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lammps/src/USER-INTEL/fix_intel.cpp
Steve Plimpton c9c2ae6c61 new neighbor list changes
2016-09-07 13:42:58 -06:00

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: W. Michael Brown (Intel)
Anupama Kurpad (Intel) - Host Affinitization
------------------------------------------------------------------------- */
#include "comm.h"
#include "error.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "pair.h"
#include "pair_hybrid.h"
#include "pair_hybrid_overlay.h"
#include "timer.h"
#include "universe.h"
#include "update.h"
#include "fix_intel.h"
#include <string.h>
#include <stdlib.h>
#include <stdio.h>
#ifdef _LMP_INTEL_OFFLOAD
#ifndef INTEL_OFFLOAD_NOAFFINITY
#include <unistd.h>
#endif
#endif
#include "suffix.h"
using namespace LAMMPS_NS;
using namespace FixConst;
#ifdef __INTEL_OFFLOAD
#ifndef _LMP_INTEL_OFFLOAD
#warning "Not building Intel package with Xeon Phi offload support."
#endif
#endif
enum{NSQ,BIN,MULTI};
/* ---------------------------------------------------------------------- */
FixIntel::FixIntel(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR,"Illegal package intel command");
int ncops = force->inumeric(FLERR,arg[3]);
_nbor_pack_width = 1;
_precision_mode = PREC_MODE_MIXED;
_offload_balance = 1.0;
_overflow_flag[LMP_OVERFLOW] = 0;
_off_overflow_flag[LMP_OVERFLOW] = 0;
_offload_affinity_balanced = 0;
_offload_threads = 0;
_offload_tpc = 4;
_force_array_s = 0;
_force_array_m = 0;
_force_array_d = 0;
_ev_array_s = 0;
_ev_array_d = 0;
#ifdef _LMP_INTEL_OFFLOAD
if (ncops < 0) error->all(FLERR,"Illegal package intel command");
_offload_affinity_set = 0;
_off_force_array_s = 0;
_off_force_array_m = 0;
_off_force_array_d = 0;
_off_ev_array_s = 0;
_off_ev_array_d = 0;
_balance_fixed = 0.0;
_cop = 0;
#endif
// optional keywords
int nomp = 0, no_affinity = 0;
_allow_separate_buffers = 1;
_offload_ghost = -1;
_lrt = 0;
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"omp") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal package intel command");
nomp = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"mode") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal package intel command");
if (strcmp(arg[iarg+1],"single") == 0)
_precision_mode = PREC_MODE_SINGLE;
else if (strcmp(arg[iarg+1],"mixed") == 0)
_precision_mode = PREC_MODE_MIXED;
else if (strcmp(arg[iarg+1],"double") == 0)
_precision_mode = PREC_MODE_DOUBLE;
else error->all(FLERR,"Illegal package intel command");
iarg += 2;
} else if (strcmp(arg[iarg],"balance") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal package intel command");
_offload_balance = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg], "ghost") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal package intel command");
if (strcmp(arg[iarg+1],"yes") == 0) _offload_ghost = 1;
else if (strcmp(arg[iarg+1],"no") == 0) _offload_ghost = 0;
else error->all(FLERR,"Illegal package intel command");
iarg += 2;
} else if (strcmp(arg[iarg], "tpc") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal package intel command");
_offload_tpc = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"tptask") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal package intel command");
_offload_threads = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"no_affinity") == 0) {
no_affinity = 1;
iarg++;
} else if (strcmp(arg[iarg], "lrt") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal package intel command");
if (strcmp(arg[iarg+1],"yes") == 0) _lrt = 1;
else if (strcmp(arg[iarg+1],"no") == 0) _lrt = 0;
else error->all(FLERR,"Illegal package intel command");
iarg += 2;
}
// undocumented options
else if (strcmp(arg[iarg],"offload_affinity_balanced") == 0) {
_offload_affinity_balanced = 1;
iarg++;
} else if (strcmp(arg[iarg],"buffers") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal package intel command");
_allow_separate_buffers = atoi(arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal package intel command");
}
// if ncops is zero, just run on the cpu
if (ncops < 1) {
ncops = -1;
_offload_balance = 0.0;
}
// if using LRT mode, create the integrate style
if (_lrt) {
char *str;
