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Fix code for AVX and remove warnings

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2022-11-08 15:30:37 +01:00
parent 437b380229
commit 493915fe95
10 changed files with 51 additions and 36 deletions
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4
Makefile
View File

@ -73,6 +73,10 @@ ifeq ($(strip $(SIMD_KERNEL_AVAILABLE)),true)
DEFINES += -DSIMD_KERNEL_AVAILABLE
endif
ifeq ($(strip $(NO_AVX2)),true)
DEFINES += -DNO_AVX2
endif
ifeq ($(strip $(AVX512)),true)
DEFINES += -DAVX512
endif

8
common/eam_utils.c
View File

@ -54,10 +54,10 @@ void read_eam_file(Funcfl* file, const char* filename) {
}
int tmp;
fgets(line, MAXLINE, fptr);
fgets(line, MAXLINE, fptr);
readline(line, fptr);
readline(line, fptr);
sscanf(line, "%d %lg", &tmp, &(file->mass));
fgets(line, MAXLINE, fptr);
readline(line, fptr);
sscanf(line, "%d %lg %d %lg %lg", &file->nrho, &file->drho, &file->nr, &file->dr, &file->cut);
//printf("Read: %lf %i %lf %i %lf %lf\n",file->mass,file->nrho,file->drho,file->nr,file->dr,file->cut);
@ -261,7 +261,7 @@ void grab(FILE* fptr, int n, MD_FLOAT* list) {
int i = 0;
while(i < n) {
fgets(line, MAXLINE, fptr);
readline(line, fptr);
ptr = strtok(line, " \t\n\r\f");
list[i++] = atof(ptr);
while(ptr = strtok(NULL, " \t\n\r\f")) list[i++] = atof(ptr);

7
common/includes/simd/avx_avx2_double.h
View File

@ -71,6 +71,7 @@ static inline MD_SIMD_FLOAT simd_reciprocal(MD_SIMD_FLOAT a) { return _mm256_cvt
static inline MD_SIMD_FLOAT simd_fma(MD_SIMD_FLOAT a, MD_SIMD_FLOAT b, MD_SIMD_FLOAT c) { return simd_add(simd_mul(a, b), c); }
static inline MD_SIMD_FLOAT simd_masked_add(MD_SIMD_FLOAT a, MD_SIMD_FLOAT b, MD_SIMD_MASK m) { return simd_add(a, _mm256_and_pd(b, m)); }
static inline MD_SIMD_MASK simd_mask_cond_lt(MD_SIMD_FLOAT a, MD_SIMD_FLOAT b) { return _mm256_cmp_pd(a, b, _CMP_LT_OQ); }
static inline MD_SIMD_MASK simd_mask_int_cond_lt(MD_SIMD_INT a, MD_SIMD_INT b) { return _mm256_cvtepi32_pd(_mm_cmplt_epi32(a, b)); }
static inline MD_SIMD_MASK simd_mask_and(MD_SIMD_MASK a, MD_SIMD_MASK b) { return _mm256_and_pd(a, b); }
// TODO: Initialize all diagonal cases and just select the proper one (all bits set or diagonal) based on cond0
static inline MD_SIMD_MASK simd_mask_from_u32(unsigned int a) {
@ -96,6 +97,7 @@ static inline MD_SIMD_FLOAT simd_reciprocal(MD_SIMD_FLOAT a) { return _mm256_rcp
static inline MD_SIMD_FLOAT simd_fma(MD_SIMD_FLOAT a, MD_SIMD_FLOAT b, MD_SIMD_FLOAT c) { return _mm256_fmadd_pd(a, b, c); }
static inline MD_SIMD_FLOAT simd_masked_add(MD_SIMD_FLOAT a, MD_SIMD_FLOAT b, MD_SIMD_MASK m) { return _mm256_mask_add_pd(a, m, a, b); }
static inline MD_SIMD_MASK simd_mask_cond_lt(MD_SIMD_FLOAT a, MD_SIMD_FLOAT b) { return _mm256_cmp_pd_mask(a, b, _CMP_LT_OQ); }
static inline MD_SIMD_MASK simd_mask_int_cond_lt(MD_SIMD_INT a, MD_SIMD_INT b) { return _mm_cmplt_epi32_mask(a, b); }
static inline MD_SIMD_MASK simd_mask_and(MD_SIMD_MASK a, MD_SIMD_MASK b) { return _kand_mask8(a, b); }
static inline MD_SIMD_MASK simd_mask_from_u32(unsigned int a) { return _cvtu32_mask8(a); }
static inline unsigned int simd_mask_to_u32(MD_SIMD_MASK a) { return _cvtmask8_u32(a); }
@ -109,13 +111,13 @@ static inline MD_FLOAT simd_h_reduce_sum(MD_SIMD_FLOAT a) {
return *((MD_FLOAT *) &a0);
}
#endif
static inline void simd_h_decr3(MD_FLOAT *m, MD_SIMD_FLOAT a0, MD_SIMD_FLOAT a1, MD_SIMD_FLOAT a2) {
fprintf(stderr, "simd_h_decr3(): Not implemented for AVX/AVX2 with double precision!");
exit(-1);
}
#endif
// Functions used in LAMMPS kernel
static inline MD_SIMD_FLOAT simd_gather(MD_SIMD_INT vidx, const MD_FLOAT *m, int s) { return _mm256_i32gather_pd(m, vidx, s); }
static inline MD_SIMD_INT simd_int_broadcast(int scalar) { return _mm_set1_epi32(scalar); }
@ -125,4 +127,3 @@ static inline MD_SIMD_INT simd_int_load(const int *m) { return _mm_load_si128((_
static inline MD_SIMD_INT simd_int_add(MD_SIMD_INT a, MD_SIMD_INT b) { return _mm_add_epi32(a, b); }
static inline MD_SIMD_INT simd_int_mul(MD_SIMD_INT a, MD_SIMD_INT b) { return _mm_mul_epi32(a, b); }
static inline MD_SIMD_INT simd_int_mask_load(const int *m, MD_SIMD_MASK k) { return simd_int_load(m) & _mm256_cvtpd_epi32(k); }
static inline MD_SIMD_MASK simd_mask_int_cond_lt(MD_SIMD_INT a, MD_SIMD_INT b) { return _mm256_cvtepi32_pd(_mm_cmplt_epi32(a, b)); }

