Fix code for AVX and remove warnings

Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>

Makefile

@@ -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

common/eam_utils.c

@@ -54,10 +54,10 @@ void read_eam_file(Funcfl* file, const char* filename) {
     }
 
     int tmp;
-    fgets(line, MAXLINE, fptr);
+    readline(line, fptr);
-    fgets(line, MAXLINE, 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);

common/includes/simd/avx_avx2_double.h

@@ -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)); }

common/includes/util.h

@@ -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

common/parameter.c

@@ -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';
 

common/util.c

@@ -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);
+    }
+}

gromacs/atom.c

@@ -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, " "));

include_ISA.mk

@@ -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

include_NVCC.mk

@@ -6,7 +6,7 @@ ANSI_CFLAGS += -std=c99
 ANSI_CFLAGS += -pedantic
 ANSI_CFLAGS += -Wextra
 
-CFLAGS   = -O3 -march=native  -ffast-math -funroll-loops --forward-unknown-to-host-compiler # -fopenmp
+CFLAGS   = -O3 -march=native -ffast-math -funroll-loops --forward-unknown-to-host-compiler # -fopenmp
 #CFLAGS   = -O3 -march=cascadelake  -ffast-math -funroll-loops --forward-unknown-to-host-compiler # -fopenmp
 #CFLAGS   = -O3 -g # -fopenmp
 #CFLAGS   = -O0 -g  -std=c99 -fargument-noalias

lammps/atom.c

@@ -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, " ");