diff --git a/CMakeLists.txt b/CMakeLists.txt
index ba9af2cc7b7acd761dd9da644ca3d8c00775e338..48e52961a95d50264b201eec50ccb3a462f39c54 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -204,6 +204,11 @@ include(external/snappy)    # download snappy
 include(external/snappystream)
 include(external/threadpool)
 
+include(flags)              # set paddle compile flags
+include(cudnn)              # set cudnn libraries, must before configure
+include(cupti)
+include(configure)          # add paddle env configuration
+
 if(WITH_GPU)
     include(cuda)
     include(tensorrt)
@@ -212,10 +217,6 @@ elseif()
     set(WITH_ANAKIN OFF CACHE STRING "Anakin is used in GPU only now." FORCE)
 endif()
 
-include(flags)              # set paddle compile flags
-include(cudnn)              # set cudnn libraries, must before configure
-include(cupti)
-include(configure)          # add paddle env configuration
 include(generic)            # simplify cmake module
 include(package)            # set paddle packages
 include(ccache)             # set ccache for compilation
diff --git a/cmake/configure.cmake b/cmake/configure.cmake
index 0a8d891b081deaa1142a63f952667bfb516c5215..e03e15bfc017ce33e06192a7fa8010ffe060adcb 100644
--- a/cmake/configure.cmake
+++ b/cmake/configure.cmake
@@ -112,8 +112,11 @@ if(WITH_GPU)
         endif()
     endif()
     if(WITH_ANAKIN)
-        set(ENV{CUDNN_INCLUDE_DIR} ${CUDNN_INCLUDE_DIR})
-        set(ENV{CUDNN_LIBRARY} ${CUDNN_LIBRARY})
+        # NOTICE(minqiyang): the end slash is important because $CUDNN_INCLUDE_DIR
+        # is a softlink to real cudnn.h directory
+        set(ENV{CUDNN_INCLUDE_DIR} "${CUDNN_INCLUDE_DIR}/")
+        get_filename_component(CUDNN_LIBRARY_DIR ${CUDNN_LIBRARY} DIRECTORY)
+        set(ENV{CUDNN_LIBRARY} ${CUDNN_LIBRARY_DIR})
     endif()
 elseif(WITH_AMD_GPU)
     add_definitions(-DPADDLE_WITH_HIP)
diff --git a/cmake/external/anakin.cmake b/cmake/external/anakin.cmake
index 855897394a602736f3a4fa1132c634f8cb537468..5d11d238cd73653b60623bf7e32b94f5f1ac9ecc 100644
--- a/cmake/external/anakin.cmake
+++ b/cmake/external/anakin.cmake
@@ -19,17 +19,17 @@ execute_process(COMMAND bash -c "cd ${ANAKIN_SOURCE_DIR}; wget -q --no-check-cer
 include_directories(${ANAKIN_INCLUDE})
 include_directories(${ANAKIN_INCLUDE}/saber/)
 
-set(ANAKIN_COMPILE_EXTRA_FLAGS 
+set(ANAKIN_COMPILE_EXTRA_FLAGS
     -Wno-error=unused-but-set-variable -Wno-unused-but-set-variable
-    -Wno-error=unused-variable -Wno-unused-variable 
+    -Wno-error=unused-variable -Wno-unused-variable
     -Wno-error=format-extra-args -Wno-format-extra-args
-    -Wno-error=comment -Wno-comment 
-    -Wno-error=format -Wno-format 
+    -Wno-error=comment -Wno-comment
+    -Wno-error=format -Wno-format
     -Wno-error=switch -Wno-switch
-    -Wno-error=return-type -Wno-return-type 
+    -Wno-error=return-type -Wno-return-type
     -Wno-error=non-virtual-dtor -Wno-non-virtual-dtor
     -Wno-sign-compare
-    -Wno-reorder 
+    -Wno-reorder
     -Wno-error=cpp)
 
 ExternalProject_Add(
@@ -47,6 +47,7 @@ ExternalProject_Add(
                         -DPROTOBUF_ROOT=${THIRD_PARTY_PATH}/install/protobuf
                         -DMKLML_ROOT=${THIRD_PARTY_PATH}/install/mklml
                         -DCUDNN_ROOT=${CUDNN_ROOT}
+                        -DCUDNN_INCLUDE_DIR=${CUDNN_INCLUDE_DIR}
                         ${EXTERNAL_OPTIONAL_ARGS}
     CMAKE_CACHE_ARGS    -DCMAKE_INSTALL_PREFIX:PATH=${ANAKIN_INSTALL_DIR}
 )