t size_hblkhd = static_cast<size_t>( meminfo.hblkhd );
size_t size_uordblks = static_cast<unsigned int>( meminfo.uordblks ); size_t size_uordblks = static_cast<size_t>( meminfo.uordblks );
N_bytes = size_hblkhd + size_uordblks; N_bytes = static_cast<size_t>( size_hblkhd + size_uordblks );
#elif defined(USE_MAC) #elif defined(USE_MAC)
struct task_basic_info t_info; struct task_basic_info t_info;
mach_msg_type_number_t t_info_count = TASK_BASIC_INFO_COUNT; mach_msg_type_number_t t_info_count = TASK_BASIC_INFO_COUNT;
@ -347,11 +347,3 @@ std::vector<int> Utilities::factor(size_t number)
std::sort( factors.begin(), factors.end() ); std::sort( factors.begin(), factors.end() );
return factors; return factors;
} }
// Dummy function to prevent compiler from optimizing away variable
void Utilities::nullUse( void* data )
{
NULL_USE(data);
}

3
common/Utilities.h
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@ -61,9 +61,6 @@ namespace Utilities
//! Factor a number into it's prime factors //! Factor a number into it's prime factors
std::vector<int> factor(size_t number); std::vector<int> factor(size_t number);
//! Print AMP Banner
void nullUse( void* );
} // namespace Utilities } // namespace Utilities