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Thu, Jul 25, 17:04

verlet_cuda.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
Original Version:
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
See the README file in the top-level LAMMPS directory.
-----------------------------------------------------------------------
USER-CUDA Package and associated modifications:
https://sourceforge.net/projects/lammpscuda/
Christian Trott, christian.trott@tu-ilmenau.de
Lars Winterfeld, lars.winterfeld@tu-ilmenau.de
Theoretical Physics II, University of Technology Ilmenau, Germany
See the README file in the USER-CUDA directory.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
#include <cstdlib>
#include <cstdio>
#include <cstring>
#include "verlet_cuda.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "atom.h"
#include "atom_vec.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "kspace.h"
#include "output.h"
#include "update.h"
#include "modify_cuda.h"
#include "compute.h"
#include "fix.h"
#include "timer.h"
#include "memory.h"
#include "error.h"
#include "cuda_wrapper_cu.h"
#include "thermo.h"
#include "cuda_pair_cu.h"
#include "cuda.h"
#include <ctime>
#include <cmath>
using namespace LAMMPS_NS;
#define MAKETIMEING
VerletCuda::VerletCuda(LAMMPS *lmp, int narg, char **arg) : Verlet(lmp, narg, arg) {
cuda = lmp->cuda;
if(cuda == NULL)
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
modify_cuda=(ModifyCuda*) modify;
}
/* ----------------------------------------------------------------------
setup before run
------------------------------------------------------------------------- */
void VerletCuda::setup()
{
//debug related variables
cuda->debugdata[0]=0;
cuda->cu_debugdata->upload();
dotestatom=cuda->dotestatom;
int testatom=cuda->testatom;//48267;
MYDBG(printf("# CUDA VerletCuda::setup start\n"); )
cuda->oncpu = true;
cuda->begin_setup = true;
cuda->finished_run = false;
time_pair=0;
time_kspace=0;
time_comm=0;
time_modify=0;
time_fulliterate=0;
atom->setup();
cuda_shared_atom* cu_atom = & cuda->shared_data.atom;
cuda_shared_domain* cu_domain = & cuda->shared_data.domain;
cuda_shared_pair* cu_pair = & cuda->shared_data.pair;
cu_atom->update_nlocal=1;
cu_atom->update_nmax=1;
if(atom->molecular||(force->kspace&&(not cuda->shared_data.pppm.cudable_force))) cuda->shared_data.pair.collect_forces_later = true;
cuda->setDomainParams();
if(cuda->shared_data.me==0)
printf("# CUDA: VerletCuda::setup: Allocate memory on device for maximum of %i atoms...\n", atom->nmax);
if(cuda->shared_data.me==0)
printf("# CUDA: Using precision: Global: %u X: %u V: %u F: %u PPPM: %u \n", CUDA_PRECISION==1?4:8,sizeof(X_FLOAT),sizeof(V_FLOAT),sizeof(F_FLOAT),sizeof(PPPM_FLOAT));
cuda->allocate();
if (comm->me == 0 && screen) fprintf(screen,"Setting up run ...\n");
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
if (atom->sortfreq > 0) atom->sort();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
cuda->setSystemParams();
cuda->checkResize();
if(cuda->shared_data.me==0)
printf("# CUDA: VerletCuda::setup: Upload data...\n");
cuda->uploadAll();
neighbor->build();
neighbor->ncalls = 0;
if(atom->mass)
cuda->cu_mass->upload();
if(cuda->cu_map_array)
cuda->cu_map_array->upload();
// compute all forces
ev_set(update->ntimestep);
if(elist_atom) cuda->shared_data.atom.need_eatom = 1;
if(vlist_atom) cuda->shared_data.atom.need_vatom = 1;
if(elist_atom||vlist_atom) cuda->checkResize();
int test_BpA_vs_TpA = true;
timespec starttime;
timespec endtime;
#ifdef NO_PREC_TIMING
double startsec,endsec;
#endif
//if(atom->molecular||(force->kspace&&(not cuda->shared_data.pppm.cudable_force))) cuda->shared_data.pair.collect_forces_later = false;
if(test_BpA_vs_TpA && cuda->shared_data.pair.cudable_force && force->pair &&(cuda->shared_data.pair.override_block_per_atom<0))
