lammps/lib/gpu/pair_gpu_nbor.cpp

/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   http://lammps.sandia.gov, Sandia National Laboratories
   Steve Plimpton, sjplimp@sandia.gov

   Copyright (2003) Sandia Corporation.  Under the terms of Contract
   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
   certain rights in this software.  This software is distributed under 
   the GNU General Public License.

   See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
 
/* ----------------------------------------------------------------------
   Contributing authors: Mike Brown (ORNL), brownw@ornl.gov
                         Peng Wang (Nvidia), penwang@nvidia.com
------------------------------------------------------------------------- */

#include "pair_gpu_precision.h"
#include "pair_gpu_nbor.h"
#include "pair_gpu_device.h"
#include "math.h"

int PairGPUNbor::bytes_per_atom(const int max_nbors) const {
  if (_gpu_nbor)
    return (max_nbors+2)*sizeof(int);
  else if (_use_packing)
    return ((max_nbors+2)*2)*sizeof(int);
  else
    return (max_nbors+3)*sizeof(int);
}

bool PairGPUNbor::init(PairGPUNborShared *shared, const int inum,
                       const int host_inum, const int max_nbors, 
                       const int maxspecial, UCL_Device &devi, 
                       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) {
  clear();

  _block_cell_2d=block_cell_2d;
  _block_cell_id=block_cell_id;
  _block_nbor_build=block_nbor_build;
  _shared=shared;
  dev=&devi;
  _gpu_nbor=gpu_nbor;
  if (gpu_host==0)
    _gpu_host=false;
  else if (gpu_host==1)
    _gpu_host=true;
  else 
    // Not yet implemented
    assert(0==1);
  
  if (pre_cut || gpu_nbor==false)
    _alloc_packed=true;
  else
    _alloc_packed=false;

  bool success=true;
    
  // Initialize timers for the selected GPU
  time_nbor.init(*dev);
  time_kernel.init(*dev);
  time_nbor.zero();
  time_kernel.zero();

  _max_atoms=static_cast<int>(static_cast<double>(inum)*1.10);
  if (_max_atoms==0)
    _max_atoms=1000;
    
  _max_host=static_cast<int>(static_cast<double>(host_inum)*1.10);
  _max_nbors=max_nbors;

  _maxspecial=maxspecial;
  if (gpu_nbor==false)
    _maxspecial=0;

  if (gpu_nbor==false)
    success=success && (host_packed.alloc(2*IJ_SIZE,*dev,
                                          UCL_WRITE_OPTIMIZED)==UCL_SUCCESS);
  alloc(success);
  if (!success)
    return false;
    
  if (_use_packing==false)
    _shared->compile_kernels(devi,gpu_nbor);

  return success;
}

void PairGPUNbor::alloc(bool &success) { 
  dev_nbor.clear();
  host_acc.clear();
  int nt=_max_atoms+_max_host;
  if (_use_packing==false || _gpu_nbor) 
    success=success && (dev_nbor.alloc((_max_nbors+2)*_max_atoms,*dev,
                                       UCL_READ_ONLY)==UCL_SUCCESS);
  else 
    success=success && (dev_nbor.alloc(3*_max_atoms,*dev,
                                       UCL_READ_ONLY)==UCL_SUCCESS);
  success=success && (host_acc.alloc(nt*2,*dev,
                                     UCL_WRITE_OPTIMIZED)==UCL_SUCCESS);

  _c_bytes=dev_nbor.row_bytes();
  if (_alloc_packed) {
    dev_packed.clear();
    success=success && (dev_packed.alloc((_max_nbors+2)*_max_atoms,*dev,
                                         UCL_READ_ONLY)==UCL_SUCCESS);
    _c_bytes+=dev_packed.row_bytes();                                         
  } 
  if (_max_host>0) {
    host_nbor.clear();
    dev_host_nbor.clear();
    dev_host_numj.clear();
    host_ilist.clear();
    host_jlist.clear();
    
