diff --git a/makefiles/Makefile b/makefiles/Makefile
index 67293be056..0a4f29bd1f 100644
--- a/makefiles/Makefile
+++ b/makefiles/Makefile
@@ -27,6 +27,12 @@ EXEDIR       := $(MAINEXEDIR)/$(ARCH)
 REVISION     := $(shell $(CP2KHOME)/tools/get_revision_number $(SRCDIR))
 
 
+# Discover programs =========================================================
+ifeq ($(ALL_EXE_FILES),)
+export ALL_EXE_FILES := $(sort $(shell $(TOOLSRC)/discover_programs.py $(SRCDIR)))
+endif
+EXE_NAMES := $(basename $(notdir $(ALL_EXE_FILES)))
+
 # Once we are down to a single version ======================================
 # this only happens on stage 3 and 4
 ifneq ($(ONEVERSION),)
@@ -35,14 +41,10 @@ include $(CP2KHOME)/arch/$(ARCH).$(ONEVERSION)
 LIBDIR  := $(MAINLIBDIR)/$(ARCH)/$(ONEVERSION)
 OBJDIR  := $(MAINOBJDIR)/$(ARCH)/$(ONEVERSION)
 ifeq ($(NVCC),)
-DISCOVER_FLAGS = "--ignore-cuda-files"
+EXE_NAMES := $(basename $(notdir $(filter-out %.cu, $(ALL_EXE_FILES))))
 endif
 endif
 
-# Discover programs =========================================================
-ALL_EXE_FILES := $(sort $(shell $(TOOLSRC)/discover_programs.py $(SRCDIR) $(DISCOVER_FLAGS) ))
-EXE_NAMES := $(basename $(notdir $(ALL_EXE_FILES)))
-
 # Declare PHONY targets =====================================================
 .PHONY : $(VERSION) $(EXE_NAMES) \
          dirs makedep default_target all \
diff --git a/tools/discover_programs.py b/tools/discover_programs.py
index 5da8864e8b..0829832868 100755
--- a/tools/discover_programs.py
+++ b/tools/discover_programs.py
@@ -10,16 +10,13 @@ re_main = re.compile(r"\sint\s+main\s*\(")
 
 #============================================================================
 def main():
-    if(len(sys.argv) not in (2,3)):
-        print("Usage: discover_programs.py <src-dir> [--ignore-cuda-files]")
+    if(len(sys.argv) != 2):
+        print("Usage: discover_programs.py <src-dir>")
         sys.exit(1)
 
     srcdir = sys.argv[1]
 
-    ignore_cu_files = False
-    if(len(sys.argv) > 2):
-        assert(sys.argv[2] == "--ignore-cuda-files")
-        ignore_cu_files = True
+    sys.stderr.write("Discovering programs ...\n")
 
     programs = []
     for root, dirs, files in os.walk(srcdir):
@@ -34,11 +31,7 @@ def main():
                 if(is_fortran_program(abs_fn)):
                     programs.append(abs_fn)
 
-            elif(fn[-2:] == ".c"):
-                if(has_main_function(abs_fn)):
-                    programs.append(abs_fn)
-
-            elif(fn[-3:] == ".cu" and not ignore_cu_files):
+            elif(fn[-2:]==".c" or fn[-3:]==".cu"):
                 if(has_main_function(abs_fn)):
                     programs.append(abs_fn)