Installation error: path is prefixed in the build directory.

[rcrehuet]

Issue summary

cmake .. produces the following output. I have 2 questions:

1. -- Could NOT find Boost (missing: python36) (found suitable version "1.66.0", minimum required is "1.58") however I have the file /usr/lib64/libboost_python3.so. Isn't this what cmake is looking for?
2. How can I solve the problem with the absolute paths in caffe?

CMake Deprecation Warning at CMakeLists.txt:6 (cmake_policy):
  The OLD behavior for policy CMP0104 will be removed from a future version
  of CMake.

  The cmake-policies(7) manual explains that the OLD behaviors of all
  policies are deprecated and that a policy should be set to OLD only under
  specific short-term circumstances.  Projects should be ported to the NEW
  behavior and not rely on setting a policy to OLD.


-- Found CUDA: /usr/local/cuda (found suitable version "12.3", minimum required is "12.0") 
-- Found CUDA: /usr/local/cuda (found version "12.3") 
-- Caffe2: CUDA detected: 12.3
-- Caffe2: CUDA nvcc is: /usr/local/cuda/bin/nvcc
-- Caffe2: CUDA toolkit directory: /usr/local/cuda
-- Caffe2: Header version is: 12.3
-- /usr/local/cuda/lib64/libnvrtc.so shorthash is c9fa0fca
-- USE_CUDNN is set to 0. Compiling without cuDNN support
-- USE_CUSPARSELT is set to 0. Compiling without cuSPARSELt support
-- Autodetected CUDA architecture(s):  8.9 8.9 8.9 8.9 8.9 8.9 8.9 8.9
-- Added CUDA NVCC flags for: -gencode;arch=compute_89,code=sm_89
-- /home/ramon/progs/gnina/build/_deps/libtorch-src
-- Could NOT find libmolgrid (missing:  LIBMOLGRID_INCLUDE_DIR LIBMOLGRID_LIBRARY) 
libmolgrid will be fetched from git
-- Could NOT find Python (missing: Python_EXECUTABLE Python_INCLUDE_DIRS Python_LIBRARIES Interpreter Development Development.Module Development.Embed) 
-- CUDA detected: 12.3
-- Added CUDA NVCC flags for: sm_50 sm_60 sm_61 sm_70 sm_75 sm_80 sm_86
CMake Deprecation Warning at caffe/CMakeLists.txt:13 (cmake_policy):
  The OLD behavior for policy CMP0104 will be removed from a future version
  of CMake.

  The cmake-policies(7) manual explains that the OLD behaviors of all
  policies are deprecated and that a policy should be set to OLD only under
  specific short-term circumstances.  Projects should be ported to the NEW
  behavior and not rely on setting a policy to OLD.


-- Found Boost: /usr/include (found suitable version "1.66.0", minimum required is "1.54") found components: system thread filesystem iostreams timer chrono date_time atomic regex 
-- Could NOT find GFlags (missing:  GFLAGS_INCLUDE_DIR GFLAGS_LIBRARY) 
-- Could NOT find Glog (missing:  GLOG_INCLUDE_DIR GLOG_LIBRARY) 
-- Found PROTOBUF Compiler: /usr/bin/protoc
-- HDF5 C compiler wrapper is unable to compile a minimal HDF5 program.
-- CUDA detected: 12.3
-- Added CUDA NVCC flags for: sm_50 sm_60 sm_61 sm_70 sm_75 sm_80 sm_86
-- Found OpenBLAS libraries: /usr/lib64/libopenblas.so
-- Found OpenBLAS include: /usr/include
-- Found PythonInterp: /usr/bin/python3 (found suitable version "3.6.8", minimum required is "3.0") 
-- NumPy ver. 1.19.5 found (include: /home/ramon/.local/lib/python3.6/site-packages/numpy/core/include)
-- Could NOT find Boost (missing: python36) (found suitable version "1.66.0", minimum required is "1.58")
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) 
-- 
-- ******************* Caffe Configuration Summary *******************
-- General:
--   Version           :   1.0.0
--   Git               :   v1.1-20-ge9ba5c1d
--   System            :   Linux
--   C++ compiler      :   /opt/rh/gcc-toolset-12/root/usr/bin/c++
--   Release CXX flags :   -O3 -DNDEBUG -Wno-deprecated-declarations -Wno-unknown-pragmas -fPIC -Wall -Wno-sign-compare -Wno-uninitialized
--   Debug CXX flags   :   -g -Wno-deprecated-declarations -Wno-unknown-pragmas -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        :   0
--   USE_LEVELDB       :   0
--   USE_LMDB          :   0
--   USE_NCCL          :   0
--   ALLOW_LMDB_NOLOCK :   OFF
-- 
-- Dependencies:
--   BLAS              :   Yes (open)
--   Boost             :   Yes (ver. 1.66)
--   glog              :   Yes
--   gflags            :   Yes
--   OpenBabel         :   No
--   protobuf          :   Yes (ver. 3.5.0)
--   CUDA              :   Yes (ver. 12.3)
-- 
-- NVIDIA CUDA:
--   Target GPU(s)     :   All
--   GPU arch(s)       :   sm_50 sm_60 sm_61 sm_70 sm_75 sm_80 sm_86
--   cuDNN             :   Disabled
-- 
-- Python:
--   Interpreter       :   /usr/bin/python3 (ver. 3.6.8)
--   Libraries         :   /usr/lib64/libpython3.6m.so (ver 3.6.8)
--   NumPy             :   /home/ramon/.local/lib/python3.6/site-packages/numpy/core/include (ver 1.19.5)
-- 
-- Documentaion:
--   Doxygen           :   No
--   config_file       :   
-- 
-- Install:
--   Install path      :   /usr/local
-- 
-- Found Boost: /usr/include (found version "1.66.0") found components: program_options system iostreams timer thread serialization filesystem date_time regex unit_test_framework chrono atomic 
-- Could NOT find RDKit (missing:  RDKIT_INCLUDE_DIR RDKIT_LIBRARIES) 
CMake Warning at gninasrc/CMakeLists.txt:235 (message):
  RDKIT not found.  gninavis will NOT be built.


