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lal_atom.h
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/***************************************************************************
atom.h
-------------------
W. Michael Brown (ORNL)
Class for particle data management
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin :
email : brownw@ornl.gov
***************************************************************************/
#ifndef PAIR_GPU_ATOM_H
#define PAIR_GPU_ATOM_H
#include <math.h>
#include "mpi.h"
#if defined(USE_OPENCL)
#include "geryon/ocl_timer.h"
#include "geryon/ocl_mat.h"
#include "geryon/ocl_kernel.h"
using namespace ucl_opencl;
#elif defined(USE_CUDART)
#include "geryon/nvc_timer.h"
#include "geryon/nvc_mat.h"
#include "geryon/nvc_kernel.h"
using namespace ucl_cudart;
#else
#include "geryon/nvd_timer.h"
#include "geryon/nvd_mat.h"
#include "geryon/nvd_kernel.h"
using namespace ucl_cudadr;
#endif
#ifdef USE_CUDPP
#include "cudpp.h"
#endif
#include "lal_precision.h"
namespace LAMMPS_AL {
template <class numtyp, class acctyp>
class Atom {
public:
Atom();
~Atom() { clear(); }
/// Maximum number of atoms that can be stored with current allocation
inline int max_atoms() const { return _max_atoms; }
/// Current number of local+ghost atoms stored
inline int nall() const { return _nall; }
/// Set number of local+ghost atoms for future copy operations
inline void nall(const int n) { _nall=n; }
/// Memory usage per atom in this class
int bytes_per_atom() const;
/// Clear any previous data and set up for a new LAMMPS run
/** \param rot True if atom storage needs quaternions
* \param gpu_nbor 0 if neighboring will be performed on host
* gpu_nbor 1 if neighboring will be performed on device
* gpu_nbor 2 if binning on host and neighboring on device **/
bool init(const int nall, const bool charge, const bool rot,
UCL_Device &dev, const int gpu_nbor=0, const bool bonds=false);
/// Check if we have enough device storage and realloc if not
/** Returns true if resized with any call during this timestep **/
inline bool resize(const int nall, bool &success) {
_nall=nall;
if (nall>_max_atoms) {
clear_resize();
success = success && alloc(nall);
_resized=true;
}
return _resized;
}
/// If already initialized by another LAMMPS style, add fields as necessary
/** \param rot True if atom storage needs quaternions
* \param gpu_nbor 0 if neighboring will be performed on host
* gpu_nbor 1 if neighboring will be performed on device
* gpu_nbor 2 if binning on host and neighboring on device **/
bool add_fields(const bool charge, const bool rot, const int gpu_nbor,
const bool bonds);
/// Returns true if GPU is using charges
bool charge() { return _charge; }
/// Returns true if GPU is using quaternions
bool quaternion() { return _rot; }
/// Only free matrices of length inum or nall for resizing
void clear_resize();
/// Free all memory on host and device
void clear();
/// Return the total amount of host memory used by class in bytes
double host_memory_usage() const;
/// Sort arrays for neighbor list calculation on device
void sort_neighbor(const int num_atoms);
/// Add copy times to timers
inline void acc_timers() {
time_pos.add_to_total();
if (_charge)
time_q.add_to_total();
if (_rot)
time_quat.add_to_total();
}
/// Add copy times to timers
inline void zero_timers() {
time_pos.zero();
if (_charge)
time_q.zero();
if (_rot)
time_quat.zero();
}
/// Return the total time for host/device data transfer
/** Zeros the total so that the atom times are only included once **/
inline double transfer_time() {
double total=time_pos.total_seconds();
time_pos.zero_total();
if (_charge) {
total+=time_q.total_seconds();
time_q.zero_total();
}
if (_rot) {
total+=time_q.total_seconds();
time_quat.zero_total();
