MD-Bench/gromacs/utils.c
2023-05-09 00:44:37 +02:00

333 lines
11 KiB
C

/*
* Temporal functions for debugging, remove before proceeding with pull request
*/
#include <stdio.h>
#include <stdlib.h>
#include <utils.h>
extern void alignDataToSuperclusters(Atom *atom);
extern void alignDataFromSuperclusters(Atom *atom);
#ifdef USE_SUPER_CLUSTERS
/*
void verifyClusters(Atom *atom) {
unsigned int count = 0;
for (int i = 0; i < atom->Nsclusters_local; i++) {
for (int j = 0; j < atom->siclusters[i].nclusters; j++) {
for(int cii = 0; cii < CLUSTER_M; cii++, count++);
}
}
MD_FLOAT *x = malloc(count * sizeof(MD_FLOAT));
MD_FLOAT *y = malloc(count * sizeof(MD_FLOAT));
MD_FLOAT *z = malloc(count * sizeof(MD_FLOAT));
count = 0;
unsigned int diffs = 0;
printf("######### %d #########\r\n", atom->Nsclusters_local);
for (int i = 0; i < atom->Nsclusters_local; i++) {
printf("######### %d\t #########\r\n", atom->siclusters[i].nclusters);
for (int j = 0; j < atom->siclusters[i].nclusters; j++) {
//printf("%d\t", atom.siclusters[i].iclusters[j]);
MD_FLOAT *ci_x = &atom->cl_x[CI_VECTOR_BASE_INDEX(atom->siclusters[i].iclusters[j])];
if (atom->iclusters[atom->siclusters[i].iclusters[j]].bbminx < atom->siclusters[i].bbminx ||
atom->iclusters[atom->siclusters[i].iclusters[j]].bbmaxx > atom->siclusters[i].bbmaxx ||
atom->iclusters[atom->siclusters[i].iclusters[j]].bbminy < atom->siclusters[i].bbminy ||
atom->iclusters[atom->siclusters[i].iclusters[j]].bbmaxy > atom->siclusters[i].bbmaxy ||
atom->iclusters[atom->siclusters[i].iclusters[j]].bbminz < atom->siclusters[i].bbminz ||
atom->iclusters[atom->siclusters[i].iclusters[j]].bbmaxz > atom->siclusters[i].bbmaxz) diffs++;
for(int cii = 0; cii < CLUSTER_M; cii++, count++) {
x[count] = ci_x[CL_X_OFFSET + cii];
y[count] = ci_x[CL_Y_OFFSET + cii];
z[count] = ci_x[CL_Z_OFFSET + cii];
//printf("x: %f\ty: %f\tz: %f\r\n", ci_x[CL_X_OFFSET + cii], ci_x[CL_Y_OFFSET + cii], ci_x[CL_Z_OFFSET + cii]);
}
}
printf("######### \t #########\r\n");
}
printf("######### Diffs: %d\t #########\r\n", diffs);
printf("\r\n");
count = 0;
diffs = 0;
for (int i = 0; i < atom->Nclusters_local; i++) {
MD_FLOAT *ci_x = &atom->cl_x[CI_VECTOR_BASE_INDEX(i)];
for(int cii = 0; cii < CLUSTER_M; cii++, count++) {
if (ci_x[CL_X_OFFSET + cii] != x[count] ||
ci_x[CL_Y_OFFSET + cii] != y[count] ||
ci_x[CL_Z_OFFSET + cii] != z[count]) diffs++;
}
}
printf("######### Diffs: %d\t #########\r\n", diffs);
}
*/
void verifyLayout(Atom *atom) {
printf("verifyLayout start\r\n");
/*
unsigned int count = 0;
for (int i = 0; i < atom->Nsclusters_local; i++) {
for (int j = 0; j < atom->siclusters[i].nclusters; j++, count++);
}
MD_FLOAT *scl_x = malloc(atom->Nsclusters_local * SCLUSTER_SIZE * 3 * CLUSTER_M * sizeof(MD_FLOAT));
for (int sci = 0; sci < atom->Nsclusters_local; sci++) {
const unsigned int scl_offset = sci * SCLUSTER_SIZE * 3 * CLUSTER_M;
for (int ci = 0, scci = scl_offset; ci < atom->siclusters[sci].nclusters; ci++, scci += CLUSTER_M) {
MD_FLOAT *ci_x = &atom->cl_x[CI_VECTOR_BASE_INDEX(atom->siclusters[sci].iclusters[ci])];
const unsigned int atom_offset = scci;
