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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6053 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2011-05-02 15:02:52 +00:00
parent 2be078632d
commit 5f799182b3
70 changed files with 4489 additions and 2253 deletions
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270
lib/gpu/pair_gpu_atom.h
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@ -23,7 +23,6 @@
#ifdef USE_OPENCL
#include "geryon/ocl_device.h"
#include "geryon/ocl_timer.h"
#include "geryon/ocl_mat.h"
#include "geryon/ocl_kernel.h"
@ -32,7 +31,6 @@ using namespace ucl_opencl;
#else
#include "cudpp.h"
#include "geryon/nvd_device.h"
#include "geryon/nvd_timer.h"
#include "geryon/nvd_mat.h"
#include "geryon/nvd_kernel.h"
@ -40,10 +38,6 @@ using namespace ucl_cudadr;
#endif
#ifndef int2
struct int2 { int x; int y; };
#endif
#include "pair_gpu_precision.h"
template <class numtyp, class acctyp>
@ -56,13 +50,9 @@ class PairGPUAtom {
inline int max_atoms() const { return _max_atoms; }
/// Current number of local+ghost atoms stored
inline int nall() const { return _nall; }
/// Current number of local atoms stored
inline int inum() const { return _inum; }
/// Set number of local+ghost atoms for future copy operations
inline void nall(const int n) { _nall=n; }
/// Set number of local atoms for future copy operations
inline void inum(const int n) { _inum=n; }
/// Memory usage per atom in this class
int bytes_per_atom() const;
@ -70,21 +60,33 @@ class PairGPUAtom {
/// Clear any previous data and set up for a new LAMMPS run
/** \param rot True if atom storage needs quaternions
* \param gpu_nbor True if neighboring will be performed on device **/
bool init(const int inum, const int nall, const bool charge, const bool rot,
bool init(const int nall, const bool charge, const bool rot,
UCL_Device &dev, const bool gpu_nbor=false, const bool bonds=false);
/// Check if we have enough device storage and realloc if not
inline bool resize(const int inum, const int nall, bool &success) {
_inum=inum;
/** Returns true if resized with any call during this timestep **/
inline bool resize(const int nall, bool &success) {
_nall=nall;
if (inum>_max_local || nall>_max_atoms) {
if (nall>_max_atoms) {
clear_resize();
success = success && alloc(inum,nall);
return true;
success = success && alloc(nall);
_resized=true;
}
return false;
return _resized;
}
/// If already initialized by another LAMMPS style, add fields as necessary
/** \param rot True if atom storage needs quaternions
* \param gpu_nbor True if neighboring will be performed on device **/
bool add_fields(const bool charge, const bool rot, const bool gpu_nbor,
const bool bonds);
/// Returns true if GPU is using charges
bool charge() { return _charge; }
/// Returns true if GPU is using quaternions
bool quat() { return _rot; }
/// Only free matrices of length inum or nall for resizing
void clear_resize();
@ -100,28 +102,42 @@ class PairGPUAtom {
/// Add copy times to timers
inline void acc_timers() {
time_pos.add_to_total();
time_answer.add_to_total();
if (_other)
time_other.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();
time_answer.zero();
if (_other)
time_other.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_answer.total_seconds();
if (_other) total+=time_other.total_seconds();
