Repository: facebookarchive/caffe2

Issue #2144: mpi_test.cc.o: undefined reference to symbol '_ZN3MPI8Datatype4FreeEv
Created: 2018-03-06T00:15:39Z
Hi,
I am getting an error while running make in Caffe2. This is what it says:
/usr/bin/ld: CMakeFiles/mpi_test.dir/mpi/mpi_test.cc.o: undefined reference to symbol '_ZN3MPI8Datatype4FreeEv'
/usr/lib/libmpi_cxx.so.1: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
caffe2/CMakeFiles/mpi_test.dir/build.make: 100: recipe for target 'bin/mpi_test' failed
make[2]: *** [bin/mpi_test] Error 1
CMakeFiles/Makefile2:2518: recipe for target 'caffe2/CMakeFiles/mpi_test.dir/all' failed
make[1]: *** [caffe2/CMakeFiles/mpi_test.dir/all] Error 2
Makefile:138: recipe for target 'all' failed
make: *** [all] Error 2
Any idea how I can fix it? Any help will be appreciated.
Thanks!!
System information

Operating system: Ubuntu 16.04
Compiler version: gcc 5.4.0 20160609
CMake version: 3.5.1
CMake arguments:
CUDA 9.1
CuDNN 7.0.5

CMake summary output
******** Summary ********
-- General:
--   CMake version         : 3.5.1
--   CMake command         : /usr/bin/cmake
--   Git version           : v0.8.1-1240-g8f41717
--   System                : Linux
--   C++ compiler          : /usr/bin/c++
--   C++ compiler version  : 5.4.0
--   Protobuf compiler     : /usr/bin/protoc
--   Protobuf include path : /usr/include
--   Protobuf libraries    : optimized;/usr/lib/x86_64-linux-gnu/libprotobuf.so;debug;/usr/lib/x86_64-linux-gnu/libprotobuf.so;-pthread
--   BLAS                  : Eigen
--   CXX flags             :  -std=c++11 -O2 -fPIC -Wno-narrowing -Wno-invalid-partial-specialization
--   Build type            : Release
--   Compile definitions   :
--   BUILD_BINARY          : ON
--   BUILD_DOCS            : OFF
--   BUILD_PYTHON          : ON
--     Python version      : 2.7.12
--     Python library      : /usr/lib/x86_64-linux-gnu/libpython2.7.so
--   BUILD_SHARED_LIBS     : ON
--   BUILD_TEST            : ON
--   USE_ATEN              : OFF
--   USE_ASAN              : OFF
--   USE_CUDA              : OFF
--   USE_EIGEN_FOR_BLAS    : 1
--   USE_FFMPEG            : OFF
--   USE_GFLAGS            : ON
--   USE_GLOG              : ON
--   USE_GLOO              : ON
--   USE_LEVELDB           : ON
--     LevelDB version     : 1.18
--     Snappy version      : 1.1.3
--   USE_LITE_PROTO        : OFF
--   USE_LMDB              : ON
--     LMDB version        : 0.9.17
--   USE_METAL             : OFF
--   USE_MKL               :
--   USE_MOBILE_OPENGL     : OFF
--   USE_MPI               : ON
--   USE_NCCL              : OFF
--   USE_NERVANA_GPU       : OFF
--   USE_NNPACK            : ON
--   USE_OBSERVERS         : ON
--   USE_OPENCV            : ON
--     OpenCV version      : 2.4.9.1
--   USE_OPENMP            : OFF
--   USE_PROF              : OFF
--   USE_REDIS             : OFF
--   USE_ROCKSDB           : OFF
--   USE_THREADS           : ON
--   USE_ZMQ               : OFF
-- Configuring done
-- Generating done
-- Build files have been written to: /home/ubuntu/caffe2/build

Duplicate issue #2464: Failing to make with 8 cores
Created: 2018-03-28T14:38:05Z
I'm trying to install the dependencies for Detectron (FAIR) but I am running into difficulties with makeing Caffe2. I am following this guide under mattifrind. I've already looked at these posts, but had no success in resolving my similar issue.
Thanks!
System information
under mattifrind