str = (char *) "verlet/lrt/intel";
update->create_integrate(1,&str,0);
}
// error check
if (_offload_balance > 1.0 || _offload_threads < 0 ||
_offload_tpc <= 0 || _offload_tpc > 4 || nomp < 0)
error->all(FLERR,"Illegal package intel command");
#ifdef _LMP_INTEL_OFFLOAD
_ncops = ncops;
if (_offload_balance != 0.0) {
_real_space_comm = MPI_COMM_WORLD;
if (no_affinity == 0)
if (set_host_affinity(nomp) != 0)
error->all(FLERR,"Could not set host affinity for offload tasks");
}
int max_offload_threads = 0, offload_cores = 0;
if (_offload_balance != 0.0) {
#pragma offload target(mic:_cop) mandatory \
out(max_offload_threads,offload_cores)
{
offload_cores = omp_get_num_procs();
omp_set_num_threads(offload_cores);
max_offload_threads = omp_get_max_threads();
}
_max_offload_threads = max_offload_threads;
_offload_cores = offload_cores;
if (_offload_threads == 0) _offload_threads = offload_cores;
}
#endif
// set OpenMP threads
// nomp is user setting, default = 0
#if defined(_OPENMP)
#if defined(__INTEL_COMPILER)
kmp_set_blocktime(0);
#endif
if (nomp != 0) {
omp_set_num_threads(nomp);
comm->nthreads = nomp;
} else {
int nthreads;
#pragma omp parallel default(none) shared(nthreads)
nthreads = omp_get_num_threads();
comm->nthreads = nthreads;
}
#endif
// set offload params
#ifdef _LMP_INTEL_OFFLOAD
if (_offload_balance < 0.0) {
_balance_neighbor = 0.9;
_balance_pair = 0.9;
} else {
_balance_neighbor = _offload_balance;
_balance_pair = _offload_balance;
}
_tscreen = screen;
zero_timers();
_setup_time_cleared = false;
_timers_allocated = false;
#else
_offload_balance = 0.0;
#endif
// set precision
if (_precision_mode == PREC_MODE_SINGLE)
_single_buffers = new IntelBuffers<float,float>(lmp);
else if (_precision_mode == PREC_MODE_MIXED)
_mixed_buffers = new IntelBuffers<float,double>(lmp);
else
_double_buffers = new IntelBuffers<double,double>(lmp);
}
/* ---------------------------------------------------------------------- */
FixIntel::~FixIntel()
{
#ifdef _LMP_INTEL_OFFLOAD
output_timing_data();
if (_timers_allocated) {
double *time1 = off_watch_pair();
double *time2 = off_watch_neighbor();
int *overflow = get_off_overflow_flag();
if (_offload_balance != 0.0 && time1 != NULL && time2 != NULL &&
overflow != NULL) {
#pragma offload_transfer target(mic:_cop) \
nocopy(time1,time2,overflow:alloc_if(0) free_if(1))
}
}
#endif
if (_precision_mode == PREC_MODE_SINGLE)
delete _single_buffers;
else if (_precision_mode == PREC_MODE_MIXED)
delete _mixed_buffers;
else
delete _double_buffers;
}
/* ---------------------------------------------------------------------- */
int FixIntel::setmask()
{
int mask = 0;
mask |= PRE_REVERSE;
#ifdef _LMP_INTEL_OFFLOAD
mask |= POST_FORCE;
mask |= MIN_POST_FORCE;
#endif
return mask;
}
/* ---------------------------------------------------------------------- */
void FixIntel::init()
{
#ifdef _LMP_INTEL_OFFLOAD
output_timing_data();
_sync_mode = 0;
if (offload_balance() != 0.0) {
if (offload_noghost() || force->newton_pair == 0)
_sync_mode = 2;
else
_sync_mode = 1;
if (update->whichflag == 2) _sync_mode = 1;
}
#endif
int nstyles = 0;
if (force->pair_match("hybrid", 1) != NULL) {
PairHybrid *hybrid = (PairHybrid *) force->pair;
for (int i = 0; i < hybrid->nstyles; i++)
if (strstr(hybrid->keywords[i], "/intel") != NULL)
nstyles++;
} else if (force->pair_match("hybrid/overlay", 1) != NULL) {
PairHybridOverlay *hybrid = (PairHybridOverlay *) force->pair;
for (int i = 0; i < hybrid->nstyles; i++)
if (strstr(hybrid->keywords[i], "/intel") != NULL)
nstyles++;
else
force->pair->no_virial_fdotr_compute = 1;
}
if (nstyles > 1)
error->all(FLERR,
"Currently, cannot use more than one intel style with hybrid.");
check_neighbor_intel();
if (_precision_mode == PREC_MODE_SINGLE)
_single_buffers->zero_ev();
else if (_precision_mode == PREC_MODE_MIXED)
_mixed_buffers->zero_ev();
else
_double_buffers->zero_ev();
_need_reduce = 0;
}
/* ---------------------------------------------------------------------- */
void FixIntel::setup(int vflag)
{
if (neighbor->style != BIN)
error->all(FLERR,
"Currently, neighbor style BIN must be used with Intel package.");
if (neighbor->exclude_setting() != 0)
error->all(FLERR,
"Currently, cannot use neigh_modify exclude with Intel package.");
