forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11661 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
67afd6fb68
commit
8d9e3945dd
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/***************************************************************************
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base_dpd.cpp
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-------------------
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Trung Dac Nguyen (ORNL)
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Base class for pair styles needing per-particle data for position,
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dipole, and type.
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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 : Jan 15, 2014
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email : nguyentd@ornl.gov
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***************************************************************************/
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#include "lal_base_dpd.h"
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using namespace LAMMPS_AL;
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#define BaseDPDT BaseDPD<numtyp, acctyp>
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extern Device<PRECISION,ACC_PRECISION> global_device;
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template <class numtyp, class acctyp>
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BaseDPDT::BaseDPD() : _compiled(false), _max_bytes(0) {
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device=&global_device;
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ans=new Answer<numtyp,acctyp>();
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nbor=new Neighbor();
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}
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template <class numtyp, class acctyp>
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BaseDPDT::~BaseDPD() {
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delete ans;
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delete nbor;
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}
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template <class numtyp, class acctyp>
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int BaseDPDT::bytes_per_atom_atomic(const int max_nbors) const {
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return device->atom.bytes_per_atom()+ans->bytes_per_atom()+
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nbor->bytes_per_atom(max_nbors);
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}
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template <class numtyp, class acctyp>
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int BaseDPDT::init_atomic(const int nlocal, const int nall,
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const int max_nbors, const int maxspecial,
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const double cell_size,
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const double gpu_split, FILE *_screen,
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const void *pair_program, const char *k_name) {
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screen=_screen;
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int gpu_nbor=0;
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if (device->gpu_mode()==Device<numtyp,acctyp>::GPU_NEIGH)
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gpu_nbor=1;
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else if (device->gpu_mode()==Device<numtyp,acctyp>::GPU_HYB_NEIGH)
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gpu_nbor=2;
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int _gpu_host=0;
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int host_nlocal=hd_balancer.first_host_count(nlocal,gpu_split,gpu_nbor);
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if (host_nlocal>0)
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_gpu_host=1;
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_threads_per_atom=device->threads_per_charge();
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if (_threads_per_atom>1 && gpu_nbor==0) {
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nbor->packing(true);
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_nbor_data=&(nbor->dev_packed);
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} else
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_nbor_data=&(nbor->dev_nbor);
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int success=device->init(*ans,false,false,nlocal,host_nlocal,nall,nbor,
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maxspecial,_gpu_host,max_nbors,cell_size,false,
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_threads_per_atom,true);
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if (success!=0)
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return success;
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ucl_device=device->gpu;
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atom=&device->atom;
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_block_size=device->pair_block_size();
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_block_bio_size=device->block_bio_pair();
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compile_kernels(*ucl_device,pair_program,k_name);
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// Initialize host-device load balancer
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hd_balancer.init(device,gpu_nbor,gpu_split);
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// Initialize timers for the selected GPU
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time_pair.init(*ucl_device);
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time_pair.zero();
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pos_tex.bind_float(atom->x,4);
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vel_tex.bind_float(atom->v,4);
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_max_an_bytes=ans->gpu_bytes()+nbor->gpu_bytes();
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return success;
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}
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template <class numtyp, class acctyp>
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void BaseDPDT::estimate_gpu_overhead() {
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device->estimate_gpu_overhead(1,_gpu_overhead,_driver_overhead);
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}
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template <class numtyp, class acctyp>
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void BaseDPDT::clear_atomic() {
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// Output any timing information
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acc_timers();
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double avg_split=hd_balancer.all_avg_split();
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_gpu_overhead*=hd_balancer.timestep();
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_driver_overhead*=hd_balancer.timestep();
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device->output_times(time_pair,*ans,*nbor,avg_split,_max_bytes+_max_an_bytes,
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_gpu_overhead,_driver_overhead,_threads_per_atom,screen);
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if (_compiled) {
