MD-Bench/gromacs/main-stub.c
Rafael Ravedutti 15d43dcce5 Explicitly set half_neigh to zero on stubbed versions
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-12-14 17:21:09 +01:00

338 lines
12 KiB
C

/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.
*/
#include <stdio.h>
#include <string.h>
#include <math.h>
//---
#include <likwid-marker.h>
//---
#include <timing.h>
#include <allocate.h>
#include <neighbor.h>
#include <parameter.h>
#include <atom.h>
#include <stats.h>
#include <thermo.h>
#include <eam.h>
#include <pbc.h>
#include <timers.h>
#include <util.h>
#define HLINE "----------------------------------------------------------------------------\n"
extern double computeForceLJ_ref(Parameter*, Atom*, Neighbor*, Stats*);
extern double computeForceLJ_4xn(Parameter*, Atom*, Neighbor*, Stats*);
extern double computeForceLJ_2xnn(Parameter*, Atom*, Neighbor*, Stats*);
extern double computeForceEam(Eam*, Parameter*, Atom*, Neighbor*, Stats*);
// Patterns
#define P_SEQ 0
#define P_FIX 1
#define P_RAND 2
void init(Parameter *param) {
param->input_file = NULL;
param->force_field = FF_LJ;
param->epsilon = 1.0;
param->sigma6 = 1.0;
param->rho = 0.8442;
param->ntypes = 4;
param->ntimes = 200;
param->nx = 1;
param->ny = 1;
param->nz = 1;
param->lattice = 1.0;
param->cutforce = 1000000.0;
param->cutneigh = param->cutforce;
param->mass = 1.0;
param->half_neigh = 0;
// Unused
param->dt = 0.005;
param->dtforce = 0.5 * param->dt;
param->nstat = 100;
param->temp = 1.44;
param->reneigh_every = 20;
param->proc_freq = 2.4;
param->eam_file = NULL;
}
// Show debug messages
#define DEBUG(msg) printf(msg)
// Do not show debug messages
//#define DEBUG(msg)
void createNeighbors(Atom *atom, Neighbor *neighbor, int pattern, int nneighs, int nreps) {
const int maxneighs = nneighs * nreps;
const int jfac = MAX(1, CLUSTER_N / CLUSTER_M);
const int ncj = atom->Nclusters_local / jfac;
neighbor->numneigh = (int*) malloc(atom->Nclusters_max * sizeof(int));
neighbor->neighbors = (int*) malloc(atom->Nclusters_max * maxneighs * sizeof(int));
if(pattern == P_RAND && ncj <= nneighs) {
fprintf(stderr, "Error: P_RAND: Number of j-clusters should be higher than number of j-cluster neighbors per i-cluster!\n");
exit(-1);
}
for(int ci = 0; ci < atom->Nclusters_local; ci++) {
int *neighptr = &(neighbor->neighbors[ci * neighbor->maxneighs]);
int j = (pattern == P_SEQ) ? CJ0_FROM_CI(ci) : 0;
int m = (pattern == P_SEQ) ? ncj : nneighs;
int k = 0;
for(int k = 0; k < nneighs; k++) {
if(pattern == P_RAND) {
int found = 0;
do {
int cj = rand() % ncj;
neighptr[k] = cj;
found = 0;
for(int l = 0; l < k; l++) {
if(neighptr[l] == cj) {
found = 1;
}
}
} while(found == 1);
} else {
neighptr[k] = j;
j = (j + 1) % m;
}
}
for(int r = 1; r < nreps; r++) {
for(int k = 0; k < nneighs; k++) {
neighptr[r * nneighs + k] = neighptr[k];
}
}
neighbor->numneigh[ci] = nneighs * nreps;
}
}
int main(int argc, const char *argv[]) {
Eam eam;
Atom atom_data;
Atom *atom = (Atom *)(&atom_data);
Neighbor neighbor;
Stats stats;
Parameter param;
char *pattern_str = NULL;
int pattern = P_SEQ;
int niclusters = 256; // Number of local i-clusters
int iclusters_natoms = CLUSTER_M; // Number of valid atoms within i-clusters
int nneighs = 9; // Number of j-cluster neighbors per i-cluster
int nreps = 1;
int csv = 0;
LIKWID_MARKER_INIT;
LIKWID_MARKER_REGISTER("force");
DEBUG("Initializing parameters...\n");
