Python on RDHPCS Systems

Overview

In high-performance computing, Python is heavily used to analyze scientific data on the system. Some users require specific versions of Python or niche scientific packages to analyze their data, which may further depend on numerous other Python packages. Because of all the dependencies that some Python packages require, and all the types of data that exist, it can be quite troublesome to get different Python installations to “play nicely” with each-other, especially on an HPC system where the system environment is complicated. Virtual environments help alleviate these issues by isolating package installations into self-contained directory trees.

Although Python has a native virtual environment feature (venv), one popular virtual environment manager is Conda, a package and virtual environment manager from the Anaconda distribution. Conda allows users to easily install different versions of binary software packages and any required libraries appropriate for their computing platform. The versatility of conda allows a user to essentially build their own isolated Python environment, without having to worry about clashing dependencies and other system installations of Python. Conda is available on all RDHPCS systems, and loading the default Python module loads an Anaconda Python distribution. Loading this distribution automatically puts you in a “base” conda environment, which already includes packages that one can use for simulation, analysis, and machine learning.

For users interested in using Python with Jupyter, see our Jupyter on RDHPCS Systems page instead.

Note

The RDHPCS is working on a unified Python/Conda configuration and policies across all NOAA-managed RDHPCS systems (hera, jet, niagara, ppan). This documentation will be updated as the the configuration and policies are established.

Python Guides

Below is a list of guides created for using Python on RDHPCS systems.

• Conda Basics Guide: Goes over the basic workflow and commands of Conda

• Installing Miniconda Guide: Teaches you how to install Miniconda

• Jupyter on RDHPCS Systems: Instructions to install and access JupyterLab on the RDHPCS systems

Note

For newer users to conda, it is highly recommended to view our Conda Basics Guide, where a Quick-Reference Commands list is provided.

Module Usage

To start using Python, all you need to do is load the module:

Gaea

$ module load python

Hera

$ module load python

Jet

$ module load python

niagara

$ module load python

PPAN

$ module load python

Base Environment

Loading the Python module on all systems will put you in a “base” pre-configured environment. This option is recommended for users who do not need custom environments, and only require packages that are already installed in the base environment. This option is also recommended for users that just need a Python interpreter or standard packages like NumPy and Scipy.

To see a full list of the packages installed in the base environment, use conda list. A small preview is provided below:

Gaea

$ module load python
$ conda list

# packages in environment at ...:
#
# Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0                    py38_0
_libgcc_mutex             0.1                        main
alabaster                 0.7.12                     py_0
anaconda                  2020.07                  py38_0
anaconda-client           1.7.2                    py38_0
anaconda-project          0.8.4                      py_0
asn1crypto                1.3.0                    py38_0
astroid                   2.4.2                    py38_0
astropy                   4.0.1.post1      py38h7b6447c_1
.
.
.

Hera

$ module load python
$ conda list

# packages in environment at ...:
#
# Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0                    py37_0
_libgcc_mutex             0.1                        main
absl-py                   0.11.0                   pypi_0    pypi
alabaster                 0.7.12                   py37_0
anaconda                  2020.02                  py37_0
anaconda-client           1.7.2                    py37_0
anaconda-navigator        1.9.12                   py37_0
anaconda-project          0.8.4                      py_0
argh                      0.26.2                   py37_0
.
.
.

Jet

$ module load python
$ conda list

# packages in environment at ...:
#
# Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0                    py37_0
_libgcc_mutex             0.1                        main
absl-py                   0.11.0                   pypi_0    pypi
alabaster                 0.7.12                   py37_0
anaconda                  2020.02                  py37_0
anaconda-client           1.7.2                    py37_0
anaconda-navigator        1.9.12                   py37_0
anaconda-project          0.8.4                      py_0
argh                      0.26.2                   py37_0
.
.
.

niagara

$ module load python
$ conda list

# packages in environment at ...:
#
# Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0                    py37_0
_libgcc_mutex             0.1                        main
absl-py                   0.11.0                   pypi_0    pypi
alabaster                 0.7.12                   py37_0
anaconda                  2020.02                  py37_0
anaconda-client           1.7.2                    py37_0
anaconda-navigator        1.9.12                   py37_0
anaconda-project          0.8.4                      py_0
argh                      0.26.2                   py37_0
.
.
.

PPAN

$ module load python
$ conda list

# packages in environment at ...:
#
# Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0                    py37_0
_libgcc_mutex             0.1                        main
absl-py                   0.11.0                   pypi_0    pypi
alabaster                 0.7.12                   py37_0
anaconda                  2020.02                  py37_0
anaconda-client           1.7.2                    py37_0
anaconda-navigator        1.9.12                   py37_0
anaconda-project          0.8.4                      py_0
argh                      0.26.2                   py37_0
.
.
.