}
return total+_time_transfer/1000.0;
}
/// Return the total time for data cast/pack
/** Zeros the time so that atom times are only included once **/
inline double cast_time()
{ double t=_time_cast; _time_cast=0.0; return t; }
/// Pack LAMMPS atom type constants into matrix and copy to device
template <class dev_typ, class t1>
inline void type_pack1(const int n, const int m_size,
UCL_D_Vec<dev_typ> &dev_v, UCL_H_Vec<numtyp> &buffer,
t1 **one) {
int ii=0;
for (int i=0; i<n; i++) {
for (int j=0; j<n; j++) {
buffer[ii]=static_cast<numtyp>(one[i][j]);
ii++;
}
ii+=m_size-n;
}
UCL_H_Vec<dev_typ> view;
view.view((dev_typ*)buffer.begin(),m_size*m_size,*dev);
ucl_copy(dev_v,view,false);
}
/// Pack LAMMPS atom type constants into 2 vectors and copy to device
template <class dev_typ, class t1, class t2>
inline void type_pack2(const int n, const int m_size,
UCL_D_Vec<dev_typ> &dev_v, UCL_H_Vec<numtyp> &buffer,
t1 **one, t2 **two) {
int ii=0;
for (int i=0; i<n; i++) {
for (int j=0; j<n; j++) {
buffer[ii*2]=static_cast<numtyp>(one[i][j]);
buffer[ii*2+1]=static_cast<numtyp>(two[i][j]);
ii++;
}
ii+=m_size-n;
}
UCL_H_Vec<dev_typ> view;
view.view((dev_typ*)buffer.begin(),m_size*m_size,*dev);
ucl_copy(dev_v,view,false);
}
/// Pack LAMMPS atom type constants (3) into 4 vectors and copy to device
template <class dev_typ, class t1, class t2, class t3>
inline void type_pack4(const int n, const int m_size,
UCL_D_Vec<dev_typ> &dev_v, UCL_H_Vec<numtyp> &buffer,
t1 **one, t2 **two, t3 **three) {
int ii=0;
for (int i=0; i<n; i++) {
for (int j=0; j<n; j++) {
buffer[ii*4]=static_cast<numtyp>(one[i][j]);
buffer[ii*4+1]=static_cast<numtyp>(two[i][j]);
buffer[ii*4+2]=static_cast<numtyp>(three[i][j]);
ii++;
}
ii+=m_size-n;
}
UCL_H_Vec<dev_typ> view;
view.view((dev_typ*)buffer.begin(),m_size*m_size,*dev);
ucl_copy(dev_v,view,false);
}
/// Pack LAMMPS atom type constants (4) into 4 vectors and copy to device
template <class dev_typ, class t1, class t2, class t3, class t4>
inline void type_pack4(const int n, const int m_size,
UCL_D_Vec<dev_typ> &dev_v, UCL_H_Vec<numtyp> &buffer,
t1 **one, t2 **two, t3 **three, t4 **four) {
int ii=0;
for (int i=0; i<n; i++) {
for (int j=0; j<n; j++) {
buffer[ii*4]=static_cast<numtyp>(one[i][j]);
buffer[ii*4+1]=static_cast<numtyp>(two[i][j]);
buffer[ii*4+2]=static_cast<numtyp>(three[i][j]);
buffer[ii*4+3]=static_cast<numtyp>(four[i][j]);
ii++;
}
ii+=m_size-n;
}
UCL_H_Vec<dev_typ> view;
view.view((dev_typ*)buffer.begin(),m_size*m_size,*dev);
ucl_copy(dev_v,view,false);
}
/// Pack LAMMPS atom "self" type constants into 2 vectors and copy to device
template <class dev_typ, class t1, class t2>
inline void self_pack2(const int n, UCL_D_Vec<dev_typ> &dev_v,
UCL_H_Vec<numtyp> &buffer, t1 **one, t2 **two) {
for (int i=0; i<n; i++) {
buffer[i*2]=static_cast<numtyp>(one[i][i]);
buffer[i*2+1]=static_cast<numtyp>(two[i][i]);
}
UCL_H_Vec<dev_typ> view;
view.view((dev_typ*)buffer.begin(),n,*dev);
ucl_copy(dev_v,view,false);
}
// -------------------------COPY TO GPU ----------------------------------
/// Signal that we need to transfer atom data for next timestep
inline void data_unavail()
{ _x_avail=false; _q_avail=false; _quat_avail=false; _resized=false; }
/// Cast positions and types to write buffer
inline void cast_x_data(double **host_ptr, const int *host_type) {
if (_x_avail==false) {
double t=MPI_Wtime();
#ifdef GPU_CAST
memcpy(host_x_cast.begin(),host_ptr[0],_nall*3*sizeof(double));
memcpy(host_type_cast.begin(),host_type,_nall*sizeof(int));
#else
int wl=0;
for (int i=0; i<_nall; i++) {
x[wl]=host_ptr[i][0];
x[wl+1]=host_ptr[i][1];
x[wl+2]=host_ptr[i][2];
x[wl+3]=host_type[i];
wl+=4;
}
#endif
_time_cast+=MPI_Wtime()-t;
}
}
/// Copy positions and types to device asynchronously