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k_pair_fast.clear();
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k_pair.clear();
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delete pair_program;
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_compiled=false;
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}
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time_pair.clear();
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hd_balancer.clear();
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nbor->clear();
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ans->clear();
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device->clear();
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}
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// ---------------------------------------------------------------------------
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// Copy neighbor list from host
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// ---------------------------------------------------------------------------
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template <class numtyp, class acctyp>
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int * BaseDPDT::reset_nbors(const int nall, const int inum, int *ilist,
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int *numj, int **firstneigh, bool &success) {
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success=true;
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int mn=nbor->max_nbor_loop(inum,numj,ilist);
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resize_atom(inum,nall,success);
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resize_local(inum,mn,success);
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if (!success)
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return NULL;
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nbor->get_host(inum,ilist,numj,firstneigh,block_size());
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double bytes=ans->gpu_bytes()+nbor->gpu_bytes();
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if (bytes>_max_an_bytes)
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_max_an_bytes=bytes;
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return ilist;
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}
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// ---------------------------------------------------------------------------
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// Build neighbor list on device
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// ---------------------------------------------------------------------------
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template <class numtyp, class acctyp>
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inline void BaseDPDT::build_nbor_list(const int inum, const int host_inum,
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const int nall, double **host_x,
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int *host_type, double *sublo,
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double *subhi, tagint *tag,
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int **nspecial, tagint **special,
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bool &success) {
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success=true;
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resize_atom(inum,nall,success);
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resize_local(inum,host_inum,nbor->max_nbors(),success);
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if (!success)
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return;
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atom->cast_copy_x(host_x,host_type);
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int mn;
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nbor->build_nbor_list(host_x, inum, host_inum, nall, *atom, sublo, subhi, tag,
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nspecial, special, success, mn);
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double bytes=ans->gpu_bytes()+nbor->gpu_bytes();
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if (bytes>_max_an_bytes)
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_max_an_bytes=bytes;
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}
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// ---------------------------------------------------------------------------
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// Copy nbor list from host if necessary and then calculate forces, virials,..
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// ---------------------------------------------------------------------------
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template <class numtyp, class acctyp>
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void BaseDPDT::compute(const int f_ago, const int inum_full,
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const int nall, double **host_x, int *host_type,
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int *ilist, int *numj, int **firstneigh,
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const bool eflag, const bool vflag,
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const bool eatom, const bool vatom,
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int &host_start, const double cpu_time,
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bool &success, tagint *tag, double **host_v,
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const double dtinvsqrt, const int seed, const int timestep,
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const int nlocal, double *boxlo, double *prd) {
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acc_timers();
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if (inum_full==0) {
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host_start=0;
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// Make sure textures are correct if realloc by a different hybrid style
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resize_atom(0,nall,success);
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zero_timers();
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return;
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}
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int ago=hd_balancer.ago_first(f_ago);
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int inum=hd_balancer.balance(ago,inum_full,cpu_time);
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ans->inum(inum);
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host_start=inum;
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if (ago==0) {
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reset_nbors(nall, inum, ilist, numj, firstneigh, success);
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if (!success)
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return;
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}
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atom->cast_x_data(host_x,host_type);
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atom->cast_v_data(host_v,tag);
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hd_balancer.start_timer();
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atom->add_x_data(host_x,host_type);
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atom->add_v_data(host_v,tag);
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_dtinvsqrt = dtinvsqrt;
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_seed = seed;
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_timestep = timestep;
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loop(eflag,vflag);
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ans->copy_answers(eflag,vflag,eatom,vatom,ilist);
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device->add_ans_object(ans);
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hd_balancer.stop_timer();
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}
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// ---------------------------------------------------------------------------
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// Reneighbor on GPU if necessary and then compute forces, virials, energies
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// ---------------------------------------------------------------------------
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template <class numtyp, class acctyp>
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int** BaseDPDT::compute(const int ago, const int inum_full,
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const int nall, double **host_x, int *host_type,
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double *sublo, double *subhi, tagint *tag,
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int **nspecial, tagint **special, const bool eflag,
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const bool vflag, const bool eatom,
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const bool vatom, int &host_start,
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int **ilist, int **jnum,
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const double cpu_time, bool &success,
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double **host_v, const double dtinvsqrt,
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const int seed, const int timestep,
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double *boxlo, double *prd) {
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acc_timers();
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if (inum_full==0) {
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host_start=0;
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// Make sure textures are correct if realloc by a different hybrid style
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resize_atom(0,nall,success);
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zero_timers();
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return NULL;
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}
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hd_balancer.balance(cpu_time);
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int inum=hd_balancer.get_gpu_count(ago,inum_full);
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ans->inum(inum);
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host_start=inum;
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// Build neighbor list on GPU if necessary
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if (ago==0) {
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build_nbor_list(inum, inum_full-inum, nall, host_x, host_type,
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sublo, subhi, tag, nspecial, special, success);
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if (!success)
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return NULL;
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atom->cast_v_data(host_v,tag);
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hd_balancer.start_timer();
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} else {
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atom->cast_x_data(host_x,host_type);
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atom->cast_v_data(host_v,tag);
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hd_balancer.start_timer();
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atom->add_x_data(host_x,host_type);
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}
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atom->add_v_data(host_v,tag);
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*ilist=nbor->host_ilist.begin();
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*jnum=nbor->host_acc.begin();
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_dtinvsqrt = dtinvsqrt;
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_seed = seed;
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_timestep = timestep;
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loop(eflag,vflag);
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ans->copy_answers(eflag,vflag,eatom,vatom);
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device->add_ans_object(ans);
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hd_balancer.stop_timer();
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return nbor->host_jlist.begin()-host_start;
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}
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template <class numtyp, class acctyp>
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double BaseDPDT::host_memory_usage_atomic() const {
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return device->atom.host_memory_usage()+nbor->host_memory_usage()+
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4*sizeof(numtyp)+sizeof(BaseDPD<numtyp,acctyp>);
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}
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template <class numtyp, class acctyp>
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void BaseDPDT::compile_kernels(UCL_Device &dev, const void *pair_str,
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const char *kname) {
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if (_compiled)
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return;
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std::string s_fast=std::string(kname)+"_fast";
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pair_program=new UCL_Program(dev);
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pair_program->load_string(pair_str,device->compile_string().c_str());
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k_pair_fast.set_function(*pair_program,s_fast.c_str());
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k_pair.set_function(*pair_program,kname);
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pos_tex.get_texture(*pair_program,"pos_tex");
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vel_tex.get_texture(*pair_program,"vel_tex");
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_compiled=true;
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}
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template class BaseDPD<PRECISION,ACC_PRECISION>;
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@ -0,0 +1,203 @@
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/***************************************************************************
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base_dpd.h
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-------------------
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Trung Dac Nguyen (ORNL)
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Base class for pair styles needing per-particle data for position,
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velocity, tag, and type.
