diff --git a/.gitignore b/.gitignore
index c3b54ab8559fc61fe2007a69e2a03f0d47434f52..3b5d0fef3fa5c8b03f3d07e04ae964bc66c1c71f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -35,4 +35,5 @@ hpvm/llvm-*.src.tar.xz
 hpvm/llvm-*.src/
 hpvm/projects/hpvm-rt/hpvm-rt.ll
 hpvm/test/**/build/
+hpvm/test/**/run/
 Makefile.config
diff --git a/hpvm/test/benchmarks/hpvm-cava/Makefile b/hpvm/test/benchmarks/hpvm-cava/Makefile
index 624f67eacab85f11710284ba2558d803a9bece55..07bb7f06c0544dc87c8c4947bf04501e5e410e29 100644
--- a/hpvm/test/benchmarks/hpvm-cava/Makefile
+++ b/hpvm/test/benchmarks/hpvm-cava/Makefile
@@ -15,13 +15,14 @@ include $(CONFIG_FILE)
 
 LFLAGS += -lm -lrt
 
-# Build dirs
-ifeq ($(VERSION),)
-    VERSION = Default
+ifeq ($(TARGET),)
+    TARGET = gpu
 endif
+
+# Build dirs
 SRC_DIR = src/
 CAM_PIPE_SRC_DIR = $(SRC_DIR)
-BUILD_DIR = build/$(TARGET)_$(VERSION)
+BUILD_DIR = build/$(TARGET)
 CURRENT_DIR := $(dir $(abspath $(lastword $(MAKEFILE_LIST))))
 
 
@@ -95,8 +96,14 @@ FAILSAFE=
 endif
 
 # Targets
+
 default: $(FAILSAFE) $(BUILD_DIR) $(KERNEL_OCL) $(EXE)
 
+clean :
+	if [ -f $(EXE) ]; then rm $(EXE); fi
+	if [ -f DataflowGraph.dot ]; then rm DataflowGraph.dot*; fi
+	if [ -d $(BUILD_DIR) ]; then rm -rf $(BUILD_DIR); fi
+
 $(KERNEL_OCL) : $(KERNEL)
 	$(OCLBE) $< -o $@
 
diff --git a/hpvm/test/benchmarks/include/hpvm.h b/hpvm/test/benchmarks/include/hpvm.h
index 95482a5ffdd783d74654ee565f2846f163748159..b886ee218897b7f9a261c51618ccd56d1b3d7dce 100644
--- a/hpvm/test/benchmarks/include/hpvm.h
+++ b/hpvm/test/benchmarks/include/hpvm.h
@@ -10,7 +10,7 @@
 #define DEVICE GPU_TARGET
 #endif
 
-#include "../../include/SupportHPVM/HPVMHint.h"
+#include "../../../include/SupportHPVM/HPVMHint.h"
 #ifdef __cplusplus
 #include <cstddef>
 #else
diff --git a/hpvm/test/benchmarks/parboil/benchmarks/stencil/run/hpvm/small/128x128x32.out b/hpvm/test/benchmarks/parboil/benchmarks/stencil/run/hpvm/small/128x128x32.out
deleted file mode 100644
index 530b94020f0746e84ff14650748dc0357193da18..0000000000000000000000000000000000000000
Binary files a/hpvm/test/benchmarks/parboil/benchmarks/stencil/run/hpvm/small/128x128x32.out and /dev/null differ
diff --git a/hpvm/test/benchmarks/parboil/benchmarks/stencil/run/visc/small/128x128x32.out b/hpvm/test/benchmarks/parboil/benchmarks/stencil/run/visc/small/128x128x32.out
deleted file mode 100644
index c2bf4ffecd6f2700966cdc84ade54d013a9db4a9..0000000000000000000000000000000000000000
Binary files a/hpvm/test/benchmarks/parboil/benchmarks/stencil/run/visc/small/128x128x32.out and /dev/null differ
diff --git a/hpvm/test/benchmarks/parboil/common/mk/hpvm.mk b/hpvm/test/benchmarks/parboil/common/mk/hpvm.mk
index 24778a990159365ab024f08c0784cf2eac27f32b..9e0318600a3a2d43ed60922e2f48e7e23ea290a7 100755
--- a/hpvm/test/benchmarks/parboil/common/mk/hpvm.mk
+++ b/hpvm/test/benchmarks/parboil/common/mk/hpvm.mk
@@ -123,8 +123,8 @@ debug:
 