{
int StyleLoops=10;
if(cuda->shared_data.me==0)
printf("Test TpA\n");
cuda->shared_data.pair.use_block_per_atom = 0;
neighbor->build();
Cuda_Pair_GenerateXType(&cuda->shared_data);
if(cuda->cu_v_radius)
Cuda_Pair_GenerateVRadius(&cuda->shared_data);
if(cuda->cu_omega_rmass)
Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
force->pair->compute(eflag,vflag);
CudaWrapper_Sync();
#ifdef NO_PREC_TIMING
startsec = 1.0*clock()/CLOCKS_PER_SEC;
#endif
clock_gettime(CLOCK_REALTIME,&starttime);
for(int i=0;i<StyleLoops;i++)
{
Cuda_Pair_GenerateXType(&cuda->shared_data);
if(cuda->cu_v_radius)
Cuda_Pair_GenerateVRadius(&cuda->shared_data);
if(cuda->cu_omega_rmass)
Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
force->pair->compute(eflag,vflag);
CudaWrapper_Sync();
}
clock_gettime(CLOCK_REALTIME,&endtime);
double TpAtime=endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
#ifdef NO_PREC_TIMING
endsec = 1.0*clock()/CLOCKS_PER_SEC;
TpAtime = endsec - startsec;
#endif
if(cuda->shared_data.me==0)
printf("Test BpA\n");
cuda->shared_data.pair.use_block_per_atom = 1;
neighbor->build();
Cuda_Pair_GenerateXType(&cuda->shared_data);
if(cuda->cu_v_radius)
Cuda_Pair_GenerateVRadius(&cuda->shared_data);
if(cuda->cu_omega_rmass)
Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
force->pair->compute(eflag,vflag);
CudaWrapper_Sync();
clock_gettime(CLOCK_REALTIME,&starttime);
#ifdef NO_PREC_TIMING
startsec = 1.0*clock()/CLOCKS_PER_SEC;
#endif
for(int i=0;i<StyleLoops;i++)
{
Cuda_Pair_GenerateXType(&cuda->shared_data);
if(cuda->cu_v_radius)
Cuda_Pair_GenerateVRadius(&cuda->shared_data);
if(cuda->cu_omega_rmass)
Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
force->pair->compute(eflag,vflag);
CudaWrapper_Sync();
}
clock_gettime(CLOCK_REALTIME,&endtime);
double BpAtime=endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
#ifdef NO_PREC_TIMING
endsec = 1.0*clock()/CLOCKS_PER_SEC;
BpAtime = endsec - startsec;
#endif
if(cuda->shared_data.me==0)
printf("\n# CUDA: Timing of parallelisation layout with %i loops:\n",StyleLoops);
if(cuda->shared_data.me==0)
printf("# CUDA: BpA TpA\n %lf %lf\n",BpAtime,TpAtime);
if(BpAtime>TpAtime) cuda->shared_data.pair.use_block_per_atom = 0;
}
else
cuda->shared_data.pair.use_block_per_atom = cuda->shared_data.pair.override_block_per_atom;
//cuda->shared_data.pair.use_block_per_atom = 0;
if(atom->molecular||(force->kspace&&(not cuda->shared_data.pppm.cudable_force))) cuda->shared_data.pair.collect_forces_later = true;
neighbor->build();
neighbor->ncalls = 0;
force_clear();
cuda->cu_f->download();
if(cuda->cu_torque)
cuda->cu_torque->download();
//printf("# Verlet::setup: g f[0] = (%f, %f, %f)\n", atom->f[0][0], atom->f[0][1], atom->f[0][2]);
MYDBG( printf("# CUDA: VerletCuda::setup: initial force compute\n"); )
test_atom(testatom,"pre pair force");
if(cuda->shared_data.pair.cudable_force)
{
cuda->uploadAll();
Cuda_Pair_GenerateXType(&cuda->shared_data);
if(cuda->cu_v_radius)
Cuda_Pair_GenerateVRadius(&cuda->shared_data);
if(cuda->cu_omega_rmass)
Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
}
if (force->pair) force->pair->compute(eflag,vflag);
if(cuda->shared_data.pair.cudable_force)
{
if(cuda->shared_data.pair.collect_forces_later)
{
if(eflag) cuda->cu_eng_vdwl->upload();
if(eflag) cuda->cu_eng_coul->upload();
if(vflag) cuda->cu_virial->upload();
Cuda_Pair_CollectForces(&cuda->shared_data,eflag,vflag);
if(eflag) cuda->cu_eng_vdwl->download();
if(eflag) cuda->cu_eng_coul->download();
if(vflag) cuda->cu_virial->download();
}
cuda->downloadAll();
}
test_atom(testatom,"post pair force");
MYDBG( printf("# CUDA: VerletCuda::setup: initial force compute done\n"); )
//printf("# Verlet::setup: h f[0] = (%f, %f, %f)\n", atom->f[0][0], atom->f[0][1], atom->f[0][2]);
