Question

我创建了一个新的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
#

然后激活它并尝试使用专门的pip（而不是conda）来安装llvmlite和numba，这似乎是成功的。（注意：我也试过--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

但库未正确安装，

(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

为什么来自numba频道的llvmdev的conda安装无法正常工作＆＃34;。

在我的用例中，我来到一个有pip风格的requirements.txt文件的项目，我需要从该文件创建conda环境。一些项目开发人员将使用venv + pip，一些将使用conda，并且其中包含的一些软件包在任何anaconda渠道中都找不到，因此必须安装pip。除了requirements.txt之外，我们不想维护一个单独的envrionment.yaml，因此从conda环境中的requirements.txt安装是我约束的一部分。

除了numba / llvmlite的pip安装之外，一切似乎都没问题，因为它需要llvm 3.8+的系统依赖性。我想将其作为conda环境的一部分来满足。

如何从conda环境中确保只存在用于安装numba和llvmlite的正确llvmdev？

Answer 1

在理想情况下，安装llvmlite后应该存在所需的共享库。

(test-env) ~/condaexpts$ conda create -n test-env -c numba python=3.5.2 llvmdev=3.8
(test-env) ~/condaexpts$ source activate test-env
(test-env) ~/condaexpts$ pip install numpy==1.12.0 llvmlite==0.15 numba==0.30.1
(test-env) ~/condaexpts$ find $CONDA_PREFIX | grep libllvmlite
/home/ubuntu/condaexpts/m3/envs/test-env/lib/python3.5/site-packages/llvmlite/binding/libllvmlite.so

如果test-env中没有此文件，则在安装llvmlite时出现问题。

另外，反过来考虑这种方法。您不需要将要求文件与conda环境文件分开。您可以在conda环境文件本身中拥有两个依赖项：

(test-env) ~/condaexpts$ conda env export               
name: test-env
channels:
- !!python/unicode
  'numba'
- !!python/unicode
  'defaults'
dependencies:
- !!python/unicode
  'openssl=1.0.2k=0'
- !!python/unicode
  'pip=9.0.1=py35_1'
- !!python/unicode
  'python=3.5.2=0'
- !!python/unicode
  'readline=6.2=2'
- !!python/unicode
  'setuptools=27.2.0=py35_0'
- !!python/unicode
  'sqlite=3.13.0=0'
- !!python/unicode
  'tk=8.5.18=0'
- !!python/unicode
  'wheel=0.29.0=py35_0'
- !!python/unicode
  'xz=5.2.2=1'
- !!python/unicode
  'zlib=1.2.8=3'
- !!python/unicode
  'llvmdev=3.8.1=7'
- !!python/unicode
  'system=5.8=2'
- pip:
  - llvmlite==0.15.0
  - numba==0.30.1
  - numpy==1.12.0
prefix: !!python/unicode '/home/ubuntu/condaexpts/m3/envs/test-env'

在第二个注释中，您可以安装“numba”conda频道本身所需的预构建二进制文件。用：

(root) ~/condaexpts$ ./Miniconda3-latest-Linux-x86_64.sh -b -p m3
(root) ~/condaexpts$ source ./m3/bin/activate 
(root) ~/condaexpts$ conda create -n test-env -c numba python=3.5.2 llvmdev=3.8 numba=0.30.1 llvmlite=0.15.0
(root) ~/condaexpts$ source activate test-env
(test-env) ~/condaexpts$ 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
>>> numba.__version__
'0.30.1'

Answer 2

安装llvmdev ：通过在您的频道中添加conda-forge，可以实现从conda-forge频道安装llvmdev：

conda config --add channels conda-forge

启用conda-forge频道后，llvmdev可以安装：

conda install llvmdev

可以在您的平台上列出所有可用的llvmdev版本：

conda search llvmdev --channel conda-forge

帮助：我从他们的GitHub源克隆了相关文件，然后
 python setup.py install 
更多没有conda使用pip
 sudo pip install -U llvmlite
 sudo pip install -U numba

Answer 3

这是使用 Anaconda 环境对我有用的方法：

pip uninstall llvmlite
pip install -U --ignore-installed numba

请勿在conda环境中正确安装numba / llvmlite

3 个答案: