moebiusband/MD-Bench
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge branch 'master' of github.com:RRZE-HPC/MD-Bench

Browse Source
This commit is contained in:
Jan Eitzinger
2022-03-10 16:30:40 +01:00
parent 6203cb12b6 cecb31d6a9
commit ba3a0524f6
36 changed files with 4143 additions and 174 deletions
Download Patch File Download Diff File Expand all files Collapse all files

103
lammps/atom.c
View File

@@ -161,7 +161,108 @@ void createAtom(Atom *atom, Parameter *param)
}
}
int readAtom(Atom* atom, Parameter* param)
int type_str2int(const char *type) {
if(strncmp(type, "Ar", 2) == 0) { return 0; } // Argon
fprintf(stderr, "Invalid atom type: %s\n", type);
exit(-1);
return -1;
}
int readAtom(Atom* atom, Parameter* param) {
int len = strlen(param->input_file);
if(strncmp(&param->input_file[len - 4], ".pdb", 4) == 0) { return readAtom_pdb(atom, param); }
if(strncmp(&param->input_file[len - 4], ".dmp", 4) == 0) { return readAtom_dmp(atom, param); }
fprintf(stderr, "Invalid input file extension: %s\nValid choices are: pdb, dmp\n", param->input_file);
exit(-1);
return -1;
}
int readAtom_pdb(Atom* atom, Parameter* param) {
FILE *fp = fopen(param->input_file, "r");
char line[MAXLINE];
int read_atoms = 0;
if(!fp) {
fprintf(stderr, "Could not open input file: %s\n", param->input_file);
exit(-1);
return -1;
}
while(!feof(fp)) {
fgets(line, MAXLINE, fp);
char *item = strtok(line, " ");
if(strncmp(item, "CRYST1", 6) == 0) {
param->xlo = 0.0;
param->xhi = atof(strtok(NULL, " "));
param->ylo = 0.0;
param->yhi = atof(strtok(NULL, " "));
param->zlo = 0.0;
param->zhi = atof(strtok(NULL, " "));
param->xprd = param->xhi - param->xlo;
param->yprd = param->yhi - param->ylo;
param->zprd = param->zhi - param->zlo;
// alpha, beta, gamma, sGroup, z
} else if(strncmp(item, "ATOM", 4) == 0) {
char *label;
int atom_id, comp_id;
MD_FLOAT occupancy, charge;
atom_id = atoi(strtok(NULL, " ")) - 1;
while(atom_id + 1 >= atom->Nmax) {
growAtom(atom);
}
atom->type[atom_id] = type_str2int(strtok(NULL, " "));
label = strtok(NULL, " ");
comp_id = atoi(strtok(NULL, " "));
atom_x(atom_id) = atof(strtok(NULL, " "));
atom_y(atom_id) = atof(strtok(NULL, " "));
atom_z(atom_id) = atof(strtok(NULL, " "));
atom->vx[atom_id] = 0.0;
atom->vy[atom_id] = 0.0;
atom->vz[atom_id] = 0.0;
occupancy = atof(strtok(NULL, " "));
charge = atof(strtok(NULL, " "));
atom->ntypes = MAX(atom->type[atom_id] + 1, atom->ntypes);
atom->Natoms++;
atom->Nlocal++;
read_atoms++;
} else if(strncmp(item, "HEADER", 6) == 0 ||
strncmp(item, "REMARK", 6) == 0 ||
strncmp(item, "MODEL", 5) == 0 ||
strncmp(item, "TER", 3) == 0 ||
strncmp(item, "ENDMDL", 6) == 0) {
// Do nothing
} else {
fprintf(stderr, "Invalid item: %s\n", item);
exit(-1);
return -1;
}
}
if(!read_atoms) {
fprintf(stderr, "Input error: No atoms read!\n");
exit(-1);
return -1;
}
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;
}
fprintf(stdout, "Read %d atoms from %s\n", read_atoms, param->input_file);
fclose(fp);
return read_atoms;
}
int readAtom_dmp(Atom* atom, Parameter* param)
{
FILE *fp = fopen(param->input_file, "r");
char line[MAXLINE];

5
lammps/force_lj.c
View File

@@ -87,6 +87,11 @@ double computeForceLJFullNeigh(Parameter *param, Atom *atom, Neighbor *neighbor,
fix += delx * force;
fiy += dely * force;
fiz += delz * force;
#ifdef USE_REFERENCE_VERSION
addStat(stats->atoms_within_cutoff, 1);
} else {
addStat(stats->atoms_outside_cutoff, 1);
#endif
}
}

2
lammps/includes/atom.h
View File

@@ -42,6 +42,8 @@ typedef struct {
extern void initAtom(Atom*);
extern void createAtom(Atom*, Parameter*);
extern int readAtom(Atom*, Parameter*);
extern int readAtom_pdb(Atom*, Parameter*);
extern int readAtom_dmp(Atom*, Parameter*);
extern void growAtom(Atom*);
#ifdef AOS

1
lammps/includes/parameter.h
View File

@@ -45,6 +45,7 @@ typedef struct {
int halfneigh;
MD_FLOAT dt;
MD_FLOAT dtforce;
MD_FLOAT skin;
MD_FLOAT cutforce;
MD_FLOAT cutneigh;
int nx, ny, nz;