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);
if (force->improper) force->improper->compute(eflag,vflag);
}
if(cuda->shared_data.pppm.cudable_force)
{
cuda->cu_tag ->upload();
cuda->cu_type->upload();
cuda->cu_x ->upload();
cuda->cu_v ->upload();
cuda->cu_f ->upload();
if(cu_atom->q_flag) cuda->cu_q->upload();
}
if (force->kspace) {
force->kspace->setup();
force->kspace->compute(eflag,vflag);
}
if(cuda->shared_data.pppm.cudable_force)
{
cuda->cu_f ->download();
}
test_atom(testatom,"post kspace");
cuda->uploadAll();
if (force->newton) comm->reverse_comm();
cuda->downloadAll();
test_atom(testatom,"post reverse comm");
if(cuda->shared_data.me==0)
printf("# CUDA: Total Device Memory useage post setup: %lf MB\n",1.0*CudaWrapper_CheckMemUseage()/1024/1024);
MYDBG( printf("# CUDA: VerletCuda::setup: call modify setup\n"); )
modify->setup(vflag);
MYDBG( printf("# CUDA: VerletCuda::setup: call modify setup done\n"); )
output->setup(1);
test_atom(testatom,"post setup");
MYDBG( printf("# CUDA: VerletCuda::setup: done\n"); )
cuda->finished_setup = true;
cuda->oncpu = false;
}
//this routine is in a messy state
void VerletCuda::setup_minimal(int flag)
{
dotestatom=0;
int testatom=104;
cuda->oncpu = true;
cuda->begin_setup = true;
cuda->finished_run = false;
MYDBG(printf("# CUDA VerletCuda::setup start\n"); )
time_pair=0;
time_kspace=0;
time_comm=0;
time_modify=0;
time_fulliterate=0;
//cuda->allocate();
cuda_shared_atom* cu_atom = & cuda->shared_data.atom;
cuda_shared_domain* cu_domain = & cuda->shared_data.domain;
cuda_shared_pair* cu_pair = & cuda->shared_data.pair;
cu_atom->update_nlocal=1;
cu_atom->update_nmax=1;
if(atom->molecular) cuda->shared_data.pair.collect_forces_later = true;
cuda->setDomainParams();
if(cuda->shared_data.me==0)
printf("# CUDA: VerletCuda::setup: Allocate memory on device for maximum of %i atoms...\n", atom->nmax);
cuda->allocate();
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
if (flag) {
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
cuda->setSystemParams();
cuda->checkResize();
neighbor->build();
neighbor->ncalls = 0;
}
if(cuda->shared_data.me==0)
printf("# CUDA: VerletCuda::setup: Upload data...\n");
cuda->uploadAll();
cuda->uploadAllNeighborLists();
if(atom->mass)
cuda->cu_mass->upload();
if(cuda->cu_map_array)
cuda->cu_map_array->upload();
// compute all forces
ev_set(update->ntimestep);
if(elist_atom) cuda->shared_data.atom.need_eatom = 1;
if(vlist_atom) cuda->shared_data.atom.need_vatom = 1;
if(elist_atom||vlist_atom) cuda->checkResize();
force_clear();
cuda->cu_f->download();
//printf("# Verlet::setup: g f[0] = (%f, %f, %f)\n", atom->f[0][0], atom->f[0][1], atom->f[0][2]);
cuda->cu_mass->upload();
MYDBG( printf("# CUDA: VerletCuda::setup: initial force compute\n"); )
test_atom(testatom,"pre pair force");
if(cuda->shared_data.pair.cudable_force)
{
cuda->uploadAll();
Cuda_Pair_GenerateXType(&cuda->shared_data);
if(cuda->cu_v_radius)
Cuda_Pair_GenerateVRadius(&cuda->shared_data);
if(cuda->cu_omega_rmass)
Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
}
if (force->pair) force->pair->compute(eflag,vflag);
if(cuda->shared_data.pair.cudable_force)
{
if(cuda->shared_data.pair.collect_forces_later)
{
if(eflag) cuda->cu_eng_vdwl->upload();
if(eflag) cuda->cu_eng_coul->upload();
if(vflag) cuda->cu_virial->upload();
Cuda_Pair_CollectForces(&cuda->shared_data,eflag,vflag);
if(eflag) cuda->cu_eng_vdwl->download();
if(eflag) cuda->cu_eng_coul->download();
if(vflag) cuda->cu_virial->download();
}
cuda->downloadAll();
}
test_atom(testatom,"post pair force");
MYDBG( printf("# CUDA: VerletCuda::setup: initial force compute done\n"); )
//printf("# Verlet::setup: h f[0] = (%f, %f, %f)\n", atom->f[0][0], atom->f[0][1], atom->f[0][2]);
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);