    success=success && (host_nbor.alloc(_max_nbors*_max_host,*dev,
                                        UCL_RW_OPTIMIZED)==UCL_SUCCESS);
    success=success && (dev_host_nbor.alloc(_max_nbors*_max_host,
                                            *dev,UCL_WRITE_ONLY)==UCL_SUCCESS);
    success=success && (dev_host_numj.alloc(_max_host,*dev,
                                            UCL_WRITE_ONLY)==UCL_SUCCESS);
    success=success && (host_ilist.alloc(nt,*dev,UCL_NOT_PINNED)==UCL_SUCCESS);
    if (!success)
      return;
    for (int i=0; i<nt; i++)
      host_ilist[i]=i;
    success=success && (host_jlist.alloc(_max_host,*dev,
                                         UCL_NOT_PINNED)==UCL_SUCCESS);
    if (!success)
      return;
    int *ptr=host_nbor.begin();
    for (int i=0; i<_max_host; i++) {
      host_jlist[i]=ptr;
      ptr+=_max_nbors;
    }                                                 
    _c_bytes+=dev_host_nbor.row_bytes()+dev_host_numj.row_bytes();
  }
  if (_maxspecial>0) {
    dev_nspecial.clear();
    dev_special.clear();
    dev_special_t.clear();
    int at=_max_atoms+_max_host;
    success=success && (dev_nspecial.alloc(3*at,*dev,
                                           UCL_READ_ONLY)==UCL_SUCCESS);
    success=success && (dev_special.alloc(_maxspecial*at,*dev,
                                          UCL_READ_ONLY)==UCL_SUCCESS);
    success=success && (dev_special_t.alloc(_maxspecial*at,*dev,
                                            UCL_READ_ONLY)==UCL_SUCCESS);
    _gpu_bytes+=dev_nspecial.row_bytes()+dev_special.row_bytes()+
                dev_special_t.row_bytes();
  }

  _allocated=true;
}
  
void PairGPUNbor::clear() {
  _gpu_bytes=0.0;
  _cell_bytes=0.0;
  _c_bytes=0.0;
  if (_allocated) {
    _allocated=false;

    host_packed.clear();
    host_acc.clear();
    dev_nbor.clear();
    dev_host_nbor.clear();
    dev_packed.clear();
    host_nbor.clear();
    dev_host_numj.clear();
    host_ilist.clear();
    host_jlist.clear();
    dev_nspecial.clear();
    dev_special.clear();
    dev_special_t.clear();

    time_kernel.clear();
    time_nbor.clear();
  }
}

double PairGPUNbor::host_memory_usage() const {
  if (_gpu_nbor) {
    if (_gpu_host)
      return host_nbor.row_bytes()*host_nbor.rows()+host_ilist.row_bytes()+
             host_jlist.row_bytes();
    else
      return 0;
  } else 
    return host_packed.row_bytes()*host_packed.rows()+host_acc.row_bytes()+
           sizeof(PairGPUNbor);
}

void PairGPUNbor::get_host(const int inum, int *ilist, int *numj,
                           int **firstneigh, const int block_size) {  
  time_nbor.start();

  UCL_H_Vec<int> ilist_view;
  ilist_view.view(ilist,inum,*dev);
  ucl_copy(dev_nbor,ilist_view,false);

  UCL_D_Vec<int> nbor_offset;
  UCL_H_Vec<int> host_offset;

  int copy_count=0;
  int ij_count=0;
  int acc_count=0;
  int dev_count=0;
  int *h_ptr=host_packed.begin();
  _nbor_pitch=inum;
  
  for (int ii=0; ii<inum; ii++) {
    int i=ilist[ii];
    int nj=numj[i];
    host_acc[ii]=nj;
    host_acc[ii+inum]=acc_count;

    acc_count+=nj;
    
    int *jlist=firstneigh[i];
    for (int jj=0; jj<nj; jj++) {
      *h_ptr=jlist[jj];
      h_ptr++;
      ij_count++;
       