/** Copies nall() elements **/
inline void add_x_data(double **host_ptr, int *host_type) {
time_pos.start();
if (_x_avail==false) {
#ifdef GPU_CAST
x_cast.update_device(_nall*3,true);
type_cast.update_device(_nall,true);
int block_size=64;
int GX=static_cast<int>(ceil(static_cast<double>(_nall)/block_size));
k_cast_x.set_size(GX,block_size);
k_cast_x.run(&x, &x_cast, &type_cast, &_nall);
#else
x.update_device(_nall*4,true);
#endif
_x_avail=true;
}
time_pos.stop();
}
/// Calls cast_x_data and add_x_data and times the routines
inline void cast_copy_x(double **host_ptr, int *host_type) {
cast_x_data(host_ptr,host_type);
add_x_data(host_ptr,host_type);
}
// Cast charges to write buffer
template<class cpytyp>
inline void cast_q_data(cpytyp *host_ptr) {
if (_q_avail==false) {
double t=MPI_Wtime();
// If double precision, still memcpy for async transfers
if (_host_view) {
q.host.view((numtyp*)host_ptr,_nall,*dev);
q.device.view(q.host);
} else if (sizeof(numtyp)==sizeof(double))
memcpy(q.host.begin(),host_ptr,_nall*sizeof(numtyp));
else
for (int i=0; i<_nall; i++) q[i]=host_ptr[i];
_time_cast+=MPI_Wtime()-t;
}
}
// Copy charges to device asynchronously
inline void add_q_data() {
if (_q_avail==false) {
q.update_device(_nall,true);
_q_avail=true;
}
}
// Cast quaternions to write buffer
template<class cpytyp>
inline void cast_quat_data(cpytyp *host_ptr) {
if (_quat_avail==false) {
double t=MPI_Wtime();
if (_host_view) {
quat.host.view((numtyp*)host_ptr,_nall*4,*dev);
quat.device.view(quat.host);
} else if (sizeof(numtyp)==sizeof(double))
memcpy(quat.host.begin(),host_ptr,_nall*4*sizeof(numtyp));
else
for (int i=0; i<_nall*4; i++) quat[i]=host_ptr[i];
_time_cast+=MPI_Wtime()-t;
}
}
// Copy quaternions to device
/** Copies nall()*4 elements **/
inline void add_quat_data() {
if (_quat_avail==false) {
quat.update_device(_nall*4,true);
_quat_avail=true;
}
}
/// Add in casting time from additional data (seconds)
inline void add_cast_time(double t) { _time_cast+=t; }
/// Add in transfer time from additional data (ms)
inline void add_transfer_time(double t) { _time_transfer+=t; }
/// Return number of bytes used on device
inline double max_gpu_bytes()
{ double m=_max_gpu_bytes; _max_gpu_bytes=0.0; return m; }
/// Returns true if the device is addressing memory on the host
inline bool host_view() { return _host_view; }
// ------------------------------ DATA ----------------------------------
/// Atom coordinates and types ([0] is x, [1] is y, [2] is z, [3] is type
UCL_Vector<numtyp,numtyp> x;
/// Charges
UCL_Vector<numtyp,numtyp> q;
/// Quaterions
UCL_Vector<numtyp,numtyp> quat;
#ifdef GPU_CAST
UCL_Vector<double,double> x_cast;
UCL_Vector<int,int> type_cast;
#endif
/// Cell list identifiers for device nbor builds
UCL_D_Vec<unsigned> dev_cell_id;
/// Cell list identifiers for device nbor builds
UCL_D_Vec<int> dev_particle_id;
/// Atom tag information for device nbor builds
UCL_D_Vec<int> dev_tag;
/// Cell list identifiers for hybrid nbor builds
UCL_H_Vec<int> host_cell_id;
/// Cell list identifiers for hybrid nbor builds
UCL_H_Vec<int> host_particle_id;
/// Device timers
UCL_Timer time_pos, time_q, time_quat;
/// Geryon device
UCL_Device *dev;
private:
#ifdef GPU_CAST
UCL_Program *atom_program;
UCL_Kernel k_cast_x;
void compile_kernels(UCL_Device &dev);
#endif
bool _compiled;
// True if data has been copied to device already
bool _x_avail, _q_avail, _quat_avail, _resized;
bool alloc(const int nall);
bool _allocated, _rot, _charge, _bonds, _other;
int _max_atoms, _nall, _gpu_nbor;
bool _host_view;
double _time_cast, _time_transfer;
double _max_gpu_bytes;
#ifdef USE_CUDPP
CUDPPConfiguration sort_config;
CUDPPHandle sort_plan;
#endif
};
}
#endif

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