if (force->improper) force->improper->compute(eflag,vflag);
}
if(cuda->shared_data.pppm.cudable_force)
{
cuda->cu_tag ->upload();
cuda->cu_type->upload();
cuda->cu_x ->upload();
cuda->cu_v ->upload();
cuda->cu_f ->upload();
if(cu_atom->q_flag) cuda->cu_q->upload();
}
if (force->kspace) {
force->kspace->setup();
force->kspace->compute(eflag,vflag);
}
if(cuda->shared_data.pppm.cudable_force)
{
cuda->cu_f ->download();
}
test_atom(testatom,"post kspace");
cuda->uploadAll();
if (force->newton) comm->reverse_comm();
cuda->downloadAll();
test_atom(testatom,"post reverse comm");
if(cuda->shared_data.me==0)
printf("# CUDA: Total Device Memory useage post setup: %lf MB\n",1.0*CudaWrapper_CheckMemUseage()/1024/1024);
MYDBG( printf("# CUDA: VerletCuda::setup: call modify setup\n"); )
modify->setup(vflag);
MYDBG( printf("# CUDA: VerletCuda::setup: done\n"); )
cuda->finished_setup=true;
cuda->oncpu=false;
}
//#define TESTATOM
/* ----------------------------------------------------------------------
iterate for n steps
------------------------------------------------------------------------- */
void VerletCuda::run(int n)
{
dotestatom=cuda->dotestatom;
int testatom=cuda->testatom;//48267;
timespec starttime;
timespec endtime;
timespec starttotal;
timespec endtotal;
cuda->setTimingsZero();
static double testtime=0.0;
// clock_gettime(CLOCK_REALTIME,&starttime);
// clock_gettime(CLOCK_REALTIME,&endtime);
// testtime+=endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
// printf("Time: %lf\n",testtime);*/
cuda_shared_domain* cu_domain = & cuda->shared_data.domain;
int nflag,ntimestep,sortflag;
int n_initial_integrate = modify_cuda->n_initial_integrate;
int n_post_integrate = modify_cuda->n_post_integrate;
int n_final_integrate = modify_cuda->n_final_integrate;
int n_pre_exchange = modify_cuda->n_pre_exchange;
int n_pre_neighbor = modify_cuda->n_pre_neighbor;
int n_pre_force = modify_cuda->n_pre_force;
int n_post_force = modify_cuda->n_post_force;
int n_end_of_step = modify_cuda->n_end_of_step;
MYDBG(printf("# CUDA: Fixes: i_int: %i p_int: %i f_int: %i pr_exc: %i pr_neigh: %i pr_f: %i p_f: %i eos: %i\n",
n_initial_integrate,n_post_integrate,n_final_integrate,n_pre_exchange,n_pre_neighbor,n_pre_force,n_post_force,n_end_of_step);)
if (atom->sortfreq > 0) sortflag = 1;
else sortflag = 0;
if(cuda->shared_data.me==0)
{
if((not cuda->shared_data.pair.cudable_force)&&(force->pair))
error->warning(FLERR,"# CUDA: You asked for a Verlet integration using Cuda, "
"but selected a pair force which has not yet been ported to Cuda");
if((not cuda->shared_data.pppm.cudable_force)&&(force->kspace))
error->warning(FLERR,"# CUDA: You asked for a Verlet integration using Cuda, "
"but selected a kspace force which has not yet been ported to Cuda");
if(modify_cuda->n_post_integrate_host+modify_cuda->n_pre_exchange_host+modify_cuda->n_pre_neighbor_host+modify_cuda->n_pre_force_host+modify_cuda->n_post_force_host+modify_cuda->n_end_of_step_host+modify_cuda->n_initial_integrate_host+modify_cuda->n_final_integrate_host)
error->warning(FLERR,"# CUDA: You asked for a Verlet integration using Cuda, "
"but several fixes have not yet been ported to Cuda.\n"
"This can cause a severe speed penalty due to frequent data synchronization between host and GPU.");
if(atom->firstgroupname)
error->warning(FLERR,"Warning: firstgroupname is used, this will cause additional data transfers.");
}
cuda->uploadAll();
if(cuda->neighbor_decide_by_integrator && cuda->cu_xhold)
{
const int n=cuda->shared_data.atom.maxhold;
CudaWrapper_CopyData(cuda->cu_xhold->dev_data(),cuda->cu_x->dev_data(),n*sizeof(X_FLOAT));
CudaWrapper_CopyData((void*) &((X_FLOAT*)cuda->cu_xhold->dev_data())[n],(void*) &((X_FLOAT*)cuda->cu_x->dev_data())[atom->nmax],n*sizeof(X_FLOAT));
