在Ubuntu服务器上安装h5py

Question

我在一台Ubuntu服务器上安装h5py，但似乎出现了一个错误，提示找不到h5py.h。无论是用pip还是setup.py文件安装，都会出现同样的错误信息。我这里缺少了什么呢？

我有Numpy版本1.8.1，这个版本比要求的1.6或更高的版本要高。

完整的输出如下：

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

我需要在我的arm64设备上安装两个东西，分别是 libhdf5-dev 和 cython3，我用的是Ubuntu 18.04，Python版本是3.5。

sudo apt install libhdf5-dev
sudo apt install cython3

Answer 2

一般来说，使用 pip 来安装软件比手动安装要好，因为 pip 会自动帮你安装所有需要的 Python 依赖包。不过，你还是需要准备好你的头文件。

所以：

sudo apt-get install libhdf5-dev
pip install h5py

Answer 3

在我的情况下（Ubuntu 15.04），仅仅安装 libhdf5-dev 还不够。

我还需要运行：

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

这样才能让它正常工作。

Answer 4

你可以使用 python-h5py 这个库。

你可以在终端输入这条命令来安装它：

sudo apt-get install python-h5py

安装完成后，在你的Python文件里试试下面的代码：

import h5py

Answer 5

你需要安装 libhdf5-dev 来获取所需的头文件。只需运行

sudo apt-get install libhdf5-dev

这样就会自动安装这个软件包和它需要的其他东西。

别担心 NumPy 的警告，这只是说明软件包的开发者在用一个旧版本的接口，但一切仍然可以正常使用。