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On O2, we encourage cluster users to install the packages and software they need. One method to install packages and manage environments is to use conda, which is available through the conda2/4.2.13 module or miniconda3/4.10.3 module. Conda manages dependencies by default when you install packages, which can make it easier to install software. Packages that can be installed with conda include Python modules, libraries, or executable programs. Conda includes its own version of Python (2.7.12), though you can explicitly request to use Python 3 if you would prefer.
Commonly used commands, examples
Command | Meaning |
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module spider conda | shows the versions of conda installed on O2 |
module load |
miniconda3/version | loads an individual conda module (replace version with an actual version) |
conda info --envs | see available conda environments |
conda create -n test_env | create conda environment named test_env (name the environment whatever you'd like) |
conda create -n aligners_env bwa bowtie star | create conda environment, and install some packages (bwa, bowtie, and star) on the fly |
source activate test_env | "activate" a conda environment named test_env |
source deactivate | exit current conda environment |
conda-env remove -n test_env | delete a conda environment named test_env |
conda search numpy | search for a package (replace numpy with the package of your choice) |
conda install numpy | install a package, and must be within a conda environment or this command will fail. (replace numpy with the package of your choice) |
Setup
To install packages on O2 using conda, you must first create a conda environment. Environments are simply directories in ~/.conda/envs/ that contain packages you installed. You "source" an environment to use those packages, and can "deactivate" to exit the environment. You can have multiple environments, and can switch between them.
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mfk8@compute-a-01-01:~$ module load conda2miniconda3/4.210.133 |
Then the conda command will be available:
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mfk8@compute-a-01-01:~$ which conda /n/app/conda2miniconda3/4.10.3/bin/conda |
Running conda info will return information about the current conda installation:
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(test_env) mfk8@compute-a-01-01:~$ which python /n/app/conda2miniconda3/4.10.3/bin/python |
The default version of Python that's available through the conda module is Python 2.7.12:
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(test_env) mfk8@compute-a-01-01:~$ python --version Python 23.7.12 :: Continuum Analytics, Inc.9.5 |
If you want to use conda and Python 3a specific version of Python with conda, you can create a conda environment and install Python 3 to it. For example to create an environment using Python 3.6.5:
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mfk8@login01:~$ srun --pty -p interactive -t 0-2 bash mfk8@compute-a-01-01:~$ module load conda2miniconda3/4.210.133 mfk8@compute-a-01-01:~$ module list Currently Loaded Modules: 1) conda2miniconda3/4.210.133 (E) Where: E: Experimental mfk8@compute-a-01-01:~$ conda create -n my_env # truncated mfk8@compute-a-01-01:~$ source activate my_env # install example python package, scipy, which is available through conda: (my_env) mfk8@compute-a-01-01:~$ conda install scipy # truncated # see list of packages available in this conda environment: (my_env) mfk8@compute-a-01-01:~$ conda list # truncated # will report scipy in the list # test importing scipy in python to verify it is installed correctly (my_env) mfk8@compute-a-01-01:~$ python -c "import scipy" (my_env) mfk8@compute-a-01-01:~$ # exit environment (my_env) mfk8@compute-a-01-01:~$ source deactivate mfk8@compute-a-01-01:~$ |
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The centralized conda installation, available through the conda2/4.2.13 modulethe conda modules, includes several channels that we support. Channels are repositories where conda looks for packages. This is done with a centralized .condarc file that contains:
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