diff --git a/hpvm/projects/hpvm-rt/CMakeLists.txt b/hpvm/projects/hpvm-rt/CMakeLists.txt
index ad78c35828cf9be9f66f23301fbe4d207222d4d1..48cf16282661862a86a254b6e40097a830cc2d43 100644
--- a/hpvm/projects/hpvm-rt/CMakeLists.txt
+++ b/hpvm/projects/hpvm-rt/CMakeLists.txt
@@ -20,4 +20,4 @@ add_custom_command(
     ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/hpvm-rt.dir/hpvm-rt.cpp.o
     ${CMAKE_CURRENT_BINARY_DIR}/hpvm-rt.bc
 )
-add_custom_target(hpvm-rt.bc ALL DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/hpvm-rt.bc")
+add_custom_target(hpvm-rt-bc ALL DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/hpvm-rt.bc")
diff --git a/hpvm/test/dnn_benchmarks/hpvm-c/CMakeLists.txt b/hpvm/test/dnn_benchmarks/hpvm-c/CMakeLists.txt
index 6664827014d40c8a101f0aa30499228345edc460..d429bca23cd56cafc70a84fe79a35fed38912bec 100644
--- a/hpvm/test/dnn_benchmarks/hpvm-c/CMakeLists.txt
+++ b/hpvm/test/dnn_benchmarks/hpvm-c/CMakeLists.txt
@@ -4,18 +4,21 @@ get_filename_component(APPROXHPVM_PY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/approxhpv
 # Each source file contains a @MODEL_PARAMS_DIR@ waiting to be filled in.
 set(MODEL_PARAMS_DIR "${CMAKE_CURRENT_SOURCE_DIR}/../model_params/")
 set(test_compile_targets "")
-function(compile_hpvm_c bin_filename src_filepath codegen_target)
-  set(generated_file_path "${CMAKE_CURRENT_BINARY_DIR}/${bin_filename}.cpp")
+function(compile_hpvm_c target_name src_filepath codegen_target)
+  set(generated_file_path "${CMAKE_CURRENT_BINARY_DIR}/${target_name}.cpp")
+  set(output_bin_path "${CMAKE_CURRENT_BINARY_DIR}/hpvm_${target_name}")
   configure_file(${src_filepath} ${generated_file_path})
+  # Add an "hpvm_" prefix here because Ninja generator doesn't like
+  # the name of output file and custom target to clash.
   add_custom_command(
-    OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/${bin_filename}
+    OUTPUT ${output_bin_path}
     DEPENDS ${generated_file_path} approxhpvm.py
     COMMAND ${APPROXHPVM_PY}
-      ${generated_file_path} ${CMAKE_CURRENT_BINARY_DIR}/${bin_filename}
+      ${generated_file_path} ${output_bin_path}
       -t ${codegen_target} -I ${CMAKE_CURRENT_SOURCE_DIR}/include ${ARGN}
   )
-  add_custom_target(${bin_filename} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/${bin_filename})
-  set(test_compile_targets ${test_compile_targets} ${bin_filename} PARENT_SCOPE)
+  add_custom_target(${target_name} DEPENDS ${output_bin_path})
+  set(test_compile_targets ${test_compile_targets} ${target_name} PARENT_SCOPE)
 endfunction(compile_hpvm_c)
 
 function(hpvm_add_dnn_test benchmark_target)
@@ -29,7 +32,8 @@ function(hpvm_add_dnn_test benchmark_target)
   # Removes the final_accuracy file
   llvm_test_run(EXECUTABLE rm final_accuracy)
   # llvm_add_test creates .test file to given output path for given binary.
-  llvm_add_test(${benchmark_target}.test ${CMAKE_CURRENT_BINARY_DIR}/${benchmark_target})
+  # Also add "hpvm_" prefix here because compile_hpvm_c() did.
+  llvm_add_test(${benchmark_target}.test ${CMAKE_CURRENT_BINARY_DIR}/hpvm_${benchmark_target})
   # TODO: add_dependencies
 endfunction(hpvm_add_dnn_test)
 
diff --git a/hpvm/test/hpvm_pass/CMakeLists.txt b/hpvm/test/hpvm_pass/CMakeLists.txt
index fe929f4d6316b54e4b4b19db1221ae146534ee0b..a2be31fd4fc27dcdb83c5ed7424c6577eefb3d5d 100644
--- a/hpvm/test/hpvm_pass/CMakeLists.txt
+++ b/hpvm/test/hpvm_pass/CMakeLists.txt
@@ -7,7 +7,7 @@ configure_lit_site_cfg(
 
 set(
   HPVM_TEST_DEPENDS
-  opt hpvm-rt.bc
+  opt hpvm-rt-bc
   # Passes:
   LLVMGenHPVM LLVMBuildDFG LLVMLocalMem LLVMClearDFG
   LLVMDFG2LLVM_CPU LLVMDFG2LLVM_OpenCL
diff --git a/hpvm/tools/py-approxhpvm/CMakeLists.txt b/hpvm/tools/py-approxhpvm/CMakeLists.txt
index f9d9d6ec60825fc1e858a28e0598189fd6b1cda5..1e5eeb891d35fc028d1aa85c5e5e679902a4dad7 100644
--- a/hpvm/tools/py-approxhpvm/CMakeLists.txt
+++ b/hpvm/tools/py-approxhpvm/CMakeLists.txt
@@ -43,7 +43,7 @@ file(GENERATE OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/main.py INPUT ${CMAKE_CURRENT_B
 # so we can set these dependencies on it
 set(
     DEPS
-    tensor_runtime hpvm-rt.bc clang opt llvm-link ${AVAILABLE_PASSES}
+    tensor_runtime hpvm-rt-bc clang opt llvm-link ${AVAILABLE_PASSES}
 )
 add_custom_command(
     OUTPUT ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/approxhpvm.py