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Simplify macros for data structure access.

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Still segvaults for AoS.
This commit is contained in:
Jan Eitzinger 2021-03-23 09:26:41 +01:00
parent cb0ae2b0bb
commit 6679b6c8aa
7 changed files with 50 additions and 59 deletions
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2
Makefile
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@ -5,7 +5,7 @@ TARGET = MDBench-$(TAG)
BUILD_DIR = ./$(TAG) BUILD_DIR = ./$(TAG)
SRC_DIR = ./src SRC_DIR = ./src
MAKE_DIR = ./ MAKE_DIR = ./
FLAGS = #-DAOS FLAGS = -DAOS
Q ?= @ Q ?= @
#DO NOT EDIT BELOW #DO NOT EDIT BELOW

6
include_CLANG.mk
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@ -1,5 +1,5 @@
CC = cc CC = cc
CXX = cc CXX = gcc
LINKER = $(CC) LINKER = $(CC)
ANSI_CFLAGS = -ansi ANSI_CFLAGS = -ansi
@ -7,11 +7,11 @@ ANSI_CFLAGS += -std=c99
ANSI_CFLAGS += -pedantic ANSI_CFLAGS += -pedantic
ANSI_CFLAGS += -Wextra ANSI_CFLAGS += -Wextra
CFLAGS = -Ofast $(ANSI_CFLAGS) -Xpreprocessor -fopenmp #-g CFLAGS = -Ofast $(ANSI_CFLAGS) -g #-Xpreprocessor -fopenmp -g
ASFLAGS = -masm=intel ASFLAGS = -masm=intel
CXXFLAGS = $(CFLAGS) CXXFLAGS = $(CFLAGS)
FCFLAGS = FCFLAGS =
LFLAGS = LFLAGS =
DEFINES = -D_GNU_SOURCE -DALIGNMENT=64 -DPRECISION=2 DEFINES = -D_GNU_SOURCE -DALIGNMENT=64 -DPRECISION=2
INCLUDES = INCLUDES =
LIBS = -lomp LIBS = #-lomp

12
src/atom.c
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@ -1,8 +1,10 @@
/* /*
* ======================================================================================= * =======================================================================================
* *
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de * Authors: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 RRZE, University Erlangen-Nuremberg * Rafael Ravedutti (rr), rafaelravedutti@gmail.com
*
* Copyright (c) 2021 RRZE, University Erlangen-Nuremberg
* *
* This file is part of MD-Bench. * This file is part of MD-Bench.
* *
@ -111,9 +113,9 @@ void createAtom(Atom *atom, Parameter *param)
growAtom(atom); growAtom(atom);
} }
set_atom_x(atom, atom->Nlocal, xtmp); atom_x(atom->Nlocal) = xtmp;
set_atom_y(atom, atom->Nlocal, ytmp); atom_y(atom->Nlocal) = ytmp;
set_atom_z(atom, atom->Nlocal, ztmp); atom_z(atom->Nlocal) = ztmp;
atom->vx[atom->Nlocal] = vxtmp; atom->vx[atom->Nlocal] = vxtmp;
atom->vy[atom->Nlocal] = vytmp; atom->vy[atom->Nlocal] = vytmp;
atom->vz[atom->Nlocal] = vztmp; atom->vz[atom->Nlocal] = vztmp;

25
src/includes/atom.h
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@ -2,7 +2,7 @@
* ======================================================================================= * =======================================================================================
* *
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de * Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 RRZE, University Erlangen-Nuremberg * Copyright (c) 2021 RRZE, University Erlangen-Nuremberg
* *
* This file is part of MD-Bench. * This file is part of MD-Bench.
* *
@ -38,25 +38,14 @@ extern void growAtom(Atom*);
#ifdef AOS #ifdef AOS
#define POS_DATA_LAYOUT "AoS" #define POS_DATA_LAYOUT "AoS"
/* FIXME: these macros are resulting in segfault #define atom_x(i) atom->x[i * 3 + 0]
#define set_atom_x(atom, i, v) (atom->x[i * 3 + 0] = v) #define atom_y(i) atom->x[i * 3 + 1]
#define set_atom_y(atom, i, v) (atom->x[i * 3 + 1] = v) #define atom_z(i) atom->x[i * 3 + 2]
#define set_atom_z(atom, i, v) (atom->x[i * 3 + 2] = v)
*/
inline void set_atom_x(Atom *atom, int i, MD_FLOAT x) { atom->x[i * 3 + 0] = x; }
inline void set_atom_y(Atom *atom, int i, MD_FLOAT y) { atom->x[i * 3 + 1] = y; }
inline void set_atom_z(Atom *atom, int i, MD_FLOAT z) { atom->x[i * 3 + 2] = z; }
#define get_atom_x(atom, i) (atom->x[i * 3 + 0])
#define get_atom_y(atom, i) (atom->x[i * 3 + 1])
#define get_atom_z(atom, i) (atom->x[i * 3 + 2])
#else #else
#define POS_DATA_LAYOUT "SoA" #define POS_DATA_LAYOUT "SoA"
#define set_atom_x(atom, i, v) (atom->x[i] = v) #define atom_x(i) atom->x[i]
#define set_atom_y(atom, i, v) (atom->y[i] = v) #define atom_y(i) atom->y[i]
#define set_atom_z(atom, i, v) (atom->z[i] = v) #define atom_z(i) atom->z[i]
#define get_atom_x(atom, i) (atom->x[i])
#define get_atom_y(atom, i) (atom->y[i])
#define get_atom_z(atom, i) (atom->z[i])
#endif #endif
#endif #endif