/*
for(int cii = 0, scii = atom_offset; cii < CLUSTER_M; cii++, scii += 3) {
scl_x[CL_X_OFFSET + scii] = ci_x[CL_X_OFFSET + cii];
scl_x[CL_Y_OFFSET + scii] = ci_x[CL_Y_OFFSET + cii];
scl_x[CL_Z_OFFSET + scii] = ci_x[CL_Z_OFFSET + cii];
//printf("x: %f\ty: %f\tz: %f\r\n", ci_x[CL_X_OFFSET + cii], ci_x[CL_Y_OFFSET + cii], ci_x[CL_Z_OFFSET + cii]);
}
memcpy(&scl_x[atom_offset], &ci_x[0], CLUSTER_M * sizeof(MD_FLOAT));
memcpy(&scl_x[atom_offset + SCLUSTER_SIZE * CLUSTER_M], &ci_x[0 + CLUSTER_M], CLUSTER_M * sizeof(MD_FLOAT));
memcpy(&scl_x[atom_offset + 2 * SCLUSTER_SIZE * CLUSTER_M], &ci_x[0 + 2 * CLUSTER_M], CLUSTER_M * sizeof(MD_FLOAT));
}
}
*/
//alignDataToSuperclusters(atom);
//for (int sci = 0; sci < 2; sci++) {
for (int sci = 4; sci < 6; sci++) {
const unsigned int scl_offset = sci * SCLUSTER_SIZE;
MD_FLOAT *sci_x = &atom->scl_f[SCI_VECTOR_BASE_INDEX(sci)];
for (int cii = 0; cii < SCLUSTER_M; ++cii) {
const unsigned int cl_idx = cii / CLUSTER_M;
const unsigned int ciii = cii % CLUSTER_M;
/*
printf("%d\t%f\t%f\t%f\r\n", cl_idx, sci_x[cii],
sci_x[cii + SCLUSTER_SIZE * CLUSTER_M], sci_x[cii + 2 * SCLUSTER_SIZE * CLUSTER_M]);
*/
printf("%d\t%d\t%f\t%f\t%f\r\n", atom->icluster_idx[SCLUSTER_SIZE * sci + cl_idx], cl_idx, sci_x[SCL_CL_X_OFFSET(cl_idx) + ciii],
sci_x[SCL_CL_Y_OFFSET(cl_idx) + ciii], sci_x[SCL_CL_Z_OFFSET(cl_idx) + ciii]);
}
/*
//for (int cii = 0; cii < SCLUSTER_M; ++cii) {
for (int cii = 0; cii < SCLUSTER_M; ++cii) {
const unsigned int cl_idx = cii / CLUSTER_M;
const unsigned int ciii = cii % CLUSTER_M;
/*
printf("%d\t%f\t%f\t%f\r\n", cl_idx, sci_x[SCL_X_OFFSET(cl_idx) + cii],
sci_x[SCL_Y_OFFSET(cl_idx) + cii], sci_x[SCL_Z_OFFSET(cl_idx) + cii]);
*/
/*
printf("%d\t%f\t%f\t%f\r\n", cl_idx, sci_x[SCL_X_OFFSET(cl_idx) + ciii],
sci_x[SCL_Y_OFFSET(cl_idx) + ciii], sci_x[SCL_Z_OFFSET(cl_idx) + ciii]);
}
*/
/*
for (int scii = scl_offset; scii < scl_offset + SCLUSTER_SIZE; scii++) {
for (int cii = 0; cii < CLUSTER_M; ++cii) {
printf("%f\t%f\t%f\r\n", sci_x[SCL_X_OFFSET(scii) + cii],
sci_x[SCL_Y_OFFSET(scii) + cii], sci_x[SCL_Z_OFFSET(scii) + cii]);
}
/*
const unsigned int cl_offset = scii * 3 * CLUSTER_M;
//MD_FLOAT *sci_x = &scl_x[CI_VECTOR_BASE_INDEX(scii)];
for (int cii = cl_offset; cii < cl_offset + CLUSTER_M; ++cii) {
printf("%f\t%f\t%f\r\n", sci_x[CL_X_OFFSET + cii],
sci_x[CL_Y_OFFSET + cii], sci_x[CL_Z_OFFSET + cii]);
}
*/
/*
for (int cii = cl_offset; cii < cl_offset + CLUSTER_M; ++cii) {
printf("%f\t%f\t%f\r\n", scl_x[CL_X_OFFSET + cii],
scl_x[CL_Y_OFFSET + cii], scl_x[CL_Z_OFFSET + cii]);
}
*/
//}
printf("##########\t##########\r\n");
}
printf("\r\n");
//for (int ci = 0; ci < 16; ci++) {
for (int ci = 35; ci < 37; ci++) {
printf("$$$$$$$$$$\t%d\t%d\t$$$$$$$$$$\r\n", ci, atom->icluster_bin[ci]);
MD_FLOAT *ci_x = &atom->cl_f[CI_VECTOR_BASE_INDEX(ci)];
//for(int cii = 0; cii < CLUSTER_M; cii++, count++) {
for(int cii = 0; cii < CLUSTER_M; cii++) {
printf("%f\t%f\t%f\r\n", ci_x[CL_X_OFFSET + cii],
ci_x[CL_Y_OFFSET + cii],
ci_x[CL_Z_OFFSET + cii]);
}
printf("##########\t##########\r\n");
}
printf("verifyLayout end\r\n");