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;
}
/// Return the total time for data cast/pack
inline double cast_time() { return _time_cast; }
/** 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>
@ -216,43 +232,52 @@ class PairGPUAtom {
// -------------------------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) {
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
numtyp *_write_loc=host_x.begin();
for (int i=0; i<_nall; i++) {
*_write_loc=host_ptr[i][0];
_write_loc++;
*_write_loc=host_ptr[i][1];
_write_loc++;
*_write_loc=host_ptr[i][2];
_write_loc++;
*_write_loc=host_type[i];
_write_loc++;
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
numtyp *_write_loc=host_x.begin();
for (int i=0; i<_nall; i++) {
*_write_loc=host_ptr[i][0];
_write_loc++;
*_write_loc=host_ptr[i][1];
_write_loc++;
*_write_loc=host_ptr[i][2];
_write_loc++;
*_write_loc=host_type[i];
_write_loc++;
}
#endif
_time_cast+=MPI_Wtime()-t;
}
#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();
#ifdef GPU_CAST
ucl_copy(dev_x_cast,host_x_cast,_nall*3,true);
ucl_copy(dev_type_cast,host_type_cast,_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(&dev_x.begin(), &dev_x_cast.begin(), &dev_type_cast.begin(),
&_nall);
#else
ucl_copy(dev_x,host_x,_nall*4,true);
#endif
if (_x_avail==false) {
#ifdef GPU_CAST
ucl_copy(dev_x_cast,host_x_cast,_nall*3,true);
ucl_copy(dev_type_cast,host_type_cast,_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(&dev_x.begin(), &dev_x_cast.begin(), &dev_type_cast.begin(),
&_nall);
#else
ucl_copy(dev_x,host_x,_nall*4,true);
#endif
_x_avail=true;
}
time_pos.stop();
}
@ -262,87 +287,68 @@ class PairGPUAtom {
add_x_data(host_ptr,host_type);
}
/// Cast charges to write buffer
// Cast charges to write buffer
template<class cpytyp>
inline void cast_q_data(cpytyp *host_ptr) {
double t=MPI_Wtime();
if (dev->device_type()==UCL_CPU) {
if (sizeof(numtyp)==sizeof(double)) {
host_q.view((numtyp*)host_ptr,_nall,*dev);
dev_q.view(host_q);
} else
for (int i=0; i<_nall; i++) host_q[i]=host_ptr[i];
} else {
if (sizeof(numtyp)==sizeof(double))
memcpy(host_q.begin(),host_ptr,_nall*sizeof(numtyp));
else
for (int i=0; i<_nall; i++) host_q[i]=host_ptr[i];
if (_q_avail==false) {
double t=MPI_Wtime();
if (dev->device_type()==UCL_CPU) {
if (sizeof(numtyp)==sizeof(double)) {
host_q.view((numtyp*)host_ptr,_nall,*dev);
dev_q.view(host_q);
} else
for (int i=0; i<_nall; i++) host_q[i]=host_ptr[i];
} else {
if (sizeof(numtyp)==sizeof(double))
memcpy(host_q.begin(),host_ptr,_nall*sizeof(numtyp));
else
for (int i=0; i<_nall; i++) host_q[i]=host_ptr[i];
}
_time_cast+=MPI_Wtime()-t;
}
_time_cast+=MPI_Wtime()-t;
}
/// Copy charges to device asynchronously
// Copy charges to device asynchronously
inline void add_q_data() {
ucl_copy(dev_q,host_q,_nall,true);
if (_q_avail==false) {
ucl_copy(dev_q,host_q,_nall,true);
_q_avail=true;
}
}
/// Cast quaternions to write buffer
// Cast quaternions to write buffer
template<class cpytyp>
inline void cast_quat_data(cpytyp *host_ptr) {
double t=MPI_Wtime();
if (dev->device_type()==UCL_CPU) {
if (sizeof(numtyp)==sizeof(double)) {
host_quat.view((numtyp*)host_ptr,_nall*4,*dev);
dev_quat.view(host_quat);
} else
for (int i=0; i<_nall*4; i++) host_quat[i]=host_ptr[i];
} else {
if (sizeof(numtyp)==sizeof(double))
memcpy(host_quat.begin(),host_ptr,_nall*4*sizeof(numtyp));
else