Warning

It is not recommended to try to install new packages into the base environment. Instead, you can either clone the base environment for yourself and install packages into the clone, or create a brand new (empty) environment and install packages into it. An example for cloning the base environment is provided in Best Practices below, while creating new environments is covered directly below in Custom Environments.

Custom Environments

You can also create your own custom environments after loading the Python module. This option is recommended for users that require a different version of Python than the default version available, or for users that want a personal environment to manage specialized packages. This is possible via conda or using Python’s native venv feature instead.

Note

A more complete list of conda commands is provided in the Quick-Reference Commands section of the Conda Basics Guide. More information on using the venv command can be found in Python’s Official Documentation.

To create and activate an environment:

Gaea

#1. Load the module
$ module load python

#2a. Create "my_env" with Python version X.Y at the desired path
$ conda create -p /path/to/my_env python=X.Y

#2b. Create "my_env" with Python version X.Y with a specific name (defaults to $HOME directory)
$ conda create --name my_env python=X.Y

#3. Activate "my_env"
$ conda activate /path/to/my_env

Hera

#1. Load the module
$ module load python

#2a. Create "my_env" with Python version X.Y at the desired path
$ conda create -p /path/to/my_env python=X.Y

#2b. Create "my_env" with Python version X.Y with a specific name (defaults to $HOME directory)
$ conda create --name my_env python=X.Y

#3. Activate "my_env"
$ conda activate /path/to/my_env

Jet

#1. Load the module
$ module load cray-python

#2. Create "my_env" at the desired path (uses same Python version as module)
$ python3 -m venv /path/to/my_env

#3. Activate "my_env"
$ conda /path/to/my_env/bin/activate

Niagara

#1. Load the module
$ module load cray-python

#2. Create "my_env" at the desired path (uses same Python version as module)
$ python3 -m venv /path/to/my_env

#3. Activate "my_env"
$ conda /path/to/my_env/bin/activate

PPAN

#1. Load the module
$ module load cray-python

#2. Create "my_env" at the desired path (uses same Python version as module)
$ python3 -m venv /path/to/my_env

#3. Activate "my_env"
$ conda /path/to/my_env/bin/activate

Note

It is highly recommended to create new environments in the “Project Home” directory (see file system summary). This space avoids purges, allows for potential collaboration within your project, and works better with the compute nodes. It is also recommended, for convenience, that you use environment names that indicate the hostname, as virtual environments created on one system will not necessarily work on others.

It is always recommended to deactivate an environment before activating a new one. Deactivating an environment can be achieved through:

Gaea

# Deactivate the current environment
$ conda deactivate

Hera

# Deactivate the current environment
$ conda deactivate

Jet

# Deactivate the current environment
$ conda deactivate

Niagara

# Deactivate the current environment
$ conda deactivate

PPAN

# Deactivate the current environment
$ conda deactivate

How to Run

Warning

Remember, at larger scales both your performance and your fellow users’ performance will suffer if you do not run on the compute nodes. It is always highly recommended to run on the compute nodes (through the use of a batch job or interactive batch job).

The OS-provided Python is no longer accessible as python (including variations like /usr/bin/python or /usr/bin/env python); rather, you must specify it as python2 or python3. If you are using python from one of the module files rather than the version in /usr/bin, this change should not affect how you invoke python in your scripts, although we encourage specifying python2 or python3 as a best practice.

RDHPCS Compute Nodes

Before jumping into batch scripts, remember to check out the Module Usage section first, which details the differences between Python modules and environments on our different systems.

Batch Script

On most RDHPCS systems, you are already on a compute node once you are in a batch job. Therefore, you only need to use srun if you plan to run parallel-enabled Python, and you do not need to specify srun if you are running a serial application.

Additionally, $PATH issues are known to occur if not submitting from a fresh login shell, which can result in the wrong environment being detected. To avoid this, you must use the --export=NONE flag, which ensures that no previously set environment variables are passed into the batch job:

$ sbatch --export=NONE submit.sl

This means you will have to load your modules and activate your environment inside the batch script. An example batch script for is provided below:

