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Implement stubbed version for GROMACS

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2022-11-15 16:01:13 +01:00
parent bc06220aeb
commit 56d9613028
1 changed files with 154 additions and 115 deletions
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269
gromacs/main-stub.c
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@ -6,6 +6,7 @@
*/ */
#include <stdio.h> #include <stdio.h>
#include <string.h> #include <string.h>
#include <math.h>
//--- //---
#include <likwid-marker.h> #include <likwid-marker.h>
//--- //---
@ -23,24 +24,29 @@
#define HLINE "----------------------------------------------------------------------------\n" #define HLINE "----------------------------------------------------------------------------\n"
#define LATTICE_DISTANCE 10.0 extern double computeForceLJ_ref(Parameter*, Atom*, Neighbor*, Stats*);
#define NEIGH_DISTANCE 1.0 extern double computeForceLJ_4xn(Parameter*, Atom*, Neighbor*, Stats*);
extern double computeForceLJ_2xnn(Parameter*, Atom*, Neighbor*, Stats*);
extern double computeForceLJ(Parameter*, Atom*, Neighbor*, Stats*);
extern double computeForceEam(Eam*, 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) { void init(Parameter *param) {
param->input_file = NULL; param->input_file = NULL;
param->force_field = FF_LJ;
param->epsilon = 1.0; param->epsilon = 1.0;
param->sigma6 = 1.0; param->sigma6 = 1.0;
param->rho = 0.8442; param->rho = 0.8442;
param->ntypes = 4; param->ntypes = 4;
param->ntimes = 200; param->ntimes = 200;
param->nx = 4; param->nx = 1;
param->ny = 4; param->ny = 1;
param->nz = 2; param->nz = 1;
param->lattice = LATTICE_DISTANCE; param->lattice = 1.0;
param->cutforce = 5.0; param->cutforce = 1000000.0;
param->cutneigh = param->cutforce; param->cutneigh = param->cutforce;
param->mass = 1.0; param->mass = 1.0;
// Unused // Unused
@ -48,7 +54,7 @@ void init(Parameter *param) {
param->dtforce = 0.5 * param->dt; param->dtforce = 0.5 * param->dt;
param->nstat = 100; param->nstat = 100;
param->temp = 1.44; param->temp = 1.44;
param->every = 20; param->reneigh_every = 20;
param->proc_freq = 2.4; param->proc_freq = 2.4;
param->eam_file = NULL; param->eam_file = NULL;
} }
@ -58,13 +64,53 @@ void init(Parameter *param) {
// Do not show debug messages // Do not show debug messages
//#define DEBUG(msg) //#define DEBUG(msg)
#define ADD_ATOM(x, y, z, vx, vy, vz) atom_x(atom->Nlocal) = base_x + x * NEIGH_DISTANCE; \
atom_y(atom->Nlocal) = base_y + y * NEIGH_DISTANCE; \ void createNeighbors(Atom *atom, Neighbor *neighbor, int pattern, int nneighs, int nreps) {
atom_z(atom->Nlocal) = base_z + z * NEIGH_DISTANCE; \ const int maxneighs = nneighs * nreps;
atom->vx[atom->Nlocal] = vy; \ const int jfac = MAX(1, CLUSTER_N / CLUSTER_M);
atom->vy[atom->Nlocal] = vy; \ const int ncj = atom->Nclusters_local / jfac;
atom->vz[atom->Nlocal] = vz; \ neighbor->numneigh = (int*) malloc(atom->Nclusters_max * sizeof(int));
atom->Nlocal++ 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[]) { int main(int argc, const char *argv[]) {
Eam eam; Eam eam;
@ -73,7 +119,12 @@ int main(int argc, const char *argv[]) {
Neighbor neighbor; Neighbor neighbor;
Stats stats; Stats stats;