/*
for (int i = 0; i < atom->Nclusters_local; i++) {
MD_FLOAT *ci_x = &atom->cl_x[CI_VECTOR_BASE_INDEX(i)];
for(int cii = 0; cii < CLUSTER_M; cii++, count++) {
if (ci_x[CL_X_OFFSET + cii] != x[count] ||
ci_x[CL_Y_OFFSET + cii] != y[count] ||
ci_x[CL_Z_OFFSET + cii] != z[count]) diffs++;
}
}
*/
}
void checkAlignment(Atom *atom) {
alignDataToSuperclusters(atom);
for (int sci = 4; sci < 6; sci++) {
MD_FLOAT *sci_x = &atom->scl_x[SCI_VECTOR_BASE_INDEX(sci)];
for (int cii = 0; cii < SCLUSTER_M; ++cii) {
const unsigned int cl_idx = cii / CLUSTER_M;
const unsigned int ciii = cii % CLUSTER_M;
printf("%d\t%f\t%f\t%f\r\n", cl_idx, sci_x[SCL_CL_X_OFFSET(cl_idx) + ciii],
sci_x[SCL_CL_Y_OFFSET(cl_idx) + ciii], sci_x[SCL_CL_Z_OFFSET(cl_idx) + ciii]);
}
}
for (int ci = 35; ci < 37; ci++) {
printf("$$$$$$$$$$\t%d\t%d\t$$$$$$$$$$\r\n", ci, atom->icluster_bin[ci]);
MD_FLOAT *ci_x = &atom->cl_x[CI_VECTOR_BASE_INDEX(ci)];
for(int cii = 0; cii < CLUSTER_M; cii++) {
printf("%f\t%f\t%f\r\n", ci_x[CL_X_OFFSET + cii],
ci_x[CL_Y_OFFSET + cii],
ci_x[CL_Z_OFFSET + cii]);
}
printf("##########\t##########\r\n");
}
}
void showSuperclusters(Atom *atom) {
for (int sci = 4; sci < 6; sci++) {
MD_FLOAT *sci_x = &atom->scl_x[SCI_VECTOR_BASE_INDEX(sci)];
for (int cii = 0; cii < SCLUSTER_M; ++cii) {
const unsigned int cl_idx = cii / CLUSTER_M;
const unsigned int ciii = cii % CLUSTER_M;
printf("%d\t%f\t%f\t%f\r\n", cl_idx, sci_x[SCL_CL_X_OFFSET(cl_idx) + ciii],
sci_x[SCL_CL_Y_OFFSET(cl_idx) + ciii], sci_x[SCL_CL_Z_OFFSET(cl_idx) + ciii]);
}
}
}
void printNeighs(Atom *atom, Neighbor *neighbor) {
for (int i = 0; i < atom->Nclusters_local; ++i) {
int neigh_num = neighbor->numneigh[i];
for (int j = 0; j < neigh_num; j++) {
printf("%d ", neighbor->neighbors[ i * neighbor->maxneighs + j]);
}
printf("\r\n");
}
}
void printClusterIndices(Atom *atom) {
for (int i = 0; i < atom->Nsclusters_local; ++i) {
int clusters_num = atom->siclusters[i].nclusters;
for (int j = 0; j < clusters_num; j++) {
printf("%d ", atom->icluster_idx[j + SCLUSTER_SIZE * i]);
}
printf("\r\n");
}
}
void verifyNeigh(Atom *atom, Neighbor *neighbor) {
buildNeighbor(atom, neighbor);
int *numneigh = (int*) malloc(atom->Nclusters_local * sizeof(int));
int *neighbors = (int*) malloc(atom->Nclusters_local * neighbor->maxneighs * sizeof(int*));
for (int i = 0; i < atom->Nclusters_local; ++i) {
int neigh_num = neighbor->numneigh[i];
numneigh[i] = neighbor->numneigh[i];
neighbor->numneigh[i] = 0;
for (int j = 0; j < neigh_num; j++) {
neighbors[i * neighbor->maxneighs + j] = neighbor->neighbors[i * neighbor->maxneighs + j];
neighbor->neighbors[i * neighbor->maxneighs + j] = 0;
}
}
buildNeighborGPU(atom, neighbor);
unsigned int num_diff = 0;
unsigned int neigh_diff = 0;
for (int i = 0; i < atom->Nclusters_local; ++i) {
int neigh_num = neighbor->numneigh[i];
if (numneigh[i] != neigh_num) num_diff++;
for (int j = 0; j < neigh_num; j++) {
if (neighbors[i * neighbor->maxneighs + j] !=
neighbor->neighbors[ i * neighbor->maxneighs + j]) neigh_diff++;
}
}
printf("%d\t%d\r\n", num_diff, neigh_diff);
}
#endif //USE_SUPER_CLUSTERS