-- Found Boost: /usr/include (found version "1.66.0") found components: unit_test_framework system 
-- Found PythonInterp: /usr/bin/python3 (found version "3.6.8") 
-- Configuring done (2.1s)
CMake Error in caffe/src/caffe/CMakeLists.txt:
  Target "caffe" INTERFACE_INCLUDE_DIRECTORIES property contains path:

    "/home/ramon/progs/gnina/build/external/glog-install/include"

  which is prefixed in the build directory.


CMake Error in caffe/src/caffe/CMakeLists.txt:
  Target "caffe" INTERFACE_INCLUDE_DIRECTORIES property contains path:

    "/home/ramon/progs/gnina/build/external/glog-install/include"

  which is prefixed in the build directory.Target "caffe"
  INTERFACE_INCLUDE_DIRECTORIES property contains path:

    "/home/ramon/progs/gnina/build/external/glog-install/include"

  which is prefixed in the source directory.


CMake Error in caffe/src/caffe/CMakeLists.txt:
  Target "caffe" INTERFACE_INCLUDE_DIRECTORIES property contains path:

    "/home/ramon/progs/gnina/build/external/gflags-install/include"

  which is prefixed in the build directory.


CMake Error in caffe/src/caffe/CMakeLists.txt:
  Target "caffe" INTERFACE_INCLUDE_DIRECTORIES property contains path:

    "/home/ramon/progs/gnina/build/external/gflags-install/include"

  which is prefixed in the build directory.Target "caffe"
  INTERFACE_INCLUDE_DIRECTORIES property contains path:

    "/home/ramon/progs/gnina/build/external/gflags-install/include"

  which is prefixed in the source directory.


-- Generating done (0.5s)
CMake Generate step failed.  Build files cannot be regenerated correctly.

Steps to reproduce

mkdir build
cmake ..

Your system configuration

Operating system: Rocky linux 8
Compiler: gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-7)
CUDA version (if applicable): Cuda compilation tools, release 12.3, V12.3.52
CUDNN version (if applicable): 9
Python version: 3.6

[dkoes]

Presumably /usr/lib64/libboost_python3.so isn't the python36 version.

Did cmake create the glog directory? I haven't seen that, but I have it installed on the system.

[rcrehuet]

Thanks for the answer. The libboost_python3.so and the python I'm using are from the distribution (I'm not using anaconda). How can I check its python version?
I found this ./build/external/glog-prefix/src/glog, but it is empty.

[dkoes]

Usually the unversioned library is a symlink to a versioned library:
/usr/lib/x86_64-linux-gnu/libboost_python310.so -> libboost_python310.so.1.74.0
You should check to see if you have multiple versions of python installed - if so, set PYTHON_EXECUTABLE to the version that is compatible with the installed boost (or, alternatively, look for a libboost_python package for the default python version).

[mainguyenanhvu]

How can I define for new libboost_python310 when doing cmake ..?