if (vflag_atom)
error->all(FLERR,
"Cannot currently get per-atom virials with Intel package.");
#ifdef _LMP_INTEL_OFFLOAD
post_force(vflag);
#endif
}
/* ---------------------------------------------------------------------- */
void FixIntel::pair_init_check(const bool cdmessage)
{
#ifdef INTEL_VMASK
atom->sortfreq = 1;
if (neighbor->binsizeflag && atom->userbinsize <= 0.0)
atom->userbinsize = neighbor->binsize_user;
#endif
_nbor_pack_width = 1;
#ifdef _LMP_INTEL_OFFLOAD
if (_offload_balance != 0.0) atom->sortfreq = 1;
if (force->newton_pair == 0)
_offload_noghost = 0;
else if (_offload_ghost == 0)
_offload_noghost = 1;
set_offload_affinity();
if (!_timers_allocated) {
double *time1 = off_watch_pair();
double *time2 = off_watch_neighbor();
int *overflow = get_off_overflow_flag();
if (_offload_balance !=0.0 && time1 != NULL && time2 != NULL &&
overflow != NULL) {
#pragma offload_transfer target(mic:_cop) \
nocopy(time1,time2:length(1) alloc_if(1) free_if(0)) \
in(overflow:length(5) alloc_if(1) free_if(0))
}
_timers_allocated = true;
}
#endif
_nthreads = comm->nthreads;
if (_offload_balance != 0.0 && comm->me == 0) {
#ifndef __INTEL_COMPILER_BUILD_DATE
error->warning(FLERR, "Unknown Intel Compiler Version\n");
#else
if (__INTEL_COMPILER_BUILD_DATE != 20131008 &&
__INTEL_COMPILER_BUILD_DATE < 20141023)
error->warning(FLERR, "Unsupported Intel Compiler.");
#endif
#if !defined(__INTEL_COMPILER)
error->warning(FLERR, "Unsupported Intel Compiler.");
#endif
}
int need_tag = 0;
if (atom->molecular) need_tag = 1;
// Clear buffers used for pair style
char kmode[80];
if (_precision_mode == PREC_MODE_SINGLE) {
strcpy(kmode, "single");
get_single_buffers()->need_tag(need_tag);
} else if (_precision_mode == PREC_MODE_MIXED) {
strcpy(kmode, "mixed");
get_mixed_buffers()->need_tag(need_tag);
} else {
strcpy(kmode, "double");
get_double_buffers()->need_tag(need_tag);
}
#ifdef _LMP_INTEL_OFFLOAD
set_offload_affinity();
#endif
if (comm->me == 0) {
if (screen) {
fprintf(screen,
"----------------------------------------------------------\n");
if (_offload_balance != 0.0) {
fprintf(screen,"Using Intel Coprocessor with %d threads per core, ",
_offload_tpc);
fprintf(screen,"%d threads per task\n",_offload_threads);
} else {
fprintf(screen,"Using Intel Package without Coprocessor.\n");
}
fprintf(screen,"Precision: %s\n",kmode);
if (cdmessage) {
#ifdef LMP_USE_AVXCD
fprintf(screen,"AVX512 CD Optimizations: Enabled\n");
#else
fprintf(screen,"AVX512 CD Optimizations: Disabled\n");
#endif
}
fprintf(screen,
"----------------------------------------------------------\n");
}
}
}
/* ---------------------------------------------------------------------- */
void FixIntel::bond_init_check()
{
if (_offload_balance != 0.0 && atom->molecular &&
force->newton_pair != force->newton_bond)
error->all(FLERR,
"USER-INTEL package requires same setting for newton bond and non-bond.");
int intel_pair = 0;
if (force->pair_match("/intel", 0) != NULL)
intel_pair = 1;
else if (force->pair_match("hybrid", 1) != NULL) {
PairHybrid *hybrid = (PairHybrid *) force->pair;
for (int i = 0; i < hybrid->nstyles; i++)
if (strstr(hybrid->keywords[i], "/intel") != NULL)
intel_pair = 1;
} else if (force->pair_match("hybrid/overlay", 1) != NULL) {
PairHybridOverlay *hybrid = (PairHybridOverlay *) force->pair;
for (int i = 0; i < hybrid->nstyles; i++)
if (strstr(hybrid->keywords[i], "/intel") != NULL)
intel_pair = 1;
}
if (intel_pair == 0)
error->all(FLERR, "Intel styles for bond/angle/dihedral/improper "
"require intel pair style.");
}
/* ---------------------------------------------------------------------- */
void FixIntel::kspace_init_check()
{
int intel_pair = 0;
if (force->pair_match("/intel", 0) != NULL)
intel_pair = 1;
else if (force->pair_match("hybrid", 1) != NULL) {
PairHybrid *hybrid = (PairHybrid *) force->pair;
for (int i = 0; i < hybrid->nstyles; i++)
if (strstr(hybrid->keywords[i], "/intel") != NULL)
intel_pair = 1;
} else if (force->pair_match("hybrid/overlay", 1) != NULL) {
PairHybridOverlay *hybrid = (PairHybridOverlay *) force->pair;
for (int i = 0; i < hybrid->nstyles; i++)
if (strstr(hybrid->keywords[i], "/intel") != NULL)
intel_pair = 1;