      if (ij_count==IJ_SIZE) {
        dev_nbor.sync();
        host_offset.view_offset(IJ_SIZE*(copy_count%2),host_packed,IJ_SIZE);
        nbor_offset.view_offset(dev_count,dev_packed,IJ_SIZE);
        ucl_copy(nbor_offset,host_offset,true);
        copy_count++;
        ij_count=0;
        dev_count+=IJ_SIZE;
        h_ptr=host_packed.begin()+(IJ_SIZE*(copy_count%2));
      }
    }
  }
  if (ij_count!=0) {
    dev_nbor.sync();
    host_offset.view_offset(IJ_SIZE*(copy_count%2),host_packed,ij_count);
    nbor_offset.view_offset(dev_count,dev_packed,ij_count);
    ucl_copy(nbor_offset,host_offset,true);
  }
  UCL_D_Vec<int> acc_view;
  acc_view.view_offset(inum,dev_nbor,inum*2);
  ucl_copy(acc_view,host_acc,true);
  time_nbor.stop();
  
  if (_use_packing==false) {
    time_kernel.start();
    int GX=static_cast<int>(ceil(static_cast<double>(inum)/block_size));
    _shared->k_nbor.set_size(GX,block_size);
    _shared->k_nbor.run(&dev_nbor.begin(), &dev_packed.begin(), &inum);
    time_kernel.stop();
  }
}

template <class numtyp, class acctyp>
void PairGPUNbor::build_nbor_list(const int inum, const int host_inum,
                                  const int nall, 
                                  PairGPUAtom<numtyp,acctyp> &atom, 
                                  double *sublo, double *subhi, int *tag, 
                                  int **nspecial, int **special, bool &success,
                                  int &mn) {
  const int nt=inum+host_inum;
  if (_maxspecial>0) {
    time_nbor.start();
    UCL_H_Vec<int> view_nspecial, view_special, view_tag;
    view_nspecial.view(nspecial[0],nt*3,*dev);
    view_special.view(special[0],nt*_maxspecial,*dev);
    view_tag.view(tag,nall,*dev);
    ucl_copy(dev_nspecial,view_nspecial,nt*3,false);
    ucl_copy(dev_special_t,view_special,nt*_maxspecial,false);
    ucl_copy(atom.dev_tag,view_tag,nall,false);
    time_nbor.stop();
    time_nbor.add_to_total();
    time_kernel.start();
    const int b2x=_block_cell_2d;
    const int b2y=_block_cell_2d;
    const int g2x=static_cast<int>(ceil(static_cast<double>(_maxspecial)/b2x));
    const int g2y=static_cast<int>(ceil(static_cast<double>(nt)/b2y));
    _shared->k_transpose.set_size(g2x,g2y,b2x,b2y);
    _shared->k_transpose.run(&dev_special.begin(),&dev_special_t.begin(),
                             &_maxspecial,&nt);        
  } else
    time_kernel.start();

  _nbor_pitch=inum;
  _shared->neigh_tex.bind_float(atom.dev_x,4);

  int ncellx, ncelly, ncellz, ncell_3d;
  ncellx = static_cast<int>(ceil(((subhi[0] - sublo[0]) +
                                  2.0*_cell_size)/_cell_size));
  ncelly = static_cast<int>(ceil(((subhi[1] - sublo[1]) +
                                  2.0*_cell_size)/_cell_size));
  ncellz = static_cast<int>(ceil(((subhi[2] - sublo[2]) +
                                  2.0*_cell_size)/_cell_size));
  ncell_3d = ncellx * ncelly * ncellz;
  UCL_D_Vec<int> cell_counts;
  cell_counts.alloc(ncell_3d+1,dev_nbor);
  _cell_bytes=cell_counts.row_bytes();

  /* build cell list on GPU */
  const int neigh_block=_block_cell_id;
  const int GX=(int)ceil((float)nall/neigh_block);
  const numtyp sublo0=static_cast<numtyp>(sublo[0]);
  const numtyp sublo1=static_cast<numtyp>(sublo[1]);
  const numtyp sublo2=static_cast<numtyp>(sublo[2]);
  const numtyp subhi0=static_cast<numtyp>(subhi[0]);
  const numtyp subhi1=static_cast<numtyp>(subhi[1]);
  const numtyp subhi2=static_cast<numtyp>(subhi[2]);
  const numtyp cell_size_cast=static_cast<numtyp>(_cell_size);
  _shared->k_cell_id.set_size(GX,neigh_block);
  _shared->k_cell_id.run(&atom.dev_x.begin(), &atom.dev_cell_id.begin(), 
                         &atom.dev_particle_id.begin(),
  				               &sublo0, &sublo1, &sublo2, &subhi0, &subhi1, 
  				               &subhi2, &cell_size_cast, &ncellx, &ncelly, &nall);

  atom.sort_neighbor(nall);