Parameter param; Parameter param;
int atoms_per_unit_cell = 8; 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; int csv = 0;
LIKWID_MARKER_INIT; LIKWID_MARKER_INIT;
@ -81,64 +132,67 @@ int main(int argc, const char *argv[]) {
DEBUG("Initializing parameters...\n"); DEBUG("Initializing parameters...\n");
init(&param); init(&param);
for(int i = 0; i < argc; i++) for(int i = 0; i < argc; i++) {
{ if((strcmp(argv[i], "-f") == 0)) {
if((strcmp(argv[i], "-f") == 0))
{
if((param.force_field = str2ff(argv[++i])) < 0) { if((param.force_field = str2ff(argv[++i])) < 0) {
fprintf(stderr, "Invalid force field!\n"); fprintf(stderr, "Invalid force field!\n");
exit(-1); exit(-1);
} }
continue; continue;
} }
if((strcmp(argv[i], "-e") == 0)) 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]); param.eam_file = strdup(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "-n") == 0) || (strcmp(argv[i], "--nsteps") == 0)) if((strcmp(argv[i], "-n") == 0) || (strcmp(argv[i], "--nsteps") == 0)) {
{
param.ntimes = atoi(argv[++i]); param.ntimes = atoi(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "-nx") == 0)) if((strcmp(argv[i], "-ni") == 0)) {
{ niclusters = atoi(argv[++i]);
param.nx = atoi(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "-ny") == 0)) if((strcmp(argv[i], "-na") == 0)) {
{ iclusters_natoms = atoi(argv[++i]);
param.ny = atoi(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "-nz") == 0)) if((strcmp(argv[i], "-nn") == 0)) {
{ nneighs = atoi(argv[++i]);
param.nz = atoi(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "-na") == 0)) if((strcmp(argv[i], "-nr") == 0)) {
{ nreps = atoi(argv[++i]);
atoms_per_unit_cell = atoi(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "--freq") == 0)) if((strcmp(argv[i], "--freq") == 0)) {
{
param.proc_freq = atof(argv[++i]); param.proc_freq = atof(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "--csv") == 0)) if((strcmp(argv[i], "--csv") == 0)) {
{
csv = 1; csv = 1;
continue; continue;
} }
if((strcmp(argv[i], "-h") == 0) || (strcmp(argv[i], "--help") == 0)) if((strcmp(argv[i], "-h") == 0) || (strcmp(argv[i], "--help") == 0)) {
{
printf("MD Bench: A minimalistic re-implementation of miniMD\n"); printf("MD Bench: A minimalistic re-implementation of miniMD\n");
printf(HLINE); printf(HLINE);
printf("-f <string>: force field (lj or eam), default lj\n"); printf("-f <string>: force field (lj or eam), default lj\n");
printf("-n / --nsteps <int>: set number of timesteps for simulation\n"); printf("-p <string>: pattern for data accesses (seq, fix or rand)\n");
printf("-nx/-ny/-nz <int>: set linear dimension of systembox in x/y/z direction\n"); printf("-n / --nsteps <int>: number of timesteps for simulation\n");
printf("-na <int>: set number of atoms per unit cell\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("--freq <real>: set CPU frequency (GHz) and display average cycles per atom and neighbors\n");
printf("--csv: set output as CSV style\n"); printf("--csv: set output as CSV style\n");
printf(HLINE); printf(HLINE);
@ -146,16 +200,15 @@ int main(int argc, const char *argv[]) {
} }
} }
if(pattern_str == NULL) {
pattern_str = strdup("seq\0");
}
if(param.force_field == FF_EAM) { if(param.force_field == FF_EAM) {
DEBUG("Initializing EAM parameters...\n"); DEBUG("Initializing EAM parameters...\n");
initEam(&eam, &param); initEam(&eam, &param);
} }
param.xprd = param.nx * LATTICE_DISTANCE;
param.yprd = param.ny * LATTICE_DISTANCE;
param.zprd = param.nz * LATTICE_DISTANCE;
DEBUG("Initializing atoms...\n"); DEBUG("Initializing atoms...\n");
initAtom(atom); initAtom(atom);
initStats(&stats); initStats(&stats);
@ -173,97 +226,83 @@ int main(int argc, const char *argv[]) {
} }
DEBUG("Creating atoms...\n"); DEBUG("Creating atoms...\n");
for(int i = 0; i < param.nx; ++i) { while(atom->Nmax < niclusters * iclusters_natoms) {
for(int j = 0; j < param.ny; ++j) { growAtom(atom);
for(int k = 0; k < param.nz; ++k) { }
int added_atoms = 0;
int fac_x = 1;
int fac_y = 1;
int fac_z = 1;
int fmod = 0;
MD_FLOAT base_x = i * LATTICE_DISTANCE;
MD_FLOAT base_y = j * LATTICE_DISTANCE;
MD_FLOAT base_z = k * LATTICE_DISTANCE;
MD_FLOAT vx = 0.0;
MD_FLOAT vy = 0.0;
MD_FLOAT vz = 0.0;
while(atom->Nlocal > atom->Nmax - atoms_per_unit_cell) { while(atom->Nclusters_max < niclusters) {
growAtom(atom); growClusters(atom);
} }
while(fac_x * fac_y * fac_z < atoms_per_unit_cell) { for(int ci = 0; ci < niclusters; ++ci) {
if(fmod == 0) { fac_x *= 2; } int ci_sca_base = CI_SCALAR_BASE_INDEX(ci);
if(fmod == 1) { fac_y *= 2; } int ci_vec_base = CI_VECTOR_BASE_INDEX(ci);
if(fmod == 2) { fac_z *= 2; } MD_FLOAT *ci_x = &atom->cl_x[ci_vec_base];
fmod = (fmod + 1) % 3; MD_FLOAT *ci_v = &atom->cl_v[ci_vec_base];
} int *ci_type = &atom->cl_type[ci_sca_base];
MD_FLOAT offset_x = (fac_x > 1) ? 1.0 / (fac_x - 1) : (int)fac_x; for(int cii = 0; cii < iclusters_natoms; ++cii) {
MD_FLOAT offset_y = (fac_y > 1) ? 1.0 / (fac_y - 1) : (int)fac_y; ci_x[CL_X_OFFSET + cii] = (MD_FLOAT)(ci * iclusters_natoms + cii) * 0.00001;
MD_FLOAT offset_z = (fac_z > 1) ? 1.0 / (fac_z - 1) : (int)fac_z; ci_x[CL_Y_OFFSET + cii] = (MD_FLOAT)(ci * iclusters_natoms + cii) * 0.00001;
for(int ii = 0; ii < fac_x; ++ii) { ci_x[CL_Z_OFFSET + cii] = (MD_FLOAT)(ci * iclusters_natoms + cii) * 0.00001;
for(int jj = 0; jj < fac_y; ++jj) { ci_v[CL_X_OFFSET + cii] = 0.0;
for(int kk = 0; kk < fac_z; ++kk) { ci_v[CL_Y_OFFSET + cii] = 0.0;
if(added_atoms < atoms_per_unit_cell) { ci_v[CL_Z_OFFSET + cii] = 0.0;
atom->type[atom->Nlocal] = rand() % atom->ntypes; ci_type[cii] = rand() % atom->ntypes;
ADD_ATOM(ii * offset_x, jj * offset_y, kk * offset_z, vx, vy, vz); atom->Nlocal++;
added_atoms++;
}
}
}
}
}
} }
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_atom_volume = (double)(atom->Nlocal * 3 * sizeof(MD_FLOAT));
const double estim_neighbors_volume = (double)(atom->Nlocal * (atoms_per_unit_cell - 1 + 2) * sizeof(int)); 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); const double estim_volume = (double)(atom->Nlocal * 6 * sizeof(MD_FLOAT) + estim_neighbors_volume);
if(!csv) { if(!csv) {
printf("Pattern: %s\n", pattern_str);
printf("Number of timesteps: %d\n", param.ntimes); printf("Number of timesteps: %d\n", param.ntimes);
printf("System size (unit cells): %dx%dx%d\n", param.nx, param.ny, param.nz); printf("Number of i-clusters: %d\n", niclusters);
printf("Atoms per unit cell: %d\n", atoms_per_unit_cell); printf("Number of atoms per i-cluster: %d\n", iclusters_natoms);
