This page documents the “anaconda” installation on Bessemer. This is the recommended way of using Python, and the best way to be able to configure custom sets of packages for your use.
“conda” a Python package manager, allows you to create “environments” which are sets of packages that you can modify. It does this by installing them in your home area. This page will guide you through loading conda and then creating and modifying environments so you can install and use whatever Python packages you need.
Using Conda Python¶
After connecting to Bessemer (see Establishing a SSH connection), start an interactive session with the
srun --pty bash -i command.
Anaconda Python can be loaded with one of the following:
module load Anaconda3/2019.07 module load Anaconda3/5.3.0
root conda environment (the default) provides Python 3 and no extra
modules, it is automatically updated, and not recommended for general use, just
as a base for your own environments.
Due to Anaconda being installed in a module you must use the
source command instead of
when activating or deactivating environments!
Creating a Conda Environment¶
Every user can create their own environments, and packages shared with the
system-wide environments will not be reinstalled or copied to your file store,
they will be symlinked, this reduces the space you need in your
directory to install many different Python environments.
To create a clean environment with just Python 3.8 and numpy you can run:
conda create -n mynumpy python=3.8 numpy
This will download the latest release of Python 3.8 and numpy, and create an
Any version of Python or list of packages can be provided:
conda create -n myscience python=3.5 numpy=1.15.2 scipy
If you wish to modify an existing environment, such as one of the anaconda
installations, you can
clone that environment:
conda create --clone myscience -n myexperiment
This will create an environment called
myexperiment which has all the
same conda packages as the
Installing Packages Inside a Conda Environment¶
Once you have created your own environment you can install additional packages
or different versions of packages into it. There are two methods for doing
pip, if a package is available through conda it is
strongly recommended that you use conda to install packages. You can search for
packages using conda:
conda search pandas
then install the package using:
conda install pandas
if you are not in your environment you will get a permission denied error when trying to install packages, if this happens, create or activate an environment you own.
If a package is not available through conda you can search for and install it using pip, i.e.:
pip search colormath pip install colormath
Using conda Environments¶
Once the conda module is loaded you have to load or create the desired conda environments. For the documentation on conda environments see the conda documentation.
You can load a conda environment with:
source activate myexperiment
myexperiment is the name of the environment, and unload one with:
which will return you to the
It is possible to list all the available environments with:
conda env list
Provided system-wide are a set of anaconda environments, these will be installed with the anaconda version number in the environment name, and never modified. They will therefore provide a static base for derivative environments or for using directly.
Using Conda and Python in a batch job¶
Create a batch job submission script called
myscript.slurm that is similar to the following:
#!/bin/bash #SBATCH --ntasks=1 #SBATCH --time=10:00 #SBATCH --mem-per-cpu=100 export SLURM_EXPORT_ENV=ALL module load Anaconda3/2019.07 # We assume that the conda environment 'myexperiment' has already been created source activate myexperiment srun python mywork.py
Then submit this to Slurm by running:
Further Conda Python Learning Resources¶
The resources and training courses below may be of interest: