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/***************************************************************************
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lj_gromacs.cpp
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-------------------
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Trung Dac Nguyen (ORNL)
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Class for acceleration of the lj/gromacs pair style.
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__________________________________________________________________________
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This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
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__________________________________________________________________________
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begin :
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email : nguyentd@ornl.gov
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***************************************************************************/
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#if defined(USE_OPENCL)
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#include "lj_gromacs_cl.h"
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#elif defined(USE_CUDART)
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const char *lj_gromacs=0;
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#else
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#include "lj_gromacs_cubin.h"
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#endif
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#include "lal_lj_gromacs.h"
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#include <cassert>
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using namespace LAMMPS_AL;
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#define LJGROMACST LJGROMACS<numtyp, acctyp>
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extern Device<PRECISION,ACC_PRECISION> device;
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template <class numtyp, class acctyp>
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LJGROMACST::LJGROMACS() : BaseAtomic<numtyp,acctyp>(),
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_allocated(false) {
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}
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template <class numtyp, class acctyp>
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LJGROMACST::~LJGROMACS() {
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clear();
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}
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template <class numtyp, class acctyp>
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int LJGROMACST::bytes_per_atom(const int max_nbors) const {
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return this->bytes_per_atom_atomic(max_nbors);
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}
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template <class numtyp, class acctyp>
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int LJGROMACST::init(const int ntypes, double **host_cutsq,
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double **host_lj1, double **host_lj2, double **host_lj3,
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double **host_lj4, double *host_special_lj,
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const int nlocal, const int nall, const int max_nbors,
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const int maxspecial, const double cell_size,
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const double gpu_split, FILE *_screen,
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double **host_ljsw1, double **host_ljsw2, double **host_ljsw3,
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double **host_ljsw4, double **host_ljsw5,
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double **cut_inner, double **cut_inner_sq) {
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int success;
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success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split,
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_screen,lj_gromacs,"k_lj_gromacs");
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if (success!=0)
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return success;
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// If atom type constants fit in shared memory use fast kernel
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int lj_types=ntypes;
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shared_types=false;
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int max_shared_types=this->device->max_shared_types();
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if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
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lj_types=max_shared_types;
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shared_types=true;
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}
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_lj_types=lj_types;
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// Allocate a host write buffer for data initialization
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UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
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UCL_WRITE_ONLY);
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for (int i=0; i<lj_types*lj_types; i++)
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host_write[i]=0.0;
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lj1.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
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this->atom->type_pack4(ntypes,lj_types,lj1,host_write,host_lj1,host_lj2,
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host_cutsq,cut_inner_sq);
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lj3.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
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this->atom->type_pack4(ntypes,lj_types,lj3,host_write,host_lj3,host_lj4,
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cut_inner,host_ljsw5);
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ljsw.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
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this->atom->type_pack4(ntypes,lj_types,ljsw,host_write,host_ljsw1,host_ljsw2,
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host_ljsw3,host_ljsw4);
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UCL_H_Vec<double> dview;
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sp_lj.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
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dview.view(host_special_lj,4,*(this->ucl_device));
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ucl_copy(sp_lj,dview,false);
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_allocated=true;
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this->_max_bytes=lj1.row_bytes()+lj3.row_bytes()
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+ljsw.row_bytes()+sp_lj.row_bytes();
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return 0;
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}
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template <class numtyp, class acctyp>
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void LJGROMACST::clear() {
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if (!_allocated)
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return;
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_allocated=false;
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lj1.clear();
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lj3.clear();
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ljsw.clear();
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sp_lj.clear();
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this->clear_atomic();
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}
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template <class numtyp, class acctyp>
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double LJGROMACST::host_memory_usage() const {
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return this->host_memory_usage_atomic()+sizeof(LJGROMACS<numtyp,acctyp>);
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}
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// ---------------------------------------------------------------------------
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// Calculate energies, forces, and torques
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// ---------------------------------------------------------------------------
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template <class numtyp, class acctyp>
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void LJGROMACST::loop(const bool _eflag, const bool _vflag) {
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// Compute the block size and grid size to keep all cores busy
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const int BX=this->block_size();
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int eflag, vflag;
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if (_eflag)
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eflag=1;
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else
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eflag=0;
