Introduce common directory

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

Makefile

@@ -3,6 +3,7 @@ TARGET	   = MDBench-$(TAG)-$(OPT_SCHEME)
 BUILD_DIR  = ./$(TAG)-$(OPT_SCHEME)
 SRC_DIR    = ./$(OPT_SCHEME)
 ASM_DIR    = ./asm
+COMMON_DIR = ./common
 CUDA_DIR   = ./$(SRC_DIR)/cuda
 MAKE_DIR   = ./
 Q         ?= @
@@ -13,7 +14,7 @@ include $(MAKE_DIR)/include_$(TAG).mk
 include $(MAKE_DIR)/include_LIKWID.mk
 include $(MAKE_DIR)/include_ISA.mk
 include $(MAKE_DIR)/include_GROMACS.mk
-INCLUDES  += -I./$(SRC_DIR)/includes
+INCLUDES  += -I./$(SRC_DIR)/includes -I./$(COMMON_DIR)/includes
 
 ifeq ($(strip $(DATA_LAYOUT)),AOS)
     DEFINES +=  -DAOS
@@ -89,6 +90,7 @@ ASM       = $(patsubst $(SRC_DIR)/%.c, $(BUILD_DIR)/%.s,$(wildcard $(SRC_DIR)/*.
 OVERWRITE:= $(patsubst $(ASM_DIR)/%-new.s, $(BUILD_DIR)/%.o,$(wildcard $(ASM_DIR)/*-new.s))
 OBJ       = $(filter-out $(BUILD_DIR)/main% $(OVERWRITE),$(patsubst $(SRC_DIR)/%.c, $(BUILD_DIR)/%.o,$(wildcard $(SRC_DIR)/*.c)))
 OBJ      += $(patsubst $(ASM_DIR)/%.s, $(BUILD_DIR)/%.o,$(wildcard $(ASM_DIR)/*.s))
+OBJ      += $(patsubst $(COMMON_DIR)/%.c, $(BUILD_DIR)/%-common.o,$(wildcard $(COMMON_DIR)/*.c))
 ifeq ($(strip $(TAG)),NVCC)
 OBJ      += $(patsubst $(CUDA_DIR)/%.cu, $(BUILD_DIR)/%-cuda.o,$(wildcard $(CUDA_DIR)/*.cu))
 endif
@@ -114,6 +116,11 @@ $(BUILD_DIR)/%.o:  %.c
 	$(Q)$(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@
 	$(Q)$(CC) $(CPPFLAGS) -MT $@ -MM  $< > $(BUILD_DIR)/$*.d
 
+$(BUILD_DIR)/%-common.o:  $(COMMON_DIR)/%.c
+	$(info ===>  COMPILE  $@)
+	$(Q)$(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@
+	$(Q)$(CC) $(CPPFLAGS) -MT $@ -MM  $< > $(BUILD_DIR)/$*.d
+
 $(BUILD_DIR)/%-cuda.o:  %.cu
 	$(info ===>  COMPILE  $@)
 	$(Q)$(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@

gromacs/includes/util.h

@@ -1,61 +0,0 @@
-/*
- * =======================================================================================
- *
- *   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/>.
- * =======================================================================================
- */
-#ifndef __UTIL_H_
-#define __UTIL_H_
-
-#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
-#   define DEBUG_MESSAGE
-#endif
-
-#ifndef MAXLINE
-#   define MAXLINE 4096
-#endif
-
-#if PRECISION == 1
-#   define PRECISION_STRING "single"
-#else
-#   define PRECISION_STRING "double"
-#endif
-
-#define FF_LJ   0
-#define FF_EAM  1
-
-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);
-#endif

gromacs/util.c

@@ -1,95 +0,0 @@
-/*
- * =======================================================================================
- *
- *   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 <string.h>
-
-#include <util.h>
-
-/* Park/Miller RNG w/out MASKING, so as to be like f90s version */
-#define IA 16807
-#define IM 2147483647
-#define AM (1.0/IM)
-#define IQ 127773
-#define IR 2836
-#define MASK 123459876
-
-double myrandom(int* seed)
-{
-    int k= (*seed) / IQ;
-    double ans;
-
-    *seed = IA * (*seed - k * IQ) - IR * k;
-    if(*seed < 0) *seed += IM;
-    ans = AM * (*seed);
-    return ans;
-}
-
-void random_reset(int *seed, int ibase, double *coord)
-{
-  int i;
-  char *str = (char *) &ibase;
-  int n = sizeof(int);
-  unsigned int hash = 0;
-
-  for (i = 0; i < n; i++) {
-    hash += str[i];
-    hash += (hash << 10);
-    hash ^= (hash >> 6);
-  }
-
-  str = (char *) coord;
-  n = 3 * sizeof(double);
-  for (i = 0; i < n; i++) {
-    hash += str[i];
-    hash += (hash << 10);
-    hash ^= (hash >> 6);
-  }
-
-  hash += (hash << 3);
-  hash ^= (hash >> 11);
-  hash += (hash << 15);
-
-  // keep 31 bits of unsigned int as new seed
-  // do not allow seed = 0, since will cause hang in gaussian()
-
-  *seed = hash & 0x7ffffff;
-  if (!(*seed)) *seed = 1;
-
-  // warm up the RNG
-
-  for (i = 0; i < 5; i++) myrandom(seed);
-  //save = 0;
-}
-
-int str2ff(const char *string)
-{
-    if(strncmp(string, "lj", 2) == 0) return FF_LJ;
-    if(strncmp(string, "eam", 3) == 0) return FF_EAM;
-    return -1;
-}
-
-const char* ff2str(int ff)
-{
-    if(ff == FF_LJ) { return "lj"; }
-    if(ff == FF_EAM) { return "eam"; }
-    return "invalid";
-}