From 56d9613028c94ed7589fd5f5780256c24ab522f5 Mon Sep 17 00:00:00 2001 From: Rafael Ravedutti Date: Tue, 15 Nov 2022 16:01:13 +0100 Subject: [PATCH] Implement stubbed version for GROMACS Signed-off-by: Rafael Ravedutti --- gromacs/main-stub.c | 269 +++++++++++++++++++++++++------------------- 1 file changed, 154 insertions(+), 115 deletions(-) diff --git a/gromacs/main-stub.c b/gromacs/main-stub.c index 5afa090..c868710 100644 --- a/gromacs/main-stub.c +++ b/gromacs/main-stub.c @@ -6,6 +6,7 @@ */ #include #include +#include //--- #include //--- @@ -23,24 +24,29 @@ #define HLINE "----------------------------------------------------------------------------\n" -#define LATTICE_DISTANCE 10.0 -#define NEIGH_DISTANCE 1.0 - -extern double computeForceLJ(Parameter*, Atom*, Neighbor*, Stats*); +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 = 4; - param->ny = 4; - param->nz = 2; - param->lattice = LATTICE_DISTANCE; - param->cutforce = 5.0; + 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; // Unused @@ -48,7 +54,7 @@ void init(Parameter *param) { param->dtforce = 0.5 * param->dt; param->nstat = 100; param->temp = 1.44; - param->every = 20; + param->reneigh_every = 20; param->proc_freq = 2.4; param->eam_file = NULL; } @@ -58,13 +64,53 @@ void init(Parameter *param) { // Do not show debug messages //#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; \ - atom_z(atom->Nlocal) = base_z + z * NEIGH_DISTANCE; \ - atom->vx[atom->Nlocal] = vy; \ - atom->vy[atom->Nlocal] = vy; \ - atom->vz[atom->Nlocal] = vz; \ - atom->Nlocal++ + +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; @@ -73,7 +119,12 @@ int main(int argc, const char *argv[]) { Neighbor neighbor; Stats stats; 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; LIKWID_MARKER_INIT; @@ -81,64 +132,67 @@ int main(int argc, const char *argv[]) { DEBUG("Initializing parameters...\n"); init(¶m); - for(int i = 0; i < argc; i++) - { - if((strcmp(argv[i], "-f") == 0)) - { + 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], "-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]); 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]); continue; } - if((strcmp(argv[i], "-nx") == 0)) - { - param.nx = atoi(argv[++i]); + if((strcmp(argv[i], "-ni") == 0)) { + niclusters = atoi(argv[++i]); continue; } - if((strcmp(argv[i], "-ny") == 0)) - { - param.ny = atoi(argv[++i]); + if((strcmp(argv[i], "-na") == 0)) { + iclusters_natoms = atoi(argv[++i]); continue; } - if((strcmp(argv[i], "-nz") == 0)) - { - param.nz = atoi(argv[++i]); + if((strcmp(argv[i], "-nn") == 0)) { + nneighs = atoi(argv[++i]); continue; } - if((strcmp(argv[i], "-na") == 0)) - { - atoms_per_unit_cell = atoi(argv[++i]); + if((strcmp(argv[i], "-nr") == 0)) { + nreps = atoi(argv[++i]); continue; } - if((strcmp(argv[i], "--freq") == 0)) - { + if((strcmp(argv[i], "--freq") == 0)) { param.proc_freq = atof(argv[++i]); continue; } - if((strcmp(argv[i], "--csv") == 0)) - { + if((strcmp(argv[i], "--csv") == 0)) { csv = 1; 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(HLINE); printf("-f : force field (lj or eam), default lj\n"); - printf("-n / --nsteps : set number of timesteps for simulation\n"); - printf("-nx/-ny/-nz : set linear dimension of systembox in x/y/z direction\n"); - printf("-na : set number of atoms per unit cell\n"); + printf("-p : pattern for data accesses (seq, fix or rand)\n"); + printf("-n / --nsteps : number of timesteps for simulation\n"); + printf("-ni : number of i-clusters (default 256)\n"); + printf("-na : number of atoms per i-cluster (default %d)\n", CLUSTER_M); + printf("-nn : number of j-cluster neighbors per i-cluster (default 9)\n"); + printf("-nr : number of times neighbor lists should be replicated (default 1)\n"); printf("--freq : set CPU frequency (GHz) and display average cycles per atom and neighbors\n"); printf("--csv: set output as CSV style\n"); 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) { DEBUG("Initializing EAM parameters...