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Final MPI version

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This commit is contained in:
JairoBuitrago
2024-04-15 16:53:25 +02:00
parent a6a269703d
commit a13a0f3bae
33 changed files with 3568 additions and 624 deletions
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19
gromacs/includes/atom.h
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@@ -5,6 +5,7 @@
* license that can be found in the LICENSE file.
*/
#include <parameter.h>
#include <box.h>
#ifndef __ATOM_H_
#define __ATOM_H_
@@ -102,7 +103,7 @@ typedef struct {
typedef struct {
int Natoms, Nlocal, Nghost, Nmax;
int Nclusters, Nclusters_local, Nclusters_ghost, Nclusters_max;
int Nclusters, Nclusters_local, Nclusters_ghost, Nclusters_max, NmaxGhost,ncj;
MD_FLOAT *x, *y, *z;
MD_FLOAT *vx, *vy, *vz;
int *border_map;
@@ -112,6 +113,7 @@ typedef struct {
MD_FLOAT *sigma6;
MD_FLOAT *cutforcesq;
MD_FLOAT *cutneighsq;
//track the movement of a particle along boundaries
int *PBCx, *PBCy, *PBCz;
// Data in cluster format
MD_FLOAT *cl_x;
@@ -128,6 +130,9 @@ typedef struct {
unsigned int masks_2xnn_fn[8];
unsigned int masks_4xn_hn[16];
unsigned int masks_4xn_fn[16];
//Info Subdomain
Box mybox;
} Atom;
extern void initAtom(Atom*);
@@ -140,6 +145,18 @@ extern int readAtom_dmp(Atom*, Parameter*);
extern void growAtom(Atom*);
extern void growClusters(Atom*);
int packGhost(Atom*, int, MD_FLOAT* , int*);
int unpackGhost(Atom*, int, MD_FLOAT*);
int packExchange(Atom*, int, MD_FLOAT*);
int unpackExchange(Atom*, int, MD_FLOAT*);
void packForward(Atom*, int, int*, MD_FLOAT*, int*);
void unpackForward(Atom*, int, int, MD_FLOAT*);
void packReverse(Atom* , int , int , MD_FLOAT*);
void unpackReverse(Atom*, int, int*, MD_FLOAT*);
void pbc(Atom*);
void copy(Atom*, int, int);
#ifdef AOS
# define POS_DATA_LAYOUT "AoS"
# define atom_x(i) atom->x[(i) * 3 + 0]