 clean :
 	rm -rf $(BUILDDIR)/*
-	if [ -a $(BIN) ]; then rm $(BIN); fi
-	if [ -a DataflowGraph.dot ]; then rm DataflowGraph.dot*; fi
+	if [ -f $(BIN) ]; then rm $(BIN); fi
+	if [ -f DataflowGraph.dot ]; then rm DataflowGraph.dot*; fi
 	if [ -d $(BUILDDIR) ]; then rm -rf $(BUILDDIR); fi
 	if [ -d $(RUNDIR) ]; then rm -rf $(RUNDIR); fi
 
diff --git a/hpvm/test/benchmarks/pipeline/Makefile b/hpvm/test/benchmarks/pipeline/Makefile
index 06c896e270c7b628b7aa3815c2cd23499b9dd6f0..7a246a651a06ea67246578371d8797682aea5bfd 100644
--- a/hpvm/test/benchmarks/pipeline/Makefile
+++ b/hpvm/test/benchmarks/pipeline/Makefile
@@ -15,6 +15,10 @@ include $(CONFIG_FILE)
 
 LFLAGS += -lm -lrt
 
+ifeq ($(TARGET),)
+    TARGET = gpu
+endif
+
 # Build dirs
 SRC_DIR = src/
 BUILD_DIR = build/$(TARGET)
@@ -82,6 +86,11 @@ endif
 # Targets
 default: $(FAILSAFE) $(BUILD_DIR) $(KERNEL_OCL) $(EXE)
 
+clean :
+	if [ -f $(EXE) ]; then rm $(EXE); fi
+	if [ -f DataflowGraph.dot ]; then rm DataflowGraph.dot*; fi
+	if [ -d $(BUILD_DIR) ]; then rm -rf $(BUILD_DIR); fi
+
 $(KERNEL_OCL) : $(KERNEL)
 	$(OCLBE) $< -o $@
 
diff --git a/hpvm/test/benchmarks/template/Makefile b/hpvm/test/benchmarks/template/Makefile
index 7825096558de5f8e08dd751a64952c84ef6f6047..5524f05286be7fb8bea1aac163f5732e1f31c966 100644
--- a/hpvm/test/benchmarks/template/Makefile
+++ b/hpvm/test/benchmarks/template/Makefile
@@ -4,7 +4,7 @@
 # Paths to some dependencies (e.g., HPVM, LLVM) must exist in Makefile.config,
 # which can be copied from Makefile.config.example for a start.
 
-CONFIG_FILE := Makefile.config
+CONFIG_FILE := ../include/Makefile.config
 
 ifeq ($(wildcard $(CONFIG_FILE)),)
     $(error $(CONFIG_FILE) not found. See $(CONFIG_FILE).example)
@@ -17,6 +17,10 @@ EXE_NAME = "exe"
 # Compiler Flags
 LFLAGS += -lm -lrt
 
+ifeq ($(TARGET),)
+    TARGET = gpu
+endif
+
 # Build dirs
 SRC_DIR = src/
 BUILD_DIR = build/$(TARGET)
@@ -41,7 +45,7 @@ OBJS_CFLAGS = $(APP_CFLAGS) $(PLATFORM_CFLAGS)
 CXXFLAGS = $(APP_CXXFLAGS) $(PLATFORM_CXXFLAGS)
 LDFLAGS= $(APP_LDFLAGS) $(PLATFORM_LDFLAGS)
 
-HPVM_RT_PATH = $(LLVM_BUILD_ROOT)/../build/tools/hpvm/projects/hpvm-rt
+HPVM_RT_PATH = $(LLVM_BUILD_DIR)/../build/tools/hpvm/projects/hpvm-rt
 HPVM_RT_LIB = $(HPVM_RT_PATH)/hpvm-rt.bc
 
 TESTGEN_OPTFLAGS = -load LLVMGenHPVM.so -genhpvm -globaldce
@@ -85,6 +89,11 @@ endif
 # Targets
 default: $(FAILSAFE) $(BUILD_DIR) $(KERNEL_OCL) $(EXE)
 
+clean :
+	if [ -f $(EXE) ]; then rm $(EXE); fi
+	if [ -f DataflowGraph.dot ]; then rm DataflowGraph.dot*; fi
+	if [ -d $(BUILD_DIR) ]; then rm -rf $(BUILD_DIR); fi
+
 $(KERNEL_OCL) : $(KERNEL)
 	$(OCLBE) $< -o $@