\n"); initEam(&eam, ¶m); } - param.xprd = param.nx * LATTICE_DISTANCE; - param.yprd = param.ny * LATTICE_DISTANCE; - param.zprd = param.nz * LATTICE_DISTANCE; - DEBUG("Initializing atoms...\n"); initAtom(atom); initStats(&stats); @@ -173,97 +226,83 @@ int main(int argc, const char *argv[]) { } DEBUG("Creating atoms...\n"); - for(int i = 0; i < param.nx; ++i) { - for(int j = 0; j < param.ny; ++j) { - 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->Nmax < niclusters * iclusters_natoms) { + growAtom(atom); + } - while(atom->Nlocal > atom->Nmax - atoms_per_unit_cell) { - growAtom(atom); - } + while(atom->Nclusters_max < niclusters) { + growClusters(atom); + } - while(fac_x * fac_y * fac_z < atoms_per_unit_cell) { - if(fmod == 0) { fac_x *= 2; } - if(fmod == 1) { fac_y *= 2; } - if(fmod == 2) { fac_z *= 2; } - fmod = (fmod + 1) % 3; - } + 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]; - MD_FLOAT offset_x = (fac_x > 1) ? 1.0 / (fac_x - 1) : (int)fac_x; - MD_FLOAT offset_y = (fac_y > 1) ? 1.0 / (fac_y - 1) : (int)fac_y; - MD_FLOAT offset_z = (fac_z > 1) ? 1.0 / (fac_z - 1) : (int)fac_z; - for(int ii = 0; ii < fac_x; ++ii) { - for(int jj = 0; jj < fac_y; ++jj) { - for(int kk = 0; kk < fac_z; ++kk) { - if(added_atoms < atoms_per_unit_cell) { - atom->type[atom->Nlocal] = rand() % atom->ntypes; - ADD_ATOM(ii * offset_x, jj * offset_y, kk * offset_z, vx, vy, vz); - added_atoms++; - } - } - } - } - } + 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 * (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); if(!csv) { + printf("Pattern: %s\n", pattern_str); printf("Number of timesteps: %d\n", param.ntimes); - printf("System size (unit cells): %dx%dx%d\n", param.nx, param.ny, param.nz); - printf("Atoms per unit cell: %d\n", atoms_per_unit_cell); - printf("Total number of atoms: %d\n", atom->Nlocal); + 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, ¶m); - DEBUG("Setting up neighbor lists...\n"); - setupNeighbor(¶m); - DEBUG("Building neighbor lists...\n"); - buildNeighbor(atom, &neighbor); + DEBUG("Creating neighbor lists...\n"); + createNeighbors(atom, &neighbor, pattern, nneighs, nreps); DEBUG("Computing forces...\n"); - if(param.force_field == FF_EAM) { - computeForceEam(&eam, ¶m, atom, &neighbor, &stats); - } else { - computeForceLJ(¶m, atom, &neighbor, &stats); - } - double S, E; - S = getTimeStamp(); + double T_accum = 0.0; for(int i = 0; i < param.ntimes; i++) { - -#if defined(MEM_TRACER) || defined(INDEX_TRACER) + #if defined(MEM_TRACER) || defined(INDEX_TRACER) traceAddresses(¶m, atom, &neighbor, i + 1); -#endif + #endif if(param.force_field == FF_EAM) { - computeForceEam(&eam, ¶m, atom, &neighbor, &stats); + T_accum += computeForceEam(&eam, ¶m, atom, &neighbor, &stats); } else { - computeForceLJ(¶m, atom, &neighbor, &stats); + T_accum += computeForceLJ(¶m, atom, &neighbor, &stats); } } - E = getTimeStamp(); - double T_accum = E-S; + 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)(atoms_per_unit_cell - 1); + 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); @@ -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); } } 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) { printf(",cy/atom,cy/neigh"); } printf("\n"); - printf("%d,%dx%dx%d,%d,%d,%.4f,%.4f,%.4f,%.4f,%.4f", - param.ntimes, param.nx, param.ny, param.nz, atoms_per_unit_cell, atom->Nlocal, + 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) {