linux终端安装sundials库,如何构建和分发依赖第三方libFoo.so的Python / Cython软件包...

小编典典

您可能知道，建议使用分发格式来分发带有已编译组件的Python模块。似乎没有任何标准的跨平台方式将第三方本机库捆绑到一个轮子中。但是，有用于此目的的特定于平台的工具。

在Linux上，使用auditwheel。

auditwheel修改现有的Linux wheel文件以添加基本的“

manylinux ”标准中未包含的任何第三方库。以下是在全新安装的Ubuntu

17.10上如何将其与项目一起使用的演练：

首先，安装基本的Python开发工具，以及带有其标头的第三方库：

root@ubuntu-17:~# apt-get install cython python-pip unzip

root@ubuntu-17:~# apt-get install libsundials-serial-dev

然后将您的项目构建到wheel文件中：

root@ubuntu-17:~# cd cython-example/

root@ubuntu-17:~/cython-example# python setup.py bdist_wheel

[...]

root@ubuntu-17:~/cython-example# cd dist/

root@ubuntu-17:~/cython-example/dist# ll

total 80

drwxr-xr-x 2 root root 4096 Nov 8 11:28 ./

drwxr-xr-x 7 root root 4096 Nov 8 11:28 ../

-rw-r--r-- 1 root root 70135 Nov 8 11:28 poc-0.0.0-cp27-cp27mu-linux_x86_64.whl

root@ubuntu-17:~/cython-example/dist# unzip -l poc-0.0.0-cp27-cp27mu-linux_x86_64.whl

Archive: poc-0.0.0-cp27-cp27mu-linux_x86_64.whl

Length Date Time Name

--------- ---------- ----- ----

62440 2017-11-08 11:28 poc/do_stuff.so

2 2017-11-08 11:28 poc/__init__.py

116648 2017-11-08 11:28 poc/cython_extensions/helloworld.so

2 2017-11-08 11:28 poc/cython_extensions/__init__.py

10 2017-11-08 11:28 poc-0.0.0.dist-info/DESCRIPTION.rst

211 2017-11-08 11:28 poc-0.0.0.dist-info/metadata.json

4 2017-11-08 11:28 poc-0.0.0.dist-info/top_level.txt

105 2017-11-08 11:28 poc-0.0.0.dist-info/WHEEL

167 2017-11-08 11:28 poc-0.0.0.dist-info/METADATA

793 2017-11-08 11:28 poc-0.0.0.dist-info/RECORD

--------- -------

180382 10 files

wheel文件现在可以在本地安装并经过测试：

root@ubuntu-17:~/cython-example/dist# pip install poc-0.0.0-cp27-cp27mu-linux_x86_64.whl

[...]

root@ubuntu-17:~/cython-example/dist# python -c "from poc.do_stuff import hello; hello()"

hello cython

0.841470984808

trying to load the sundials program

3-species kinetics problem

At t = 2.6391e-01 y = 9.899653e-01 3.470564e-05 1.000000e-02

rootsfound[] = 0 1

At t = 4.0000e-01 y = 9.851641e-01 3.386242e-05 1.480205e-02

[...]

现在我们安装该auditwheel工具。它需要Python 3，但是能够处理Python 2或3的轮子。

root@ubuntu-17:~/cython-example/dist# apt-get install python3-pip

root@ubuntu-17:~/cython-example/dist# pip3 install auditwheel

auditwheel使用另一个称为“patchelf工作”的工具。不幸的是，patchelfUbuntu

17.10随附的版本缺少一个错误修正，没有该修正，auditwheel将无法运行。因此，我们必须从源代码构建脚本(脚本取自manylinux

Docker映像)：

root@ubuntu-17:~# apt-get install autoconf

root@ubuntu-17:~# PATCHELF_VERSION=6bfcafbba8d89e44f9ac9582493b4f27d9d8c369

root@ubuntu-17:~# curl -sL -o patchelf.tar.gz https://github.com/NixOS/patchelf/archive/$PATCHELF_VERSION.tar.gz

root@ubuntu-17:~# tar -xzf patchelf.tar.gz

root@ubuntu-17:~# (cd patchelf-$PATCHELF_VERSION && ./bootstrap.sh && ./configure && make && make install)

