Modificado los Makefile. Ahora funciona correctamente

Codes/IOcodes/Makefile

-objects := ini.o read_ini.o results.o
-DISTRI_LOC = $(TOP)/malleability/distribution_methods/block_distribution.h
-CC := gcc
-MCC := mpicc
-CFLAGS := -Wall -Wextra
-
-all: $(objects)
-
-ini.o: ini.c ini.h
-	echo $(BUILDDIR)
-	$(CC) $(CFLAGS) -c -o $(BUILDDIR)/$@ $<
-
-read_ini.o: read_ini.c read_ini.h ini.h $(DISTRI_LOC)
-	$(MCC) $(CFLAGS) -c -o $(BUILDDIR)/$@ $<
-
-results.o: results.c results.h
-	$(MCC) $(CFLAGS) -c -o $(BUILDDIR)/$@ $<
-
-#$@ --> Objeto
-#$< --> Source

Codes/Main/Makefile

-objects1 := computing_func comunication_func linear_reg
-objects2 := process_stage
-objects3 := Main
-
-#Pasar nombre a level -- Los objects/headers/source añadir sufijo
-
-DISTRI_LOC = $(TOP)/malleability/distribution_methods/block_distribution.h
-MALLEABILITY_DEPENDS = $(TOP)/malleability/CommDist.h $(TOP)/malleability/malleabilityStates.h $(TOP)/malleability/malleabilityManager.h
-DEPENDS := Main_datatypes.h
-CC := gcc
-MCC := mpicc
-CFLAGS := -Wall -Wextra
-
-all: $(objects1) $(objects2) $(objects3)
-
-$(objects1): %: %.c %.h $(DEPENDS)
-	$(MCC) $(CFLAGS) -c -o $(BUILDDIR)/$@.o $<
-$(objects2): %: %.c %.h $(objects1).h $(DEPENDS) $(DISTRI_LOC)
-	$(MCC) $(CFLAGS) -c -o $(BUILDDIR)/$@.o $<
-$(objects3): %: %.c $(objects2).h $(DEPENDS) $(TOP)/IOcodes/read_ini.h $(TOP)/IOcodes/results.h $(MALLEABILITY_DEPENDS)
-	$(MCC) $(CFLAGS) -c -o $(BUILDDIR)/$@.o $<
-

Codes/Makefile

-export TOP := $(dir $(CURDIR)/$(word $(words $(MAKEFILE_LIST)),$(MAKEFILE_LIST)))
-BUILD := build
-EXEC := exec
-
-EXECDIR := $(addprefix $(TOP),$(EXEC))
-export BUILDDIR = $(addprefix $(TOP),$(BUILD))
-SUBDIRS := IOcodes Main malleability
-
-.PHONY: subdirs $(SUBDIRS) build all clean clear
-#
-#
-#
-#
-CC := gcc
-MCC := mpicc
-CFLAGS := -Wall -Wextra
-LIBFLAGS := -lm -lslurm -pthread
-#
-#
-#
-#
-
-all: subdirs exec
-install: 
-	#runTests
-
-exec: subdirs
-	mkdir -p $(EXECDIR) all
-	$(MCC) $(CFLAGS) -o $(EXECDIR)/a.out $(wildcard $(BUILDDIR)/*.o) $(LIBFLAGS)
-
-subdirs: $(SUBDIRS)
-$(SUBDIRS): | $(BUILD)
-	$(MAKE) -C $@
-
-
-# Carpeta en la que almacenar los compilados y los ejecutables
-$(BUILD):
-	mkdir -p $(BUILDDIR)
+CC = gcc
+MCC = mpicc
+C_FLAGS_ALL = -Wfatal-errors -Wall -Wextra -Wpedantic -Wconversion -Wshadow
+C_FLAGS = -Wall
+LD_FLAGS = -lm -lslurm -pthread
+
+.PHONY : clean clear
+
+# Final binary
+BIN = a.out
+# 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 = $(OBJ:%.o=%.d)
+
+# Default target named after the binary.
+$(BIN) : $(BUILD_DIR)/$(BIN)
+
+# Actual target of the binary - depends on all .o files.
+$(BUILD_DIR)/$(BIN) : $(OBJ)
+	$(MCC) $(C_FLAGS) $^ -o $@ $(LD_FLAGS)
+
+# Include all .d files
+# .d files are used for knowing the dependencies of each source file
+-include $(DEP)
+
+# 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) -MMD -c $< -o $@
 
 clean:
-	-rm $(BUILDDIR)/*.o
+	-rm $(BUILD_DIR)/$(BIN) $(OBJ) $(DEP)
 clear:
 	-rm -rf $(BUILDDIR)
-	-rm -rf $(EXECDIR)
+
+install: 
 

