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neighbor.h
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/***************************************************************************
neighbor.h
-------------------
W. Michael Brown (ORNL)
Peng Wang (Nvidia)
Class for handling neighbor lists
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin :
email : brownw@ornl.gov, penwang@nvidia.com
***************************************************************************/
#ifndef LAL_NEIGHBOR_H
#define LAL_NEIGHBOR_H
#include "atom.h"
#include "neighbor_shared.h"
#define IJ_SIZE 131072
#ifdef USE_OPENCL
#include "geryon/ocl_timer.h"
#include "geryon/ocl_mat.h"
using namespace ucl_opencl;
#else
#include "geryon/nvd_timer.h"
#include "geryon/nvd_mat.h"
using namespace ucl_cudadr;
#endif
class Neighbor {
public:
Neighbor() : _allocated(false), _use_packing(false) {}
~Neighbor() { clear(); }
/// Determine whether neighbor unpacking should be used
/** If false, twice as much memory is reserved to allow unpacking neighbors by
* atom for coalesced access. **/
void packing(const bool use_packing) { _use_packing=use_packing; }
/// Clear any old data and setup for new LAMMPS run
/** \param inum Initial number of particles whose neighbors stored on device
* \param host_inum Initial number of particles whose nbors copied to host
* \param max_nbors Initial number of rows in the neighbor matrix
* \param gpu_nbor True if device will perform neighboring
* \param gpu_host 0 if host will not perform force calculations,
* 1 if gpu_nbor is true, and host needs a half nbor list,
* 2 if gpu_nbor is true, and host needs a full nbor list
* \param pre_cut True if cutoff test will be performed in separate kernel
* than the force kernel **/
bool init(NeighborShared *shared, const int inum, const int host_inum,
const int max_nbors, const int maxspecial, UCL_Device &dev,
const bool gpu_nbor, const int gpu_host, const bool pre_cut,
const int block_cell_2d, const int block_cell_id,
const int block_nbor_build);
/// Set the size of the cutoff+skin
inline void cell_size(const double size) { _cell_size=size; }
/// Get the size of the cutoff+skin
inline double cell_size() const { return _cell_size; }
/// Check if there is enough memory for neighbor data and realloc if not
/** \param inum Number of particles whose nbors will be stored on device
* \param max_nbor Current max number of neighbors for a particle
* \param success False if insufficient memory **/
inline void resize(const int inum, const int max_nbor, bool &success) {
if (inum>_max_atoms || max_nbor>_max_nbors) {
_max_atoms=static_cast<int>(static_cast<double>(inum)*1.10);
if (max_nbor>_max_nbors)
_max_nbors=static_cast<int>(static_cast<double>(max_nbor)*1.10);
alloc(success);
}
}
/// Check if there is enough memory for neighbor data and realloc if not
/** \param inum Number of particles whose nbors will be stored on device
* \param host_inum Number of particles whose nbors will be copied to host
* \param max_nbor Current max number of neighbors for a particle
* \param success False if insufficient memory **/
inline void resize(const int inum, const int host_inum, const int max_nbor,
bool &success) {
if (inum>_max_atoms || max_nbor>_max_nbors || host_inum>_max_host) {
_max_atoms=static_cast<int>(static_cast<double>(inum)*1.10);
_max_host=static_cast<int>(static_cast<double>(host_inum)*1.10);
if (max_nbor>_max_nbors)
_max_nbors=static_cast<int>(static_cast<double>(max_nbor)*1.10);
alloc(success);
}
}
/// Free all memory on host and device
void clear();
/// Bytes per atom used on device
int bytes_per_atom(const int max_nbors) const;
/// Total host memory used by class
double host_memory_usage() const;
/// True if neighboring performed on GPU
inline bool gpu_nbor() const { return _gpu_nbor; }
/// Make a copy of unpacked nbor lists in the packed storage area (for gb)
inline void copy_unpacked(const int inum, const int maxj)
{ ucl_copy(dev_packed,dev_nbor,inum*(maxj+2),true); }
/// Copy neighbor list from host (first time or from a rebuild)
void get_host(const int inum, int *ilist, int *numj,
int **firstneigh, const int block_size);
/// Return the stride in elements for each nbor row
inline int nbor_pitch() const { return _nbor_pitch; }
/// Return the maximum number of atoms that can currently be stored
inline int max_atoms() const { return _max_atoms; }
/// Return the maximum number of nbors for a particle based on current alloc
inline int max_nbors() const { return _max_nbors; }
/// Loop through neighbor count array and return maximum nbors for a particle
inline int max_nbor_loop(const int inum, int *numj, int *ilist) const {
int mn=0;
for (int i=0; i<inum; i++)
mn=std::max(mn,numj[ilist[i]]);
return mn;
}
/// Build nbor list on the device
template <class numtyp, class acctyp>
void build_nbor_list(const int inum, const int host_inum, const int nall,
Atom<numtyp,acctyp> &atom, double *sublo,
double *subhi, int *tag, int **nspecial, int **special,
bool &success, int &max_nbors);
/// Return the number of bytes used on device
inline double gpu_bytes() {
double res = _gpu_bytes + _c_bytes + _cell_bytes;
if (_gpu_nbor==false)
res += 2*IJ_SIZE*sizeof(int);
return res;
}
// ------------------------------- Data -------------------------------
/// Device neighbor matrix
/** - 1st row is i (index into atom data)
* - 2nd row is numj (number of neighbors)
* - 3rd row is starting location in packed nbors
* - Remaining rows are the neighbors arranged for coalesced access **/
UCL_D_Vec<int> dev_nbor;
/// Packed storage for neighbor lists copied from host
UCL_D_Vec<int> dev_packed;
/// Host buffer for copying neighbor lists
UCL_H_Vec<int> host_packed;
/// Host storage for nbor counts (row 1) & accumulated neighbor counts (row2)
UCL_H_Vec<int> host_acc;
// ----------------- Data for GPU Neighbor Calculation ---------------
/// Host storage for device calculated neighbor lists
/** Same storage format as device matrix **/
UCL_H_Vec<int> host_nbor;
/// Device storage for neighbor list matrix that will be copied to host
/** - 1st row is numj
* - Remaining rows are by atom, columns are nbors **/
UCL_D_Vec<int> dev_host_nbor;
UCL_D_Vec<int> dev_host_numj;
UCL_H_Vec<int> host_ilist;
UCL_H_Vec<int*> host_jlist;
/// Device storage for special neighbor counts
UCL_D_Vec<int> dev_nspecial;
/// Device storage for special neighbors
UCL_D_Vec<int> dev_special, dev_special_t;
/// Device timers
UCL_Timer time_nbor, time_kernel;
private:
NeighborShared *_shared;
UCL_Device *dev;
bool _allocated, _use_packing;
int _max_atoms, _max_nbors, _max_host, _nbor_pitch, _maxspecial;
bool _gpu_nbor, _gpu_host, _alloc_packed;
double _cell_size;
double _gpu_bytes, _c_bytes, _cell_bytes;
void alloc(bool &success);
int _block_cell_2d, _block_cell_id, _block_nbor_build;
};
#endif

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