现在，我们可以检查方向盘需要哪些第三方库：

root@ubuntu-17:~/cython-example/dist# auditwheel show poc-0.0.0-cp27-cp27mu-linux_x86_64.whl

poc-0.0.0-cp27-cp27mu-linux_x86_64.whl is consistent with the

following platform tag: "linux_x86_64".

The wheel references external versioned symbols in these system-

provided shared libraries: libc.so.6 with versions {'GLIBC_2.4',

'GLIBC_2.2.5', 'GLIBC_2.3.4'}

The following external shared libraries are required by the wheel:

{

"libblas.so.3": "/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1",

"libc.so.6": "/lib/x86_64-linux-gnu/libc-2.26.so",

"libgcc_s.so.1": "/lib/x86_64-linux-gnu/libgcc_s.so.1",

"libgfortran.so.4": "/usr/lib/x86_64-linux-gnu/libgfortran.so.4.0.0",

"liblapack.so.3": "/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1",

"libm.so.6": "/lib/x86_64-linux-gnu/libm-2.26.so",

"libpthread.so.0": "/lib/x86_64-linux-gnu/libpthread-2.26.so",

"libquadmath.so.0": "/usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0",

"libsundials_cvodes.so.2": "/usr/lib/libsundials_cvodes.so.2.0.0",

"libsundials_nvecserial.so.0": "/usr/lib/libsundials_nvecserial.so.0.0.2"

}

In order to achieve the tag platform tag "manylinux1_x86_64" the

following shared library dependencies will need to be eliminated:

libblas.so.3, libgfortran.so.4, liblapack.so.3, libquadmath.so.0,

libsundials_cvodes.so.2, libsundials_nvecserial.so.0

并创建一个捆绑它们的新轮子：

root@ubuntu-17:~/cython-example/dist# auditwheel repair poc-0.0.0-cp27-cp27mu-linux_x86_64.whl

Repairing poc-0.0.0-cp27-cp27mu-linux_x86_64.whl

Grafting: /usr/lib/libsundials_nvecserial.so.0.0.2 -> poc/.libs/libsundials_nvecserial-42b4120e.so.0.0.2

Grafting: /usr/lib/libsundials_cvodes.so.2.0.0 -> poc/.libs/libsundials_cvodes-50fde5ee.so.2.0.0

Grafting: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1 -> poc/.libs/liblapack-549933c4.so.3.7.1

Grafting: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 -> poc/.libs/libblas-52fa99c8.so.3.7.1

Grafting: /usr/lib/x86_64-linux-gnu/libgfortran.so.4.0.0 -> poc/.libs/libgfortran-2df4b07d.so.4.0.0

Grafting: /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0 -> poc/.libs/libquadmath-0d7c3070.so.0.0.0

Setting RPATH: poc/cython_extensions/helloworld.so to "$ORIGIN/../.libs"

Previous filename tags: linux_x86_64

New filename tags: manylinux1_x86_64

Previous WHEEL info tags: cp27-cp27mu-linux_x86_64

New WHEEL info tags: cp27-cp27mu-manylinux1_x86_64

Fixed-up wheel written to /root/cython-example/dist/wheelhouse/poc-0.0.0-cp27-cp27mu-manylinux1_x86_64.whl

root@ubuntu-17:~/cython-example/dist# unzip -l wheelhouse/poc-0.0.0-cp27-cp27mu-manylinux1_x86_64.whl

