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Adjust ISA options and improve output

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2022-08-16 18:36:47 +02:00
parent 0caeea0494
commit 911ba63336
9 changed files with 70 additions and 53 deletions
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8
Makefile
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@ -64,8 +64,12 @@ ifneq ($(VECTOR_WIDTH),)
DEFINES += -DVECTOR_WIDTH=$(VECTOR_WIDTH)
endif
ifeq ($(strip $(NO_AVX2)),true)
DEFINES += -DNO_AVX2
ifeq ($(strip $(MASK_REGISTERS)),true)
DEFINES += -DMASK_REGISTERS
endif
ifeq ($(strip $(SIMD_KERNEL_AVAILABLE)),true)
DEFINES += -DSIMD_KERNEL_AVAILABLE
endif
ifeq ($(strip $(AVX512)),true)

3
config.mk
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@ -2,6 +2,9 @@
TAG ?= ICC
# Instruction set (SSE/AVX/AVX2/AVX512)
ISA ?= AVX512
# Use mask registers (AVX512 must be available in the target CPU)
# This is always true when ISA is set to AVX512
MASK_REGISTERS ?= true
# Optimization scheme (lammps/gromacs/clusters_per_bin)
OPT_SCHEME ?= lammps
# Enable likwid (true or false)

6
gromacs/includes/simd/avx_avx2_double.h
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@ -28,10 +28,10 @@
#define MD_SIMD_FLOAT __m256d
#define MD_SIMD_INT __m128i
#ifdef NO_AVX2
# define MD_SIMD_MASK __m256d
#else
#ifdef MASK_REGISTERS
# define MD_SIMD_MASK __mmask8
#else
# define MD_SIMD_MASK __m256d
#endif
static inline MD_SIMD_FLOAT simd_broadcast(MD_FLOAT scalar) { return _mm256_set1_pd(scalar); }

3
include_ISA.mk
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@ -2,12 +2,13 @@ ifeq ($(strip $(ISA)), SSE)
_VECTOR_WIDTH=2
else ifeq ($(strip $(ISA)), AVX)
# Vector width is 4 but AVX2 instruction set is not supported
NO_AVX2=true
_VECTOR_WIDTH=4
else ifeq ($(strip $(ISA)), AVX2)
#SIMD_KERNEL_AVAILABLE=true
_VECTOR_WIDTH=4
else ifeq ($(strip $(ISA)), AVX512)
AVX512=true
SIMD_KERNEL_AVAILABLE=true
_VECTOR_WIDTH=8
endif

8
lammps/force_dem.c
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@ -21,16 +21,14 @@
* =======================================================================================
*/
#include <math.h>
//---
#include <atom.h>
#include <likwid-marker.h>
#include <timing.h>
#include <neighbor.h>
#include <parameter.h>
#include <atom.h>
#include <stats.h>
#include <timing.h>
// TODO: Joint common files for gromacs and lammps variants
#include "../gromacs/includes/simd.h"
double computeForceDemFullNeigh(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
int Nlocal = atom->Nlocal;

25
lammps/force_lj.c
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@ -20,16 +20,20 @@
* with MD-Bench. If not, see <https://www.gnu.org/licenses/>.
* =======================================================================================
*/
#include <stdio.h>
#include <stdlib.h>
//---
#include <atom.h>
#include <likwid-marker.h>
#include <timing.h>
#include <neighbor.h>
#include <parameter.h>
#include <atom.h>
#include <stats.h>
#include <timing.h>
// TODO: Joint common files for gromacs and lammps variants
#ifdef SIMD_KERNEL_AVAILABLE
#include "../gromacs/includes/simd.h"
#endif
double computeForceLJFullNeigh_plain_c(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
int Nlocal = atom->Nlocal;
@ -194,11 +198,6 @@ double computeForceLJFullNeigh_simd(Parameter *param, Atom *atom, Neighbor *neig
MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
MD_FLOAT sigma6 = param->sigma6;
MD_FLOAT epsilon = param->epsilon;
MD_SIMD_FLOAT cutforcesq_vec = simd_broadcast(cutforcesq);
MD_SIMD_FLOAT sigma6_vec = simd_broadcast(sigma6);
MD_SIMD_FLOAT eps_vec = simd_broadcast(epsilon);
MD_SIMD_FLOAT c48_vec = simd_broadcast(48.0);
MD_SIMD_FLOAT c05_vec = simd_broadcast(0.5);
for(int i = 0; i < Nlocal; i++) {
atom_fx(i) = 0.0;
@ -209,10 +208,16 @@ double computeForceLJFullNeigh_simd(Parameter *param, Atom *atom, Neighbor *neig
double S = getTimeStamp();
LIKWID_MARKER_START("force");
#ifdef NO_AVX2
fprintf(stderr, "Error: SIMD kernel implemented for AVX2 and AVX512 only!");
#ifndef SIMD_KERNEL_AVAILABLE
fprintf(stderr, "Error: SIMD kernel not implemented for specified instruction set!");
exit(-1);
#else
MD_SIMD_FLOAT cutforcesq_vec = simd_broadcast(cutforcesq);
MD_SIMD_FLOAT sigma6_vec = simd_broadcast(sigma6);
MD_SIMD_FLOAT eps_vec = simd_broadcast(epsilon);
MD_SIMD_FLOAT c48_vec = simd_broadcast(48.0);
MD_SIMD_FLOAT c05_vec = simd_broadcast(0.5);
#pragma omp parallel for
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];