printf("Total number of atoms: %d\n", atom->Nlocal); 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 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 atom data volume (kB): %.4f\n", estim_atom_volume / 1000.0);
printf("Estimated neighborlist data volume (kB): %.4f\n", estim_neighbors_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"); DEBUG("Initializing neighbor lists...\n");
initNeighbor(&neighbor, &param); initNeighbor(&neighbor, &param);
DEBUG("Setting up neighbor lists...\n"); DEBUG("Creating neighbor lists...\n");
setupNeighbor(&param); createNeighbors(atom, &neighbor, pattern, nneighs, nreps);
DEBUG("Building neighbor lists...\n");
buildNeighbor(atom, &neighbor);
DEBUG("Computing forces...\n"); DEBUG("Computing forces...\n");
if(param.force_field == FF_EAM) {
computeForceEam(&eam, &param, atom, &neighbor, &stats);
} else {
computeForceLJ(&param, atom, &neighbor, &stats);
}
double S, E; double T_accum = 0.0;
S = getTimeStamp();
for(int i = 0; i < param.ntimes; i++) { for(int i = 0; i < param.ntimes; i++) {
#if defined(MEM_TRACER) || defined(INDEX_TRACER)
#if defined(MEM_TRACER) || defined(INDEX_TRACER)
traceAddresses(&param, atom, &neighbor, i + 1); traceAddresses(&param, atom, &neighbor, i + 1);
#endif #endif
if(param.force_field == FF_EAM) { if(param.force_field == FF_EAM) {
computeForceEam(&eam, &param, atom, &neighbor, &stats); T_accum += computeForceEam(&eam, &param, atom, &neighbor, &stats);
} else { } else {
computeForceLJ(&param, atom, &neighbor, &stats); T_accum += computeForceLJ(&param, atom, &neighbor, &stats);
} }
} }
E = getTimeStamp();
double T_accum = E-S;
double freq_hz = param.proc_freq * 1.e9; double freq_hz = param.proc_freq * 1.e9;
const double atoms_updates_per_sec = (double)(atom->Nlocal) / T_accum * (double)(param.ntimes); 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_atom = T_accum / (double)(atom->Nlocal) / (double)(param.ntimes) * freq_hz;
const double cycles_per_neigh = cycles_per_atom / (double)(atoms_per_unit_cell - 1); const double cycles_per_neigh = cycles_per_atom / (double)(nneighs);
if(!csv) { if(!csv) {
printf("Total time: %.4f, Mega atom updates/s: %.4f\n", T_accum, atoms_updates_per_sec / 1.e6); printf("Total time: %.4f, Mega atom updates/s: %.4f\n", T_accum, atoms_updates_per_sec / 1.e6);
@ -271,14 +310,14 @@ int main(int argc, const char *argv[]) {
printf("Cycles per atom: %.4f, Cycles per neighbor: %.4f\n", cycles_per_atom, cycles_per_neigh); printf("Cycles per atom: %.4f, Cycles per neighbor: %.4f\n", cycles_per_atom, cycles_per_neigh);
} }
} else { } else {
printf("steps,unit cells,atoms/unit cell,total atoms,total vol.(kB),atoms vol.(kB),neigh vol.(kB),time(s),atom upds/s(M)"); 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) { if(param.proc_freq > 0.0) {
printf(",cy/atom,cy/neigh"); printf(",cy/atom,cy/neigh");
} }
printf("\n"); printf("\n");
printf("%d,%dx%dx%d,%d,%d,%.4f,%.4f,%.4f,%.4f,%.4f", printf("%d,%s,%d,%d,%d,%d,%.4f,%.4f,%.4f,%.4f,%.4f",
param.ntimes, param.nx, param.ny, param.nz, atoms_per_unit_cell, atom->Nlocal, 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); 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) { if(param.proc_freq > 0.0) {