}
if (intel_pair == 0)
error->all(FLERR, "Intel styles for kspace require intel pair style.");
}
/* ---------------------------------------------------------------------- */
void FixIntel::check_neighbor_intel()
{
#ifdef _LMP_INTEL_OFFLOAD
_full_host_list = 0;
#endif
const int nrequest = neighbor->nrequest;
for (int i = 0; i < nrequest; ++i) {
#ifdef _LMP_INTEL_OFFLOAD
if (_offload_balance != 0.0 && neighbor->requests[i]->intel == 0) {
_full_host_list = 1;
_offload_noghost = 0;
}
#endif
if (neighbor->requests[i]->skip)
error->all(FLERR, "Cannot yet use hybrid styles with Intel package.");
}
}
/* ---------------------------------------------------------------------- */
void FixIntel::pre_reverse(int eflag, int vflag)
{
if (_force_array_m != 0) {
if (_need_reduce) {
reduce_results(_force_array_m);
_need_reduce = 0;
}
add_results(_force_array_m, _ev_array_d, _results_eatom, _results_vatom, 0);
_force_array_m = 0;
} else if (_force_array_d != 0) {
if (_need_reduce) {
reduce_results(_force_array_d);
_need_reduce = 0;
}
add_results(_force_array_d, _ev_array_d, _results_eatom, _results_vatom, 0);
_force_array_d = 0;
} else if (_force_array_s != 0) {
if (_need_reduce) {
reduce_results(_force_array_s);
_need_reduce = 0;
}
add_results(_force_array_s, _ev_array_s, _results_eatom, _results_vatom, 0);
_force_array_s = 0;
}
#ifdef _LMP_INTEL_OFFLOAD
if (_sync_mode == 1) sync_coprocessor();
#endif
}
/* ---------------------------------------------------------------------- */
template <class ft>
void FixIntel::reduce_results(ft * _noalias const f_start)
{
int o_range, f_stride;
if (force->newton_pair)
o_range = atom->nlocal + atom->nghost;
else
o_range = atom->nlocal;
IP_PRE_get_stride(f_stride, o_range, sizeof(ft), lmp->atom->torque);
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(o_range, f_stride)
#endif
{
int iifrom, iito, tid;
IP_PRE_omp_range_id_align(iifrom, iito, tid, o_range, _nthreads,
sizeof(ft));
int t_off = f_stride;
if (_results_eatom) {
for (int t = 1; t < _nthreads; t++) {
_use_simd_pragma("vector nontemporal")
_use_simd_pragma("novector")
for (int n = iifrom; n < iito; n++) {
f_start[n].x += f_start[n + t_off].x;
f_start[n].y += f_start[n + t_off].y;
f_start[n].z += f_start[n + t_off].z;
f_start[n].w += f_start[n + t_off].w;
}
t_off += f_stride;
}
} else {
for (int t = 1; t < _nthreads; t++) {
_use_simd_pragma("vector nontemporal")
_use_simd_pragma("novector")
for (int n = iifrom; n < iito; n++) {
f_start[n].x += f_start[n + t_off].x;
f_start[n].y += f_start[n + t_off].y;
f_start[n].z += f_start[n + t_off].z;
}
t_off += f_stride;
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixIntel::sync_coprocessor()
{
#ifdef _LMP_INTEL_OFFLOAD
if (_offload_balance != 0.0) {
if (_off_force_array_m != 0) {
add_off_results(_off_force_array_m, _off_ev_array_d);
_off_force_array_m = 0;
} else if (_off_force_array_d != 0) {
add_off_results(_off_force_array_d, _off_ev_array_d);
_off_force_array_d = 0;
} else if (_off_force_array_s != 0) {
add_off_results(_off_force_array_s, _off_ev_array_s);
_off_force_array_s = 0;
}
}
#endif
}
/* ---------------------------------------------------------------------- */
template <class ft, class acc_t>
void FixIntel::add_results(const ft * _noalias const f_in,
const acc_t * _noalias const ev_global,
const int eatom, const int vatom,
const int offload) {
start_watch(TIME_PACK);
int f_length;
#ifdef _LMP_INTEL_OFFLOAD
if (_separate_buffers) {
if (offload) {
add_oresults(f_in, ev_global, eatom, vatom, 0, _offload_nlocal);
if (force->newton_pair) {
const acc_t * _noalias const enull = 0;
int offset = _offload_nlocal;
if (atom->torque) offset *= 2;
add_oresults(f_in + offset, enull, eatom, vatom,
_offload_min_ghost, _offload_nghost);
}
} else {
add_oresults(f_in, ev_global, eatom, vatom,
_host_min_local, _host_used_local);
if (force->newton_pair) {
const acc_t * _noalias const enull = 0;
int offset = _host_used_local;
if (atom->torque) offset *= 2;
add_oresults(f_in + offset, enull, eatom,
vatom, _host_min_ghost, _host_used_ghost);
}
}
stop_watch(TIME_PACK);
return;
}
if (force->newton_pair && (_offload_noghost == 0 || offload == 0))
f_length = atom->nlocal + atom->nghost;
else
