diff --git a/makefiles/Makefile b/makefiles/Makefile
index 26c1d33a84..41a119d3a5 100644
--- a/makefiles/Makefile
+++ b/makefiles/Makefile
@@ -69,19 +69,20 @@ LIBCUSMM_DIR := $(shell find $(SRCDIR) -type d -name "libcusmm")
 ALL_PREPRETTY_DIRS = $(shell find $(SRCDIR) -type d -name preprettify)
 
 ALL_PKG_FILES  = $(shell find $(SRCDIR) ! -path "*/preprettify/*" -name "PACKAGE")
-OBJ_SRC_FILES  = $(shell find $(SRCDIR) ! -path "*/preprettify/*" -name "*.F")
-OBJ_SRC_FILES += $(shell find $(SRCDIR) ! -path "*/preprettify/*" -name "*.c")
-OBJ_SRC_FILES += $(shell find $(SRCDIR) ! -path "*/preprettify/*" -name "*.cpp")
-OBJ_SRC_FILES += $(shell find $(SRCDIR) ! -path "*/preprettify/*" -name "*.cxx")
-OBJ_SRC_FILES += $(shell find $(SRCDIR) ! -path "*/preprettify/*" -name "*.cc")
+OBJ_SRC_FILES  = $(shell cd $(SRCDIR); find  ! -path "*/preprettify/*" -name "*.F")
+OBJ_SRC_FILES += $(shell cd $(SRCDIR); find  ! -path "*/preprettify/*" -name "*.c")
+OBJ_SRC_FILES += $(shell cd $(SRCDIR); find  ! -path "*/preprettify/*" -name "*.cpp")
+OBJ_SRC_FILES += $(shell cd $(SRCDIR); find  ! -path "*/preprettify/*" -name "*.cxx")
+OBJ_SRC_FILES += $(shell cd $(SRCDIR); find  ! -path "*/preprettify/*" -name "*.cc")
+
 
 ifneq ($(NVCC),)
-OBJ_SRC_FILES += $(shell find $(SRCDIR) ! -path "*/preprettify/*" ! -name "libcusmm.cu" -name "*.cu")
+OBJ_SRC_FILES += $(shell cd $(SRCDIR);  find  ! -path "*/preprettify/*" ! -name "libcusmm.cu" -name "*.cu")
 OBJ_SRC_FILES += $(LIBCUSMM_DIR)/libcusmm.cu
 endif
 
 # Include also source files which won't compile into an object file
-ALL_SRC_FILES  = $(OBJ_SRC_FILES)
+ALL_SRC_FILES  = $(strip $(subst $(NULL) .,$(NULL) $(SRCDIR),$(NULL) $(OBJ_SRC_FILES)))
 ALL_SRC_FILES += $(shell find $(SRCDIR) ! -path "*/preprettify/*" -name "*.f90")
 ALL_SRC_FILES += $(shell find $(SRCDIR) ! -path "*/preprettify/*" -name "*.h")
 ALL_SRC_FILES += $(shell find $(SRCDIR) ! -path "*/preprettify/*" -name "*.hpp")
@@ -355,7 +356,7 @@ ifeq ($(LD_SHARED),)
 	@$(TOOLSRC)/build_utils/check_archives.py $(firstword $(AR)) $(SRCDIR) $(LIBDIR)
 endif
 	@echo "Resolving dependencies for $(ONEVERSION) ... "
-	@$(TOOLSRC)/build_utils/makedep.py $(OBJDIR)/all.dep $(MODDEPS) $(MAKEDEPMODE) $(ARCHIVE_EXT) $(OBJ_SRC_FILES)
+	@$(TOOLSRC)/build_utils/makedep.py $(OBJDIR)/all.dep $(MODDEPS) $(MAKEDEPMODE) $(ARCHIVE_EXT) $(SRCDIR) $(OBJ_SRC_FILES)
 
 # on stage 4, load the rules generated by makedep.py
 ifeq ($(INCLUDE_DEPS), true)
diff --git a/tools/build_utils/makedep.py b/tools/build_utils/makedep.py
index 67f7609c32..040f04281c 100755
--- a/tools/build_utils/makedep.py
+++ b/tools/build_utils/makedep.py
@@ -25,7 +25,13 @@ def main():
     mod_format = sys.argv[2]
     mode = sys.argv[3]
     archive_ext = sys.argv[4]
-    src_files = sys.argv[5:]
+    src_dir = sys.argv[5]
+    src_files_tmp = sys.argv[6:]
+    src_files = []
+    for fn_part in src_files_tmp:
+        fn_part = fn_part[1:]
+        fn = src_dir + fn_part
+        src_files.append(fn)
     if(mod_format not in ('lower', 'upper', 'no')):
         error('Module filename format must be eighter of "lower", "upper", or "no".')
     if(mode not in ('normal', 'hackdep', 'mod_compiler')):