/* ---------------------------------------------------------------------- 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 #include #include #ifdef _LMP_INTEL_OFFLOAD #ifndef INTEL_OFFLOAD_NOAFFINITY #include #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]); _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; #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; 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++; } // 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; } // 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 (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(lmp); else if (_precision_mode == PREC_MODE_MIXED) _mixed_buffers = new IntelBuffers(lmp); else _double_buffers = new IntelBuffers(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; return mask; } /* ---------------------------------------------------------------------- */ void FixIntel::init() { #ifdef _LMP_INTEL_OFFLOAD output_timing_data(); #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."); neighbor->fix_intel = (void *)this; 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(); } /* ---------------------------------------------------------------------- */ 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."); } /* ---------------------------------------------------------------------- */ void FixIntel::pair_init_check() { #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; } if (update->whichflag == 2 && _offload_balance != 0.0) { if (_offload_balance == 1.0 && _offload_noghost == 0) _sync_at_pair = 1; else _sync_at_pair = 2; } else { _sync_at_pair = 0; if (strstr(update->integrate_style,"intel") == 0) error->all(FLERR, "Specified run_style does not support the Intel package."); } #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 } // Clear buffers used for pair style char kmode[80]; if (_precision_mode == PREC_MODE_SINGLE) { strcpy(kmode, "single"); get_single_buffers()->free_all_nbor_buffers(); } else if (_precision_mode == PREC_MODE_MIXED) { strcpy(kmode, "mixed"); get_mixed_buffers()->free_all_nbor_buffers(); } else { strcpy(kmode, "double"); get_double_buffers()->free_all_nbor_buffers(); } #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); fprintf(screen, "----------------------------------------------------------\n"); } } } /* ---------------------------------------------------------------------- */ 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::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 } /* ---------------------------------------------------------------------- */ 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::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=cpu,core,socket | 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) \ in(buf1:length(pragma_size) alloc_if(1) free_if(0)) \ signal(&sig1) {} #pragma offload_wait target(mic:0) wait(&sig1) #pragma offload target (mic:0) \ out(buf1:length(pragma_size) alloc_if(0) free_if(1)) \ signal(&sig2) {} #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