f_length = atom->nlocal;
#else
if (force->newton_pair)
f_length = atom->nlocal + atom->nghost;
else
f_length = atom->nlocal;
#endif
add_oresults(f_in, ev_global, eatom, vatom, 0, f_length);
stop_watch(TIME_PACK);
}
/* ---------------------------------------------------------------------- */
template <class ft, class acc_t>
void FixIntel::add_oresults(const ft * _noalias const f_in,
const acc_t * _noalias const ev_global,
const int eatom, const int vatom,
const int out_offset, const int nall) {
lmp_ft * _noalias const f = (lmp_ft *) lmp->atom->f[0] + out_offset;
if (atom->torque) {
if (f_in[1].w)
if (f_in[1].w == 1)
error->all(FLERR,"Bad matrix inversion in mldivide3");
else
error->all(FLERR,
"Sphere particles not yet supported for gayberne/intel");
}
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
{
#if defined(_OPENMP)
const int tid = omp_get_thread_num();
#else
const int tid = 0;
#endif
int ifrom, ito;
IP_PRE_omp_range_align(ifrom, ito, tid, nall, _nthreads, sizeof(acc_t));
if (atom->torque) {
int ii = ifrom * 2;
lmp_ft * _noalias const tor = (lmp_ft *) lmp->atom->torque[0] +
out_offset;
if (eatom) {
double * _noalias const lmp_eatom = force->pair->eatom + out_offset;
#if defined(LMP_SIMD_COMPILER)
#pragma novector
#endif
for (int i = ifrom; i < ito; i++) {
f[i].x += f_in[ii].x;
f[i].y += f_in[ii].y;
f[i].z += f_in[ii].z;
lmp_eatom[i] += f_in[ii].w;
tor[i].x += f_in[ii+1].x;
tor[i].y += f_in[ii+1].y;
tor[i].z += f_in[ii+1].z;
ii += 2;
}
} else {
#if defined(LMP_SIMD_COMPILER)
#pragma novector
#endif
for (int i = ifrom; i < ito; i++) {
f[i].x += f_in[ii].x;
f[i].y += f_in[ii].y;
f[i].z += f_in[ii].z;
tor[i].x += f_in[ii+1].x;
tor[i].y += f_in[ii+1].y;
tor[i].z += f_in[ii+1].z;
ii += 2;
}
}
} else {
if (eatom) {
double * _noalias const lmp_eatom = force->pair->eatom + out_offset;
#if defined(LMP_SIMD_COMPILER)
#pragma novector
#endif
for (int i = ifrom; i < ito; i++) {
f[i].x += f_in[i].x;
f[i].y += f_in[i].y;
f[i].z += f_in[i].z;
lmp_eatom[i] += f_in[i].w;
}
} else {
#if defined(LMP_SIMD_COMPILER)
#pragma novector
#endif
for (int i = ifrom; i < ito; i++) {
f[i].x += f_in[i].x;
f[i].y += f_in[i].y;
f[i].z += f_in[i].z;
}
}
}
}
if (ev_global != NULL) {
force->pair->eng_vdwl += ev_global[0];
force->pair->eng_coul += ev_global[1];
force->pair->virial[0] += ev_global[2];
force->pair->virial[1] += ev_global[3];
force->pair->virial[2] += ev_global[4];
force->pair->virial[3] += ev_global[5];
force->pair->virial[4] += ev_global[6];
force->pair->virial[5] += ev_global[7];
}
}
/* ---------------------------------------------------------------------- */
double FixIntel::memory_usage()
{
double bytes;
if (_precision_mode == PREC_MODE_SINGLE)
bytes = _single_buffers->memory_usage(_nthreads);
else if (_precision_mode == PREC_MODE_MIXED)
bytes = _mixed_buffers->memory_usage(_nthreads);
else
bytes = _double_buffers->memory_usage(_nthreads);
return bytes;
}
/* ---------------------------------------------------------------------- */
#ifdef _LMP_INTEL_OFFLOAD
/* ---------------------------------------------------------------------- */
void FixIntel::post_force(int vflag)
{
if (_sync_mode == 2) sync_coprocessor();
}
/* ---------------------------------------------------------------------- */
template <class ft, class acc_t>
void FixIntel::add_off_results(const ft * _noalias const f_in,
const acc_t * _noalias const ev_global) {
if (_offload_balance < 0.0)
_balance_other_time = MPI_Wtime() - _balance_other_time;
start_watch(TIME_OFFLOAD_WAIT);
#ifdef _LMP_INTEL_OFFLOAD
if (neighbor->ago == 0) {
#pragma offload_wait target(mic:_cop) wait(atom->tag,f_in)
} else {
#pragma offload_wait target(mic:_cop) wait(f_in)
}
#endif
double wait_time = stop_watch(TIME_OFFLOAD_WAIT);
int nlocal = atom->nlocal;
if (neighbor->ago == 0) {
if (_off_overflow_flag[LMP_OVERFLOW])
error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
_offload_nlocal = _off_overflow_flag[LMP_LOCAL_MAX] + 1;
_offload_min_ghost = _off_overflow_flag[LMP_GHOST_MIN];
_offload_nghost = _off_overflow_flag[LMP_GHOST_MAX] + 1 -
_offload_min_ghost;
if (_offload_nghost < 0) _offload_nghost = 0;
_offload_nall = _offload_nlocal + _offload_nghost;
_offload_nlocal;
}
// Load balance?
