Modified structure of Codes directory, now code is divided into SAM and MaM....

Modified structure of Codes directory, now code is divided into SAM and MaM. Exec files must be updated to consider changes in configuration

Codes/Makefile

-CC = gcc
-MCC = mpicc
-#C_FLAGS_ALL = -Wconversion -Wpedantic
-C_FLAGS = -Wall -Wextra -Wshadow -Wfatal-errors
-LD_FLAGS = -lm -pthread
-
 MAM_USE_SLURM ?= 0
 MAM_USE_BARRIERS ?= 0
 MAM_DEBUG ?= 0
-DEF = -DMAM_USE_SLURM=$(MAM_USE_SLURM) -DMAM_USE_BARRIERS=$(MAM_USE_BARRIERS) -DMAM_DEBUG=$(MAM_DEBUG)
-
-ifeq ($(MAM_USE_SLURM),1)
-    LD_FLAGS += -lslurm
-endif
 
-ifeq ($(shell test $(MAM_DEBUG) -gt 0; echo $$?),0)
-    C_FLAGS += -g
-endif
-
-# Final binary
-BIN = a.out
 CONFIG = config.txt
+PROTEO_HOME := $(shell realpath -z $$(echo "$$(pwd)/..") | tr -d '\0')
+
 # Put all auto generated stuff to this build dir.
 BUILD_DIR = ./build
 
-# List of all directories where source files are located
-SRCDIRS = IOcodes Main malleability malleability/spawn_methods malleability/distribution_methods
-
-# List of all .c source files.
-C_FILES = $(foreach dire, $(SRCDIRS), $(wildcard $(dire)/*.c))
-
-# All .o files go to build dir.
-OBJ = $(C_FILES:%.c=$(BUILD_DIR)/%.o)
-# Gcc will create these .d files containing dependencies.
-DEP = $(OBJ:%.o=%.d)
-
 # BASIC RULES
-.PHONY : clean clear install
+.PHONY : all install sam mam clean sam_clean mam_clean clear sam_clear mam_clear
 
 all: install
 
-clean:
-	-rm $(BUILD_DIR)/$(BIN) $(BUILD_DIR)/$(CONFIG) $(OBJ) $(DEP)
-clear:
-	-rm -rf $(BUILD_DIR)
-
-install: $(BIN) $(CONFIG)
-	echo "Done"
-
-# SPECIFIC RULES
 # Default configuration file
 $(CONFIG) : $(BUILD_DIR)/$(CONFIG)
-# Default target named after the binary.
-$(BIN) : $(BUILD_DIR)/$(BIN)
+$(BUILD_DIR)/$(CONFIG):
+	@ mkdir -p $(@D)
+	@ echo "export PROTEO_HOME=$(PROTEO_HOME)" > $(BUILD_DIR)/$(CONFIG)
+	@ echo "export PROTEO_BIN=$(PROTEO_HOME)/Codes/SAM/build/a.out" >> $(BUILD_DIR)/$(CONFIG)
+	@ echo "export PATH=\$$PATH:\$$PROTEO_HOME/Codes/MaM" >> $(BUILD_DIR)/$(CONFIG)
+	@ echo "export LD_LIBRARY_PATH=\$$LD_LIBRARY_PATH:\$$PROTEO_HOME/Codes/MaM/build" >> $(BUILD_DIR)/$(CONFIG)
+	@ echo "codeDir=\"/Codes\"" >> $(BUILD_DIR)/$(CONFIG)
+	@ echo "execDir=\"/Exec\"" >> $(BUILD_DIR)/$(CONFIG)
+
 
-$(BUILD_DIR)/$(CONFIG) :
-	@mkdir -p $(@D)
-	@ echo -n "dir=\"" > $(BUILD_DIR)/$(CONFIG)
-	@ realpath -z $$(echo "$$(pwd)/..") | tr -d '\0' >> $(BUILD_DIR)/$(CONFIG)
-	@ echo "\"" >> $(BUILD_DIR)/$(CONFIG)
+mam:
+	@echo "Compiling MaM"
+	$(MAKE) -C MaM MAM_USE_SLURM=$(MAM_USE_SLURM) MAM_USE_BARRIERS=$(MAM_USE_BARRIERS) MAM_DEBUG=$(MAM_DEBUG)
 
-# Actual target of the binary - depends on all .o files.
-$(BUILD_DIR)/$(BIN) : $(OBJ)
-	$(MCC) $(C_FLAGS) $^ -o $@ $(LD_FLAGS)
+sam: mam
+	@echo "Compiling SAM"
+	$(MAKE) -C SAM
 
-# Include all .d files
-# .d files are used for knowing the dependencies of each source file
--include $(DEP)
+install: mam sam $(CONFIG)
+	echo "Done"
+
+#Clean rules
+sam_clean:
+	@echo "Cleaning SAM"
+	$(MAKE) -C SAM clean
+mam_clean:
+	@echo "Cleaning MaM"
+	$(MAKE) -C MaM clean
+clean: sam_clean mam_clean
+	-rm $(BUILD_DIR)/$(CONFIG)
+
+#Clear rules
+sam_clear:
+	@echo "Clearing SAM"
+	$(MAKE) -C SAM clear
+mam_clear:
+	@echo "Clearing MaM"
+	$(MAKE) -C MaM clear
+clear: sam_clear mam_clear
+	-rm -rf $(BUILD_DIR)
 
-# Build target for every single object file.
-# The potential dependency on header files is covered
-# by calling `-include $(DEP)`.
-# The -MMD flags additionaly creates a .d file with
-# the same name as the .o file.
-$(BUILD_DIR)/%.o : %.c
-	@mkdir -p $(@D)
-	$(MCC) $(C_FLAGS) $(DEF) -MMD -c $< -o $@

Codes/IOcodes/read_ini.c → Codes/SAM/IOcodes/read_ini.c

@@ -3,7 +3,7 @@
 #include <string.h>
 #include "read_ini.h"
 #include "ini.h"
-#include "../malleability/MAM.h"
+#include "../MaM/MAM.h"
 
 
 ext_functions_t *user_functions;