To install a new environment start with creating an environment yaml file and store it in a safe location (ideally in your source code repository). This step is optional but we really recommend it so you and everyone in your team is able to produce the same python environment.

name: my-env
dependencies:
  - python=3.10
  - tensorflow-gpu=2.6.0

# load the miniconda package
$ module load miniconda3

# executes bash hooks for the tool to function
# and enters the "base" environment
$ eval "$(conda shell.bash hook)"

# create your environment via environment file
(base) $ conda create -n my-env --file my_env.yaml

# after creation you can activate the environment to run code in it
(base) $ conda activate my-env

# test python version to make sure we have the right one
(my-env) $ python --version
Python 3.10.11

You can now start developing and even just use the environment in a slurm script

#!/bin/bash

#SBATCH --job-name=slurm_conda_example
#SBATCH --time 00-00:05:00
#SBATCH --ntasks=2
#SBATCH --mem=2GB

# modify SBATCH options according to needs

# see "Setup Conda" above or consult "module avail miniconda3" to get the right package name
module load MINICONDA3_PACKAGE_NAME
eval "$(conda shell.bash hook)"
conda activate myenv

# print out some info of the python executable in use
# this should point to the python version from "myenv"
which python
python --version

I see the error 'ModuleNotFoundError: No module named “conda”' in my slurm job logfile. What is wrong>?

The default for sbatch is to use the current user environment and start the job in the context of this environment. Since conda is depending on environment variables being setup correctly you need to ake sure to start the job script from a clean environment. Alternatively you can also use sbatch with the '–export=NONE' argument.

Python is comparatively fast evolving programming language, so different versions behave very differently. We provide multiple varieties of python installations, please always use spack to find and load them.

The VSC team makes sure to have the most used packages readily available via spack. The installed python packages are always named in the following format py-mypackagename e.g. py-numpy or py-scipy. If you can, please always consider using those packages first. See spack on how to find and load them.

There are many additional python packages, some with long dependency chains. Because of this we simply cannot install all of them for all the different python versions we provide. If you need a specific package and its a very popular one, consider dropping us a mail so we can make it generally available.

Apart from loading packages via spack you should always consider creating a virtual environment for your project. This way it will be easier to install other packages / specific package versions and its also possible to exactly track them to produce consistent results. For most of the python packages this is the easiest way to get you up and running in no time.

Note: Before you start, make sure that you have loaded the python version you need! The virtual environment will be created using this version.

cd my_project_folder
python -m venv venv --system-site-packages
source venv/bin/activate
pip install autopep8

The above commands create a new virtual environment in the folder 'venv' (including the system provided packages), activate it and install the package autopep8 into it.

To be able to reproduce the venv, consider specifying the exact versions of the packages as well as tracking your packages in a requirements.txt file (also see python4HPC Development Tools Lecture and Installing packages using pip and virtual environments for more information).

Sometimes, especially in a scientific context, there will be cases were you cannot use pip e.g. some packages need to be compiled. Again this creates the problem that we simply cannot each and every package and package version in our infrastructure.

In this case you can use conda (see Anaconda) instead of pip to set up a consistent local python environment. Conda provides ready made binary distributions for many scientific packages and can thus be used to circumvent this problem.

To use the conda tool on our clusters search for the miniconda3 package. At the time of writing the miniconda3 package is available in all environments on both VSC-4 & VSC-5 and can be loaded with

module load miniconda3

If you plan to use conda more frequently you can simple add the load statement to your ~/.bashrc file to have it loaded automatically after logging in.

To fully utilize the conda command it needs to load runtime hooks. If you want to have conda completely initialized directly after logging in you can execute the following statements to add the conda startup code to your ~/.bashrc file as well.

conda init bash --dry-run --verbose | grep "# >>> conda initialize" -A 100 | grep "# <<< conda initialize" -B 100 | sed 's/+//g' > ~/.bashrc
source ~/.bashrc

After executing these steps you will see that your prompt changed to (base) [myname@l51 ~]$ which signifies that conda is active and the base environment is active.

If you already have an environment you can also add conda activate myenv to your ~/.bashrc file

The default conda channel points to anacondas repository. However this repo does not always contain the latest packages. There are a number of community driven channels (e.g. conda-forge) that have many more packages and most of the time the newer versions readily available.

Popular channels

1. conda-forge - https://conda-forge.org/feedstock-outputs/
2. bioconda - https://bioconda.github.io/conda-package_index.html

To use e.g. conda-forge you need to specify –channel conda-forge when executing conda install commands.

If you want to set e.g. conda-forge as default for your user you can achieve this by executing the following statement:

conda config --add channels conda-forge

This is the recommended method to create new conda environments since it makes environment creation reproducible. The file can be easily shared or e.g. added to your version control system

First decide which python version and packages you need. In case you don't know the exact versions upfront you can also just create a first draft of the env-file without pinned version to get the latest libraries. With that information in mind we now write our environment file called “myenv.yml”

name: myenv
channels:
  - conda-forge
dependencies:
  - python=3.10
  - pytorch=1.13.1

After this we run the conda solver to create and install the new environment

conda env create -f myenv.yml

Conda will now take its time and solve the environment and then download and install the packages. After this has been done the environment can be activated with

conda activate myenv

Note: this method is only for illustrating how conda works and is not recommended since it does not create a reproducible environment specification

In order to create your own user environment you need to do the following steps. To also give a short example for a package which we do not provide via spack we will install phono3py (available onconda forge) into our conda environment (myenv) with conda:

# create conda env 'myenv', set conda-forge channel as default and use the latest python 3.11
conda create --name myenv --channel conda-forge python=3.11
conda activate myenv
conda install --channel conda-forge numpy phono3py

With the above statements conda will create a new environment, activate it and install the requested packages into it. You should see that your prompt now changed to (myenv) [myname@l51 ~]$'

The following commands provide a bit of introspection to make sure that everything is setup as expected:

(myenv) [myname@l51 ~]$ which python
~/.conda/envs/myenv/bin/python
(myenv) [myname@l51 ~]$ python --version
Python 3.11.0
(myenv) [myname@l51 ~]$ which phono3py
~/.conda/envs/myenv/bin/phono3py

Starting python in this conda environment (myenv) and loading the packages also works:

(myenv) myname@l51:~$ python
Python 3.11.0 | packaged by conda-forge | (main, Jan 14 2023, 12:27:40) [GCC 11.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> import phono3py
>>> exit()

See the following minimal example to use conda with slurm in your batch script. See slurm for detailed information about slurm in general.

#!/bin/bash
 
#SBATCH --job-name=slurm_conda_example
#SBATCH --time 00-00:05:00
#SBATCH --ntasks=2
#SBATCH --mem=2GB
 
# modify SBATCH options according to needs
 
# see "Setup Conda" above or consult "module avail miniconda3" to get the right package name
module load MINICONDA3_PACKAGE_NAME
eval "$(conda shell.bash hook)"
conda activate myenv
 
# print out some info of the python executable in use
# this should point to the python version from "myenv"
which python
python --version

In case you need visualization capabilities or you need to do some preprocessing also consider using our JupyterHub service jupyterhub.

Please note that you should still use slurm and batch processing for actual computation runs since JupyterHub is mainly reserved for interactive use and runs on shared nodes.