init(&param);
for(int i = 0; i < argc; i++) {
if((strcmp(argv[i], "-f") == 0)) {
if((param.force_field = str2ff(argv[++i])) < 0) {
fprintf(stderr, "Invalid force field!\n");
exit(-1);
}
continue;
}
if((strcmp(argv[i], "-p") == 0)) {
pattern_str = strdup(argv[++i]);
if(strncmp(pattern_str, "seq", 3) == 0) { pattern = P_SEQ; }
else if(strncmp(pattern_str, "fix", 3) == 0) { pattern = P_FIX; }
else if(strncmp(pattern_str, "rand", 3) == 0) { pattern = P_RAND; }
else {
fprintf(stderr, "Invalid pattern!\n");
exit(-1);
}
continue;
}
if((strcmp(argv[i], "-e") == 0)) {
param.eam_file = strdup(argv[++i]);
continue;
}
if((strcmp(argv[i], "-n") == 0) || (strcmp(argv[i], "--nsteps") == 0)) {
param.ntimes = atoi(argv[++i]);
continue;
}
if((strcmp(argv[i], "-ni") == 0)) {
niclusters = atoi(argv[++i]);
continue;
}
if((strcmp(argv[i], "-na") == 0)) {
iclusters_natoms = atoi(argv[++i]);
continue;
}
if((strcmp(argv[i], "-nn") == 0)) {
nneighs = atoi(argv[++i]);
continue;
}
if((strcmp(argv[i], "-nr") == 0)) {
nreps = atoi(argv[++i]);
continue;
}
if((strcmp(argv[i], "--freq") == 0)) {
param.proc_freq = atof(argv[++i]);
continue;
}
if((strcmp(argv[i], "--csv") == 0)) {
csv = 1;
continue;
}
if((strcmp(argv[i], "-h") == 0) || (strcmp(argv[i], "--help") == 0)) {
printf("MD Bench: A minimalistic re-implementation of miniMD\n");
printf(HLINE);
printf("-f <string>: force field (lj or eam), default lj\n");
printf("-p <string>: pattern for data accesses (seq, fix or rand)\n");
printf("-n / --nsteps <int>: number of timesteps for simulation\n");
printf("-ni <int>: number of i-clusters (default 256)\n");
printf("-na <int>: number of atoms per i-cluster (default %d)\n", CLUSTER_M);
printf("-nn <int>: number of j-cluster neighbors per i-cluster (default 9)\n");
printf("-nr <int>: number of times neighbor lists should be replicated (default 1)\n");
printf("--freq <real>: set CPU frequency (GHz) and display average cycles per atom and neighbors\n");
printf("--csv: set output as CSV style\n");
printf(HLINE);
exit(EXIT_SUCCESS);
}
}
if(pattern_str == NULL) {
pattern_str = strdup("seq\0");
}
if(param.force_field == FF_EAM) {
DEBUG("Initializing EAM parameters...\n");
initEam(&eam, &param);
}
DEBUG("Initializing atoms...\n");
initAtom(atom);
initStats(&stats);
atom->ntypes = param.ntypes;
atom->epsilon = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
atom->sigma6 = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
atom->cutforcesq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
atom->cutneighsq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
for(int i = 0; i < atom->ntypes * atom->ntypes; i++) {
atom->epsilon[i] = param.epsilon;
atom->sigma6[i] = param.sigma6;
atom->cutneighsq[i] = param.cutneigh * param.cutneigh;
atom->cutforcesq[i] = param.cutforce * param.cutforce;
}
DEBUG("Creating atoms...\n");
while(atom->Nmax < niclusters * iclusters_natoms) {
growAtom(atom);
}
while(atom->Nclusters_max < niclusters) {
growClusters(atom);
}
for(int ci = 0; ci < niclusters; ++ci) {
int ci_sca_base = CI_SCALAR_BASE_INDEX(ci);
int ci_vec_base = CI_VECTOR_BASE_INDEX(ci);
MD_FLOAT *ci_x = &atom->cl_x[ci_vec_base];
MD_FLOAT *ci_v = &atom->cl_v[ci_vec_base];
int *ci_type = &atom->cl_type[ci_sca_base];
for(int cii = 0; cii < iclusters_natoms; ++cii) {
ci_x[CL_X_OFFSET + cii] = (MD_FLOAT)(ci * iclusters_natoms + cii) * 0.00001;
ci_x[CL_Y_OFFSET + cii] = (MD_FLOAT)(ci * iclusters_natoms + cii) * 0.00001;