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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 : Jan 15, 2014
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email : nguyentd@ornl.gov
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***************************************************************************/
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#ifndef LAL_BASE_DPD_H
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#define LAL_BASE_DPD_H
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#include "lal_device.h"
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#include "lal_balance.h"
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#include "mpi.h"
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#ifdef USE_OPENCL
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#include "geryon/ocl_texture.h"
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#else
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#include "geryon/nvd_texture.h"
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#endif
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namespace LAMMPS_AL {
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template <class numtyp, class acctyp>
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class BaseDPD {
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public:
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BaseDPD();
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virtual ~BaseDPD();
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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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* \param k_name name for the kernel for force calculation
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*
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* Returns:
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* - 0 if successfull
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* - -1 if fix gpu not found
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* - -3 if there is an out of memory error
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* - -4 if the GPU library was not compiled for GPU
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* - -5 Double precision is not supported on card **/
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int init_atomic(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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const void *pair_program, const char *k_name);
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/// Estimate the overhead for GPU context changes and CPU driver
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void estimate_gpu_overhead();
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/// Check if there is enough storage for atom arrays and realloc if not
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/** \param success set to false if insufficient memory **/
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inline void resize_atom(const int inum, const int nall, bool &success) {
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if (atom->resize(nall, success)) {
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pos_tex.bind_float(atom->x,4);
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vel_tex.bind_float(atom->v,4);
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}
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ans->resize(inum,success);
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}
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/// Check if there is enough storage for neighbors and realloc if not
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/** \param nlocal number of particles whose nbors must be stored on device
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* \param host_inum number of particles whose nbors need to copied to host
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* \param current maximum number of neighbors
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* \note olist_size=total number of local particles **/
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inline void resize_local(const int inum, const int max_nbors, bool &success) {
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nbor->resize(inum,max_nbors,success);
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}
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/// Check if there is enough storage for neighbors and realloc if not
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/** \param nlocal number of particles whose nbors must be stored on device
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* \param host_inum number of particles whose nbors need to copied to host
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* \param current maximum number of neighbors
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* \note host_inum is 0 if the host is performing neighboring
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* \note nlocal+host_inum=total number local particles
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* \note olist_size=0 **/
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inline void resize_local(const int inum, const int host_inum,
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const int max_nbors, bool &success) {
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nbor->resize(inum,host_inum,max_nbors,success);
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}
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/// Clear all host and device data
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/** \note This is called at the beginning of the init() routine **/
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void clear_atomic();
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/// Returns memory usage on device per atom
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int bytes_per_atom_atomic(const int max_nbors) const;
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/// Total host memory used by library for pair style
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double host_memory_usage_atomic() const;
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/// Accumulate timers
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inline void acc_timers() {
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if (device->time_device()) {
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nbor->acc_timers();
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time_pair.add_to_total();
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atom->acc_timers();
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ans->acc_timers();
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}
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}
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/// Zero timers
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inline void zero_timers() {
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time_pair.zero();
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atom->zero_timers();
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ans->zero_timers();
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}
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/// Copy neighbor list from host
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int * reset_nbors(const int nall, const int inum, int *ilist, int *numj,
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int **firstneigh, bool &success);
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/// Build neighbor list on device
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void build_nbor_list(const int inum, const int host_inum,
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const int nall, double **host_x, int *host_type,
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double *sublo, double *subhi, tagint *tag, int **nspecial,
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tagint **special, bool &success);
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/// Pair loop with host neighboring
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void compute(const int f_ago, const int inum_full, const int nall,
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double **host_x, int *host_type, int *ilist, int *numj,
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int **firstneigh, const bool eflag, const bool vflag,
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const bool eatom, const bool vatom, int &host_start,
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const double cpu_time, bool &success, tagint *tag,
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double **v, const double dtinvsqrt, const int seed,
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const int timestep, const int nlocal, double *boxlo, double *prd);
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/// Pair loop with device neighboring
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int** compute(const int ago, const int inum_full, const int nall,
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double **host_x, int *host_type, double *sublo,
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double *subhi, tagint *tag, int **nspecial,
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tagint **special, const bool eflag, const bool vflag,
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const bool eatom, const bool vatom, int &host_start,
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int **ilist, int **numj, const double cpu_time, bool &success,
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double **v, const double dtinvsqrt, const int seed,
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const int timestep, double *boxlo, double *prd);
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// -------------------------- DEVICE DATA -------------------------
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/// Device Properties and Atom and Neighbor storage
|
||||
Device<numtyp,acctyp> *device;
|
||||
|
||||
/// Geryon device
|
||||
UCL_Device *ucl_device;
|
||||
|
||||
/// Device Timers
|
||||
UCL_Timer time_pair;
|
||||
|
||||
/// Host device load balancer
|
||||
Balance<numtyp,acctyp> hd_balancer;
|
||||
|
||||
/// LAMMPS pointer for screen output
|
||||
FILE *screen;
|
||||
|
||||
// --------------------------- ATOM DATA --------------------------
|
||||
|
||||
/// Atom Data
|
||||
Atom<numtyp,acctyp> *atom;
|
||||
|
||||
|
||||
// ------------------------ FORCE/ENERGY DATA -----------------------
|
||||
|
||||
Answer<numtyp,acctyp> *ans;
|
||||
|
||||
// --------------------------- NBOR DATA ----------------------------
|
||||
|
||||
/// Neighbor data
|
||||
Neighbor *nbor;
|
||||
|
||||
// ------------------------- DEVICE KERNELS -------------------------
|
||||
UCL_Program *pair_program;
|
||||
UCL_Kernel k_pair_fast, k_pair;
|
||||
inline int block_size() { return _block_size; }
|
||||
|
||||
// --------------------------- TEXTURES -----------------------------
|
||||
UCL_Texture pos_tex;
|
||||
UCL_Texture vel_tex;
|
||||
|
||||
// ------------------------- COMMON VARS ----------------------------
|
||||
numtyp _dtinvsqrt;
|
||||
int _seed, _timestep;
|
||||
|
||||
protected:
|
||||
bool _compiled;
|
||||
int _block_size, _block_bio_size, _threads_per_atom;
|
||||
double _max_bytes, _max_an_bytes;
|
||||
double _gpu_overhead, _driver_overhead;
|
||||
UCL_D_Vec<int> *_nbor_data;
|
||||
|
||||
void compile_kernels(UCL_Device &dev, const void *pair_string, const char *k);
|
||||
virtual void loop(const bool _eflag, const bool _vflag) = 0;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
|
|
@ -0,0 +1,170 @@
|
|||
/***************************************************************************
|
||||
dpd.cpp
|
||||
-------------------
|
||||
Trung Dac Nguyen (ORNL)
|
||||
|
||||
Class for acceleration of the dpd pair style.
|
||||
|
||||
__________________________________________________________________________
|
||||
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
|
||||
__________________________________________________________________________
|
||||
|
||||
begin : Jan 15, 2014
|
||||
email : nguyentd@ornl.gov
|
||||
***************************************************************************/
|
||||
|
||||
#if defined(USE_OPENCL)
|
||||
#include "dpd_cl.h"
|
||||
#elif defined(USE_CUDART)
|
||||
const char *dpd=0;
|
||||
#else
|
||||
#include "dpd_cubin.h"
|
||||
#endif
|
||||
|
||||
#include "lal_dpd.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
#define DPDT DPD<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
DPDT::DPD() : BaseDPD<numtyp,acctyp>(), _allocated(false) {
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
DPDT::~DPD() {
|
||||
clear();
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
int DPDT::bytes_per_atom(const int max_nbors) const {
|
||||
return this->bytes_per_atom_atomic(max_nbors);
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
int DPDT::init(const int ntypes,
|
||||
double **host_cutsq, double **host_a0,
|
||||
double **host_gamma, double **host_sigma,
|
||||
double **host_cut, double *host_special_lj,
|
||||
const bool tstat_only,
|
||||
const int nlocal, const int nall,
|
||||
const int max_nbors, const int maxspecial,
|
||||
const double cell_size,
|
||||
const double gpu_split, FILE *_screen) {
|
||||
int success;
|
||||
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split,_screen,dpd,"k_dpd");
|
||||
if (success!=0)
|
||||
return success;
|
||||
|
||||
// If atom type constants fit in shared memory use fast kernel
|
||||
int lj_types=ntypes;
|
||||
shared_types=false;
|
||||
int max_shared_types=this->device->max_shared_types();
|
||||
if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
|
||||
lj_types=max_shared_types;
|
||||
shared_types=true;
|
||||
}
|
||||
_lj_types=lj_types;
|
||||
|
||||
// Allocate a host write buffer for data initialization
|
||||
UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
|
||||
UCL_WRITE_ONLY);
|
||||
|
||||
for (int i=0; i<lj_types*lj_types; i++)
|
||||
host_write[i]=0.0;
|
||||
|
||||
coeff.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
|
||||
this->atom->type_pack4(ntypes,lj_types,coeff,host_write,host_a0,host_gamma,
|
||||
host_sigma,host_cut);
|
||||
|
||||
UCL_H_Vec<numtyp> host_rsq(lj_types*lj_types,*(this->ucl_device),
|
||||
UCL_WRITE_ONLY);
|
||||
cutsq.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
|
||||
this->atom->type_pack1(ntypes,lj_types,cutsq,host_rsq,host_cutsq);
|
||||
|
||||
UCL_H_Vec<double> dview;
|
||||
sp_lj.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
|
||||
dview.view(host_special_lj,4,*(this->ucl_device));
|
||||
ucl_copy(sp_lj,dview,false);
|
||||
|
||||
_tstat_only = 0;
|
||||
if (tstat_only) _tstat_only=1;
|
||||
|
||||
_allocated=true;
|
||||
this->_max_bytes=coeff.row_bytes()+cutsq.row_bytes()+sp_lj.row_bytes();
|
||||
return 0;
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
void DPDT::clear() {
|
||||
if (!_allocated)
|
||||
return;
|
||||
_allocated=false;
|
||||
|
||||
coeff.clear();
|
||||
cutsq.clear();
|
||||
sp_lj.clear();
|
||||
this->clear_atomic();
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
double DPDT::host_memory_usage() const {
|
||||
return this->host_memory_usage_atomic()+sizeof(DPD<numtyp,acctyp>);
|
||||
}
|
||||
|
||||
// ---------------------------------------------------------------------------
|
||||
// Calculate energies, forces, and torques
|
||||
// ---------------------------------------------------------------------------
|
||||
template <class numtyp, class acctyp>
|
||||
void DPDT::loop(const bool _eflag, const bool _vflag) {
|
||||
// Compute the block size and grid size to keep all cores busy
|
||||
const int BX=this->block_size();
|
||||
int eflag, vflag;
|
||||
if (_eflag)
|
||||
eflag=1;
|
||||
else
|
||||
eflag=0;
|
||||
|
||||
if (_vflag)
|
||||
vflag=1;
|
||||
else
|
||||
vflag=0;
|
||||
|
||||
int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
|
||||
(BX/this->_threads_per_atom)));
|
||||
|
||||
int ainum=this->ans->inum();
|
||||
int nbor_pitch=this->nbor->nbor_pitch();
|
||||
this->time_pair.start();
|
||||
if (shared_types) {
|
||||
this->k_pair_fast.set_size(GX,BX);
|
||||
this->k_pair_fast.run(&this->atom->x, &coeff, &sp_lj,
|
||||
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
|
||||
&this->ans->force, &this->ans->engv, &eflag,
|
||||
&vflag, &ainum, &nbor_pitch, &this->atom->v, &cutsq,
|
||||
&this->_dtinvsqrt, &this->_seed, &this->_timestep,
|
||||
&this->_tstat_only, &this->_threads_per_atom);
|
||||
} else {
|
||||
this->k_pair.set_size(GX,BX);
|
||||
this->k_pair.run(&this->atom->x, &coeff, &_lj_types, &sp_lj,
|
||||
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
|
||||
&this->ans->force, &this->ans->engv, &eflag, &vflag,
|
||||
&ainum, &nbor_pitch, &this->atom->v, &cutsq, &this->_dtinvsqrt,
|
||||
&this->_seed, &this->_timestep, &this->_tstat_only,
|
||||
&this->_threads_per_atom);
|
||||
}
|
||||
this->time_pair.stop();
|
||||
}
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
void DPDT::update_coeff(int ntypes, double **host_a0, double **host_gamma,
|
||||
double **host_sigma, double **host_cut)
|
||||
{
|
||||
UCL_H_Vec<numtyp> host_write(_lj_types*_lj_types*32,*(this->ucl_device),
|
||||
UCL_WRITE_ONLY);
|
||||
this->atom->type_pack4(ntypes,_lj_types,coeff,host_write,host_a0,host_gamma,
|
||||
host_sigma,host_cut);
|
||||
}
|
||||
|
||||
template class DPD<PRECISION,ACC_PRECISION>;
|
||||
|
|
@ -0,0 +1,86 @@
|
|||
/***************************************************************************
|
||||
dpd.h
|
||||
-------------------
|
||||
Trung Dac Nguyen (ORNL)
|
||||
|
||||
Class for acceleration of the dpd pair style.