if (_offload_balance < 0.0) {
if (neighbor->ago == 0)
_balance_pair = _balance_neighbor;
double mic_time;
mic_time = *_stopwatch_offload_pair;
if (_balance_pair_time + _balance_other_time < mic_time) {
double ft = _balance_pair_time + _balance_other_time + wait_time -
mic_time;
_balance_fixed = (1.0 - INTEL_LB_MEAN_WEIGHT) * _balance_fixed +
INTEL_LB_MEAN_WEIGHT * ft;
}
double ctps = _balance_pair_time / (1.0-_balance_pair);
double otps = mic_time / _balance_pair;
double new_balance = (ctps + _balance_other_time - _balance_fixed) /
(otps + ctps);
_balance_neighbor = (1.0 - INTEL_LB_MEAN_WEIGHT) *_balance_neighbor +
INTEL_LB_MEAN_WEIGHT * new_balance;
}
#ifdef TIME_BALANCE
start_watch(TIME_IMBALANCE);
MPI_Barrier(_real_space_comm);
stop_watch(TIME_IMBALANCE);
#endif
acc_timers();
if (atom->torque)
if (f_in[1].w < 0.0)
error->all(FLERR, "Bad matrix inversion in mldivide3");
add_results(f_in, ev_global, _off_results_eatom, _off_results_vatom, 1);
}
/* ---------------------------------------------------------------------- */
void FixIntel::output_timing_data() {
if (_im_real_space_task == 0 || _offload_affinity_set == 0) return;
double timer_total = 0.0;
int size, rank;
double timers[NUM_ITIMERS];
MPI_Comm_size(_real_space_comm, &size);
MPI_Comm_rank(_real_space_comm, &rank);
MPI_Allreduce(&_timers, &timers, NUM_ITIMERS, MPI_DOUBLE, MPI_SUM,
_real_space_comm);
for (int i=0; i < NUM_ITIMERS; i++) {
timers[i] /= size;
timer_total += timers[i];
}
#ifdef TIME_BALANCE
double timers_min[NUM_ITIMERS], timers_max[NUM_ITIMERS];
MPI_Allreduce(&_timers, &timers_max, NUM_ITIMERS, MPI_DOUBLE, MPI_MAX,
_real_space_comm);
MPI_Allreduce(&_timers, &timers_min, NUM_ITIMERS, MPI_DOUBLE, MPI_MIN,
_real_space_comm);
#endif
if (timer_total > 0.0) {
double balance_out[2], balance_in[2];
balance_out[0] = _balance_pair;
balance_out[1] = _balance_neighbor;
MPI_Reduce(balance_out, balance_in, 2, MPI_DOUBLE, MPI_SUM,
0, _real_space_comm);
balance_in[0] /= size;
balance_in[1] /= size;
if (rank == 0 && _tscreen) {
fprintf(_tscreen, "\n------------------------------------------------\n");
fprintf(_tscreen, " Offload Timing Data\n");
fprintf(_tscreen, "------------------------------------------------\n");
fprintf(_tscreen, " Data Pack/Cast Seconds %f\n",
timers[TIME_PACK]);
if (_offload_balance != 0.0) {
fprintf(_tscreen, " Host Neighbor Seconds %f\n",
timers[TIME_HOST_NEIGHBOR]);
fprintf(_tscreen, " Host Pair Seconds %f\n",
timers[TIME_HOST_PAIR]);
fprintf(_tscreen, " Offload Neighbor Seconds %f\n",
timers[TIME_OFFLOAD_NEIGHBOR]);
fprintf(_tscreen, " Offload Pair Seconds %f\n",
timers[TIME_OFFLOAD_PAIR]);
fprintf(_tscreen, " Offload Wait Seconds %f\n",
timers[TIME_OFFLOAD_WAIT]);
fprintf(_tscreen, " Offload Latency Seconds %f\n",
timers[TIME_OFFLOAD_LATENCY]);
fprintf(_tscreen, " Offload Neighbor Balance %f\n",
balance_in[1]);
fprintf(_tscreen, " Offload Pair Balance %f\n",
balance_in[0]);
fprintf(_tscreen, " Offload Ghost Atoms ");
if (_offload_noghost) fprintf(_tscreen,"No\n");
else fprintf(_tscreen,"Yes\n");
#ifdef TIME_BALANCE
fprintf(_tscreen, " Offload Imbalance Seconds %f\n",
timers[TIME_IMBALANCE]);
fprintf(_tscreen, " Offload Min/Max Seconds ");
for (int i = 0; i < NUM_ITIMERS; i++)
fprintf(_tscreen, "[%f, %f] ",timers_min[i],timers_max[i]);
fprintf(_tscreen, "\n");
#endif
double ht = timers[TIME_HOST_NEIGHBOR] + timers[TIME_HOST_PAIR] +
timers[TIME_OFFLOAD_WAIT];
double ct = timers[TIME_OFFLOAD_NEIGHBOR] +
timers[TIME_OFFLOAD_PAIR];