1
common/includes/util.h
View File

@ -44,5 +44,6 @@ 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();
extern void readline(char *line, FILE *fp);
#endif

2
common/parameter.c
View File

@ -67,7 +67,7 @@ void readParameter(Parameter *param, const char *filename) {
while(!feof(fp)) {
line[0] = '\0';
fgets(line, MAXLINE, fp);
readline(line, fp);
for(i = 0; line[i] != '\0' && line[i] != '#'; i++);
line[i] = '\0';

8
common/util.c
View File

@ -4,6 +4,7 @@
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <util.h>
@ -80,3 +81,10 @@ int get_num_threads() {
const char *num_threads_env = getenv("NUM_THREADS");
return (num_threads_env == NULL) ? 32 : atoi(num_threads_env);
}
void readline(char *line, FILE *fp) {
if(fgets(line, MAXLINE, fp) == NULL) {
fprintf(stderr, "readline(): Error: could not read line!\n");
exit(-1);
}
}

24
gromacs/atom.c
View File

@ -147,7 +147,7 @@ int readAtom_pdb(Atom* atom, Parameter* param) {
}
while(!feof(fp)) {
fgets(line, MAXLINE, fp);
readline(line, fp);
char *item = strtok(line, " ");
if(strncmp(item, "CRYST1", 6) == 0) {
param->xlo = 0.0;
@ -234,15 +234,15 @@ int readAtom_gro(Atom* atom, Parameter* param) {
return -1;
}
fgets(desc, MAXLINE, fp);
readline(desc, fp);
for(i = 0; desc[i] != '\n'; i++);
desc[i] = '\0';
fgets(line, MAXLINE, fp);
readline(line, fp);
atoms_to_read = atoi(strtok(line, " "));
fprintf(stdout, "System: %s with %d atoms\n", desc, atoms_to_read);
while(!feof(fp) && read_atoms < atoms_to_read) {
fgets(line, MAXLINE, fp);
readline(line, fp);
char *label = strtok(line, " ");
int type = type_str2int(strtok(NULL, " "));
int atom_id = atoi(strtok(NULL, " ")) - 1;
@ -265,7 +265,7 @@ int readAtom_gro(Atom* atom, Parameter* param) {
}
if(!feof(fp)) {
fgets(line, MAXLINE, fp);
readline(line, fp);
param->xlo = 0.0;
param->xhi = atof(strtok(line, " "));
param->ylo = 0.0;
@ -314,15 +314,15 @@ int readAtom_dmp(Atom* atom, Parameter* param) {
}
while(!feof(fp) && ts < 1 && !read_atoms) {
fgets(line, MAXLINE, fp);
readline(line, fp);
if(strncmp(line, "ITEM: ", 6) == 0) {
char *item = &line[6];
if(strncmp(item, "TIMESTEP", 8) == 0) {
fgets(line, MAXLINE, fp);
readline(line, fp);
ts = atoi(line);
} else if(strncmp(item, "NUMBER OF ATOMS", 15) == 0) {
fgets(line, MAXLINE, fp);
readline(line, fp);
natoms = atoi(line);
atom->Natoms = natoms;
atom->Nlocal = natoms;
@ -330,23 +330,23 @@ int readAtom_dmp(Atom* atom, Parameter* param) {
growAtom(atom);
}
} else if(strncmp(item, "BOX BOUNDS pp pp pp", 19) == 0) {
fgets(line, MAXLINE, fp);
readline(line, fp);
param->xlo = atof(strtok(line, " "));
param->xhi = atof(strtok(NULL, " "));
param->xprd = param->xhi - param->xlo;
fgets(line, MAXLINE, fp);
readline(line, fp);
param->ylo = atof(strtok(line, " "));
param->yhi = atof(strtok(NULL, " "));
param->yprd = param->yhi - param->ylo;
fgets(line, MAXLINE, fp);
readline(line, fp);
param->zlo = atof(strtok(line, " "));
param->zhi = atof(strtok(NULL, " "));
param->zprd = param->zhi - param->zlo;
} else if(strncmp(item, "ATOMS id type x y z vx vy vz", 28) == 0) {
for(int i = 0; i < natoms; i++) {
fgets(line, MAXLINE, fp);
readline(line, fp);
atom_id = atoi(strtok(line, " ")) - 1;
atom->type[atom_id] = atoi(strtok(NULL, " "));
atom_x(atom_id) = atof(strtok(NULL, " "));

1
include_ISA.mk
View File

@ -2,6 +2,7 @@ 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

30
lammps/atom.c
View File

@ -4,8 +4,8 @@
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.
*/
#include <stdlib.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
@ -186,7 +186,7 @@ int readAtom_pdb(Atom* atom, Parameter* param) {
}
while(!feof(fp)) {
fgets(line, MAXLINE, fp);
readline(line, fp);
char *item = strtok(line, " ");
if(strncmp(item, "CRYST1", 6) == 0) {
param->xlo = 0.0;
@ -273,15 +273,15 @@ int readAtom_gro(Atom* atom, Parameter* param) {
return -1;
}
fgets(desc, MAXLINE, fp);
readline(desc, fp);
for(i = 0; desc[i] != '\n'; i++);
desc[i] = '\0';
fgets(line, MAXLINE, fp);
readline(line, fp);
atoms_to_read = atoi(strtok(line, " "));
fprintf(stdout, "System: %s with %d atoms\n", desc, atoms_to_read);
while(!feof(fp) && read_atoms < atoms_to_read) {
fgets(line, MAXLINE, fp);
readline(line, fp);
char *label = strtok(line, " ");
int type = type_str2int(strtok(NULL, " "));
int atom_id = atoi(strtok(NULL, " ")) - 1;
@ -304,7 +304,7 @@ int readAtom_gro(Atom* atom, Parameter* param) {
}
if(!feof(fp)) {
fgets(line, MAXLINE, fp);
readline(line, fp);
param->xlo = 0.0;
param->xhi = atof(strtok(line, " "));
param->ylo = 0.0;
@ -353,15 +353,15 @@ int readAtom_dmp(Atom* atom, Parameter* param) {
}
while(!feof(fp) && ts < 1 && !read_atoms) {
fgets(line, MAXLINE, fp);
readline(line, fp);
if(strncmp(line, "ITEM: ", 6) == 0) {
char *item = &line[6];
if(strncmp(item, "TIMESTEP", 8) == 0) {
fgets(line, MAXLINE, fp);
readline(line, fp);
ts = atoi(line);
} else if(strncmp(item, "NUMBER OF ATOMS", 15) == 0) {
fgets(line, MAXLINE, fp);
readline(line, fp);
natoms = atoi(line);
atom->Natoms = natoms;
atom->Nlocal = natoms;
@ -369,23 +369,23 @@ int readAtom_dmp(Atom* atom, Parameter* param) {
growAtom(atom);
}
} else if(strncmp(item, "BOX BOUNDS pp pp pp", 19) == 0) {
fgets(line, MAXLINE, fp);
readline(line, fp);
param->xlo = atof(strtok(line, " "));
param->xhi = atof(strtok(NULL, " "));
param->xprd = param->xhi - param->xlo;
fgets(line, MAXLINE, fp);
readline(line, fp);
param->ylo = atof(strtok(line, " "));
param->yhi = atof(strtok(NULL, " "));
param->yprd = param->yhi - param->ylo;
fgets(line, MAXLINE, fp);
readline(line, fp);
param->zlo = atof(strtok(line, " "));
param->zhi = atof(strtok(NULL, " "));
param->zprd = param->zhi - param->zlo;
} else if(strncmp(item, "ATOMS id type x y z vx vy vz", 28) == 0) {
for(int i = 0; i < natoms; i++) {
fgets(line, MAXLINE, fp);
readline(line, fp);
atom_id = atoi(strtok(line, " ")) - 1;
atom->type[atom_id] = atoi(strtok(NULL, " "));
atom_x(atom_id) = atof(strtok(NULL, " "));
@ -442,7 +442,7 @@ int readAtom_in(Atom* atom, Parameter* param) {
return -1;
}
fgets(line, MAXLINE, fp);
readline(line, fp);
natoms = atoi(strtok(line, " "));
param->xlo = atof(strtok(NULL, " "));
param->xhi = atof(strtok(NULL, " "));
@ -459,7 +459,7 @@ int readAtom_in(Atom* atom, Parameter* param) {
}
for(int i = 0; i < natoms; i++) {
fgets(line, MAXLINE, fp);
readline(line, fp);
// TODO: store mass per atom
char *s_mass = strtok(line, " ");