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if (_vflag)
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vflag=1;
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else
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vflag=0;
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int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
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(BX/this->_threads_per_atom)));
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int ainum=this->ans->inum();
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int nbor_pitch=this->nbor->nbor_pitch();
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this->time_pair.start();
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if (shared_types) {
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this->k_pair_fast.set_size(GX,BX);
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this->k_pair_fast.run(&this->atom->x, &lj1, &lj3, &ljsw,
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&sp_lj, &this->nbor->dev_nbor,
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&this->_nbor_data->begin(),
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&this->ans->force, &this->ans->engv,
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&eflag, &vflag, &ainum, &nbor_pitch,
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&this->_threads_per_atom);
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} else {
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this->k_pair.set_size(GX,BX);
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this->k_pair.run(&this->atom->x, &lj1, &lj3, &ljsw, &_lj_types,
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&sp_lj, &this->nbor->dev_nbor,
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&this->_nbor_data->begin(),
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&this->ans->force, &this->ans->engv,
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&eflag, &vflag, &ainum, &nbor_pitch,
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&this->_threads_per_atom);
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}
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this->time_pair.stop();
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}
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template class LJGROMACS<PRECISION,ACC_PRECISION>;
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@ -0,0 +1,233 @@
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// **************************************************************************
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// lj_gromacs.cu
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// -------------------
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// Trung Dac Nguyen (ORNL)
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//
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// Device code for acceleration of the gromacs/coul/long pair style
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//
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// __________________________________________________________________________
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// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
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// __________________________________________________________________________
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//
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// begin :
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// email : nguyentd@ornl.gov
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// ***************************************************************************/
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#ifdef NV_KERNEL
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#include "lal_aux_fun1.h"
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#ifndef _DOUBLE_DOUBLE
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texture<float4> pos_tex;
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#else
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texture<int4,1> pos_tex;
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#endif
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#else
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#define pos_tex x_
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#endif
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__kernel void k_lj_gromacs(const __global numtyp4 *restrict x_,
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const __global numtyp4 *restrict lj1,
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const __global numtyp4 *restrict lj3,
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const __global numtyp4 *restrict ljsw,
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const int lj_types,
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const __global numtyp *restrict sp_lj_in,
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const __global int *dev_nbor,
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const __global int *dev_packed,
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__global acctyp4 *restrict ans,
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__global acctyp *restrict engv,
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const int eflag, const int vflag, const int inum,
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const int nbor_pitch, const int t_per_atom) {
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int tid, ii, offset;
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atom_info(t_per_atom,ii,tid,offset);
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__local numtyp sp_lj[4];
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sp_lj[0]=sp_lj_in[0];
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sp_lj[1]=sp_lj_in[1];
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sp_lj[2]=sp_lj_in[2];
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sp_lj[3]=sp_lj_in[3];
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acctyp energy=(acctyp)0;
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acctyp4 f;
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f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
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acctyp virial[6];
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for (int i=0; i<6; i++)
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virial[i]=(acctyp)0;
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if (ii<inum) {
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const __global int *nbor, *list_end;
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int i, numj;
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__local int n_stride;
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nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
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n_stride,list_end,nbor);
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numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
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int itype=ix.w;
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numtyp factor_lj;
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for ( ; nbor<list_end; nbor+=n_stride) {
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int j=*nbor;
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factor_lj = sp_lj[sbmask(j)];
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j &= NEIGHMASK;
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numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
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int jtype=jx.w;
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// Compute r12
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numtyp delx = ix.x-jx.x;
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numtyp dely = ix.y-jx.y;
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numtyp delz = ix.z-jx.z;
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numtyp rsq = delx*delx+dely*dely+delz*delz;
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int mtype=itype*lj_types+jtype;
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if (rsq<lj1[mtype].z) {
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numtyp r2inv=ucl_recip(rsq);
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numtyp force_lj, force, r6inv, t;
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r6inv = r2inv*r2inv*r2inv;
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force_lj = r6inv*(lj1[mtype].x*r6inv-lj1[mtype].y);
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if (rsq > lj1[mtype].w) {
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numtyp r = ucl_sqrt(rsq);
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t = r - lj3[mtype].z;
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numtyp fswitch = r*t*t*(ljsw[mtype].x + ljsw[mtype].y*t);
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force_lj += fswitch;
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}
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force = factor_lj*force_lj * r2inv;
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f.x+=delx*force;
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f.y+=dely*force;
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f.z+=delz*force;
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if (eflag>0) {