for (int i=0; i<_nall*4; i++) host_quat[i]=host_ptr[i];
if (_quat_avail==false) {
double t=MPI_Wtime();
if (dev->device_type()==UCL_CPU) {
if (sizeof(numtyp)==sizeof(double)) {
host_quat.view((numtyp*)host_ptr,_nall*4,*dev);
dev_quat.view(host_quat);
} else
for (int i=0; i<_nall*4; i++) host_quat[i]=host_ptr[i];
} else {
if (sizeof(numtyp)==sizeof(double))
memcpy(host_quat.begin(),host_ptr,_nall*4*sizeof(numtyp));
else
for (int i=0; i<_nall*4; i++) host_quat[i]=host_ptr[i];
}
_time_cast+=MPI_Wtime()-t;
}
_time_cast+=MPI_Wtime()-t;
}
/// Copy quaternions to device
// Copy quaternions to device
/** Copies nall()*4 elements **/
inline void add_quat_data() {
ucl_copy(dev_quat,host_quat,_nall*4,true);
if (_quat_avail==false) {
ucl_copy(dev_quat,host_quat,_nall*4,true);
_quat_avail=true;
}
}
/// Copy data other than pos and data to device
inline void add_other_data() {
time_other.start();
if (_charge)
add_q_data();
if (_rot)
add_quat_data();
time_other.stop();
}
/// Return number of bytes used on device
inline double gpu_bytes() { return _gpu_bytes; }
// -------------------------COPY FROM GPU -------------------------------
/// Copy answers from device into read buffer asynchronously
void copy_answers(const bool eflag, const bool vflag,
const bool ef_atom, const bool vf_atom);
/// Copy answers from device into read buffer asynchronously
void copy_answers(const bool eflag, const bool vflag,
const bool ef_atom, const bool vf_atom, int *ilist);
/// Copy energy and virial data into LAMMPS memory
double energy_virial(double *eatom, double **vatom, double *virial);
/// Copy energy and virial data into LAMMPS memory
double energy_virial(double *eatom, double **vatom, double *virial,
double &ecoul);
/// Add forces and torques from the GPU into a LAMMPS pointer
void get_answers(double **f, double **tor);
inline double max_gpu_bytes()
{ double m=_max_gpu_bytes; _max_gpu_bytes=0.0; return m; }
// ------------------------------ DATA ----------------------------------
@ -352,10 +358,6 @@ class PairGPUAtom {
UCL_D_Vec<numtyp> dev_q;
/// Quaterions
UCL_D_Vec<numtyp> dev_quat;
/// Force and possibly torque
UCL_D_Vec<acctyp> dev_ans;
/// Energy and virial per-atom storage
UCL_D_Vec<acctyp> dev_engv;
#ifdef GPU_CAST
UCL_D_Vec<double> dev_x_cast;
@ -370,10 +372,6 @@ class PairGPUAtom {
UCL_H_Vec<numtyp> host_q;
/// Buffer for moving quat data to GPU
UCL_H_Vec<numtyp> host_quat;
/// Force and possibly torque data on host
UCL_H_Vec<acctyp> host_ans;
/// Energy/virial data on host
UCL_H_Vec<acctyp> host_engv;
/// Cell list identifiers for device nbor builds
UCL_D_Vec<unsigned> dev_cell_id;
@ -383,7 +381,7 @@ class PairGPUAtom {
UCL_D_Vec<int> dev_tag;
/// Device timers
UCL_Timer time_pos, time_other, time_answer;
UCL_Timer time_pos, time_q, time_quat;
/// Geryon device
UCL_Device *dev;
@ -396,19 +394,19 @@ class PairGPUAtom {
#endif
bool _compiled;
bool alloc(const int inum, const int nall);
bool _allocated, _eflag, _vflag, _ef_atom, _vf_atom, _rot, _charge, _other;
int _max_local, _max_atoms, _nall, _inum, _e_fields, _ev_fields;
// 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, _other;
int _max_atoms, _nall;
bool _gpu_nbor, _bonds;
int *_ilist;
double _time_cast;
double _gpu_bytes;
double _max_gpu_bytes;
bool _newton;
#ifndef USE_OPENCL
CUDPPConfiguration sort_config;
CUDPPHandle sort_plan;