CudaWrapper_CopyData((void*) &((X_FLOAT*)cuda->cu_xhold->dev_data())[2*n],(void*) &((X_FLOAT*)cuda->cu_x->dev_data())[2*atom->nmax],n*sizeof(X_FLOAT));
}
cuda->shared_data.atom.reneigh_flag=0;
cuda->shared_data.atom.update_nlocal=1;
cuda->shared_data.atom.update_nmax=1;
cuda->shared_data.atom.update_neigh=1;
cuda->shared_data.domain.update=1;
cuda->shared_data.buffer_new=1;
cuda->uploadtime=0;
cuda->downloadtime=0;
int firstreneigh=1;
for(int i = 0; i < n; i++)
{
ntimestep = ++update->ntimestep;
ev_set(ntimestep);
// initial time integration
test_atom(testatom,"Pre initial");
MYDBG( printf("# CUDA VerletCuda::iterate: before initial_integrate\n"); )
modify->initial_integrate(vflag);
MYDBG( printf("# CUDA VerletCuda::iterate: after initial_integrate\n"); )
if(n_post_integrate) modify->post_integrate();
// regular communication vs neighbor list rebuild
test_atom(testatom,"Pre Exchange");
MYDBG( printf("# CUDA VerletCuda::iterate: before neighbor decide\n"); )
nflag = neighbor->decide();
if(nflag == 0)
{
MYDBG( printf("# CUDA VerletCuda::iterate: communicate\n"); )
timer->stamp();
if((not (eflag||vflag))&&(cuda->shared_data.overlap_comm))
{
//overlap forward communication of ghost atom positions with inner force calculation (interactions between local atoms)
//build communication buffers
// printf("Pre forward_comm(1)\n");
clock_gettime(CLOCK_REALTIME,&starttotal);
cuda->shared_data.atom.reneigh_flag=0;
clock_gettime(CLOCK_REALTIME,&starttime);
timer->stamp();
comm->forward_comm(1);
timer->stamp(TIME_COMM);
clock_gettime(CLOCK_REALTIME,&endtime);
cuda->shared_data.cuda_timings.comm_forward_total+=
endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
//prepare force calculation
// printf("Pre force_clear\n");
force_clear();
// printf("Pre Generate XType\n");
Cuda_Pair_GenerateXType(&cuda->shared_data);
if(cuda->cu_v_radius)
Cuda_Pair_GenerateVRadius(&cuda->shared_data);
if(cuda->cu_omega_rmass)
Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
//start force calculation asynchronus
cuda->shared_data.comm.comm_phase=1;
force->pair->compute(eflag, vflag);
timer->stamp(TIME_PAIR);
//CudaWrapper_Sync();
//download comm buffers from GPU, perform MPI communication and upload buffers again
clock_gettime(CLOCK_REALTIME,&starttime);
comm->forward_comm(2);
clock_gettime(CLOCK_REALTIME,&endtime);
cuda->shared_data.cuda_timings.comm_forward_total+=
endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
timer->stamp(TIME_COMM);
//wait for force calculation
CudaWrapper_Sync();
timer->stamp(TIME_PAIR);
//unpack communication buffers
clock_gettime(CLOCK_REALTIME,&starttime);
comm->forward_comm(3);
clock_gettime(CLOCK_REALTIME,&endtime);
cuda->shared_data.cuda_timings.comm_forward_total+=
endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
timer->stamp(TIME_COMM);
MYDBG( printf("# CUDA VerletCuda::iterate: communicate done\n"); )
cuda->shared_data.cuda_timings.test1+=
endtotal.tv_sec-starttotal.tv_sec+1.0*(endtotal.tv_nsec-starttotal.tv_nsec)/1000000000;
}
else
{
//perform standard forward communication
clock_gettime(CLOCK_REALTIME,&starttime);
comm->forward_comm();
clock_gettime(CLOCK_REALTIME,&endtime);
cuda->shared_data.cuda_timings.comm_forward_total+=
endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
timer->stamp(TIME_COMM);
MYDBG( printf("# CUDA VerletCuda::iterate: communicate done\n"); )
}
}
else
{
int nlocalold=cuda->shared_data.atom.nlocal;
if(firstreneigh)
{
cuda->shared_data.atom.update_nlocal=1;
cuda->shared_data.atom.update_nmax=1;
firstreneigh=0;
}
cuda->shared_data.buffer_new=1;
MYDBG( printf("# CUDA VerletCuda::iterate: neighbor\n"); )
cuda->setDomainParams();
if(n_pre_exchange) modify->pre_exchange();
if(atom->nlocal!=cuda->shared_data.atom.nlocal) //did someone add atoms during pre_exchange?
