moebiusband/MD-Bench
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Introduce common directory

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti
2022-08-17 17:20:57 +02:00
parent 418f392a11
commit 47db9e86b0
5 changed files with 8 additions and 157 deletions
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9
Makefile
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@@ -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 $@

0
lammps/includes/util.h → common/includes/util.h
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0
lammps/util.c → common/util.c
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61
gromacs/includes/util.h
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@@ -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

95
gromacs/util.c
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@@ -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";
}