|
||||
|
||||
__________________________________________________________________________
|
||||
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
|
||||
__________________________________________________________________________
|
||||
|
||||
begin : Jan 15, 2014
|
||||
email : nguyentd@ornl.gov
|
||||
***************************************************************************/
|
||||
|
||||
#ifndef LAL_DPD_H
|
||||
#define LAL_DPD_H
|
||||
|
||||
#include "lal_base_dpd.h"
|
||||
|
||||
namespace LAMMPS_AL {
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
class DPD : public BaseDPD<numtyp, acctyp> {
|
||||
public:
|
||||
DPD();
|
||||
~DPD();
|
||||
|
||||
/// Clear any previous data and set up for a new LAMMPS run
|
||||
/** \param max_nbors initial number of rows in the neighbor matrix
|
||||
* \param cell_size cutoff + skin
|
||||
* \param gpu_split fraction of particles handled by device
|
||||
*
|
||||
* Returns:
|
||||
* - 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_a0,
|
||||
double **host_gamma, double **host_sigma, double **host_cut,
|
||||
double *host_special_lj, bool tstat_only, const int nlocal,
|
||||
const int nall, const int max_nbors, const int maxspecial,
|
||||
const double cell_size, const double gpu_split, FILE *screen);
|
||||
|
||||
/// 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;
|
||||
|
||||
/// Update coeff if needed (tstat only)
|
||||
void update_coeff(int ntypes, double **host_a0, double **host_gamma,
|
||||
double **host_sigma, double **host_cut);
|
||||
|
||||
// --------------------------- TYPE DATA --------------------------
|
||||
|
||||
/// coeff.x = a0, coeff.y = gamma, coeff.z = sigma, coeff.w = cut
|
||||
UCL_D_Vec<numtyp4> coeff;
|
||||
|
||||
UCL_D_Vec<numtyp> cutsq;
|
||||
|
||||
/// Special LJ values
|
||||
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;
|
||||
|
||||
/// Only used for thermostat
|
||||
int _tstat_only;
|
||||
|
||||
private:
|
||||
bool _allocated;
|
||||
void loop(const bool _eflag, const bool _vflag);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
|
|
@ -0,0 +1,133 @@
|
|||
/***************************************************************************
|
||||
dpd_ext.cpp
|
||||
-------------------
|
||||
Trung Dac Nguyen (ORNL)
|
||||
|
||||
Functions for LAMMPS access to dpd acceleration routines.
|
||||
|
||||
__________________________________________________________________________
|
||||
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
|
||||
__________________________________________________________________________
|
||||
|
||||
begin : Jan 15, 2014
|
||||
email : nguyentd@ornl.gov
|
||||
***************************************************************************/
|
||||
|
||||
#include <iostream>
|
||||
#include <cassert>
|
||||
#include <math.h>
|
||||
|
||||
#include "lal_dpd.h"
|
||||
|
||||
using namespace std;
|
||||
using namespace LAMMPS_AL;
|
||||
|
||||
static DPD<PRECISION,ACC_PRECISION> DPDMF;
|
||||
|
||||
// ---------------------------------------------------------------------------
|
||||
// Allocate memory on host and device and copy constants to device
|
||||
// ---------------------------------------------------------------------------
|
||||
int dpd_gpu_init(const int ntypes, double **cutsq, double **host_a0,
|
||||