64
gromacs/includes/integrate.h
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@@ -9,10 +9,13 @@
#include <atom.h>
#include <parameter.h>
#include <util.h>
#include <timers.h>
#include <timing.h>
#include <simd.h>
/*
void cpuInitialIntegrate(Parameter *param, Atom *atom) {
DEBUG_MESSAGE("cpuInitialIntegrate start\n");
for(int ci = 0; ci < atom->Nclusters_local; ci++) {
int ci_vec_base = CI_VECTOR_BASE_INDEX(ci);
MD_FLOAT *ci_x = &atom->cl_x[ci_vec_base];
@@ -32,9 +35,9 @@ void cpuInitialIntegrate(Parameter *param, Atom *atom) {
DEBUG_MESSAGE("cpuInitialIntegrate end\n");
}
void cpuFinalIntegrate(Parameter *param, Atom *atom) {
DEBUG_MESSAGE("cpuFinalIntegrate start\n");
void cpuFinalIntegrate(Parameter *param, Atom *atom) {
DEBUG_MESSAGE("cpuFinalIntegrate start\n");
for(int ci = 0; ci < atom->Nclusters_local; ci++) {
int ci_vec_base = CI_VECTOR_BASE_INDEX(ci);
MD_FLOAT *ci_v = &atom->cl_v[ci_vec_base];
@@ -46,6 +49,56 @@ void cpuFinalIntegrate(Parameter *param, Atom *atom) {
ci_v[CL_Z_OFFSET + cii] += param->dtforce * ci_f[CL_Z_OFFSET + cii];
}
}
DEBUG_MESSAGE("cpuFinalIntegrate end\n");
}
*/
void cpuInitialIntegrate(Parameter *param, Atom *atom) {
DEBUG_MESSAGE("cpuInitialIntegrate start\n");
for(int ci = 0; ci < atom->Nclusters_local; ci+=2) {
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];
MD_FLOAT *ci_f = &atom->cl_f[ci_vec_base];
MD_SIMD_FLOAT dtforce = simd_broadcast(param->dtforce);
MD_SIMD_FLOAT dt = simd_broadcast(param->dt);
MD_SIMD_FLOAT vx_vector = simd_fma(simd_load(&ci_f[CL_X_OFFSET]), dtforce, simd_load(&ci_v[CL_X_OFFSET]));
MD_SIMD_FLOAT vy_vector = simd_fma(simd_load(&ci_f[CL_Y_OFFSET]), dtforce, simd_load(&ci_v[CL_Y_OFFSET]));
MD_SIMD_FLOAT vz_vector = simd_fma(simd_load(&ci_f[CL_Z_OFFSET]), dtforce, simd_load(&ci_v[CL_Z_OFFSET]));
MD_SIMD_FLOAT x_vector = simd_fma(vx_vector, dt, simd_load(&ci_x[CL_X_OFFSET]));
MD_SIMD_FLOAT y_vector = simd_fma(vy_vector, dt, simd_load(&ci_x[CL_Y_OFFSET]));
MD_SIMD_FLOAT z_vector = simd_fma(vz_vector, dt, simd_load(&ci_x[CL_Z_OFFSET]));
simd_store(&ci_v[CL_X_OFFSET], vx_vector);
simd_store(&ci_v[CL_Y_OFFSET], vy_vector);
simd_store(&ci_v[CL_Z_OFFSET], vz_vector);
simd_store(&ci_x[CL_X_OFFSET], x_vector);
simd_store(&ci_x[CL_Y_OFFSET], y_vector);
simd_store(&ci_x[CL_Z_OFFSET], z_vector);
}
DEBUG_MESSAGE("cpuInitialIntegrate end\n");
}
void cpuFinalIntegrate(Parameter *param, Atom *atom) {
DEBUG_MESSAGE("cpuFinalIntegrate start\n");
for(int ci = 0; ci < atom->Nclusters_local; ci+=2) {
int ci_vec_base = CI_VECTOR_BASE_INDEX(ci);
MD_FLOAT *ci_v = &atom->cl_v[ci_vec_base];
MD_FLOAT *ci_f = &atom->cl_f[ci_vec_base];
MD_SIMD_FLOAT dtforce = simd_broadcast(param->dtforce);
MD_SIMD_FLOAT vx_vector = simd_fma(simd_load(&ci_f[CL_X_OFFSET]), dtforce, simd_load(&ci_v[CL_X_OFFSET]));
MD_SIMD_FLOAT vy_vector = simd_fma(simd_load(&ci_f[CL_Y_OFFSET]), dtforce, simd_load(&ci_v[CL_Y_OFFSET]));
MD_SIMD_FLOAT vz_vector = simd_fma(simd_load(&ci_f[CL_Z_OFFSET]), dtforce, simd_load(&ci_v[CL_Z_OFFSET]));
simd_store(&ci_v[CL_X_OFFSET], vx_vector);
simd_store(&ci_v[CL_Y_OFFSET], vy_vector);
simd_store(&ci_v[CL_Z_OFFSET], vz_vector);
}
DEBUG_MESSAGE("cpuFinalIntegrate end\n");
}
@@ -54,3 +107,6 @@ void cpuFinalIntegrate(Parameter *param, Atom *atom) {
void cudaInitialIntegrate(Parameter*, Atom*);
void cudaFinalIntegrate(Parameter*, Atom*);
#endif

17
gromacs/includes/neighbor.h
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@@ -25,6 +25,11 @@
#define NBNXN_INTERACTION_MASK_DIAG_J8_0 0xf0f8fcfeU
#define NBNXN_INTERACTION_MASK_DIAG_J8_1 0x0080c0e0U
typedef struct {
int cluster;
int atom;
} Pair;
typedef struct {
int every;
int ncalls;
@@ -34,8 +39,20 @@ typedef struct {
int half_neigh;
int* neighbors;
unsigned int* neighbors_imask;
//MPI
/*
int Nshell; //# of atoms in listShell(Cluster here cover all possible ghost interactions)
int *numNeighShell; //# of neighs for each atom in listShell
Pair *neighshell; //list of neighs for each atom in listShell
Pair *listshell; //Atoms to compute the force
*/
int Nshell; //# of cluster in listShell(Cluster here cover all possible ghost interactions)
int *numNeighShell; //# of neighs for each atom in listShell
int *neighshell; //list of neighs for each atom in listShell
int *listshell; //Atoms to compute the force
} Neighbor;
extern void initNeighbor(Neighbor*, Parameter*);
extern void setupNeighbor(Parameter*, Atom*);
extern void binatoms(Atom*);

3
gromacs/includes/vtk.h
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@@ -5,6 +5,8 @@
* license that can be found in the LICENSE file.
*/
#include <atom.h>
#include <comm.h>
#include <parameter.h>
#ifndef __VTK_H_
#define __VTK_H_
@@ -13,4 +15,5 @@ extern int write_local_atoms_to_vtk_file(const char* filename, Atom* atom, int t
extern int write_ghost_atoms_to_vtk_file(const char* filename, Atom* atom, int timestep);
extern int write_local_cluster_edges_to_vtk_file(const char* filename, Atom* atom, int timestep);
extern int write_ghost_cluster_edges_to_vtk_file(const char* filename, Atom* atom, int timestep);
extern void printvtk(const char* filename, Comm* comm, Atom* atom ,Parameter* param, int timestep);
#endif