{
cuda->checkResize();
cuda->uploadAll();
}
//check domain changes
if(domain->triclinic) domain->x2lamda(atom->nlocal);
MYDBG( printf("# CUDA VerletCuda::iterate: neighbor pbc\n"); )
domain->pbc();
if(domain->box_change)
{
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
}
timer->stamp();
MYDBG( printf("# CUDA VerletCuda::iterate: neighbor exchange\n"); )
//perform exchange of local atoms
clock_gettime(CLOCK_REALTIME,&starttime);
comm->exchange();
clock_gettime(CLOCK_REALTIME,&endtime);
//special and nspecial fields of the atom data are not currently transfered via the GPU buffer might be changed in the future
if(comm->nprocs>1)
{
clock_gettime(CLOCK_REALTIME,&starttime);
if(atom->special)
cuda->cu_special->upload();
if(atom->nspecial)
cuda->cu_nspecial->upload();
clock_gettime(CLOCK_REALTIME,&endtime);
cuda->shared_data.cuda_timings.test1+=
endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
}
cuda->shared_data.cuda_timings.comm_exchange_total+=
endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
if(nlocalold!=cuda->shared_data.atom.nlocal) cuda->shared_data.atom.update_nlocal=2;
//sort atoms
if (sortflag && ntimestep >= atom->nextsort) atom->sort();
MYDBG( printf("# CUDA VerletCuda::iterate: neighbor borders\n"); )
//generate ghost atom lists, and transfer ghost atom data
clock_gettime(CLOCK_REALTIME,&starttime);
comm->borders();
clock_gettime(CLOCK_REALTIME,&endtime);
cuda->shared_data.cuda_timings.comm_border_total+=
endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
clock_gettime(CLOCK_REALTIME,&starttime);
//atom index maps are generated on CPU, and need to be transfered to GPU if they are used
if(cuda->cu_map_array)
cuda->cu_map_array->upload();
if(domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
if(n_pre_neighbor) modify->pre_neighbor();
cuda->shared_data.buffer_new=2;
if(atom->molecular) cuda->cu_molecule->download();
MYDBG( printf("# CUDA VerletCuda::iterate: neighbor build\n"); )
timer->stamp(TIME_COMM);
clock_gettime(CLOCK_REALTIME,&endtime);
cuda->shared_data.cuda_timings.test2+=
endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
//rebuild neighbor list
test_atom(testatom,"Pre Neighbor");
neighbor->build();
timer->stamp(TIME_NEIGHBOR);
MYDBG( printf("# CUDA VerletCuda::iterate: neighbor done\n"); )
//if bonded interactions are used (in this case collect_forces_later is true), transfer data which only changes upon exchange/border routines from GPU to CPU
if(cuda->shared_data.pair.collect_forces_later)
{
if(cuda->cu_molecule) cuda->cu_molecule->download();
cuda->cu_tag->download();
cuda->cu_type->download();
cuda->cu_mask->download();
if(cuda->cu_q) cuda->cu_q->download();
}
cuda->shared_data.comm.comm_phase=3;
}
test_atom(testatom,"Post Exchange");
// force computations
//only do force_clear if it has not been done during overlap of communication with local interactions
if(not((not (eflag||vflag))&&(cuda->shared_data.overlap_comm)&&(cuda->shared_data.comm.comm_phase<3)))
force_clear();
if(n_pre_force) modify->pre_force(vflag);
timer->stamp();
//if overlap of bonded interactions with nonbonded interactions takes place, download forces and positions
/* if(cuda->shared_data.pair.collect_forces_later)
{
cuda->cu_x->downloadAsync(2);
cuda->cu_f->downloadAsync(2);
}*/
if(force->pair)
{
if((not (eflag||vflag))&&(cuda->shared_data.overlap_comm)&&(cuda->shared_data.comm.comm_phase<3)&&cuda->shared_data.pair.cudable_force)
{
//second part of force calculations in case of overlaping it with commuincation. Only interactions between local and ghost atoms are done now
//regenerate data layout for force computations, its actually only needed for the ghost atoms
cuda->shared_data.comm.comm_phase=2;
timespec atime1,atime2;
clock_gettime(CLOCK_REALTIME,&atime1);
Cuda_Pair_GenerateXType(&cuda->shared_data);
if(cuda->cu_v_radius)
Cuda_Pair_GenerateVRadius(&cuda->shared_data);
if(cuda->cu_omega_rmass)
Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
clock_gettime(CLOCK_REALTIME,&atime2);
cuda->shared_data.cuda_timings.pair_xtype_conversion+=
