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Integrate LAMMPS CUDA versions into master branch

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti
2022-08-09 18:53:53 +02:00
parent eb77e1a3bd
commit c18124b066
19 changed files with 1004 additions and 92 deletions
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23
lammps/includes/atom.h
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@@ -25,6 +25,29 @@
#ifndef __ATOM_H_
#define __ATOM_H_
#ifdef CUDA_TARGET
# define KERNEL_NAME "CUDA"
# define computeForceLJFullNeigh computeForceLJFullNeigh_cuda
# define initialIntegrate initialIntegrate_cuda
# define finalIntegrate finalIntegrate_cuda
# define buildNeighbor buildNeighbor_cuda
# define updatePbc updatePbc_cuda
# define updateAtomsPbc updateAtomsPbc_cuda
#else
# ifdef USE_SIMD_KERNEL
# define KERNEL_NAME "SIMD"
# define computeForceLJFullNeigh computeForceLJFullNeigh_simd
# else
# define KERNEL_NAME "plain-C"
# define computeForceLJFullNeigh computeForceLJFullNeigh_plain_c
# endif
# define initialIntegrate initialIntegrate_cpu
# define finalIntegrate finalIntegrate_cpu
# define buildNeighbor buildNeighbor_cpu
# define updatePbc updatePbc_cpu
# define updateAtomsPbc updateAtomsPbc_cpu
#endif
typedef struct {
int Natoms, Nlocal, Nghost, Nmax;
MD_FLOAT *x, *y, *z;

10
lammps/includes/cuda_atom.h Normal file
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@@ -0,0 +1,10 @@
#include <cuda_runtime.h>
//---
#include <atom.h>
#include <neighbor.h>
#ifndef __CUDA_ATOM_H_
#define __CUDA_ATOM_H_
extern void initCuda(Atom*, Neighbor*, Atom*, Neighbor*);
extern void checkCUDAError(const char *msg, cudaError_t err);
#endif

48
lammps/includes/integrate.h Normal file
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@@ -0,0 +1,48 @@
/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 RRZE, University Erlangen-Nuremberg
*
* This file is part of MD-Bench.
*
* MD-Bench is free software: you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* MD-Bench is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
* PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License along
* with MD-Bench. If not, see <https://www.gnu.org/licenses/>.
* =======================================================================================
*/
#include <parameter.h>
#include <atom.h>
void initialIntegrate_cpu(bool reneigh, Parameter *param, Atom *atom, Atom *c_atom) {
for(int i = 0; i < atom->Nlocal; i++) {
atom_vx(i) += param->dtforce * atom_fx(i);
atom_vy(i) += param->dtforce * atom_fy(i);
atom_vz(i) += param->dtforce * atom_fz(i);
atom_x(i) = atom_x(i) + param->dt * atom_vx(i);
atom_y(i) = atom_y(i) + param->dt * atom_vy(i);
atom_z(i) = atom_z(i) + param->dt * atom_vz(i);
}
}
void finalIntegrate_cpu(bool reneigh, Parameter *param, Atom *atom, Atom *c_atom) {
for(int i = 0; i < atom->Nlocal; i++) {
atom_vx(i) += param->dtforce * atom_fx(i);
atom_vy(i) += param->dtforce * atom_fy(i);
atom_vz(i) += param->dtforce * atom_fz(i);
}
}
#ifdef CUDA_TARGET
void initialIntegrate_cuda(bool, Parameter*, Atom*, Atom*);
void finalIntegrate_cuda(bool, Parameter*, Atom*, Atom*);
#endif

22
lammps/includes/neighbor.h
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@@ -34,9 +34,29 @@ typedef struct {
int* numneigh;
} Neighbor;
typedef struct {
MD_FLOAT xprd; MD_FLOAT yprd; MD_FLOAT zprd;
MD_FLOAT bininvx; MD_FLOAT bininvy; MD_FLOAT bininvz;
int mbinxlo; int mbinylo; int mbinzlo;
int nbinx; int nbiny; int nbinz;
int mbinx; int mbiny; int mbinz;
} Neighbor_params;
typedef struct {
int* bincount;
int* bins;
int mbins;
int atoms_per_bin;
} Binning;
extern void initNeighbor(Neighbor*, Parameter*);
extern void setupNeighbor(Parameter*);
extern void binatoms(Atom*);
extern void buildNeighbor(Atom*, Neighbor*);
extern void buildNeighbor_cpu(Atom*, Neighbor*, Atom*, Neighbor*);
extern void sortAtom(Atom*);
#ifdef CUDA_TARGET
extern void buildNeighbor_cuda(Atom*, Neighbor*, Atom*, Neighbor*);
#endif
#endif

12
lammps/includes/pbc.h
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@@ -20,13 +20,21 @@
* with MD-Bench. If not, see <https://www.gnu.org/licenses/>.
* =======================================================================================
*/
#include <stdbool.h>
//---
#include <atom.h>
#include <parameter.h>
#ifndef __PBC_H_
#define __PBC_H_
extern void initPbc();
extern void updatePbc(Atom*, Parameter*);
extern void updateAtomsPbc(Atom*, Parameter*);
extern void updatePbc_cpu(Atom*, Atom*, Parameter*, bool);
extern void updateAtomsPbc_cpu(Atom*, Atom*, Parameter*);
extern void setupPbc(Atom*, Parameter*);
#ifdef CUDA_TARGET
extern void updatePbc_cuda(Atom*, Atom*, Parameter*, bool);
extern void updateAtomsPbc_cuda(Atom*, Atom*, Parameter*);
#endif
#endif

2
lammps/includes/util.h
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@@ -50,4 +50,6 @@ extern double myrandom(int*);
extern void random_reset(int *seed, int ibase, double *coord);
extern int str2ff(const char *string);
extern const char* ff2str(int ff);
extern int get_num_threads();
#endif