2
lammps/includes/stats.h
View File

@@ -28,6 +28,8 @@
typedef struct {
long long int total_force_neighs;
long long int total_force_iters;
long long int atoms_within_cutoff;
long long int atoms_outside_cutoff;
} Stats;
void initStats(Stats *s);

44
lammps/main.c
View File

@@ -64,7 +64,8 @@ void init(Parameter *param)
param->ny = 32;
param->nz = 32;
param->cutforce = 2.5;
param->cutneigh = param->cutforce + 0.30;
param->skin = 0.3;
param->cutneigh = param->cutforce + param->skin;
param->temp = 1.44;
param->nstat = 100;
param->mass = 1.0;
@@ -188,56 +189,54 @@ int main(int argc, char** argv)
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) {
fprintf(stderr, "Invalid force field!\n");
exit(-1);
}
continue;
}
if((strcmp(argv[i], "-i") == 0))
{
if((strcmp(argv[i], "-i") == 0)) {
param.input_file = strdup(argv[++i]);
continue;
}
if((strcmp(argv[i], "-e") == 0))
{
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))
{
if((strcmp(argv[i], "-nx") == 0)) {
param.nx = atoi(argv[++i]);
continue;
}
if((strcmp(argv[i], "-ny") == 0))
{
if((strcmp(argv[i], "-ny") == 0)) {
param.ny = atoi(argv[++i]);
continue;
}
if((strcmp(argv[i], "-nz") == 0))
{
if((strcmp(argv[i], "-nz") == 0)) {
param.nz = atoi(argv[++i]);
continue;
}
if((strcmp(argv[i], "--freq") == 0))
{
if((strcmp(argv[i], "-r") == 0) || (strcmp(argv[i], "--radius") == 0)) {
param.cutforce = atof(argv[++i]);
continue;
}
if((strcmp(argv[i], "-s") == 0) || (strcmp(argv[i], "--skin") == 0)) {
param.skin = atof(argv[++i]);
continue;
}
if((strcmp(argv[i], "--freq") == 0)) {
param.proc_freq = atof(argv[++i]);
continue;
}
if((strcmp(argv[i], "--vtk") == 0))
{
if((strcmp(argv[i], "--vtk") == 0)) {
param.vtk_file = strdup(argv[++i]);
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 <string>: force field (lj or eam), default lj\n");
@@ -245,6 +244,8 @@ int main(int argc, char** argv)
printf("-e <string>: input file for EAM\n");
printf("-n / --nsteps <int>: set number of timesteps for simulation\n");
printf("-nx/-ny/-nz <int>: set linear dimension of systembox in x/y/z direction\n");
printf("-r / --radius <real>: set cutoff radius\n");
printf("-s / --skin <real>: set skin (verlet buffer)\n");
printf("--freq <real>: processor frequency (GHz)\n");
printf("--vtk <string>: VTK file for visualization\n");
printf(HLINE);
@@ -252,6 +253,7 @@ int main(int argc, char** argv)
}
}
param.cutneigh = param.cutforce + param.skin;
setup(&param, &eam, &atom, &neighbor, &stats);
computeThermo(0, &param, &atom);
#if defined(MEM_TRACER) || defined(INDEX_TRACER)

15
lammps/stats.c
View File

@@ -8,17 +8,22 @@
void initStats(Stats *s) {
s->total_force_neighs = 0;
s->total_force_iters = 0;
s->atoms_within_cutoff = 0;
s->atoms_outside_cutoff = 0;
}
void displayStatistics(Atom *atom, Parameter *param, Stats *stats, double *timer) {
#ifdef COMPUTE_STATS
double force_useful_volume = 1e-9 * ( (double)(atom->Nlocal * (param->ntimes + 1)) * (sizeof(MD_FLOAT) * 6 + sizeof(int)) +
(double)(stats->total_force_neighs) * (sizeof(MD_FLOAT) * 3 + sizeof(int)) );
double avg_neigh = stats->total_force_neighs / (double)(atom->Nlocal * (param->ntimes + 1));
double avg_simd = stats->total_force_iters / (double)(atom->Nlocal * (param->ntimes + 1));
#ifdef EXPLICIT_TYPES
#ifdef EXPLICIT_TYPES
force_useful_volume += 1e-9 * (double)((atom->Nlocal * (param->ntimes + 1)) + stats->total_force_neighs) * sizeof(int);
#endif
#endif
printf("Statistics:\n");
printf("\tVector width: %d, Processor frequency: %.4f GHz\n", VECTOR_WIDTH, param->proc_freq);
printf("\tAverage neighbors per atom: %.4f\n", avg_neigh);
@@ -27,5 +32,11 @@ void displayStatistics(Atom *atom, Parameter *param, Stats *stats, double *timer
printf("\tTotal number of SIMD iterations: %lld\n", stats->total_force_iters);
printf("\tUseful read data volume for force computation: %.2fGB\n", force_useful_volume);
printf("\tCycles/SIMD iteration: %.4f\n", timer[FORCE] * param->proc_freq * 1e9 / stats->total_force_iters);
#ifdef USE_REFERENCE_VERSION
const double eff_pct = (double)stats->atoms_within_cutoff / (double)(stats->atoms_within_cutoff + stats->atoms_outside_cutoff) * 100.0;
printf("\tAtoms within/outside cutoff radius: %lld/%lld (%.2f%%)\n", stats->atoms_within_cutoff, stats->atoms_outside_cutoff, eff_pct);
#endif
#endif
}