18
src/main.c
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@ -123,9 +123,9 @@ void initialIntegrate(Parameter *param, Atom *atom)
vx[i] += param->dtforce * fx[i]; vx[i] += param->dtforce * fx[i];
vy[i] += param->dtforce * fy[i]; vy[i] += param->dtforce * fy[i];
vz[i] += param->dtforce * fz[i]; vz[i] += param->dtforce * fz[i];
set_atom_x(atom, i, get_atom_x(atom, i) + param->dt * vx[i]); atom_x(i) = atom_x(i) + param->dt * vx[i];
set_atom_y(atom, i, get_atom_y(atom, i) + param->dt * vy[i]); atom_y(i) = atom_y(i) + param->dt * vy[i];
set_atom_z(atom, i, get_atom_z(atom, i) + param->dt * vz[i]); atom_z(i) = atom_z(i) + param->dt * vz[i];
} }
} }
@ -164,9 +164,9 @@ double computeForce(Parameter *param, Atom *atom, Neighbor *neighbor)
for(int i = 0; i < Nlocal; i++) { for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs]; neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i]; int numneighs = neighbor->numneigh[i];
MD_FLOAT xtmp = get_atom_x(atom, i); MD_FLOAT xtmp = atom_x(i);
MD_FLOAT ytmp = get_atom_y(atom, i); MD_FLOAT ytmp = atom_y(i);
MD_FLOAT ztmp = get_atom_z(atom, i); MD_FLOAT ztmp = atom_z(i);
MD_FLOAT fix = 0; MD_FLOAT fix = 0;
MD_FLOAT fiy = 0; MD_FLOAT fiy = 0;
@ -174,9 +174,9 @@ double computeForce(Parameter *param, Atom *atom, Neighbor *neighbor)
for(int k = 0; k < numneighs; k++) { for(int k = 0; k < numneighs; k++) {
int j = neighs[k]; int j = neighs[k];
MD_FLOAT delx = xtmp - get_atom_x(atom, j); MD_FLOAT delx = xtmp - atom_x(j);
MD_FLOAT dely = ytmp - get_atom_y(atom, j); MD_FLOAT dely = ytmp - atom_y(j);
MD_FLOAT delz = ztmp - get_atom_z(atom, j); MD_FLOAT delz = ztmp - atom_z(j);
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz; MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
if(rsq < cutforcesq) { if(rsq < cutforcesq) {

