cmake HDF5 library safe linker path warning

[Eduards Slava]

I am trying to install on remote CentOS server without root priviliges and therefore usa conda install in digits_env environment. Never used cmake before and don't know if configured it correctly but it seems that I have warning related to HDF5 library and its search path. I have probably one system wide and other from conda directory.

If I fallow this stackexchange issue then it removes search path warning:

Cannot generate a safe linker search path for target caffe because files in

  some directories may conflict with libraries in implicit directories:

    link library [libhdf5_hl.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

    link library [libhdf5.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

  Some of these libraries may not be found correctly.

However multiple warnings of library linking still remain:

WARNING: Target "caffe" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

 1) Are these two seperate issues or single problem of HDF5 library path?

 2) How do I fix this?

Full cmake command and output:

(digits_env) [eduardss@ui-1 build]$ cmake -DUSE_LEVELDB=OFF -DUSE_OPENCV=OFF -DBOOST_ROOT=/mnt/home/eduardss/.conda/envs/digits_env/include/boost/ -DCMAKE_PREFIX_PATH=~/.conda/envs/digits_env/ -DPYTHON_EXECUTABLE:FILEPATH=/mnt/home/eduardss/.conda/envs/digits_env/bin/python3.6/ -DPYTHON_LIBRARY=/mnt/home/eduardss/.conda/envs/digits_env/lib/ -DPYTHON_INCLUDE_DIR=/mnt/home/eduardss/.conda/envs/digits_env/include/python3.6m/ ..

-- Boost version: 1.65.1

-- Found the following Boost libraries:

--   system

--   thread

--   filesystem

-- Found gflags  (include: /mnt/home/eduardss/.conda/envs/digits_env/include, library: /mnt/home/eduardss/.conda/envs/digits_env/lib/libgflags.so)

-- Found glog    (include: /mnt/home/eduardss/.conda/envs/digits_env/include, library: /mnt/home/eduardss/.conda/envs/digits_env/lib/libglog.so)

-- Found PROTOBUF Compiler: /mnt/home/eduardss/.conda/envs/digits_env/bin/protoc

-- Found lmdb    (include: /mnt/home/eduardss/.conda/envs/digits_env/include, library: /mnt/home/eduardss/.conda/envs/digits_env/lib/liblmdb.so)

-- CUDA detected: 8.0

-- Found cuDNN: ver. 6.0.21 found (include: /opt/exp_soft/cuda/cuda-8.0/include, library: /opt/exp_soft/cuda/cuda-8.0/lib64/libcudnn.so)

-- Automatic GPU detection failed. Building for all known architectures.

-- Added CUDA NVCC flags for: sm_20 sm_21 sm_30 sm_35 sm_50

-- Found Atlas (include: /usr/include, library: /mnt/home/eduardss/.conda/envs/digits_env/lib/libatlas.a)

-- NumPy ver. 1.14.1 found (include: /mnt/home/eduardss/.conda/envs/digits_env/lib/python3.6/site-packages/numpy/core/include)

-- Boost version: 1.65.1

-- Found the following Boost libraries:

--   python

-- Found NCCL (include: /mnt/home/eduardss/.conda/envs/digits_env/include, library: /mnt/home/eduardss/.conda/envs/digits_env/lib/libnccl.so)

-- Detected Doxygen OUTPUT_DIRECTORY: ./doxygen/

-- 

-- ******************* Caffe Configuration Summary *******************

-- General:

--   Version           :   0.15.14

--   Git               :   v0.15.14-16-g4b8d54d-dirty

--   System            :   Linux

--   C++ compiler      :   /usr/bin/c++

--   Release CXX flags :   -O3 -DNDEBUG -fPIC -Wall -Wno-sign-compare -Wno-uninitialized

--   Debug CXX flags   :   -g -fPIC -Wall -Wno-sign-compare -Wno-uninitialized

--   Build type        :   Release

-- 

--   BUILD_SHARED_LIBS :   ON

--   BUILD_python      :   ON

--   BUILD_matlab      :   OFF

--   BUILD_docs        :   ON

--   CPU_ONLY          :   OFF

--   USE_OPENCV        :   OFF

--   USE_LEVELDB       :   OFF

--   USE_LMDB          :   ON

--   ALLOW_LMDB_NOLOCK :   OFF

-- 

-- Dependencies:

--   BLAS              :   Yes (Atlas)

--   Boost             :   Yes (ver. 1.65)

--   glog              :   Yes

--   gflags            :   Yes

--   protobuf          :   Yes (ver. 3.5.1)

--   lmdb              :   Yes (ver. 0.9.21)

--   CUDA              :   Yes (ver. 8.0)

-- 

-- NVIDIA CUDA:

--   Target GPU(s)     :   Auto

--   GPU arch(s)       :   sm_20 sm_21 sm_30 sm_35 sm_50

--   cuDNN             :   Yes (ver. 6.0.21)

--   NCCL              :   Yes

-- 

-- Python:

--   Interpreter       :   /mnt/home/eduardss/.conda/envs/digits_env/bin/python3.6 (ver. 3.6.4)

--   Libraries         :   /mnt/home/eduardss/.conda/envs/digits_env/lib (ver 3.6.4)

--   NumPy             :   /mnt/home/eduardss/.conda/envs/digits_env/lib/python3.6/site-packages/numpy/core/include (ver 1.14.1)

-- 

-- Documentaion:

--   Doxygen           :   /usr/bin/doxygen (1.8.5)

--   config_file       :   /mnt/home/eduardss/Code/packages/caffe/.Doxyfile

-- 

-- Install:

--   Install path      :   /mnt/home/eduardss/Code/packages/caffe/build/install

-- 

WARNING: Target "caffe" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

WARNING: Target "caffe" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

-- Configuring done

WARNING: Target "caffe" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

WARNING: Target "caffe" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

CMake Warning at src/caffe/CMakeLists.txt:20 (add_library):

  Cannot generate a safe linker search path for target caffe because files in

  some directories may conflict with libraries in implicit directories:

    link library [libhdf5_hl.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

    link library [libhdf5.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

  Some of these libraries may not be found correctly.

WARNING: Target "test.testbin" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

CMake Warning at src/caffe/test/CMakeLists.txt:29 (add_executable):

  Cannot generate a safe linker search path for target test.testbin because

  files in some directories may conflict with libraries in implicit

  directories:

    link library [libhdf5_hl.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

    link library [libhdf5.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

  Some of these libraries may not be found correctly.

WARNING: Target "caffe.bin" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

CMake Warning at tools/CMakeLists.txt:14 (add_executable):

  Cannot generate a safe linker search path for target caffe.bin because

  files in some directories may conflict with libraries in implicit

  directories:

    link library [libhdf5_hl.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

    link library [libhdf5.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

  Some of these libraries may not be found correctly.

WARNING: Target "compute_image_mean" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

CMake Warning at tools/CMakeLists.txt:14 (add_executable):

  Cannot generate a safe linker search path for target compute_image_mean

  because files in some directories may conflict with libraries in implicit

  directories:

    link library [libhdf5_hl.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

    link library [libhdf5.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

  Some of these libraries may not be found correctly.

WARNING: Target "convert_imageset" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

CMake Warning at tools/CMakeLists.txt:14 (add_executable):

  Cannot generate a safe linker search path for target convert_imageset

  because files in some directories may conflict with libraries in implicit

  directories:

    link library [libhdf5_hl.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

    link library [libhdf5.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

  Some of these libraries may not be found correctly.

WARNING: Target "device_query" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

CMake Warning at tools/CMakeLists.txt:14 (add_executable):

  Cannot generate a safe linker search path for target device_query because

  files in some directories may conflict with libraries in implicit

  directories:

    link library [libhdf5_hl.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

    link library [libhdf5.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

  Some of these libraries may not be found correctly.

WARNING: Target "extract_features" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

CMake Warning at tools/CMakeLists.txt:14 (add_executable):

  Cannot generate a safe linker search path for target extract_features

  because files in some directories may conflict with libraries in implicit

  directories:

    link library [libhdf5_hl.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

    link library [libhdf5.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

  Some of these libraries may not be found correctly.

WARNING: Target "finetune_net" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

CMake Warning at tools/CMakeLists.txt:14 (add_executable):

  Cannot generate a safe linker search path for target finetune_net because

  files in some directories may conflict with libraries in implicit

  directories:

    link library [libhdf5_hl.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

    link library [libhdf5.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

  Some of these libraries may not be found correctly.

