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Building of super clusters complete, force computation kernel WIP

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This commit is contained in:
Andropov Arsenii
2022-12-18 14:28:29 +01:00
parent b20e8c6986
commit ee3f6de050
14 changed files with 1326 additions and 4 deletions
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73
gromacs/includes/atom.h
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@@ -22,7 +22,25 @@
# define KERNEL_NAME "CUDA"
# define CLUSTER_M 8
# define CLUSTER_N VECTOR_WIDTH
#ifdef USE_SUPER_CLUSTERS
# define XX 0
# define YY 1
# define ZZ 2
# define SCLUSTER_SIZE_X 2
# define SCLUSTER_SIZE_Y 2
# define SCLUSTER_SIZE_Z 2
# define SCLUSTER_SIZE (SCLUSTER_SIZE_X * SCLUSTER_SIZE_Y * SCLUSTER_SIZE_Z)
# define DIM_COORD(dim,coord) ((dim == XX) ? atom_x(coord) : ((dim == YY) ? atom_y(coord) : atom_z(coord)))
# define MIN(a,b) ({int _a = (a), _b = (b); _a < _b ? _a : _b; })
# define SCLUSTER_M CLUSTER_M * SCLUSTER_SIZE
# define computeForceLJ computeForceLJSup_cuda
#else
# define computeForceLJ computeForceLJ_cuda
#endif //USE_SUPER_CLUSTERS
# define initialIntegrate cudaInitialIntegrate
# define finalIntegrate cudaFinalIntegrate
# define updatePbc cudaUpdatePbc
@@ -55,16 +73,28 @@
# define CJ1_FROM_CI(a) (a)
# define CI_BASE_INDEX(a,b) ((a) * CLUSTER_N * (b))
# define CJ_BASE_INDEX(a,b) ((a) * CLUSTER_N * (b))
#ifdef USE_SUPER_CLUSTERS
# define SCI_BASE_INDEX(a,b) ((a) * CLUSTER_N * SCLUSTER_SIZE * (b))
# define SCJ_BASE_INDEX(a,b) ((a) * CLUSTER_N * SCLUSTER_SIZE * (b))
#endif //USE_SUPER_CLUSTERS
#elif CLUSTER_M == CLUSTER_N * 2 // M > N
# define CJ0_FROM_CI(a) ((a) << 1)
# define CJ1_FROM_CI(a) (((a) << 1) | 0x1)
# define CI_BASE_INDEX(a,b) ((a) * CLUSTER_M * (b))
# define CJ_BASE_INDEX(a,b) (((a) >> 1) * CLUSTER_M * (b) + ((a) & 0x1) * (CLUSTER_M >> 1))
#ifdef USE_SUPER_CLUSTERS
# define SCI_BASE_INDEX(a,b) ((a) * CLUSTER_M * SCLUSTER_SIZE * (b))
# define SCJ_BASE_INDEX(a,b) (((a) >> 1) * CLUSTER_M * SCLUSTER_SIZE * (b) + ((a) & 0x1) * (SCLUSTER_SIZE * CLUSTER_M >> 1))
#endif //USE_SUPER_CLUSTERS
#elif CLUSTER_M == CLUSTER_N / 2 // M < N
# define CJ0_FROM_CI(a) ((a) >> 1)
# define CJ1_FROM_CI(a) ((a) >> 1)
# define CI_BASE_INDEX(a,b) (((a) >> 1) * CLUSTER_N * (b) + ((a) & 0x1) * (CLUSTER_N >> 1))
# define CJ_BASE_INDEX(a,b) ((a) * CLUSTER_N * (b))
#ifdef USE_SUPER_CLUSTERS
# define SCI_BASE_INDEX(a,b) (((a) >> 1) * CLUSTER_N * SCLUSTER_SIZE * (b) + ((a) & 0x1) * (CLUSTER_N * SCLUSTER_SIZE >> 1))
# define SCJ_BASE_INDEX(a,b) ((a) * CLUSTER_N * SCLUSTER_SIZE * (b))
#endif //USE_SUPER_CLUSTERS
#else
# error "Invalid cluster configuration!"
#endif
@@ -78,14 +108,37 @@
#define CJ_SCALAR_BASE_INDEX(a) (CJ_BASE_INDEX(a, 1))
#define CJ_VECTOR_BASE_INDEX(a) (CJ_BASE_INDEX(a, 3))
#ifdef USE_SUPER_CLUSTERS
#define SCI_SCALAR_BASE_INDEX(a) (SCI_BASE_INDEX(a, 1))
#define SCI_VECTOR_BASE_INDEX(a) (SCI_BASE_INDEX(a, 3))
#define SCJ_SCALAR_BASE_INDEX(a) (SCJ_BASE_INDEX(a, 1))
#define SCJ_VECTOR_BASE_INDEX(a) (SCJ_BASE_INDEX(a, 3))
#endif //USE_SUPER_CLUSTERS
#if CLUSTER_M >= CLUSTER_N
# define CL_X_OFFSET (0 * CLUSTER_M)
# define CL_Y_OFFSET (1 * CLUSTER_M)
# define CL_Z_OFFSET (2 * CLUSTER_M)
#ifdef USE_SUPER_CLUSTERS
# define SCL_CL_X_OFFSET(ci) (ci * CLUSTER_M + 0 * SCLUSTER_M)
# define SCL_CL_Y_OFFSET(ci) (ci * CLUSTER_M + 1 * SCLUSTER_M)
# define SCL_CL_Z_OFFSET(ci) (ci * CLUSTER_M + 2 * SCLUSTER_M)
# define SCL_X_OFFSET (0 * SCLUSTER_M)
# define SCL_Y_OFFSET (1 * SCLUSTER_M)
# define SCL_Z_OFFSET (2 * SCLUSTER_M)
#endif //USE_SUPER_CLUSTERS
#else
# define CL_X_OFFSET (0 * CLUSTER_N)
# define CL_Y_OFFSET (1 * CLUSTER_N)
# define CL_Z_OFFSET (2 * CLUSTER_N)
#ifdef USE_SUPER_CLUSTERS
# define SCL_X_OFFSET (0 * SCLUSTER_SIZE * CLUSTER_N)
# define SCL_Y_OFFSET (1 * SCLUSTER_SIZE * CLUSTER_N)
# define SCL_Z_OFFSET (2 * SCLUSTER_SIZE * CLUSTER_N)
#endif //USE_SUPER_CLUSTERS
#endif
typedef struct {
@@ -95,6 +148,14 @@ typedef struct {
MD_FLOAT bbminz, bbmaxz;
} Cluster;
typedef struct {
//int *iclusters;
int nclusters;
MD_FLOAT bbminx, bbmaxx;
MD_FLOAT bbminy, bbmaxy;
MD_FLOAT bbminz, bbmaxz;
} SuperCluster;
typedef struct {
int Natoms, Nlocal, Nghost, Nmax;
int Nclusters, Nclusters_local, Nclusters_ghost, Nclusters_max;
@@ -116,6 +177,17 @@ typedef struct {
Cluster *iclusters, *jclusters;
int *icluster_bin;
int dummy_cj;
#ifdef USE_SUPER_CLUSTERS
int Nsclusters, Nsclusters_local, Nsclusters_ghost, Nsclusters_max;
MD_FLOAT *scl_x;
MD_FLOAT *scl_v;
MD_FLOAT *scl_f;
int *scl_type;
int *icluster_idx;
SuperCluster *siclusters;
int *sicluster_bin;
#endif //USE_SUPER_CLUSTERS
} Atom;
extern void initAtom(Atom*);
@@ -126,6 +198,7 @@ extern int readAtom_gro(Atom*, Parameter*);
extern int readAtom_dmp(Atom*, Parameter*);
extern void growAtom(Atom*);
extern void growClusters(Atom*);
extern void growSuperClusters(Atom*);
#ifdef AOS
# define POS_DATA_LAYOUT "AoS"