atime2.tv_sec-atime1.tv_sec+1.0*(atime2.tv_nsec-atime1.tv_nsec)/1000000000;
force->pair->compute(eflag, vflag);
}
else
{
//calculate complete pair interactions
if(not cuda->shared_data.pair.cudable_force) cuda->downloadAll();
else
{
//regenerate data layout for force computations, its actually only needed for the ghost atoms
timespec atime1,atime2;
clock_gettime(CLOCK_REALTIME,&atime1);
Cuda_Pair_GenerateXType(&cuda->shared_data);
if(cuda->cu_v_radius)
Cuda_Pair_GenerateVRadius(&cuda->shared_data);
if(cuda->cu_omega_rmass)
Cuda_Pair_GenerateOmegaRmass(&cuda->shared_data);
clock_gettime(CLOCK_REALTIME,&atime2);
cuda->shared_data.cuda_timings.pair_xtype_conversion+=
atime2.tv_sec-atime1.tv_sec+1.0*(atime2.tv_nsec-atime1.tv_nsec)/1000000000;
}
cuda->shared_data.comm.comm_phase=0;
force->pair->compute(eflag, vflag);
}
if(not cuda->shared_data.pair.cudable_force) cuda->uploadAll();
//wait for force calculation in case of not using overlap with bonded interactions
if(not cuda->shared_data.pair.collect_forces_later)
CudaWrapper_Sync();
timer->stamp(TIME_PAIR);
}
//calculate bonded interactions
if(atom->molecular)
{
cuda->cu_x->downloadAsync(2);
if(n_pre_force==0) Verlet::force_clear();
else cuda->cu_f->downloadAsync(2);
timer->stamp(TIME_PAIR);
test_atom(testatom,"pre bond force");
if(force->bond) force->bond->compute(eflag, vflag);
if(force->angle) force->angle->compute(eflag, vflag);
if(force->dihedral) force->dihedral->compute(eflag, vflag);
if(force->improper) force->improper->compute(eflag, vflag);
timer->stamp(TIME_BOND);
}
//collect forces in case pair force and bonded interactions were overlapped, and either no KSPACE or a GPU KSPACE style is used
if(cuda->shared_data.pair.collect_forces_later&&cuda->shared_data.pair.cudable_force&&(not (force->kspace&&(not cuda->shared_data.pppm.cudable_force))))
{
clock_gettime(CLOCK_REALTIME,&starttime);
cuda->cu_f->uploadAsync(2);
test_atom(testatom,"post molecular force");
if(eflag) cuda->cu_eng_vdwl->upload();
if(eflag) cuda->cu_eng_coul->upload();
if(vflag) cuda->cu_virial->upload();
Cuda_Pair_CollectForces(&cuda->shared_data,eflag,vflag);
if(eflag) cuda->cu_eng_vdwl->download();
if(eflag) cuda->cu_eng_coul->download();
if(vflag) cuda->cu_virial->download();
timer->stamp(TIME_PAIR);
clock_gettime(CLOCK_REALTIME,&endtime);
cuda->shared_data.cuda_timings.pair_force_collection+=
endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
}
//compute kspace force
if(force->kspace)
{
if((not cuda->shared_data.pppm.cudable_force) && (not cuda->shared_data.pair.collect_forces_later))
cuda->downloadAll();
if((not cuda->shared_data.pppm.cudable_force) && (cuda->shared_data.pair.collect_forces_later) && (not atom->molecular))
{
cuda->cu_x->downloadAsync(2);
if(n_pre_force==0) Verlet::force_clear();
else cuda->cu_f->downloadAsync(2);
timer->stamp(TIME_PAIR);
}
force->kspace->compute(eflag,vflag);
if((not cuda->shared_data.pppm.cudable_force) && (not cuda->shared_data.pair.collect_forces_later))
cuda->uploadAll();
timer->stamp(TIME_KSPACE);
}
//collect forces in case pair forces and kspace was overlaped
if(cuda->shared_data.pair.collect_forces_later&&cuda->shared_data.pair.cudable_force&&((force->kspace&&(not cuda->shared_data.pppm.cudable_force))))
{
cuda->cu_f->uploadAsync(2);
clock_gettime(CLOCK_REALTIME,&starttime);
if(eflag) cuda->cu_eng_vdwl->upload();
if(eflag) cuda->cu_eng_coul->upload();
if(vflag) cuda->cu_virial->upload();
Cuda_Pair_CollectForces(&cuda->shared_data,eflag,vflag);
if(eflag) cuda->cu_eng_vdwl->download();
if(eflag) cuda->cu_eng_coul->download();
if(vflag) cuda->cu_virial->download();
timer->stamp(TIME_PAIR);
clock_gettime(CLOCK_REALTIME,&endtime);
cuda->shared_data.cuda_timings.pair_force_collection+=
endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000;
}
//send forces on ghost atoms back to other GPU: THIS SHOULD NEVER HAPPEN
if(force->newton)
{
comm->reverse_comm();
timer->stamp(TIME_COMM);
}
test_atom(testatom,"post force");
// force modifications, final time integration, diagnostics
if(n_post_force) modify->post_force(vflag);
test_atom(testatom,"pre final");