Operating system: Ubuntu 16.04

`rose@rose-GS73VR-7RF:~/caffe2$ sudo make -j8
-- Does not need to define long separately.
-- std::exception_ptr is supported.
-- NUMA is available
-- Current compiler supports avx2 extention. Will build perfkernels.
-- Caffe2: Found protobuf with old-style protobuf targets.
-- Caffe2 protobuf include directory: /usr/include
-- The BLAS backend of choice:Eigen
-- Could NOT find NNPACK (missing:  NNPACK_INCLUDE_DIR NNPACK_LIBRARY PTHREADPOOL_LIBRARY CPUINFO_LIBRARY)
-- Brace yourself, we are building NNPACK
-- Found PythonInterp: /usr/bin/python (found version "2.7.12")
-- Caffe2: Cannot find gflags automatically. Using legacy find.
-- Caffe2: Found gflags  (include: /usr/include, library: /usr/lib/x86_64-linux-gnu/libgflags.so)
-- Caffe2: Cannot find glog automatically. Using legacy find.
-- Caffe2: Found glog (include: /usr/include, library: /usr/lib/x86_64-linux-gnu/libglog.so)
-- git Version: v0.0.0
-- Version: 0.0.0
-- Performing Test HAVE_STD_REGEX
-- Performing Test HAVE_STD_REGEX
-- Performing Test HAVE_STD_REGEX -- success
-- Performing Test HAVE_GNU_POSIX_REGEX
-- Performing Test HAVE_GNU_POSIX_REGEX
-- Performing Test HAVE_GNU_POSIX_REGEX -- failed to compile
-- Performing Test HAVE_POSIX_REGEX
-- Performing Test HAVE_POSIX_REGEX
-- Performing Test HAVE_POSIX_REGEX -- success
-- Performing Test HAVE_STEADY_CLOCK
-- Performing Test HAVE_STEADY_CLOCK
-- Performing Test HAVE_STEADY_CLOCK -- success
-- Found lmdb    (include: /usr/include, library: /usr/lib/x86_64-linux-gnu/liblmdb.so)
-- Found LevelDB (include: /usr/include, library: /usr/lib/x86_64-linux-gnu/libleveldb.so)
-- Found Snappy  (include: /usr/include, library: /usr/lib/x86_64-linux-gnu/libsnappy.so)
-- Found Numa  (include: /usr/include, library: /usr/lib/x86_64-linux-gnu/libnuma.so)
-- OpenCV found (/usr/share/OpenCV)
CMake Warning at cmake/Dependencies.cmake:280 (find_package):
By not providing "FindEigen3.cmake" in CMAKE_MODULE_PATH this project has
asked CMake to find a package configuration file provided by "Eigen3", but
CMake did not find one.
Could not find a package configuration file provided by "Eigen3" with any
of the following names:
Eigen3Config.cmake
eigen3-config.cmake