ci_x[CL_Z_OFFSET + cii] = (MD_FLOAT)(ci * iclusters_natoms + cii) * 0.00001;
ci_v[CL_X_OFFSET + cii] = 0.0;
ci_v[CL_Y_OFFSET + cii] = 0.0;
ci_v[CL_Z_OFFSET + cii] = 0.0;
ci_type[cii] = rand() % atom->ntypes;
atom->Nlocal++;
}
for(int cii = iclusters_natoms; cii < CLUSTER_M; cii++) {
ci_x[CL_X_OFFSET + cii] = INFINITY;
ci_x[CL_Y_OFFSET + cii] = INFINITY;
ci_x[CL_Z_OFFSET + cii] = INFINITY;
}
atom->iclusters[ci].natoms = iclusters_natoms;
atom->Nclusters_local++;
}
const double estim_atom_volume = (double)(atom->Nlocal * 3 * sizeof(MD_FLOAT));
const double estim_neighbors_volume = (double)(atom->Nlocal * (nneighs + 2) * sizeof(int));
const double estim_volume = (double)(atom->Nlocal * 6 * sizeof(MD_FLOAT) + estim_neighbors_volume);
if(!csv) {
printf("Kernel: %s, MxN: %dx%d, Vector width: %d\n", KERNEL_NAME, CLUSTER_M, CLUSTER_N, VECTOR_WIDTH);
printf("Floating-point precision: %s\n", PRECISION_STRING);
printf("Pattern: %s\n", pattern_str);
printf("Number of timesteps: %d\n", param.ntimes);
printf("Number of i-clusters: %d\n", niclusters);
printf("Number of atoms per i-cluster: %d\n", iclusters_natoms);
printf("Number of j-cluster neighbors per i-cluster: %d\n", nneighs);
printf("Number of times to replicate neighbor lists: %d\n", nreps);
printf("Estimated total data volume (kB): %.4f\n", estim_volume / 1000.0);
printf("Estimated atom data volume (kB): %.4f\n", estim_atom_volume / 1000.0);
printf("Estimated neighborlist data volume (kB): %.4f\n", estim_neighbors_volume / 1000.0);
}
DEBUG("Defining j-clusters...\n");
defineJClusters(atom);
DEBUG("Initializing neighbor lists...\n");
initNeighbor(&neighbor, &param);
DEBUG("Creating neighbor lists...\n");
createNeighbors(atom, &neighbor, pattern, nneighs, nreps);
DEBUG("Computing forces...\n");
double T_accum = 0.0;
for(int i = 0; i < param.ntimes; i++) {
#if defined(MEM_TRACER) || defined(INDEX_TRACER)
traceAddresses(&param, atom, &neighbor, i + 1);
#endif
if(param.force_field == FF_EAM) {
T_accum += computeForceEam(&eam, &param, atom, &neighbor, &stats);
} else {
T_accum += computeForceLJ(&param, atom, &neighbor, &stats);
}
}
double freq_hz = param.proc_freq * 1.e9;
const double atoms_updates_per_sec = (double)(atom->Nlocal) / T_accum * (double)(param.ntimes);
const double cycles_per_atom = T_accum / (double)(atom->Nlocal) / (double)(param.ntimes) * freq_hz;
const double cycles_per_neigh = cycles_per_atom / (double)(nneighs);
if(!csv) {
printf("Total time: %.4f, Mega atom updates/s: %.4f\n", T_accum, atoms_updates_per_sec / 1.e6);
if(param.proc_freq > 0.0) {
printf("Cycles per atom: %.4f, Cycles per neighbor: %.4f\n", cycles_per_atom, cycles_per_neigh);
}
} else {
printf("steps,pattern,niclusters,iclusters_natoms,nneighs,nreps,total vol.(kB),atoms vol.(kB),neigh vol.(kB),time(s),atom upds/s(M)");
if(param.proc_freq > 0.0) {
printf(",cy/atom,cy/neigh");
}
printf("\n");
printf("%d,%s,%d,%d,%d,%d,%.4f,%.4f,%.4f,%.4f,%.4f",
param.ntimes, pattern_str, niclusters, iclusters_natoms, nneighs, nreps,
estim_volume / 1.e3, estim_atom_volume / 1.e3, estim_neighbors_volume / 1.e3, T_accum, atoms_updates_per_sec / 1.e6);
if(param.proc_freq > 0.0) {
printf(",%.4f,%.4f", cycles_per_atom, cycles_per_neigh);
}
printf("\n");
}
double timer[NUMTIMER];
timer[FORCE] = T_accum;
displayStatistics(atom, &param, &stats, timer);
LIKWID_MARKER_CLOSE;
return EXIT_SUCCESS;
}