我正在尝试创建一个奇异的图像和配方,该图像和配方将创建一个anaconda环境,然后激活该环境,以便我可以在该环境中构建项目的python wheel,以便在奇异性构建完成后100%已安装且可以正常工作
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
我已经尝试过conda activate
和source activate
并都遇到相同的错误。
+ source activate caiman
/bin/sh: 41: source: not found
ABORT: Aborting with RETVAL=255
Cleaning up...
这是我以后通过使图像可写而要做的事情吗? 那将是下一个默认的解决方案,但是如果该配方可以使用的话,那就太好了。
*编辑1
. activate caiman
返回。
+ . 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,找不到错误将消失。我所做的就是更改wget附带的Anaconda发行版,并且我也强制并进行了更新,以确保可以肯定。
# 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
答案 0 :(得分:1)
如果我没记错(这完全有可能),那么virtualenv也会发生同样的情况。
问题在于源不是命令,请尝试:
. activate caiman
代替
source activate caiman
在更新问题后进行编辑,请选中此https://github.com/conda/conda/issues/6639,您可能想调查激活程序正在做什么(似乎正在寻找不存在的文件)