Archive: wheelhouse/poc-0.0.0-cp27-cp27mu-manylinux1_x86_64.whl

Length Date Time Name

--------- ---------- ----- ----

167 2017-11-08 11:28 poc-0.0.0.dist-info/METADATA

4 2017-11-08 11:28 poc-0.0.0.dist-info/top_level.txt

10 2017-11-08 11:28 poc-0.0.0.dist-info/DESCRIPTION.rst

211 2017-11-08 11:28 poc-0.0.0.dist-info/metadata.json

1400 2017-11-08 12:08 poc-0.0.0.dist-info/RECORD

110 2017-11-08 12:08 poc-0.0.0.dist-info/WHEEL

62440 2017-11-08 11:28 poc/do_stuff.so

2 2017-11-08 11:28 poc/__init__.py

131712 2017-11-08 12:08 poc/cython_extensions/helloworld.so

2 2017-11-08 11:28 poc/cython_extensions/__init__.py

230744 2017-11-08 12:08 poc/.libs/libsundials_cvodes-50fde5ee.so.2.0.0

7005072 2017-11-08 12:08 poc/.libs/liblapack-549933c4.so.3.7.1

264024 2017-11-08 12:08 poc/.libs/libquadmath-0d7c3070.so.0.0.0

2039960 2017-11-08 12:08 poc/.libs/libgfortran-2df4b07d.so.4.0.0

17736 2017-11-08 12:08 poc/.libs/libsundials_nvecserial-42b4120e.so.0.0.2

452432 2017-11-08 12:08 poc/.libs/libblas-52fa99c8.so.3.7.1

--------- -------

10206026 16 files

如果我们卸载第三方库，则先前安装的滚轮将停止工作：

root@ubuntu-17:~/cython-example/dist# apt-get remove libsundials-serial-dev && apt-get autoremove

[...]

root@ubuntu-17:~/cython-example/dist# python -c "from poc.do_stuff import hello; hello()"

Traceback (most recent call last):

File "", line 1, in

File "poc/do_stuff.pyx", line 1, in init poc.do_stuff

ImportError: libsundials_cvodes.so.2: cannot open shared object file: No such file or directory

但是带有捆绑库的轮子可以正常工作：

root@ubuntu-17:~/cython-example/dist# pip uninstall poc

[...]

root@ubuntu-17:~/cython-example/dist# pip install wheelhouse/poc-0.0.0-cp27-cp27mu-manylinux1_x86_64.whl

[...]

root@ubuntu-17:~/cython-example/dist# python -c "from poc.do_stuff import hello; hello()"

hello cython

0.841470984808

trying to load the sundials program

3-species kinetics problem

At t = 2.6391e-01 y = 9.899653e-01 3.470564e-05 1.000000e-02

rootsfound[] = 0 1

At t = 4.0000e-01 y = 9.851641e-01 3.386242e-05 1.480205e-02

[...]

在OSX上，使用delocate。

delocateOSX的工作方式显然与auditwheel。不幸的是，我没有可用于提供演练的OSX机器。

组合示例：

使用这两种工具的一个项目是SciPy。尽管它的名称，此存储库包含所有平台(不仅仅是Mac)的官方SciPy构建过程。具体来说，将Linux构建脚本(使用auditwheel)和OSX构建脚本(使用delocate)进行比较。

要查看此过程的结果，您可能需要从PyPI下载并解压缩一些SciPy轮子。例如，scipy-1.0.0-cp27-cp27m-manylinux1_x86_64.whl包含以下内容：

38513408 2017-10-25 06:02 scipy/.libs/libopenblasp-r0-39a31c03.2.18.so

1023960 2017-10-25 06:02 scipy/.libs/libgfortran-ed201abd.so.3.0.0

虽然scipy-1.0.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl包含以下内容：

273072 2017-10-25 07:03 scipy/.dylibs/libgcc_s.1.dylib

1550456 2017-10-25 07:03 scipy/.dylibs/libgfortran.3.dylib

279932 2017-10-25 07:03 scipy/.dylibs/libquadmath.0.dylib

2020-12-20