Add the installation prefix of "Eigen3" to CMAKE_PREFIX_PATH or set
"Eigen3_DIR" to a directory containing one of the above files.  If "Eigen3"
provides a separate development package or SDK, be sure it has been
installed.
Call Stack (most recent call first):
CMakeLists.txt:103 (include)
-- Did not find system Eigen. Using third party subdirectory.
-- Found PythonInterp: /usr/bin/python (found suitable version "2.7.12", minimum required is "2.7")
-- NumPy ver. 1.14.2 found (include: /usr/local/lib/python2.7/dist-packages/numpy/core/include)
-- Could NOT find pybind11 (missing:  pybind11_INCLUDE_DIR)
-- MPI support found
-- MPI compile flags:
-- MPI include path: /usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include/usr/lib/openmpi/include/usr/lib/openmpi/include/openmpi
-- MPI LINK flags path:  -Wl,-rpath  -Wl,/usr/lib/openmpi/lib  -Wl,--enable-new-dtags
-- MPI libraries: /usr/lib/openmpi/lib/libmpi_cxx.so/usr/lib/openmpi/lib/libmpi.so
CMake Warning at cmake/Dependencies.cmake:334 (message):
OpenMPI found, but it is not built with CUDA support.
Call Stack (most recent call first):
CMakeLists.txt:103 (include)
-- Could NOT find CUDNN (missing:  CUDNN_INCLUDE_DIR CUDNN_LIBRARY)
CMake Warning at cmake/public/cuda.cmake:28 (message):
Caffe2: cudnn cannot be found.  Caffe2 CUDA depends explicitly on cudnn so
you should consider installing it.
Call Stack (most recent call first):
cmake/Dependencies.cmake:366 (include)
CMakeLists.txt:103 (include)
CMake Warning at cmake/Dependencies.cmake:374 (message):
Not compiling with CUDA.  Suppress this warning with -DUSE_CUDA=OFF.
Call Stack (most recent call first):
CMakeLists.txt:103 (include)
CMake Warning at cmake/Dependencies.cmake:384 (message):
If not using cuda, one should not use NCCL either.
Call Stack (most recent call first):
CMakeLists.txt:103 (include)
-- Could NOT find Gloo (missing:  Gloo_INCLUDE_DIR Gloo_LIBRARY)
-- MPI include path: /usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include/usr/lib/openmpi/include/usr/lib/openmpi/include/openmpi
-- MPI libraries: /usr/lib/openmpi/lib/libmpi_cxx.so/usr/lib/openmpi/lib/libmpi.so
CMake Warning at cmake/Dependencies.cmake:467 (message):
mobile opengl is only used in android or ios builds.
Call Stack (most recent call first):
CMakeLists.txt:103 (include)
CMake Warning at cmake/Dependencies.cmake:543 (message):
Metal is only used in ios builds.
Call Stack (most recent call first):
CMakeLists.txt:103 (include)
-- Could NOT find pybind11 (missing:  pybind11_INCLUDE_DIR)
-- GCC 5.4.0: Adding gcc and gcc_s libs to link line
-- NCCL operators skipped due to no CUDA support
-- CUDA RTC operators skipped due to no CUDA support
-- Including image processing operators
-- Excluding video processing operators due to no opencv
-- Excluding mkl operators as we are not using mkl
-- Include Observer library
-- Using lib/python2.7/dist-packages as python relative installation path
-- Automatically generating missing init.py files.
-- ******** Summary ********
-- General:
--   CMake version         : 3.5.1
--   CMake command         : /usr/bin/cmake
--   Git version           : v0.8.1-1483-g56bb251
--   System                : Linux
--   C++ compiler          : /usr/bin/c++
--   C++ compiler version  : 5.4.0
--   Protobuf compiler     : /usr/bin/protoc
--   Protobuf include path : /usr/include
--   Protobuf libraries    : optimized;/usr/lib/x86_64-linux-gnu/libprotobuf.so;debug;/usr/lib/x86_64-linux-gnu/libprotobuf.so;-pthread
--   BLAS                  : Eigen
--   CXX flags             :  -DONNX_NAMESPACE=onnx_c2 -O2 -fPIC -Wno-narrowing -Wno-invalid-partial-specialization
--   Build type            : Release
--   Compile definitions   :
--   BUILD_BINARY          : ON
--   BUILD_CUSTOM_PROTOBUF : OFF
--   BUILD_DOCS            : OFF
--   BUILD_PYTHON          : ON
--     Python version      : 2.7.12
--     Python includes     : /usr/include/python2.7
--   BUILD_SHARED_LIBS     : ON
--   BUILD_TEST            : ON
--   USE_ATEN              : OFF
--   USE_ASAN              : OFF
--   USE_CUDA              : OFF
--   USE_EIGEN_FOR_BLAS    : 1
--   USE_FFMPEG            : OFF
--   USE_GFLAGS            : ON
--   USE_GLOG              : ON
--   USE_GLOO              : ON
--   USE_LEVELDB           : ON
--     LevelDB version     : 1.18
--     Snappy version      : 1.1.3
--   USE_LITE_PROTO        : OFF
--   USE_LMDB              : ON
--     LMDB version        : 0.9.17
--   USE_METAL             : OFF
--   USE_MKL               :
--   USE_MOBILE_OPENGL     : OFF
--   USE_MPI               : ON
--   USE_NCCL              : OFF
--   USE_NERVANA_GPU       : OFF
--   USE_NNPACK            : ON
--   USE_OBSERVERS         : ON
--   USE_OPENCV            : ON
--     OpenCV version      : 2.4.9.1
--   USE_OPENMP            : OFF
--   USE_PROF              : OFF
--   USE_REDIS             : OFF
--   USE_ROCKSDB           : OFF
--   USE_ZMQ               : OFF
-- Configuring done
-- Generating done
-- Build files have been written to: /home/rose/caffe2/build
make[1]: Entering directory '/home/rose/caffe2/build'
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[100%] Built target split_db
[100%] Built target db_throughput
[100%] Built target convert_caffe_image_db
/usr/bin/ld: CMakeFiles/mpi_test.dir/mpi/mpi_test.cc.o: undefined reference to symbol '_ZN3MPI8Datatype4FreeEv'
//usr/lib/libmpi_cxx.so.1: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
caffe2/CMakeFiles/mpi_test.dir/build.make:101: recipe for target 'bin/mpi_test' failed
make[3]: *** [bin/mpi_test] Error 1
make[3]: Leaving directory '/home/rose/caffe2/build'
CMakeFiles/Makefile2:2738: recipe for target 'caffe2/CMakeFiles/mpi_test.dir/all' failed
make[2]: *** [caffe2/CMakeFiles/mpi_test.dir/all] Error 2
make[2]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/home/rose/caffe2/build'
[100%] Built target python_copy_files
make[2]: Leaving directory '/home/rose/caffe2/build'
Makefile:138: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/home/rose/caffe2/build'
Makefile:4: recipe for target 'all' failed
make: *** [all] Error 2
`

Closing comment (2018-03-28T16:58:45Z): This is a duplicate of #2144 ; it's related to openmpi and not to how many cores you use to build. I will close this issue as a duplicate, but you can please post the output of mpirun --version and ldd //usr/lib/libmpi_cxx.so.1 and nm /usr/lib/libmpi_cxx.so.1 | grep -E 'Datatype.*Free' on #2144?