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numtyp e=r6inv*(lj3[mtype].x*r6inv-lj3[mtype].y);
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e += lj3[mtype].w;
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if (rsq > lj1[mtype].w) {
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numtyp eswitch = t*t*t*(ljsw[mtype].z + ljsw[mtype].w*t);
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e += eswitch;
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}
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energy+=factor_lj*e;
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}
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if (vflag>0) {
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virial[0] += delx*delx*force;
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virial[1] += dely*dely*force;
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virial[2] += delz*delz*force;
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virial[3] += delx*dely*force;
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virial[4] += delx*delz*force;
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virial[5] += dely*delz*force;
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}
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}
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} // for nbor
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store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,
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vflag,ans,engv);
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} // if ii
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}
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__kernel void k_lj_gromacs_fast(const __global numtyp4 *restrict x_,
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const __global numtyp4 *restrict lj1_in,
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const __global numtyp4 *restrict lj3_in,
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const __global numtyp4 *restrict ljsw_in,
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const __global numtyp *restrict sp_lj_in,
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const __global int *dev_nbor,
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const __global int *dev_packed,
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__global acctyp4 *restrict ans,
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__global acctyp *restrict engv,
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const int eflag, const int vflag, const int inum,
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const int nbor_pitch, const int t_per_atom) {
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int tid, ii, offset;
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atom_info(t_per_atom,ii,tid,offset);
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__local numtyp4 lj1[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
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__local numtyp4 lj3[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
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__local numtyp4 ljsw[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
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__local numtyp sp_lj[4];
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if (tid<4)
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sp_lj[tid]=sp_lj_in[tid];
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if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES) {
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lj1[tid]=lj1_in[tid];
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lj3[tid]=lj3_in[tid];
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ljsw[tid]=ljsw_in[tid];
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}
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acctyp energy=(acctyp)0;
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acctyp4 f;
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f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
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acctyp virial[6];
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for (int i=0; i<6; i++)
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virial[i]=(acctyp)0;
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__syncthreads();
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if (ii<inum) {
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const __global int *nbor, *list_end;
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int i, numj;
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__local int n_stride;
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nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
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n_stride,list_end,nbor);
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numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
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int iw=ix.w;
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int itype=fast_mul((int)MAX_SHARED_TYPES,iw);
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numtyp factor_lj;
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for ( ; nbor<list_end; nbor+=n_stride) {
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int j=*nbor;
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factor_lj = sp_lj[sbmask(j)];
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j &= NEIGHMASK;
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numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
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int mtype=itype+jx.w;
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// Compute r12
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numtyp delx = ix.x-jx.x;
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numtyp dely = ix.y-jx.y;
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numtyp delz = ix.z-jx.z;
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numtyp rsq = delx*delx+dely*dely+delz*delz;
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if (rsq<lj1[mtype].z) {
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numtyp r2inv=ucl_recip(rsq);
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numtyp force_lj, force, r6inv, t;
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r6inv = r2inv*r2inv*r2inv;
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force_lj = r6inv*(lj1[mtype].x*r6inv-lj1[mtype].y);
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if (rsq > lj1[mtype].w) {
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numtyp r = ucl_sqrt(rsq);
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t = r - lj3[mtype].z;
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numtyp fswitch = r*t*t*(ljsw[mtype].x + ljsw[mtype].y*t);
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force_lj += fswitch;
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}
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force = factor_lj*force_lj * r2inv;
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f.x+=delx*force;
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f.y+=dely*force;
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f.z+=delz*force;
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if (eflag>0) {
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numtyp e=r6inv*(lj3[mtype].x*r6inv-lj3[mtype].y);
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e += lj3[mtype].w;
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if (rsq > lj1[mtype].w) {
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numtyp eswitch = t*t*t*(ljsw[mtype].z + ljsw[mtype].w*t);
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e += eswitch;
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}
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energy+=factor_lj*e;
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}
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if (vflag>0) {
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virial[0] += delx*delx*force;
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virial[1] += dely*dely*force;
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virial[2] += delz*delz*force;
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virial[3] += delx*dely*force;
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virial[4] += delx*delz*force;
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virial[5] += dely*delz*force;
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}
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}
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} // for nbor
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store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,
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vflag,ans,engv);
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} // if ii
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}
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@ -0,0 +1,84 @@
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/***************************************************************************
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lj_gromacs.h
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-------------------
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Trung Dac Nguyen (ORNL)
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Class for acceleration of the lj/gromacs pair style.