double tt = MAX(ht,ct);
if (timers[TIME_OFFLOAD_LATENCY] / tt > 0.07 && _separate_coi == 0)
error->warning(FLERR,
"Leaving a core free can improve performance for offload");
}
fprintf(_tscreen, "------------------------------------------------\n");
}
zero_timers();
_setup_time_cleared = false;
}
}
/* ---------------------------------------------------------------------- */
int FixIntel::get_ppn(int &node_rank) {
int nprocs;
int rank;
MPI_Comm_size(_real_space_comm, &nprocs);
MPI_Comm_rank(_real_space_comm, &rank);
int name_length;
char node_name[MPI_MAX_PROCESSOR_NAME];
MPI_Get_processor_name(node_name,&name_length);
node_name[name_length] = '\0';
char *node_names = new char[MPI_MAX_PROCESSOR_NAME*nprocs];
MPI_Allgather(node_name, MPI_MAX_PROCESSOR_NAME, MPI_CHAR, node_names,
MPI_MAX_PROCESSOR_NAME, MPI_CHAR, _real_space_comm);
int ppn = 0;
node_rank = 0;
for (int i = 0; i < nprocs; i++) {
if (strcmp(node_name, node_names + i * MPI_MAX_PROCESSOR_NAME) == 0) {
ppn++;
if (i < rank)
node_rank++;
}
}
return ppn;
}
/* ---------------------------------------------------------------------- */
void FixIntel::set_offload_affinity()
{
_separate_buffers = 0;
if (_allow_separate_buffers)
if (_offload_balance != 0.0 && _offload_balance < 1.0)
_separate_buffers = 1;
_im_real_space_task = 1;
if (strncmp(update->integrate_style,"verlet/split",12) == 0) {
_real_space_comm = world;
if (universe->iworld != 0) {
_im_real_space_task = 0;
return;
}
} else
_real_space_comm = universe->uworld;
if (_offload_balance == 0.0) _cop = -1;
if (_offload_balance == 0.0 || _offload_affinity_set == 1)
return;
_offload_affinity_set = 1;
int node_rank;
int ppn = get_ppn(node_rank);
if (ppn % _ncops != 0)
error->all(FLERR, "MPI tasks per node must be multiple of offload_cards");
ppn = ppn / _ncops;
_cop = node_rank / ppn;
node_rank = node_rank % ppn;
int max_threads_per_task = _offload_cores / 4 * _offload_tpc / ppn;
if (_offload_threads > max_threads_per_task)
_offload_threads = max_threads_per_task;
if (_offload_threads > _max_offload_threads)
_offload_threads = _max_offload_threads;
int offload_threads = _offload_threads;
int offload_tpc = _offload_tpc;
int offload_affinity_balanced = _offload_affinity_balanced;
#pragma offload target(mic:_cop) mandatory \
in(node_rank,offload_threads,offload_tpc,offload_affinity_balanced)
{
omp_set_num_threads(offload_threads);
#pragma omp parallel
{
int tnum = omp_get_thread_num();
kmp_affinity_mask_t mask;
kmp_create_affinity_mask(&mask);
int proc;
if (offload_affinity_balanced) {
proc = offload_threads * node_rank + tnum;
proc = proc * 4 - (proc / 60) * 240 + proc / 60 + 1;
} else {
proc = offload_threads * node_rank + tnum;
proc += (proc / 4) * (4 - offload_tpc) + 1;
}
kmp_set_affinity_mask_proc(proc, &mask);
if (kmp_set_affinity(&mask) != 0)
printf("Could not set affinity on rank %d thread %d to %d\n",
node_rank, tnum, proc);
}
}
if (_precision_mode == PREC_MODE_SINGLE)
_single_buffers->set_off_params(offload_threads, _cop, _separate_buffers);
else if (_precision_mode == PREC_MODE_MIXED)
_mixed_buffers->set_off_params(offload_threads, _cop, _separate_buffers);
else
_double_buffers->set_off_params(offload_threads, _cop, _separate_buffers);
}
/* ---------------------------------------------------------------------- */
int FixIntel::set_host_affinity(const int nomp)
{
#ifndef INTEL_OFFLOAD_NOAFFINITY
_separate_coi = 1;
int rank = comm->me;
int node_rank;
int ppn = get_ppn(node_rank);