16
src/neighbor.c
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@ -2,7 +2,7 @@
* ======================================================================================= * =======================================================================================
* *
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de * Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 RRZE, University Erlangen-Nuremberg * Copyright (c) 2021 RRZE, University Erlangen-Nuremberg
* *
* This file is part of MD-Bench. * This file is part of MD-Bench.
* *
@ -193,9 +193,9 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor)
for(int i = 0; i < atom->Nlocal; i++) { for(int i = 0; i < atom->Nlocal; i++) {
int* neighptr = &(neighbor->neighbors[i * neighbor->maxneighs]); int* neighptr = &(neighbor->neighbors[i * neighbor->maxneighs]);
int n = 0; int n = 0;
MD_FLOAT xtmp = get_atom_x(atom, i); MD_FLOAT xtmp = atom_x(i);
MD_FLOAT ytmp = get_atom_y(atom, i); MD_FLOAT ytmp = atom_y(i);
MD_FLOAT ztmp = get_atom_z(atom, i); MD_FLOAT ztmp = atom_z(i);
int ibin = coord2bin(xtmp, ytmp, ztmp); int ibin = coord2bin(xtmp, ytmp, ztmp);
for(int k = 0; k < nstencil; k++) { for(int k = 0; k < nstencil; k++) {
@ -209,9 +209,9 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor)
continue; continue;
} }
MD_FLOAT delx = xtmp - get_atom_x(atom, j); MD_FLOAT delx = xtmp - atom_x(j);
MD_FLOAT dely = ytmp - get_atom_y(atom, j); MD_FLOAT dely = ytmp - atom_y(j);
MD_FLOAT delz = ztmp - get_atom_z(atom, j); MD_FLOAT delz = ztmp - atom_z(j);
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz; MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
if( rsq <= cutneighsq ) { if( rsq <= cutneighsq ) {
@ -316,7 +316,7 @@ void binatoms(Atom *atom)
} }
for(int i = 0; i < nall; i++) { for(int i = 0; i < nall; i++) {
int ibin = coord2bin(get_atom_x(atom, i), get_atom_y(atom, i), get_atom_z(atom, i)); int ibin = coord2bin(atom_x(i), atom_y(i), atom_z(i));
if(bincount[ibin] < atoms_per_bin) { if(bincount[ibin] < atoms_per_bin) {
int ac = bincount[ibin]++; int ac = bincount[ibin]++;

30
src/pbc.c
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@ -53,9 +53,9 @@ void updatePbc(Atom *atom, Parameter *param)
MD_FLOAT zprd = param->zprd; MD_FLOAT zprd = param->zprd;
for(int i = 0; i < atom->Nghost; i++) { for(int i = 0; i < atom->Nghost; i++) {
set_atom_x(atom, nlocal + i, get_atom_x(atom, BorderMap[i]) + PBCx[i] * xprd); atom_x(nlocal + i) = atom_x(BorderMap[i]) + PBCx[i] * xprd;
set_atom_y(atom, nlocal + i, get_atom_y(atom, BorderMap[i]) + PBCy[i] * yprd); atom_y(nlocal + i) = atom_y(BorderMap[i]) + PBCy[i] * yprd;
set_atom_z(atom, nlocal + i, get_atom_z(atom, BorderMap[i]) + PBCz[i] * zprd); atom_z(nlocal + i) = atom_z(BorderMap[i]) + PBCz[i] * zprd;
} }
} }
@ -68,26 +68,26 @@ void updateAtomsPbc(Atom *atom, Parameter *param)
MD_FLOAT zprd = param->zprd; MD_FLOAT zprd = param->zprd;
for(int i = 0; i < atom->Nlocal; i++) { for(int i = 0; i < atom->Nlocal; i++) {
MD_FLOAT x = get_atom_x(atom, i); MD_FLOAT x = atom_x(i);
MD_FLOAT y = get_atom_y(atom, i); MD_FLOAT y = atom_y(i);
MD_FLOAT z = get_atom_z(atom, i); MD_FLOAT z = atom_z(i);
if(x < 0.0) { if(x < 0.0) {
set_atom_x(atom, i, x + xprd); atom_x(i) = x + xprd;
} else if(x >= xprd) { } else if(x >= xprd) {
set_atom_x(atom, i, x - xprd); atom_x(i) = x - xprd;
} }
if(y < 0.0) { if(y < 0.0) {
set_atom_y(atom, i, y + yprd); atom_y(i) = y + yprd;
} else if(y >= yprd) { } else if(y >= yprd) {
set_atom_y(atom, i, y - yprd); atom_y(i) = y - yprd;
} }
if(z < 0.0) { if(z < 0.0) {
set_atom_z(atom, i, z + zprd); atom_z(i) = z + zprd;
} else if(z >= zprd) { } else if(z >= zprd) {
set_atom_z(atom, i, z - zprd); atom_z(i) = z - zprd;
} }
} }
} }
@ -114,9 +114,9 @@ void setupPbc(Atom *atom, Parameter *param)
growPbc(); growPbc();
} }
MD_FLOAT x = get_atom_x(atom, i); MD_FLOAT x = atom_x(i);
MD_FLOAT y = get_atom_y(atom, i); MD_FLOAT y = atom_y(i);
MD_FLOAT z = get_atom_z(atom, i); MD_FLOAT z = atom_z(i);
/* Setup ghost atoms */ /* Setup ghost atoms */
/* 6 planes */ /* 6 planes */