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__________________________________________________________________________
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This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
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__________________________________________________________________________
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begin :
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email : nguyentd@ornl.gov
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***************************************************************************/
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#ifndef LAL_LJ_GROMACS_H
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#define LAL_LJ_GROMACS_H
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#include "lal_base_atomic.h"
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namespace LAMMPS_AL {
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template <class numtyp, class acctyp>
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class LJGROMACS : public BaseAtomic<numtyp, acctyp> {
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public:
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LJGROMACS();
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~LJGROMACS();
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/// Clear any previous data and set up for a new LAMMPS run
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/** \param max_nbors initial number of rows in the neighbor matrix
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* \param cell_size cutoff + skin
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* \param gpu_split fraction of particles handled by device
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*
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* Returns:
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* - 0 if successfull
|
||||
* - -1 if fix gpu not found
|
||||
* - -3 if there is an out of memory error
|
||||
* - -4 if the GPU library was not compiled for GPU
|
||||
* - -5 Double precision is not supported on card **/
|
||||
int init(const int ntypes, double **host_cutsq,
|
||||
double **host_lj1, double **host_lj2, double **host_lj3,
|
||||
double **host_lj4, double *host_special_lj,
|
||||
const int nlocal, const int nall, const int max_nbors,
|
||||
const int maxspecial, const double cell_size,
|
||||
const double gpu_split, FILE *screen,
|
||||
double **host_ljsw1, double **host_ljsw2, double **host_ljsw3,
|
||||
double **host_ljsw4, double **host_ljsw5,
|
||||
double **cut_inner, double **cut_inner_sq);
|
||||
|
||||
/// Clear all host and device data
|
||||
/** \note This is called at the beginning of the init() routine **/
|
||||
void clear();
|
||||
|
||||
/// Returns memory usage on device per atom
|
||||
int bytes_per_atom(const int max_nbors) const;
|
||||
|
||||
/// Total host memory used by library for pair style
|
||||
double host_memory_usage() const;
|
||||
|
||||
// --------------------------- TYPE DATA --------------------------
|
||||
|
||||
/// lj1.x = lj1, lj1.y = lj2, lj1.z = cutsq, lj1.w = cut_inner_sq
|
||||
UCL_D_Vec<numtyp4> lj1;
|
||||
/// lj3.x = lj3, lj3.y = lj4, lj3.z = cut_inner, lj3.w = ljsw5
|
||||
UCL_D_Vec<numtyp4> lj3;
|
||||
/// ljsw.x = ljsw1, ljsw.y = ljsw2, ljsw.z = ljsw3, ljsw.w = ljsw4
|
||||
UCL_D_Vec<numtyp4> ljsw;
|
||||
/// Special LJ values [0-3] and Special Coul values [4-7]
|
||||
UCL_D_Vec<numtyp> sp_lj;
|
||||
|
||||
/// If atom type constants fit in shared memory, use fast kernels
|
||||
bool shared_types;
|
||||
|
||||
/// Number of atom types
|
||||
int _lj_types;
|
||||
|
||||
private:
|
||||
bool _allocated;
|
||||
void loop(const bool _eflag, const bool _vflag);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
|
|
@ -0,0 +1,126 @@
|
|||
/***************************************************************************
|
||||
lj_gromacs_ext.cpp
|
||||
-------------------
|
||||
Trung Dac Nguyen (ORNL)
|
||||
|
||||
Functions for LAMMPS access to lj/gromacs acceleration routines.
