如何在 Singularity 配方中激活 Anaconda 环境

Question

我正在尝试创建一个奇点图像和配方，它将创建一个 anaconda 环境，然后激活所述环境，这样我就可以在该环境中构建项目的 python 轮子，因此它已 100% 安装并正常运行奇点构建完成后。

Bootstrap: docker
From: nvidia/cuda:9.0-cudnn7-devel-ubuntu16.04

%environment

  # use bash as default shell
  SHELL=/bin/bash

  # add CUDA paths
  CPATH="/usr/local/cuda/include:$CPATH"
  PATH="/usr/local/cuda/bin:$PATH"
  LD_LIBRARY_PATH="/usr/local/cuda/lib64:$LD_LIBRARY_PATH"
  CUDA_HOME="/usr/local/cuda"

  # add Anaconda path
  PATH="/usr/local/anaconda3/bin:$PATH"

  export PATH LD_LIBRARY_PATH CPATH CUDA_HOME
  export MKL_NUM_THREADS=1
  export OPENBLAS_NUM_THREADS=1

%setup
  # runs on host
  # the path to the image is $SINGULARITY_ROOTFS

%post
  # post-setup script

  # load environment variables
  . /environment

  # use bash as default shell
  echo "\n #Using bash as default shell \n" >> /environment
  echo 'SHELL=/bin/bash' >> /environment

  # make environment file executable
  chmod +x /environment

  # default mount paths
  mkdir /scratch /data 

  #Add CUDA paths
  echo "\n #Cuda paths \n" >> /environment
  echo 'export CPATH="/usr/local/cuda/include:$CPATH"' >> /environment
  echo 'export PATH="/usr/local/cuda/bin:$PATH"' >> /environment
  echo 'export LD_LIBRARY_PATH="/usr/local/cuda/lib64:$LD_LIBRARY_PATH"' >> /environment
  echo 'export CUDA_HOME="/usr/local/cuda"' >> /environment

  # updating and getting required packages
  apt-get update
  apt-get install -y wget git vim build-essential cmake

  # creates a build directory
  mkdir build
  cd build

  # download and install Anaconda
  CONDA_INSTALL_PATH="/usr/local/anaconda3"
  wget https://repo.continuum.io/archive/Anaconda3-5.0.1-Linux-x86_64.sh
  chmod +x Anaconda3-5.0.1-Linux-x86_64.sh
  ./Anaconda3-5.0.1-Linux-x86_64.sh -b -p $CONDA_INSTALL_PATH

  # download and install CaImAn
  git clone https://github.com/flatironinstitute/CaImAn.git
  cd CaImAn
  conda env create -n caiman -f environment.yml
  source activate caiman
  pip install .
  caimanmanager.py install
  source deactivate


%runscript
  # executes with the singularity run command
  # delete this section to use existing docker ENTRYPOINT command

%test
  # test that script is a success

我已经尝试了 conda activate 和 source activate 并且都得到了同样的错误。

+ source activate caiman
/bin/sh: 41: source: not found
ABORT: Aborting with RETVAL=255
Cleaning up...

这只是让图像可写后我必须要做的事情吗？那将是下一个默认解决方案，但如果该配方能够正常工作，那就太好了。

*编辑1 . activate caiman returns.

+ . activate caiman
+ [[ -n ]]
/bin/sh: 4: /usr/local/anaconda3/bin/activate: [[: not found
+ [[ -n ]]
/bin/sh: 7: /usr/local/anaconda3/bin/activate: [[: not found
+ echo Only bash and zsh are supported
Only bash and zsh are supported
+ return 1
ABORT: Aborting with RETVAL=255
Cleaning up...

*编辑2 通过使用较新版本的 Anaconda，未找到的错误消失了。我所做的只是更改了我使用 wget 获得的 Anaconda 发行版，并且我还强制更新以加倍确定。

# download and install Anaconda
  CONDA_INSTALL_PATH="/usr/local/anaconda3"
  wget https://repo.continuum.io/archive/Anaconda3-5.3.1-Linux-x86_64.sh
  chmod +x Anaconda3-5.3.1-Linux-x86_64.sh
  ./Anaconda3-5.3.1-Linux-x86_64.sh -b -p $CONDA_INSTALL_PATH
  conda update -n base -c defaults conda
  pip install --upgrade pip

Answer 1

如果我没记错（完全有可能），virtualenv 也会发生同样的情况。

问题是source不是命令，试试：

. activate caiman

而不是

source activate caiman

更新问题后编辑，检查此https://github.com/conda/conda/issues/6639您可能想调查您的激活正在做什么（似乎正在寻找不存在的文件）

如何在 Singularity 配方中激活 Anaconda 环境

How to activate an Anaconda environment in a Singularity recipe

python

anaconda

singularity-container