How to place object files in separate subdirectory

Since you're using GNUmake, use a pattern rule for compiling object files:

$(OBJDIR)/%.o: %.c
    $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $<

This is the makefile that I use for most of my projects,

It permits putting source files, headers and inline files in subfolders, and subfolders of subfolders and so-forth, and will automatically generate a dependency file for each object This means that modification of headers and inline files will trigger recompilation of files which are dependent.

Source files are detected via shell find command, so there is no need to explicitly specify, just keep coding to your hearts content.

It will also copy all files from a 'resources' folder, into the bin folder when the project is compiled, which I find handy most of the time.

To provide credit where it is due, the auto-dependencies feature was based largely off Scott McPeak's page that can be found HERE, with some additional modifications / tweaks for my needs.

Example Makefile

#Compiler and Linker
CC          := g++-mp-4.7

#The Target Binary Program
TARGET      := program

#The Directories, Source, Includes, Objects, Binary and Resources
SRCDIR      := src
INCDIR      := inc
BUILDDIR    := obj
TARGETDIR   := bin
RESDIR      := res
SRCEXT      := cpp
DEPEXT      := d
OBJEXT      := o

#Flags, Libraries and Includes
CFLAGS      := -fopenmp -Wall -O3 -g
LIB         := -fopenmp -lm -larmadillo
INC         := -I$(INCDIR) -I/usr/local/include
INCDEP      := -I$(INCDIR)

#---------------------------------------------------------------------------------
#DO NOT EDIT BELOW THIS LINE
#---------------------------------------------------------------------------------
SOURCES     := $(shell find $(SRCDIR) -type f -name *.$(SRCEXT))
OBJECTS     := $(patsubst $(SRCDIR)/%,$(BUILDDIR)/%,$(SOURCES:.$(SRCEXT)=.$(OBJEXT)))

#Defauilt Make
all: resources $(TARGET)

#Remake
remake: cleaner all

#Copy Resources from Resources Directory to Target Directory
resources: directories
    @cp $(RESDIR)/* $(TARGETDIR)/

#Make the Directories
directories:
    @mkdir -p $(TARGETDIR)
    @mkdir -p $(BUILDDIR)

#Clean only Objecst
clean:
    @$(RM) -rf $(BUILDDIR)

#Full Clean, Objects and Binaries
cleaner: clean
    @$(RM) -rf $(TARGETDIR)

#Pull in dependency info for *existing* .o files
-include $(OBJECTS:.$(OBJEXT)=.$(DEPEXT))

#Link
$(TARGET): $(OBJECTS)
    $(CC) -o $(TARGETDIR)/$(TARGET) $^ $(LIB)

#Compile
$(BUILDDIR)/%.$(OBJEXT): $(SRCDIR)/%.$(SRCEXT)
    @mkdir -p $(dir $@)
    $(CC) $(CFLAGS) $(INC) -c -o $@ $<
    @$(CC) $(CFLAGS) $(INCDEP) -MM $(SRCDIR)/$*.$(SRCEXT) > $(BUILDDIR)/$*.$(DEPEXT)
    @cp -f $(BUILDDIR)/$*.$(DEPEXT) $(BUILDDIR)/$*.$(DEPEXT).tmp
    @sed -e 's|.*:|$(BUILDDIR)/$*.$(OBJEXT):|' < $(BUILDDIR)/$*.$(DEPEXT).tmp > $(BUILDDIR)/$*.$(DEPEXT)
    @sed -e 's/.*://' -e 's/\\$$//' < $(BUILDDIR)/$*.$(DEPEXT).tmp | fmt -1 | sed -e 's/^ *//' -e 's/$$/:/' >> $(BUILDDIR)/$*.$(DEPEXT)
    @rm -f $(BUILDDIR)/$*.$(DEPEXT).tmp

#Non-File Targets
.PHONY: all remake clean cleaner resources

The VPATH lines are wrong, they should be

vpath %.c  src
vpath %.h  src

i.e. not capital and without the = . As it is now, it doesn't find the .h file and thinks it is a target to be made.