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Mambaforge provides mamba and conda on the cluster. Users who prefer to manage their own installation can install a Conda distribution in their home directory.

This document is not a comprehensive guide on Conda. To learn more, see the official manual. The conda intro provides a good starting point.

Using Conda with Slurm

Submitting a slurm job which includes conda activate will result in the following error:

$ srun -N1 conda activate myenv

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run

    $ conda init <SHELL_NAME>

This happens because conda activate is made available as a shell function which is not preserved when slurm executes a job.

The suggestion of executing conda init does not apply to Slurm. Instead, an environment can be activated with one of the following methods:

  • Execute conda activate while logged into a submission node, then submit the job:
$ conda activate myenv
(myenv) $ srun -N1 env | grep CONDA_PREFIX
  • Execute eval "$(conda shell.bash hook)" as part of the slurm job in order to make conda activate available:
$ cat
#!/usr/bin/env bash
eval "$(conda shell.bash hook)"
conda activate myenv
srun -N1 env | grep CONDA_PREFIX

$ sbatch

$ cat slurm-120651.out