int cop = node_rank / (ppn / _ncops);
// Get a sorted list of logical cores
int proc_list[INTEL_MAX_HOST_CORE_COUNT];
int ncores;
FILE *p;
char cmd[512];
char readbuf[INTEL_MAX_HOST_CORE_COUNT*5];
sprintf(cmd, "lscpu -p | grep -v '#' |"
"sort -t, -k 3,3n -k 2,2n | awk -F, '{print $1}'");
p = popen(cmd, "r");
if (p == NULL) return -1;
ncores = 0;
while(fgets(readbuf, 512, p)) {
proc_list[ncores] = atoi(readbuf);
ncores++;
}
pclose(p);
// Sanity checks for core list
if (ncores < 2) return -1;
int nzero = 0;
for (int i = 0; i < ncores; i++) {
if (proc_list[i] == 0) nzero++;
if (proc_list[i] < 0 || proc_list[i] >= ncores) return -1;
}
if (nzero > 1) return -1;
// Determine the OpenMP/MPI configuration
char *estring;
int nthreads = nomp;
if (nthreads == 0) {
estring = getenv("OMP_NUM_THREADS");
if (estring != NULL) {
nthreads = atoi(estring);
if (nthreads < 2) nthreads = 1;
} else
nthreads = 1;
}
// Determine how many logical cores for COI and MPI tasks
int coi_cores = 0, mpi_cores;
int subscription = nthreads * ppn;
if (subscription > ncores) {
if (rank == 0)
error->warning(FLERR,
"More MPI tasks/OpenMP threads than available cores");
return 0;
}
if (subscription == ncores)
_separate_coi = 0;
if (subscription > ncores / 2) {
coi_cores = ncores - subscription;
if (coi_cores > INTEL_MAX_COI_CORES) coi_cores = INTEL_MAX_COI_CORES;
}
mpi_cores = (ncores - coi_cores) / ppn;
// Get ids of all LWPs that COI spawned and affinitize
int lwp = 0, plwp = 0, nlwp = 0, mlwp = 0, fail = 0;
cpu_set_t cpuset;
pid_t pid = getpid();
if (coi_cores) {
sprintf(cmd, "ps -Lp %d -o lwp | awk ' (NR > 2) {print}'", pid);
p = popen(cmd, "r");
if (p == NULL) return -1;
while(fgets(readbuf, 512, p)) {
lwp = atoi(readbuf);
int first = coi_cores + node_rank * mpi_cores;
CPU_ZERO(&cpuset);
for (int i = first; i < first + mpi_cores; i++)
CPU_SET(proc_list[i], &cpuset);
if (sched_setaffinity(lwp, sizeof(cpu_set_t), &cpuset)) {
fail = 1;
break;
}
plwp++;
}
pclose(p);
// Do async offload to create COI threads
int sig1, sig2;
float *buf1;
int pragma_size = 1024;
buf1 = (float*) malloc(sizeof(float)*pragma_size);
#pragma offload target (mic:0) mandatory \
in(buf1:length(pragma_size) alloc_if(1) free_if(0)) \
signal(&sig1)
{ buf1[0] = 0.0; }
#pragma offload_wait target(mic:0) wait(&sig1)
#pragma offload target (mic:0) mandatory \
out(buf1:length(pragma_size) alloc_if(0) free_if(1)) \
signal(&sig2)
{ buf1[0] = 1.0; }
#pragma offload_wait target(mic:0) wait(&sig2)
free(buf1);
p = popen(cmd, "r");
if (p == NULL) return -1;
while(fgets(readbuf, 512, p)) {
lwp = atoi(readbuf);
nlwp++;
if (nlwp <= plwp) continue;
CPU_ZERO(&cpuset);
for(int i=0; i<coi_cores; i++)
CPU_SET(proc_list[i], &cpuset);
if (sched_setaffinity(lwp, sizeof(cpu_set_t), &cpuset)) {
fail = 1;
break;
}
}
pclose(p);
nlwp -= plwp;
// Get stats on the number of LWPs per process
MPI_Reduce(&nlwp, &mlwp, 1, MPI_INT, MPI_MAX, 0, MPI_COMM_WORLD);
}
if (screen && rank == 0) {
if (coi_cores)
fprintf(screen,"Intel Package: Affinitizing %d Offload Threads to %d Cores\n",
mlwp, coi_cores);
fprintf(screen,"Intel Package: Affinitizing MPI Tasks to %d Cores Each\n",mpi_cores);
}
if (fail) return -1;
// Affinitize MPI Ranks
CPU_ZERO(&cpuset);
int first = coi_cores + node_rank * mpi_cores;
for (int i = first; i < first+mpi_cores; i++)
CPU_SET(proc_list[i], &cpuset);
if (sched_setaffinity(pid, sizeof(cpu_set_t), &cpuset))
return -1;
#endif
return 0;
}
#endif
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