modify->final_integrate();
test_atom(testatom,"post final");
if(n_end_of_step) modify->end_of_step();
// all output
test_atom(testatom,"pre output");
if(ntimestep == output->next)
{
if(not output->thermo->cudable)
cuda->downloadAll();
timer->stamp();
output->write(ntimestep);
timer->stamp(TIME_OUTPUT);
}
test_atom(testatom,"post output");
if(cuda->shared_data.atom.update_nlocal>0)
cuda->shared_data.atom.update_nlocal--;
if(cuda->shared_data.atom.update_nmax>0)
cuda->shared_data.atom.update_nmax--;
if(cuda->shared_data.atom.update_neigh>0)
cuda->shared_data.atom.update_neigh--;
if(cuda->shared_data.domain.update>0)
cuda->shared_data.domain.update--;
if(cuda->shared_data.buffer_new>0)
cuda->shared_data.buffer_new--;
cuda->shared_data.atom.reneigh_flag=0;
}
cuda->downloadAll();
cuda->downloadAllNeighborLists();
cuda->shared_data.atom.update_nlocal=1;
cuda->shared_data.atom.update_nmax=1;
cuda->shared_data.atom.update_neigh=1;
cuda->shared_data.buffer_new=1;
cuda->shared_data.domain.update=1;
cuda->oncpu = true;
cuda->finished_run = true;
}
/* ----------------------------------------------------------------------
clear force on own & ghost atoms
setup and clear other arrays as needed
------------------------------------------------------------------------- */
void VerletCuda::force_clear()
{
cuda->cu_f->memset_device(0);
if(cuda->cu_torque) cuda->cu_torque->memset_device(0);
return;
//The rest should not be necessary
int i;
for(i=0;i<atom->nlocal;i++)
{
atom->f[i][0]=0.0;
atom->f[i][1]=0.0;
atom->f[i][2]=0.0;
}
// clear force on all particles
// if either newton flag is set, also include ghosts
if (neighbor->includegroup == 0) {
int nall;
if (force->newton) nall = atom->nlocal + atom->nghost;
else nall = atom->nlocal;
if (torqueflag) {
double **torque = atom->torque;
for (i = 0; i < nall; i++) {
torque[i][0] = 0.0;
torque[i][1] = 0.0;
torque[i][2] = 0.0;
}
}
// neighbor includegroup flag is set
// clear force only on initial nfirst particles
// if either newton flag is set, also include ghosts
} else {
int nall = atom->nfirst;
if (torqueflag) {
double **torque = atom->torque;
for (i = 0; i < nall; i++) {
torque[i][0] = 0.0;
torque[i][1] = 0.0;
torque[i][2] = 0.0;
}
}
if (force->newton) {
nall = atom->nlocal + atom->nghost;
if (torqueflag) {
double **torque = atom->torque;
for (i = atom->nlocal; i < nall; i++) {
torque[i][0] = 0.0;
torque[i][1] = 0.0;
torque[i][2] = 0.0;
}
}
}
}
}
void VerletCuda::test_atom(int aatom, char* string) //printing properties of one atom for test purposes
{
if(not dotestatom) return;
bool check=false;
if(cuda->finished_setup) cuda->downloadAll();
for(int i=0;i<atom->nlocal+atom->nghost;i++)
{
if((atom->tag[i]==aatom)&&(i<atom->nlocal))
{
printf("%i # CUDA %s: %i %i %e %e %e %i ",comm->me,string,update->ntimestep,atom->tag[i],atom->x[i][0],atom->v[i][0],atom->f[i][0],i);
if(atom->molecular && (i<atom->nlocal))
{
printf(" // %i %i %i ",atom->num_bond[i],atom->num_angle[i],atom->num_dihedral[i]);
for(int k=0;k<atom->num_bond[i];k++)
printf("// %i %i ",atom->bond_type[i][k],atom->bond_atom[i][k]);
}
printf("\n");
}
if(i<atom->nlocal)
{
if((atom->v[i][0]<-100||atom->v[i][0]>100)||
(atom->v[i][1]<-100||atom->v[i][1]>100)||
(atom->v[i][2]<-100||atom->v[i][2]>100)||
(atom->v[i][0]!=atom->v[i][0])||
(atom->v[i][1]!=atom->v[i][1])||
(atom->v[i][2]!=atom->v[i][2]))
{printf("%i # CUDA %s velocity: %i %e %e %e %i\n",comm->me,string,atom->tag[i],atom->x[i][0],atom->v[i][0],atom->f[i][0],i); check=true;}
if((atom->f[i][0]<-10000||atom->f[i][0]>10000)||
(atom->f[i][1]<-10000||atom->f[i][1]>10000)||
(atom->f[i][2]<-10000||atom->f[i][2]>10000)||
(atom->f[i][0]!=atom->f[i][0])||
(atom->f[i][1]!=atom->f[i][1])||
(atom->f[i][2]!=atom->f[i][2]))
{printf("%i # CUDA %s force: %i %e %e %e %i\n",comm->me,string,atom->tag[i],atom->x[i][0],atom->v[i][0],atom->f[i][0],i); check=true;}
if(atom->tag[i]<=0)
printf("%i # CUDA %s tag: %i %e %e %e %i\n",comm->me,string,atom->tag[i],atom->x[i][0],atom->v[i][0],atom->f[i][0],i);
}
}
if(check) exit(0);
}

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