Caffe: ***HDF5 library version mismatched error*** ...Library 1.8.14 but header 1.8.13 Mac OSX 10.10

[asampat3090]

I get the following error when I run "make runtest". I can't figure out how to change my library using homebrew so I'd like to change the header to accept HDF5 1.8.14, but I can't figure out how. Anyone else have this issue? Full error here: https://gist.github.com/asampat3090/36caf62fc6a43d48fc47

As a side note I'm trying to run caffe in CPU-only mode (I don't have an nVidia graphics card on my laptop).

[bearpaw]

If you are using Anaconda, I think may be it was caused by the wrong setting of Makefile.config

Make sure the python_lib and python_include are both set as Anaconda path.

[greatgao]

I have the same problem like it.And I checked the Makefile.config again and again.It seems no wrong setting.The file as the following:

#####***************************

Refer to http://caffe.berkeleyvision.org/installation.html

Contributions simplifying and improving our build system are welcome!

cuDNN acceleration switch (uncomment to build with cuDNN).

USE_CUDNN := 1

CPU-only switch (uncomment to build without GPU support).

CPU_ONLY := 1

To customize your choice of compiler, uncomment and set the following.

N.B. the default for Linux is g++ and the default for OSX is clang++

CUSTOM_CXX := clang++

CUDA directory contains bin/ and lib/ directories that we need.

CUDA_DIR := /usr/local/cuda

On Ubuntu 14.04, if cuda tools are installed via

"sudo apt-get install nvidia-cuda-toolkit" then use this instead:

CUDA_DIR := /usr

CUDA architecture setting: going with all of them.

For CUDA < 6.0, comment the *_50 lines for compatibility.

CUDA_ARCH := -gencode arch=compute_20,code=sm_20
-gencode arch=compute_20,code=sm_21
-gencode arch=compute_30,code=sm_30
-gencode arch=compute_35,code=sm_35
-gencode arch=compute_50,code=sm_50
-gencode arch=compute_50,code=compute_50

BLAS choice:

atlas for ATLAS (default)

mkl for MKL

open for OpenBlas

BLAS := atlas

Custom (MKL/ATLAS/OpenBLAS) include and lib directories.

Leave commented to accept the defaults for your choice of BLAS

(which should work)!

BLAS_INCLUDE := /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/Accelerate.framework/Versions/Current/Frameworks/vecLib.framework/Headers/

BLAS_LIB :=

This is required only if you will compile the matlab interface.

MATLAB directory should contain the mex binary in /bin.

MATLAB_DIR := /usr/local

MATLAB_DIR := /Applications/MATLAB_R2012b.app

NOTE: this is required only if you will compile the python interface.

We need to be able to find Python.h and numpy/arrayobject.h.

#PYTHON_INCLUDE := /usr/include/python2.7

/usr/lib/python2.7/dist-packages/numpy/core/include

#####***************************

Anaconda Python distribution is quite popular. Include path:

Verify anaconda location, sometimes it's in root.

ANACONDA_HOME := $(HOME)/anaconda
PYTHON_INCLUDE := $(ANACONDA_HOME)/include
$(ANACONDA_HOME)/include/python2.7
$(ANACONDA_HOME)/lib/python2.7/site-packages/numpy/core/include

We need to be able to find libpythonX.X.so or .dylib.

PYTHON_LIB := /usr/lib

PYTHON_LIB := $(ANACONDA_HOME)/lib

Uncomment to support layers written in Python (will link against Python libs)

WITH_PYTHON_LAYER := 1

Whatever else you find you need goes here.

INCLUDE_DIRS := $(PYTHON_INCLUDE) /usr/local/include
LIBRARY_DIRS := $(PYTHON_LIB) /usr/local/lib /usr/lib

#####***************************

Uncomment to use pkg-config to specify OpenCV library paths.

(Usually not necessary -- OpenCV libraries are normally installed in one of the above $LIBRARY_DIRS.)

USE_PKG_CONFIG := 1

BUILD_DIR := build
DISTRIBUTE_DIR := distribute

Uncomment for debugging. Does not work on OSX due to https://github.com/BVLC/caffe/issues/171

DEBUG := 1

The ID of the GPU that 'make runtest' will use to run unit tests.

TEST_GPUID := 0

enable pretty build (comment to see full commands)

Q ?= @

[shelhamer]

This is usually include vs. linking order mismatch. Please ask build questions on the caffe-users group.

[anbai106]

Is this not a bug that you should resolve??

[aabobakr]

the reason for this mismatch is that you are compiling with hdf5 lib from brew and running with anaconda one.. you may do conda uninstall hdf5 and use to the brew one.

[engineeringmath]

conda install -c anaconda hdf5=1.8.14