module load openmpi/2.1.2
module show openmpi/2.1.2
Spack Package Management
Anaconda Package Management
If most of your software requirements revolve around scientific python packages you may want to install Conda into your home or group directory. Conda is an open source package management system and environment management system that runs on Windows, macOS and Linux. Conda quickly installs, runs and updates packages and their dependencies. Conda easily creates, saves, loads and switches between environments on your local computer.
Example 1, Conda Install into your home directory.
Run the following in your home directory to install a Conda local to your accounts. (See next example to add shared Conda installs for larger groups)
For Python3 Conda installation
For Python2 Conda installation
(base) [jflilley@login1]$ which python
Since sourcing of the Conda environment is in your ~/.bashrc all compute nodes will have the proper paths set to use Conda packages. If you've setup multiple conda environments be sure that your slurm submission scripts activate the correct environment if not the default one.
Example 2, Conda Install into your groups shared directory. Complete Example 1 installation above first. Add the secondary conda environment by creating a new .condarc file in your home directory, replacing <group name directory> with your groups directory name.
- /central/groups/<group name directory>/anaconda2
Verify the environment shows up and then activate.
[jflilley@login1 ~]$ conda env list
second-shared-environment /central/groups/MICS/anaconda2/second-shared-environment base * /home/jflilley/anaconda2
conda activate second-shared-environment
/central/groups/<group name directory>/second-shared-environment/bin/python
Another method to share Conda environments while allowing flexibility for other users to self manage their own, is to export an environment to yaml that can be imported into the other users personal Conda setup.
To export an environment to share with a fellow research first activate the intended environment in Conda and run the following command.
conda env export > ~/shared-conda-environment.yml
To import the Conda invornment into another Conda installation run.
conda env create -f shared-conda-environment.yml
To verify the import list your Conda environments.
conda env list