9
lammps/includes/util.h
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@ -26,12 +26,15 @@
#ifndef MIN
# define MIN(x,y) ((x)<(y)?(x):(y))
#endif
#ifndef MAX
# define MAX(x,y) ((x)>(y)?(x):(y))
#endif
#ifndef ABS
# define ABS(a) ((a) >= 0 ? (a) : -(a))
#endif
#ifdef DEBUG
# define DEBUG_MESSAGE printf
#else
@ -46,6 +49,12 @@
#define FF_EAM 1
#define FF_DEM 2
#if PRECISION == 1
# define PRECISION_STRING "single"
#else
# define PRECISION_STRING "double"
#endif
extern double myrandom(int*);
extern void random_reset(int *seed, int ibase, double *coord);
extern int str2ff(const char *string);

9
lammps/main.c
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@ -226,6 +226,7 @@ int main(int argc, char** argv) {
param.cutneigh = param.cutforce + param.skin;
setup(&param, &eam, &atom, &neighbor, &stats);
printParameter(&param);
printf(HLINE);
printf("step\ttemp\t\tpressure\n");
computeThermo(0, &param, &atom);
@ -272,14 +273,6 @@ int main(int argc, char** argv) {
timer[TOTAL] = getTimeStamp() - timer[TOTAL];
computeThermo(-1, &param, &atom);
printf(HLINE);
printf("Force field: %s\n", ff2str(param.force_field));
printf("Data layout for positions: %s\n", POS_DATA_LAYOUT);
#if PRECISION == 1
printf("Using single precision floating point.\n");
#else
printf("Using double precision floating point.\n");
#endif
printf(HLINE);
printf("System: %d atoms %d ghost atoms, Steps: %d\n", atom.Natoms, atom.Nghost, param.ntimes);
printf("TOTAL %.2fs FORCE %.2fs NEIGH %.2fs REST %.2fs\n",

6
lammps/parameter.c
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@ -24,6 +24,7 @@
#include <stdlib.h>
#include <string.h>
//---
#include <atom.h>
#include <parameter.h>
#include <util.h>
@ -154,6 +155,9 @@ void printParameter(Parameter *param) {
}
printf("\tForce field: %s\n", ff2str(param->force_field));
printf("\tKernel: %s\n", KERNEL_NAME);
printf("\tData layout: %s\n", POS_DATA_LAYOUT);
printf("\tFloating-point precision: %s\n", PRECISION_STRING);
printf("\tUnit cells (nx, ny, nz): %d, %d, %d\n", param->nx, param->ny, param->nz);
printf("\tDomain box sizes (x, y, z): %e, %e, %e\n", param->xprd, param->yprd, param->zprd);
printf("\tPeriodic (x, y, z): %d, %d, %d\n", param->pbc_x, param->pbc_y, param->pbc_z);
@ -175,5 +179,5 @@ void printParameter(Parameter *param) {
printf("\tCutoff radius: %e\n", param->cutforce);
printf("\tSkin: %e\n", param->skin);
printf("\tHalf neighbor lists: %d\n", param->half_neigh);
printf("\tProcessor frequency (GHz): %.4f\n\n", param->proc_freq);
printf("\tProcessor frequency (GHz): %.4f\n", param->proc_freq);
}