Running Python on Cypress

Python Modules

For python as well as all other computationally intensive workloads, you should always use a compute node, either interactively or in batch, rather than a login node. (See below.)

To query your working version of python, you can always use the command python ——version regardless of whether or not you use a module or a conda virtual environment (see here).

The default version of python on Cypress is Python 2.6.6

[tulaneID@cypress1 ~]$python --version
Python 2.6.6

Other versions of python are available on Cypress via modules with the following major names. (See Module command).

• python
• anaconda
• anaconda3

For example, the following is a query in short format for modules on Cypress using the search pattern anaconda.

[tulaneID@cypress1 ~]$module avail -t anaconda 
/cm/local/modulefiles:
/cm/shared/modulefiles:
/share/apps/modulefiles:
anaconda/2.1.0
anaconda/2.5.0
anaconda3/2018.12
anaconda3/2019.03
anaconda3/2020.07
anaconda3/4.0.0
anaconda3/5.1.0
/share/apps/centos7/modulefiles:
anaconda3/2023.07

In particular, for any module listed under /share/apps/centos7, you'll need to use a compute node in partition centos7 (see here).

Anaconda

As the name implies, Anaconda and later Anaconda3 are larger versions of Python. In addition to Python 2.7.8 in Anaconda and Python 3.x in Anaconda3, over 300 of the most requested Python packages are also available. This includes

• NumPy
• Pandas
• SciPy
• Matplotlib
• IPython.

A complete list of packages available though Anaconda can be found ​here.

Install Packages to Anaconda Python

If you want to use some package but Anaconda on Cypress doesn't have it, you can install it on your home directory. See here.

Running Python Interactively

Start an interactive session using idev

[tulaneID@cypress1 pp-1.6.4]$ idev 
Requesting 1 node(s)  task(s) to normal queue of defq partition
1 task(s)/node, 20 cpu(s)/task, 2 MIC device(s)/node
Time: 0 (hr) 60 (min).
Submitted batch job 52311
Seems your requst is pending.
JOBID=52311 begin on cypress01-035
--> Creating interactive terminal session (login) on node cypress01-035.
--> You have 0 (hr) 60 (min).
[tulaneID@cypress01-035 pp-1.6.4]$ 

Load the desired Python module

[tulaneID@cypress01-035 pp-1.6.4]$ module load anaconda
[tulaneID@cypress01-035 pp-1.6.4]$ module list
Currently Loaded Modulefiles:
  1) git/2.4.1           3) idev                5) anaconda/2.1.0
  2) slurm/14.03.0       4) bbcp/amd64_rhel60

Run Python in the command line window

[tulaneID@cypress01-035 pp-1.6.4]$ ipython
Python 2.7.11 |Anaconda 2.5.0 (64-bit)| (default, Dec  6 2015, 18:08:32)
Type "copyright", "credits" or "license" for more information.

IPython 4.1.2 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]:

Running a Python script in Batch mode

You can also submit your Python job to the batch nodes (compute nodes) on Cypress. Inside your SLURM script, include a command to load the desired Python module. Then invoke python on your python script.

#!/bin/bash
#SBATCH --qos=normal            # Quality of Service
#SBATCH --job-name=python       # Job Name
#SBATCH --time=00:01:00         # WallTime
#SBATCH --nodes=1               # Number of Nodes
#SBATCH --ntasks-per-node=1     # Number of tasks (MPI processes)
#SBATCH --cpus-per-task=1       # Number of threads per task (OMP threads)

module load anaconda
python mypythonscript.py

Jupyter Notebook

The ​Jupyter Notebook is a web application that allows you to create and share documents that contain live code, equations, visualizations and explanatory text.

Here show an example.

Installing Packages

See here.