|
||||
|
||||
__________________________________________________________________________
|
||||
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
|
||||
__________________________________________________________________________
|
||||
|
||||
begin :
|
||||
email : nguyentd@ornl.gov
|
||||
***************************************************************************/
|
||||
|
||||
#include <iostream>
|
||||
#include <cassert>
|
||||
#include <math.h>
|
||||
|
||||
#include "lal_lj_gromacs.h"
|
||||
|
||||
using namespace std;
|
||||
using namespace LAMMPS_AL;
|
||||
|
||||
static LJGROMACS<PRECISION,ACC_PRECISION> LJGRMMF;
|
||||
|
||||
// ---------------------------------------------------------------------------
|
||||
// Allocate memory on host and device and copy constants to device
|
||||
// ---------------------------------------------------------------------------
|
||||
int ljgrm_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
|
||||
double **host_lj2, double **host_lj3, double **host_lj4,
|
||||
double *special_lj, const int inum,
|
||||
const int nall, const int max_nbors, const int maxspecial,
|
||||
const double cell_size, int &gpu_mode, FILE *screen,
|
||||
double **host_ljsw1, double **host_ljsw2, double **host_ljsw3,
|
||||
double **host_ljsw4, double **host_ljsw5,
|
||||
double **cut_inner, double **cut_inner_sq) {
|
||||
LJGRMMF.clear();
|
||||
gpu_mode=LJGRMMF.device->gpu_mode();
|
||||
double gpu_split=LJGRMMF.device->particle_split();
|
||||
int first_gpu=LJGRMMF.device->first_device();
|
||||
int last_gpu=LJGRMMF.device->last_device();
|
||||
int world_me=LJGRMMF.device->world_me();
|
||||
int gpu_rank=LJGRMMF.device->gpu_rank();
|
||||
int procs_per_gpu=LJGRMMF.device->procs_per_gpu();
|
||||
|
||||
LJGRMMF.device->init_message(screen,"lj/gromacs",first_gpu,last_gpu);
|
||||
|
||||
bool message=false;
|
||||
if (LJGRMMF.device->replica_me()==0 && screen)
|
||||
message=true;
|
||||
|
||||
if (message) {
|
||||
fprintf(screen,"Initializing GPU and compiling on process 0...");
|
||||
fflush(screen);
|
||||
}
|
||||
|
||||
int init_ok=0;
|
||||
if (world_me==0)
|
||||
LJGRMMF.init(ntypes, cutsq, host_lj1, host_lj2, host_lj3, host_lj4,
|
||||
special_lj, inum, nall, 300, maxspecial, cell_size,
|
||||
gpu_split, screen, host_ljsw1, host_ljsw2, host_ljsw3,
|
||||
host_ljsw4, host_ljsw5, cut_inner, cut_inner_sq);
|
||||
|
||||
LJGRMMF.device->world_barrier();
|
||||
if (message)
|
||||
fprintf(screen,"Done.\n");
|
||||
|
||||
for (int i=0; i<procs_per_gpu; i++) {
|
||||
if (message) {
|
||||
if (last_gpu-first_gpu==0)
|
||||
fprintf(screen,"Initializing GPU %d on core %d...",first_gpu,i);
|
||||
else
|
||||
fprintf(screen,"Initializing GPUs %d-%d on core %d...",first_gpu,
|
||||
last_gpu,i);
|
||||
fflush(screen);
|
||||
}
|
||||
if (gpu_rank==i && world_me!=0)
|
||||
init_ok=LJGRMMF.init(ntypes, cutsq, host_lj1, host_lj2, host_lj3, host_lj4,
|
||||
special_lj, inum, nall, 300, maxspecial, cell_size,
|
||||
gpu_split, screen, host_ljsw1, host_ljsw2, host_ljsw3,
|
||||
host_ljsw4, host_ljsw5, cut_inner, cut_inner_sq);
|
||||
|
||||
LJGRMMF.device->gpu_barrier();
|
||||
if (message)
|
||||
fprintf(screen,"Done.\n");
|
||||
}
|
||||
if (message)
|
||||
fprintf(screen,"\n");
|
||||
|
||||
if (init_ok==0)
|
||||
LJGRMMF.estimate_gpu_overhead();
|
||||
return init_ok;
|
||||
}
|
||||
|
||||
void ljgrm_gpu_clear() {
|
||||
LJGRMMF.clear();
|
||||
}
|
||||
|
||||
int ** ljgrm_gpu_compute_n(const int ago, const int inum_full,
|
||||
const int nall, double **host_x, int *host_type,
|
||||
double *sublo, double *subhi, int *tag, int **nspecial,
|
||||
int **special, const bool eflag, const bool vflag,
|
||||
const bool eatom, const bool vatom, int &host_start,
|
||||
int **ilist, int **jnum, const double cpu_time,
|
||||
bool &success) {
|
||||
return LJGRMMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
|
||||
subhi, tag, nspecial, special, eflag, vflag, eatom,
|
||||
vatom, host_start, ilist, jnum, cpu_time, success);
|
||||
}
|
||||
|
||||
void ljgrm_gpu_compute(const int ago, const int inum_full, const int nall,
|
||||
double **host_x, int *host_type, int *ilist, int *numj,
|
||||
int **firstneigh, const bool eflag, const bool vflag,
|
||||
const bool eatom, const bool vatom, int &host_start,
|
||||
const double cpu_time, bool &success) {
|
||||
LJGRMMF.compute(ago,inum_full,nall,host_x,host_type,ilist,numj,
|
||||
firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success);
|
||||
}
|
||||
|
||||
|
||||
double ljgrm_gpu_bytes() {
|
||||
return LJGRMMF.host_memory_usage();
|
||||
}
|
||||
|
||||
|
||||
Loading…
Reference in New Issue