WARNING: Target "net_speed_benchmark" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

CMake Warning at tools/CMakeLists.txt:14 (add_executable):

  Cannot generate a safe linker search path for target net_speed_benchmark

  because files in some directories may conflict with libraries in implicit

  directories:

    link library [libhdf5_hl.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

    link library [libhdf5.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

  Some of these libraries may not be found correctly.

WARNING: Target "test_net" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

CMake Warning at tools/CMakeLists.txt:14 (add_executable):

  Cannot generate a safe linker search path for target test_net because files

  in some directories may conflict with libraries in implicit directories:

    link library [libhdf5_hl.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

    link library [libhdf5.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

  Some of these libraries may not be found correctly.

WARNING: Target "train_net" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

CMake Warning at tools/CMakeLists.txt:14 (add_executable):

  Cannot generate a safe linker search path for target train_net because

  files in some directories may conflict with libraries in implicit

  directories:

    link library [libhdf5_hl.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

    link library [libhdf5.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

  Some of these libraries may not be found correctly.

WARNING: Target "upgrade_net_proto_binary" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

CMake Warning at tools/CMakeLists.txt:14 (add_executable):

  Cannot generate a safe linker search path for target

  upgrade_net_proto_binary because files in some directories may conflict

  with libraries in implicit directories:

    link library [libhdf5_hl.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

    link library [libhdf5.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

  Some of these libraries may not be found correctly.

WARNING: Target "upgrade_net_proto_text" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

CMake Warning at tools/CMakeLists.txt:14 (add_executable):

  Cannot generate a safe linker search path for target upgrade_net_proto_text

  because files in some directories may conflict with libraries in implicit

  directories:

    link library [libhdf5_hl.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

    link library [libhdf5.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

  Some of these libraries may not be found correctly.

WARNING: Target "upgrade_solver_proto_text" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

CMake Warning at tools/CMakeLists.txt:14 (add_executable):

  Cannot generate a safe linker search path for target

  upgrade_solver_proto_text because files in some directories may conflict

  with libraries in implicit directories:

    link library [libhdf5_hl.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

    link library [libhdf5.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

  Some of these libraries may not be found correctly.

WARNING: Target "classification" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

CMake Warning at examples/CMakeLists.txt:11 (add_executable):

  Cannot generate a safe linker search path for target classification because

  files in some directories may conflict with libraries in implicit

  directories:

    link library [libhdf5_hl.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

    link library [libhdf5.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

  Some of these libraries may not be found correctly.

WARNING: Target "convert_cifar_data" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

CMake Warning at examples/CMakeLists.txt:11 (add_executable):

  Cannot generate a safe linker search path for target convert_cifar_data

  because files in some directories may conflict with libraries in implicit

  directories:

    link library [libhdf5_hl.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

    link library [libhdf5.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

  Some of these libraries may not be found correctly.

WARNING: Target "convert_mnist_data" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

CMake Warning at examples/CMakeLists.txt:11 (add_executable):

  Cannot generate a safe linker search path for target convert_mnist_data

  because files in some directories may conflict with libraries in implicit

  directories:

    link library [libhdf5_hl.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

    link library [libhdf5.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

  Some of these libraries may not be found correctly.

WARNING: Target "convert_mnist_siamese_data" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

CMake Warning at examples/CMakeLists.txt:11 (add_executable):

  Cannot generate a safe linker search path for target

  convert_mnist_siamese_data because files in some directories may conflict

  with libraries in implicit directories:

    link library [libhdf5_hl.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

    link library [libhdf5.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

  Some of these libraries may not be found correctly.

WARNING: Target "pycaffe" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

WARNING: Target "pycaffe" requests linking to directory "/mnt/home/eduardss/.conda/envs/digits_env/lib".  Targets may link only to libraries.  CMake is dropping the item.

CMake Warning at python/CMakeLists.txt:9 (add_library):

  Cannot generate a safe linker search path for target pycaffe because files

  in some directories may conflict with libraries in implicit directories:

    link library [libhdf5_hl.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

    link library [libhdf5.so] in /usr/lib64 may be hidden by files in:

      /mnt/home/eduardss/.conda/envs/digits_env/lib

  Some of these libraries may not be found correctly.

-- Generating done

-- Build files have been written to: /mnt/home/eduardss/Code/packages/caffe/build