double **host_gamma, double **host_sigma, double **host_cut,
|
||||
double *special_lj, bool tstat_only, const int inum,
|
||||
const int nall, const int max_nbors, const int maxspecial,
|
||||
const double cell_size, int &gpu_mode, FILE *screen) {
|
||||
DPDMF.clear();
|
||||
gpu_mode=DPDMF.device->gpu_mode();
|
||||
double gpu_split=DPDMF.device->particle_split();
|
||||
int first_gpu=DPDMF.device->first_device();
|
||||
int last_gpu=DPDMF.device->last_device();
|
||||
int world_me=DPDMF.device->world_me();
|
||||
int gpu_rank=DPDMF.device->gpu_rank();
|
||||
int procs_per_gpu=DPDMF.device->procs_per_gpu();
|
||||
|
||||
DPDMF.device->init_message(screen,"dpd",first_gpu,last_gpu);
|
||||
|
||||
bool message=false;
|
||||
if (DPDMF.device->replica_me()==0 && screen)
|
||||
message=true;
|
||||
|
||||
if (message) {
|
||||
fprintf(screen,"Initializing Device and compiling on process 0...");
|
||||
fflush(screen);
|
||||
}
|
||||
|
||||
int init_ok=0;
|
||||
if (world_me==0)
|
||||
init_ok=DPDMF.init(ntypes, cutsq, host_a0, host_gamma, host_sigma,
|
||||
host_cut, special_lj, tstat_only, inum, nall, 300,
|
||||
maxspecial, cell_size, gpu_split, screen);
|
||||
|
||||
DPDMF.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 Device %d on core %d...",first_gpu,i);
|
||||
else
|
||||
fprintf(screen,"Initializing Devices %d-%d on core %d...",first_gpu,
|
||||
last_gpu,i);
|
||||
fflush(screen);
|
||||
}
|
||||
if (gpu_rank==i && world_me!=0)
|
||||
init_ok=DPDMF.init(ntypes, cutsq, host_a0, host_gamma, host_sigma,
|
||||
host_cut, special_lj, tstat_only, inum, nall, 300,
|
||||
maxspecial, cell_size, gpu_split, screen);
|
||||
|
||||
DPDMF.device->gpu_barrier();
|
||||
if (message)
|
||||
fprintf(screen,"Done.\n");
|
||||
}
|
||||
if (message)
|
||||
fprintf(screen,"\n");
|
||||
|
||||
if (init_ok==0)
|
||||
DPDMF.estimate_gpu_overhead();
|
||||
return init_ok;
|
||||
}
|
||||
|
||||
void dpd_gpu_clear() {
|
||||
DPDMF.clear();
|
||||
}
|
||||
|
||||
int ** dpd_gpu_compute_n(const int ago, const int inum_full, const int nall,
|
||||
double **host_x, int *host_type, double *sublo,
|
||||
double *subhi, tagint *tag, int **nspecial,
|
||||
tagint **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,
|
||||
double **host_v, const double dtinvsqrt,
|
||||
const int seed, const int timestep,
|
||||
double *boxlo, double *prd) {
|
||||
return DPDMF.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,
|
||||
host_v, dtinvsqrt, seed, timestep, boxlo, prd);
|
||||
}
|
||||
|
||||
void dpd_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, tagint *tag,
|
||||
double **host_v, const double dtinvsqrt,
|
||||
const int seed, const int timestep,
|
||||
const int nlocal, double *boxlo, double *prd) {
|
||||
DPDMF.compute(ago, inum_full, nall, host_x, host_type, ilist, numj,
|
||||
firstneigh, eflag, vflag, eatom, vatom, host_start, cpu_time, success,
|
||||
tag, host_v, dtinvsqrt, seed, timestep, nlocal, boxlo, prd);
|
||||
}
|
||||
|
||||
void dpd_gpu_update_coeff(int ntypes, double **host_a0, double **host_gamma,
|
||||
double **host_sigma, double **host_cut)
|
||||
{
|
||||
DPDMF.update_coeff(ntypes,host_a0,host_gamma,host_sigma,host_cut);
|
||||
}
|
||||
|
||||
double dpd_gpu_bytes() {
|
||||
return DPDMF.host_memory_usage();
|
||||
}
|
||||
|
||||
|
||||
Loading…
Reference in New Issue