ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8693 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2012-08-21 13:57:32 +00:00
parent 9a99e27552
commit 31551d81fd
85 changed files with 2630 additions and 2172 deletions
Download Patch File Download Diff File Expand all files Collapse all files

125
lib/gpu/lal_atom.h
View File

@ -19,20 +19,21 @@
#include <math.h>
#include "mpi.h"
#ifdef USE_OPENCL
#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
@ -92,7 +93,7 @@ class Atom {
bool charge() { return _charge; }
/// Returns true if GPU is using quaternions
bool quat() { return _rot; }
bool quaternion() { return _rot; }
/// Only free matrices of length inum or nall for resizing
void clear_resize();
@ -148,9 +149,9 @@ class Atom {
/// 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) {
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++) {
@ -167,8 +168,8 @@ class Atom {
/// 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) {
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++) {
@ -186,8 +187,8 @@ class Atom {
/// 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) {
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++) {
@ -206,8 +207,8 @@ class Atom {
/// 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) {
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++) {
@ -251,16 +252,13 @@ class Atom {
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();
int wl=0;
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++;
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;
@ -273,15 +271,14 @@ class Atom {
time_pos.start();
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);
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(&dev_x.begin(), &dev_x_cast.begin(), &dev_type_cast.begin(),
&_nall);
k_cast_x.run(&x, &x_cast, &type_cast, &_nall);
#else
ucl_copy(dev_x,host_x,_nall*4,true);
x.update_device(_nall*4,true);
#endif
_x_avail=true;
}
@ -299,18 +296,14 @@ class Atom {
inline void cast_q_data(cpytyp *host_ptr) {
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];
}
// 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;
}
}
@ -318,7 +311,7 @@ class Atom {
// Copy charges to device asynchronously
inline void add_q_data() {
if (_q_avail==false) {
ucl_copy(dev_q,host_q,_nall,true);
q.update_device(_nall,true);
_q_avail=true;
}
}
@ -328,18 +321,13 @@ class Atom {
inline void cast_quat_data(cpytyp *host_ptr) {
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];
}
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;
}
}
@ -348,7 +336,7 @@ class Atom {
/** Copies nall()*4 elements **/
inline void add_quat_data() {
if (_quat_avail==false) {
ucl_copy(dev_quat,host_quat,_nall*4,true);
quat.update_device(_nall*4,true);
_quat_avail=true;
}
}
@ -363,29 +351,23 @@ class Atom {
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_D_Vec<numtyp> dev_x;
UCL_Vector<numtyp,numtyp> x;
/// Charges
UCL_D_Vec<numtyp> dev_q;
UCL_Vector<numtyp,numtyp> q;
/// Quaterions
UCL_D_Vec<numtyp> dev_quat;
UCL_Vector<numtyp,numtyp> quat;
#ifdef GPU_CAST
UCL_D_Vec<double> dev_x_cast;
UCL_D_Vec<int> dev_type_cast;
UCL_H_Vec<double> host_x_cast;
UCL_H_Vec<int> host_type_cast;
UCL_Vector<double,double> x_cast;
UCL_Vector<int,int> type_cast;
#endif
/// Buffer for moving positions to device
UCL_H_Vec<numtyp> host_x;
/// Buffer for moving charge data to GPU
UCL_H_Vec<numtyp> host_q;
/// Buffer for moving quat data to GPU
UCL_H_Vec<numtyp> host_quat;
/// Cell list identifiers for device nbor builds
UCL_D_Vec<unsigned> dev_cell_id;
/// Cell list identifiers for device nbor builds
@ -418,9 +400,9 @@ class Atom {
bool alloc(const int nall);
bool _allocated, _rot, _charge, _other;
bool _allocated, _rot, _charge, _bonds, _other;
int _max_atoms, _nall, _gpu_nbor;
bool _bonds;
bool _host_view;
double _time_cast, _time_transfer;
double _max_gpu_bytes;
@ -434,3 +416,4 @@ class Atom {
}
#endif