Codes/malleability/Makefile

-dir_targets := distribution_methods
-objects1 := CommDist
-objects2 := malleabilityTypes ProcessDist
-objects3 := malleabilityZombies
-objects4 := malleabilityManager
-DEPENDS := $(addsuffix .h, malleabilityDataStructures malleabilityStates)
-CC := gcc
-MCC := mpicc
-CFLAGS := -Wall -Wextra
-
-.PHONY: $(dir_targets) subdir
-
-all: subdir $(objects1) $(objects2) $(objects3) $(objects4)
-
-subdir: $(dir_targets)
-$(dir_targets): %:
-	$(MAKE) -C $@
-
-$(objects1): %: %.c %.h $(DEPENDS) $(dir_targets)/block_distribution.h
-	$(MCC) $(CFLAGS) -c -o $(BUILDDIR)/$@.o $<
-
-$(objects2): %: %.c %.h $(DEPENDS)
-	$(MCC) $(CFLAGS) -c -o $(BUILDDIR)/$@.o $<
-
-$(objects3): %: %.c %.h $(DEPENDS) $(TOP)/IOcodes/results.h
-	$(MCC) $(CFLAGS) -c -o $(BUILDDIR)/$@.o $<
-
-$(objects4): %: %.c %.h $(objects1).h $(objects2).h $(objects3).h $(DEPENDS) \
-	                $(TOP)/IOcodes/read_ini.h $(TOP)/IOcodes/results.h $(TOP)/Main/Main_datatypes.h
-	$(MCC) $(CFLAGS) -c -o $(BUILDDIR)/$@.o $<

Codes/malleability/ProcessDist.h

-#ifndef PROCESS_DIST_H
-#define PROCESS_DIST_H
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <mpi.h>
-#include <string.h>
-#include <slurm/slurm.h>
-#include "malleabilityStates.h"
-
-int init_slurm_comm(char *argv, int num_cpus, int num_nodes, char *nodelist, int myId, int numP, int numC, int root, int type_dist, int type_creation, int spawn_is_single, MPI_Comm comm, MPI_Comm *child);
-int check_slurm_comm(int myId, int root, int numP, MPI_Comm *child, MPI_Comm comm, MPI_Comm comm_thread, double *end_real_time);
-
-void malleability_establish_connection(int myId, int root, MPI_Comm *intercomm);
-
-
-void proc_adapt_expand(int *numP, int numC, MPI_Comm intercomm, MPI_Comm *comm, int is_children_group);
-void proc_adapt_shrink(int numC, MPI_Comm *comm, int myId);
-
-#endif

Codes/malleability/distribution_methods/Makefile

-objects1 := block_distribution
-CC := gcc
-MCC := mpicc
-CFLAGS := -Wall -Wextra
-
-all: $(objects1)
-
-$(objects1): %: %.c %.h
-	$(MCC) $(CFLAGS) -c -o $(BUILDDIR)/$@.o $<

Codes/malleability/spawn_methods/Makefile

-objects1 := ProcessDist
-objects2 := Spawn_state
-objects3 := Baseline
-objects4 := Merge
-objects5 := GenericSpawn
-CC := gcc
-MCC := mpicc
-CFLAGS := -Wall
-
-all: $(objects1) $(objects2) $(objects3) $(objects4) $(objects5)
-
-$(objects1): %: %.c %.h
-	$(MCC) $(CFLAGS) -c -o $(BUILDDIR)/$@.o $<
-
-$(objects2): %: %.c %.h
-	$(CC) $(CFLAGS) -c -o $(BUILDDIR)/$@.o $<
-
-$(objects3): %: %.c %.h $(objects2).h
-	$(MCC) $(CFLAGS) -c -o $(BUILDDIR)/$@.o $<
-
-$(objects4): %: %.c %.h $(objects3).h
-	$(MCC) $(CFLAGS) -c -o $(BUILDDIR)/$@.o $<
-
-$(objects5): %: %.c %.h $(objects1).h $(objects2).h $(objects3).h $(objects4).h
-	$(MCC) $(CFLAGS) -c -o $(BUILDDIR)/$@.o $<