no rule to make target but file exists, compiling - makefile

Question

I can't seem to debug this, could someone please help? The *.f90 file does exists and the directory is correct. I am not sure what it could be, the gfortran compiler works fine outside of the makefile.
make[1]: Entering directory '/media/f/fv/ED-2.1/ED/build/bin'
make[1]: *** No rule to make target 'media/f/fv/ED-2.1/ED/src/utils/allometry.f90', needed by 'allometry.o'. Stop.
make[1]: Leaving directory '/media/f/fv/ED-2.1/ED/build/bin'
Makefile:24: recipe for target 'all' failed
This is the makefile
#----- Define path and compilation --------------------------------------------------------#
include paths.mk
include include.mk.$(OPT)
#----- Compiler commands. -----------------------------------------------------------------#
INCLUDES = $(PAR_INCS) -I$(ED_INCS) $(HDF5_INCS) $(MPI_INCS)
F90_COMMAND = $(F_COMP) -c $(F_OPTS) $(INCLUDES) $(PAR_DEFS)
FPP_COMMAND = $(F_COMP) -c -DUSE_INTERF=$(USE_INTERF) -DUSENC=$(USENC) -D$(CMACH) \
-DUSE_HDF5=$(USE_HDF5) -DUSE_COLLECTIVE_MPIO=$(USE_COLLECTIVE_MPIO) \
-DUSE_MPIWTIME=$(USE_MPIWTIME) $(F_OPTS) $(INCLUDES) $(PAR_DEFS)
CXX_COMMAND = $(C_COMP) -c $(C_OPTS) -D$(CMACH) $(HDF5_INCS) $(INCLUDES) $(PAR_DEFS)
#----- Define archive and executable names. -----------------------------------------------#
EXE=$(BASE)/ed_$(ED_VERSION)-$(OPT)
LIBMODEL=$(BASE)/ed_$(ED_VERSION)-$(OPT).a
include objects.mk
#----- Define targets. --------------------------------------------------------------------#
all:
make gendep
#$(info $$EXE is [${EXE}])
make $(EXE)
make $(EXE)
make $(EXE)
make $(EXE)
make $(EXE)
gendep:
#echo ""
./generate_deps.sh $(ED_ROOT)
#echo === Finished dependencies ===
$(EXE): $(LIBMODEL) $(MAINOBJ)
#echo ""
$(LOADER) -o $(EXE) edmain.o $(LOADER_OPTS) $(LIBMODEL) $(HDF5_LIBS) $(PAR_LIBS) \
$(NC_LIBS) $(LIBS) $(LOADER_OPTS)
#echo ""
#echo Finished building === $(EXE)
#echo ""
$(MAINOBJ): $(MAIN)
#echo ""
cp -f $< $(<F:.f90=.f90)
$(F90_COMMAND) $(<F:.f90=.f90)
rm -f $(<F:.f90=.f90)
$(LIBMODEL): $(OBJ_MODEL)
$(ARCHIVE) $(LIBMODEL) $(OBJ_MODEL)
FORCE:
install:
#echo ""
ln -fs `pwd`/$(EXE) ../run/$(BASE)
ln -fs `pwd`/$(EXE) ../test/$(BASE)
#echo ""
clean:
#echo ""
rm -f $(LIBMODEL) $(EXE) *.o *.mod *.F90 *.f90 *.stb *.d dependency.mk
rm -f ../$(EXE) ../$(LIBMODEL)
touch dependency.mk
#echo ""
#----- Define rules -----------------------------------------------------------------------#
include rules.mk

Answer 1

This makefile is a hot mess. Why do you have the same command make $(EXE) listed 5 times in a row in the all recipe? Why are you using $(<F:.f90=.f90) which just replaces the string .f90 with an identical string .f90, essentially a no-op?
Further, we don't have enough information here to answer your question: you haven't provided the definition of the variables MAINOBJ or OBJ_MODEL, or more importantly, MAIN. At least one of those is wrong. Unless you've mis-transcribed the error message (please always cut and paste actual errors, don't try to manually type them in!!), then this:
make[1]: *** No rule to make target 'media/f/fv/ED-2.1/ED/src/utils/allometry.f90', needed by 'allometry.o'. Stop.
tells you what the problem is; note there is no slash (/) at the beginning of this pathname, before media. So this is not an absolute path, it's a relative path. That means make is actually trying to find the file named /media/f/fv/ED-2.1/ED/build/bin/media/f/fv/ED-2.1/ED/src/utils/allometry.f90 which clearly won't exist.
We can't tell you why this is happening because you haven't provided the information about how these variables are set. Most likely the bad one is MAIN but it's hard to know for sure.