python - pip 没有在 conda 环境中正确安装 numba/llvmlite

Question

我创建一个新的conda环境

user@machine:~/project$ conda create -n test-env -c numba python=3.5.2 llvmdev=3.8
Fetching package metadata ...........
Solving package specifications: .

Package plan for installation in environment /home/user/anaconda2/envs/test-env:

The following NEW packages will be INSTALLED:

    llvmdev:    3.8.1-7       numba
    openssl:    1.0.2k-0           
    pip:        9.0.1-py35_1       
    python:     3.5.2-0            
    readline:   6.2-2              
    setuptools: 27.2.0-py35_0      
    sqlite:     3.13.0-0           
    system:     5.8-2         numba
    tk:         8.5.18-0           
    wheel:      0.29.0-py35_0      
    xz:         5.2.2-1            
    zlib:       1.2.8-3            

Proceed ([y]/n)? y

#
# To activate this environment, use:
# > source activate test-env
#
# To deactivate this environment, use:
# > source deactivate test-env
#

然后激活它并尝试专门使用 pip(不是 conda)来安装 llvmlite 和 numba，这似乎成功了。 (注意:我也尝试过 --no-cache-dir 并且它没有改变任何东西。)

user@machine:~/project$ source activate test-env
(test-env) user@machine:~/project$ pip install llvmlite==0.15 numba==0.30.1
Collecting llvmlite==0.15
Collecting numba==0.30.1
Collecting numpy (from numba==0.30.1)
  Using cached numpy-1.12.0-cp35-cp35m-manylinux1_x86_64.whl
Installing collected packages: llvmlite, numpy, numba
Successfully installed llvmlite-0.15.0 numba-0.30.1 numpy-1.12.0

但是库没有正确安装，

(test-env) user@machine:~/project$ python
Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import numba
Traceback (most recent call last):
  File "/home/user/anaconda2/envs/test-env/lib/python3.5/site-packages/llvmlite/binding/ffi.py", line 42, in <module>
    lib = ctypes.CDLL(os.path.join(_lib_dir, _lib_name))
  File "/home/user/anaconda2/envs/test-env/lib/python3.5/ctypes/__init__.py", line 347, in __init__
    self._handle = _dlopen(self._name, mode)
OSError: /home/user/anaconda2/envs/test-env/lib/python3.5/site-packages/llvmlite/binding/libllvmlite.so: undefined symbol: _ZNKSt14error_category23default_error_conditionEi

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/user/anaconda2/envs/test-env/lib/python3.5/site-packages/numba/__init__.py", line 9, in <module>
    from . import config, errors, runtests, types
  File "/home/user/anaconda2/envs/test-env/lib/python3.5/site-packages/numba/config.py", line 11, in <module>
    import llvmlite.binding as ll
  File "/home/user/anaconda2/envs/test-env/lib/python3.5/site-packages/llvmlite/binding/__init__.py", line 6, in <module>
    from .dylib import *
  File "/home/user/anaconda2/envs/test-env/lib/python3.5/site-packages/llvmlite/binding/dylib.py", line 4, in <module>
    from . import ffi
  File "/home/user/anaconda2/envs/test-env/lib/python3.5/site-packages/llvmlite/binding/ffi.py", line 47, in <module>
    lib = ctypes.CDLL(_lib_name)
  File "/home/user/anaconda2/envs/test-env/lib/python3.5/ctypes/__init__.py", line 347, in __init__
    self._handle = _dlopen(self._name, mode)
OSError: libllvmlite.so: cannot open shared object file: No such file or directory

为什么 conda 从 numba channel 安装 llvmdev 无法“正常工作”。

在我的用例中，我要进入一个具有 pip 样式的 requirements.txt 文件的项目，我需要从该文件创建 conda 环境。有的项目开发者会使用venv+pip，有的会使用conda，而它包含的一些包在任何anaconda channel 都找不到，所以pip安装是必须的。除了 requirements.txt 之外，我们不想维护单独的 envrionment.yaml，因此从 conda envrionment 内的 requirements.txt 安装是我的约束的一部分。

一切似乎都正常，除了 numba/llvmlite 的 pip 安装，它需要 llvm 3.8+ 的系统依赖。不过，我想将其作为 conda 环境的一部分来满足。

我如何才能从 conda 环境中确保仅存在用于安装 numba 和 llvmlite 的正确 llvmdev？

Answer 1

安装 llvmdev:从 conda-forge channel 安装 llvmdev 可以通过将 conda-forge 添加到您的 channel 来实现:

conda config --add channels conda-forge

启用 conda-forge channel 后，可以安装 llvmdev:

conda install llvmdev

可以列出您平台上可用的所有 llvmdev 版本:

conda search llvmdev --channel conda-forge

HELP:I cloned the relevant files from their GitHub sources and did

 python setup.py install 

for more without conda use pip

 sudo pip install -U llvmlite
 sudo pip install -U numba