1
gromacs/includes/neighbor.h
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@@ -25,6 +25,7 @@ extern void buildNeighbor(Atom*, Neighbor*);
extern void pruneNeighbor(Parameter*, Atom*, Neighbor*);
extern void sortAtom(Atom*);
extern void buildClusters(Atom*);
extern void buildClustersGPU(Atom*);
extern void defineJClusters(Atom*);
extern void binClusters(Atom*);
extern void updateSingleAtoms(Atom*);

17
gromacs/includes/utils.h Normal file
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@@ -0,0 +1,17 @@
/*
* Temporal functions for debugging, remove before proceeding with pull request
*/
#ifndef MD_BENCH_UTILS_H
#define MD_BENCH_UTILS_H
#include <atom.h>
#ifdef USE_SUPER_CLUSTERS
void verifyClusters(Atom *atom);
void verifyLayout(Atom *atom);
void checkAlignment(Atom *atom);
void showSuperclusters(Atom *atom);
#endif //USE_SUPER_CLUSTERS
#endif //MD_BENCH_UTILS_H

1
gromacs/includes/vtk.h
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@@ -9,6 +9,7 @@
#ifndef __VTK_H_
#define __VTK_H_
extern void write_data_to_vtk_file(const char *filename, Atom* atom, int timestep);
extern int write_super_clusters_to_vtk_file(const char* filename, Atom* atom, int timestep);
extern int write_local_atoms_to_vtk_file(const char* filename, Atom* atom, int timestep);
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);