在Ubuntu服务器上安装h5py

Question

在Ubuntu服务器上安装h5py

50

我正在Ubuntu服务器上安装h5py，但似乎返回错误信息说找不到h5py.h。使用pip或setup.py文件安装时都会出现相同的错误提示。我错过了什么吗？

我的Numpy版本是1.8.1，高于所需的1.6或更高版本。

完整输出如下：

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

- Devil

5个回答

22

您可以使用 python-h5py 库。

sudo apt-get install python-h5py

然后在您的 Python 文件中尝试：

import h5py

- KyungHoon Kim

19

在我的情况下（Ubuntu 15.04），安装libhdf5-dev是不够的。

我必须运行：

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

使其正常工作。

- vierja

2

谢谢！对于其他新手，如果你在Termux上，HDF5_DIR应该是HDF5_DIR=/usr/lib/aarch64-linux-gnu/hdf5/serial/。 - sguan

3

为了安装Python相关的依赖项，通常最好使用pip而不是手动安装。但你仍然需要你的头文件。

因此：

sudo apt-get install libhdf5-dev
pip install h5py

- Gx1sptDTDa

1

我必须安装libhdf5-dev和cython3（在Python 3.5的Ubuntu 18.04 arm64设备上）。

sudo apt install libhdf5-dev
sudo apt install cython3

- Niklas

网页内容由stack overflow 提供, 点击上面的

可以查看英文原文，
原文链接

- MattDMo · Accepted Answer

为获取所需的头文件，您需要安装libhdf5-dev。只需运行：

sudo apt-get install libhdf5-dev

它应该自动安装它及其依赖项。

不要担心NumPy的警告，这只是意味着软件包开发人员正在使用旧版API，但一切仍将正常工作。