Install h5py on an Ubuntu server

Question

I installed h5py on an Ubuntu server. However, it seems to return an error that was not found by h5py.h It gives the same error message when I install it using the pip file or setup.py . What am I missing here?

I have version 1.1.1 for Numpy that is higher than the required version 1.6 or higher.

The full output is as follows:

 van@Hulk:~/h5py-2.3.1⟫ sudo python setup.py install libhdf5.so: cannot open shared object file: No such file or directory HDF5 autodetection failed; building for 1.8.4+ running install running bdist_egg running egg_info writing h5py.egg-info/PKG-INFO writing top-level names to h5py.egg-info/top_level.txt writing dependency_links to h5py.egg-info/dependency_links.txt reading manifest file 'h5py.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.c' under directory 'win_include' warning: no files found matching '*.h' under directory 'win_include' writing manifest file 'h5py.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build creating build/lib.linux-x86_64-2.7 creating build/lib.linux-x86_64-2.7/h5py copying h5py/ipy_completer.py -> build/lib.linux-x86_64-2.7/h5py copying h5py/__init__.py -> build/lib.linux-x86_64-2.7/h5py copying h5py/version.py -> build/lib.linux-x86_64-2.7/h5py copying h5py/highlevel.py -> build/lib.linux-x86_64-2.7/h5py creating build/lib.linux-x86_64-2.7/h5py/_hl copying h5py/_hl/group.py -> build/lib.linux-x86_64-2.7/h5py/_hl copying h5py/_hl/files.py -> build/lib.linux-x86_64-2.7/h5py/_hl copying h5py/_hl/selections.py -> build/lib.linux-x86_64-2.7/h5py/_hl copying h5py/_hl/__init__.py -> build/lib.linux-x86_64-2.7/h5py/_hl copying h5py/_hl/filters.py -> build/lib.linux-x86_64-2.7/h5py/_hl copying h5py/_hl/base.py -> build/lib.linux-x86_64-2.7/h5py/_hl copying h5py/_hl/dims.py -> build/lib.linux-x86_64-2.7/h5py/_hl copying h5py/_hl/datatype.py -> build/lib.linux-x86_64-2.7/h5py/_hl copying h5py/_hl/dataset.py -> build/lib.linux-x86_64-2.7/h5py/_hl copying h5py/_hl/selections2.py -> build/lib.linux-x86_64-2.7/h5py/_hl copying h5py/_hl/attrs.py -> build/lib.linux-x86_64-2.7/h5py/_hl creating build/lib.linux-x86_64-2.7/h5py/tests copying h5py/tests/test_selections.py -> build/lib.linux-x86_64-2.7/h5py/tests copying h5py/tests/test_group.py -> build/lib.linux-x86_64-2.7/h5py/tests copying h5py/tests/test_h5.py -> build/lib.linux-x86_64-2.7/h5py/tests copying h5py/tests/test_attrs.py -> build/lib.linux-x86_64-2.7/h5py/tests copying h5py/tests/test_objects.py -> build/lib.linux-x86_64-2.7/h5py/tests copying h5py/tests/test_slicing.py -> build/lib.linux-x86_64-2.7/h5py/tests copying h5py/tests/test_h5t.py -> build/lib.linux-x86_64-2.7/h5py/tests copying h5py/tests/test_datatype.py -> build/lib.linux-x86_64-2.7/h5py/tests copying h5py/tests/__init__.py -> build/lib.linux-x86_64-2.7/h5py/tests copying h5py/tests/test_dimension_scales.py -> build/lib.linux-x86_64-2.7/h5py/tests copying h5py/tests/test_base.py -> build/lib.linux-x86_64-2.7/h5py/tests copying h5py/tests/test_dataset.py -> build/lib.linux-x86_64-2.7/h5py/tests copying h5py/tests/test_file.py -> build/lib.linux-x86_64-2.7/h5py/tests copying h5py/tests/test_h5p.py -> build/lib.linux-x86_64-2.7/h5py/tests copying h5py/tests/test_attrs_data.py -> build/lib.linux-x86_64-2.7/h5py/tests copying h5py/tests/common.py -> build/lib.linux-x86_64-2.7/h5py/tests copying h5py/tests/test_h5f.py -> build/lib.linux-x86_64-2.7/h5py/tests running build_ext skipping 'h5py/defs.c' Cython extension (up-to-date) building 'h5py.defs' extension creating build/temp.linux-x86_64-2.7 creating build/temp.linux-x86_64-2.7/h5py x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -DH5_USE_16_API -I/home/govinda/h5py-2.3.1/lzf -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c h5py/defs.c -o build/temp.linux-x86_64-2.7/h5py/defs.o In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from h5py/api_compat.h:26, from h5py/defs.c:342: /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ In file included from h5py/defs.c:342:0: h5py/api_compat.h:27:18: fatal error: hdf5.h: No such file or directory #include "hdf5.h" ^ compilation terminated. error: command 'x86_64-linux-gnu-gcc' failed with exit status 1 

Answer 1

You need to install libhdf5-dev to get the required header files. Just run

 sudo apt-get install libhdf5-dev 

and he should automatically install it and its dependencies.

Don't worry about the NumPy warning, it just means that the package developers are using the old version of the API, but everything will work.

Answer 2

You can use python-h5py .

sudo apt-get install python-h5py

And then in the Python file try:

import h5py

Answer 3

In my case (Ubuntu 15.04), installing libhdf5-dev was not enough.

I needed to run:

HDF5_DIR=/usr/lib/x86_64-linux-gnu/hdf5/serial/ pip install h5py

for it to work.

Answer 4

It is usually recommended to use pip instead of installing it manually, since pip will also install all python dependencies. However, you still need your header files.

So:

 sudo apt-get install libhdf5-dev pip install h5py