Gaea

#!/bin/bash
#SBATCH -A <PROJECT_ID>
#SBATCH -J python
#SBATCH -N 1
#SBATCH -p batch
#SBATCH -t 0:05:00

cd $SLURM_SUBMIT_DIR
date

module load python
conda activate my_env

python3 script.py

Hera

#!/bin/bash
#SBATCH -A <PROJECT_ID>
#SBATCH -J python
#SBATCH -N 1
#SBATCH -p batch
#SBATCH -t 0:05:00

cd $SLURM_SUBMIT_DIR
date

module load python
conda activate my_env

python3 script.py

Jet

#!/bin/bash
#SBATCH -A <PROJECT_ID>
#SBATCH -J python
#SBATCH -N 1
#SBATCH -p batch
#SBATCH -t 0:05:00

cd $SLURM_SUBMIT_DIR
date

module load python
conda activate my_env

python3 script.py

Niagara

#!/bin/bash
#SBATCH -A <PROJECT_ID>
#SBATCH -J python
#SBATCH -N 1
#SBATCH -p batch
#SBATCH -t 0:05:00

cd $SLURM_SUBMIT_DIR
date

module load python
conda activate my_env

python3 script.py

PPAN

#!/bin/bash
#SBATCH -A <PROJECT_ID>
#SBATCH -J python
#SBATCH -N 1
#SBATCH -p batch
#SBATCH -t 0:05:00

cd $SLURM_SUBMIT_DIR
date

module load python
conda activate my_env

python3 script.py

Interactive Job

To use Python in an interactive session on RDHPCS systems:

Gaea

$ salloc -A <PROJECT_ID> -N 1 -t 0:05:00
$ module load python
$ conda activate my_env
$ python3 script.py

Hera

$ salloc -A <PROJECT_ID> -N 1 -t 0:05:00
$ module load python
$ conda activate my_env
$ python3 script.py

Jet

$ salloc -A <PROJECT_ID> -N 1 -t 0:05:00
$ module load python
$ conda activate my_env
$ python3 script.py

Niagara

$ salloc -A <PROJECT_ID> -N 1 -t 0:05:00
$ module load python
$ conda activate my_env
$ python3 script.py

PPAN

$ salloc -A <PROJECT_ID> -N 1 -t 0:05:00
$ module load python
$ conda activate my_env
$ python3 script.py

When in an interactive job, if you want to use an interactive Python prompt and srun at the same time, use the --pty flag (useful when running with multiple tasks):

$ srun --pty python3

Best Practices

• Cloning the base environment using conda:

  It is not recommended to try to install new packages into the base environment. Instead, you can clone the base environment for yourself and install packages into the clone. To clone an environment, you must use the --clone <env_to_clone> flag when creating a new conda environment. An example for cloning the base environment into a specific directory called envs/ in your “Project Home” is provided below:

  $ conda create -p <project_home>/<project_id>/<user_id>/envs/baseClone --clone base
  $ conda activate <project_home>/<project_id>/<user_id>/envs/baseClone
  

• Cloning the “base environment” using venv:

  $ python3 -m venv /path/to/new_env --system-site-packages
  

• Environment locations (storage):

  It is highly recommended to create new environments in the “Project Home” directory (see file system summary). This space avoids purges, allows for potential collaboration within your project, and works better with the compute nodes.

• Adding known conda environment locations:

  For a conda environment to be callable by a “name”, it must be installed in one of the envs_dirs directories. The list of known directories can be seen by executing:

  $ conda config --show envs_dirs
  

  On RDHPCS systems, the default location is your $HOME directory. If you plan to frequently create environments in a different location other than the default, then there is an option to add directories to the envs_dirs list.

  For example, to track conda environments in a subdirectory in the Project Home you would execute:

  $ conda config --append envs_dirs <project_home>/<project_id>/<user_id>/envs
  

  This will create a .condarc file in your $HOME directory if you do not have one already, which will now contain this new envs_dirs location. This will now enable you to use the --name env_name flag when using conda commands for environments stored in the personal environments directory, instead of having to use the -p <project_home>/<project_id>/<user_id>/envs/env_name flag and specifying the full path to the environment. For example, you can do conda activate my_env instead of conda activate <project_home>/<project_id>/<user_id>/envs/my_env.

• Make note of and clean your pip cache location:

  To avoid quota issues, it is highly recommended to occasionally clean your pip cache location.

  • To find where your cache location is, use:

    $ pip cache info
    

  • To clean your cache, use:

    $ pip cache purge
    

• Clean your conda cache:

  To avoid quota issues, it is highly recommended to occasionally clean your conda cache location (in your .conda directory). To do so, run:

  $ conda clean -a
  

• Deactivate your environments before running batch jobs:

  To avoid $PATH issues, it is highly recommended to submit batch jobs or enter interactive jobs without an already activated environment – so, deactivating your environment is recommended. Alternatively, you can submit your jobs from a fresh login shell.

• Unbuffered input:

  To enable unbuffered input when running Python jobs or scripts on our systems, it is recommended to use the -u flag. For example:

  $ python3 -u script.py
  

Additional Resources

• pip User Guide

• venv Documentation

• Conda User Guide

• Anaconda Package List

• Using Pip In A Conda Environment