  /* calculate cell count */
  _shared->k_cell_counts.set_size(GX,neigh_block);
  _shared->k_cell_counts.run(&atom.dev_cell_id.begin(), &cell_counts.begin(), 
                             &nall, &ncell_3d);

  /* build the neighbor list */
  const int cell_block=_block_nbor_build;
  _shared->k_build_nbor.set_size(ncellx, ncelly*ncellz, cell_block, 1);
  _shared->k_build_nbor.run(&atom.dev_x.begin(), &atom.dev_particle_id.begin(),
                            &cell_counts.begin(), &dev_nbor.begin(),
                            &dev_host_nbor.begin(), &dev_host_numj.begin(),
                            &_max_nbors,&cell_size_cast,
                            &ncellx, &ncelly, &ncellz, &inum, &nt, &nall);

  /* Get the maximum number of nbors and realloc if necessary */
  UCL_D_Vec<int> numj;
  numj.view_offset(inum,dev_nbor,inum);
  ucl_copy(host_acc,numj,inum,false);
  if (nt>inum) {
    UCL_H_Vec<int> host_offset;
    host_offset.view_offset(inum,host_acc,nt-inum);
    ucl_copy(host_offset,dev_host_numj,nt-inum,false);
  }
  mn=host_acc[0];
  for (int i=1; i<nt; i++)
    mn=std::max(mn,host_acc[i]);

  if (mn>_max_nbors) {  
    mn=static_cast<int>(static_cast<double>(mn)*1.10);
    dev_nbor.clear();
    success=success && (dev_nbor.alloc((mn+1)*_max_atoms,atom.dev_cell_id,
                        UCL_READ_ONLY)==UCL_SUCCESS);
    _gpu_bytes=dev_nbor.row_bytes();
    if (_max_host>0) {
      host_nbor.clear();
      dev_host_nbor.clear();
      success=success && (host_nbor.alloc(mn*_max_host,dev_nbor,
                                          UCL_RW_OPTIMIZED)==UCL_SUCCESS);
      success=success && (dev_host_nbor.alloc(mn*_max_host,
                                        dev_nbor,UCL_WRITE_ONLY)==UCL_SUCCESS);
      int *ptr=host_nbor.begin();
      for (int i=0; i<_max_host; i++) {
        host_jlist[i]=ptr;
        ptr+=mn;
      }                                                 
      _gpu_bytes+=dev_host_nbor.row_bytes();
    }
    if (_alloc_packed) {
      dev_packed.clear();
      success=success && (dev_packed.alloc((mn+2)*_max_atoms,*dev,
                                           UCL_READ_ONLY)==UCL_SUCCESS);
      _gpu_bytes+=dev_packed.row_bytes();
    }
    if (!success)
      return;
    _max_nbors=mn;
    time_kernel.stop();
    time_kernel.add_to_total();
    build_nbor_list(inum, host_inum, nall, atom, sublo, subhi, tag, nspecial,
                    special, success, mn);
    return;
  }
  
  if (_maxspecial>0) {
    const int GX2=static_cast<int>(ceil(static_cast<double>(nt)/cell_block));
    _shared->k_special.set_size(GX2,cell_block);
    _shared->k_special.run(&dev_nbor.begin(), &dev_host_nbor.begin(), 
                           &dev_host_numj.begin(), &atom.dev_tag.begin(), 
                           &dev_nspecial.begin(), &dev_special.begin(), 
                           &inum, &nt, &nall, &_max_nbors);
  }
  time_kernel.stop();

  time_nbor.start();
  if (_gpu_host)
    ucl_copy(host_nbor,dev_host_nbor,false);
  time_nbor.stop();
}

template void PairGPUNbor::build_nbor_list<PRECISION,ACC_PRECISION>
     (const int inum, const int host_inum, const int nall,
      PairGPUAtom<PRECISION,ACC_PRECISION> &atom, double *sublo, double *subhi,
      int *, int **, int **, bool &success, int &mn);