Page Comparison

...

You can create as many conda environments as you need. Environments are independent (changing one environment won't affect another). They can be used for different analyses, or perhaps if you need more than one version of the same tool. You can run conda info --envs to list all of your conda environments.

Usage of conda init

At some point in their interactions with conda, users may be prompted to execute conda init. Executing conda init results in a block of initialization code being added to the bottom of the the executing user’s $HOME/.bashrc profile, causing that conda distribution’s (base) environment to be initialized upon login to O2. This block also enables the use of the conda activate command.

Research Computing does not recommend the use of conda init on O2. There are two primary reasons for this:

1. This fixes the use of the specified version of conda (and all that entails) for the user on login, which may become the cause of package dependency mismatches and errors as a user requires either alternative conda or application versions for future projects and environments.

2. There have been reports of users experiencing high latency when logging in to O2 when they have conda init blocks present in their $HOME/.bashrc files. This is due to an interaction between the login initialization processes and Research Computing’s login node process watchdog; this interaction can cause logins can take upwards of minutes to resolve.

Research Computing recommends users either comment out or outright delete the conda init block from their $HOME/.bashrc files entirely (the block will be hard to miss, as it is commented and possibly at the very bottom of the file), and get used to the source activate (and load the appropriate associated conda module beforehand) approach. In particular, while using the O2-available miniconda modules, the source activate method should always work.

If a user is leveraging their own personal anaconda/miniconda distribution (i.e., not available via O2’s module system), they can choose to ignore this section at their peril. Users that would like to request assistance in maintaining access to their local distributions without the use of conda init can contact Research Computing at rchelp@hms.harvard.edu.

Installing Packages

To search for available versions of a package that can be installed, use conda search:

...