Oscar: Sage

Loading and Launching Sage

1. Once authenticated to Oscar, use the following commands at the command line.

2. Start an interactive job by using the interact command. This command can take additional parameters to extend the resources and time allotted to the node as well as the partition that the node operates on.

3. The Sage module provides containers. To load sage to load the most recent version of Sage.

4. If your work requires an older version of Sage,them use module load sage/sage-container/10.3.

4. To start the container use apptainer shell /oscar/rt/9.52/software/0.20-generic/0.20.1/opt/spack/linux-rhel9-x86_64_v3/gcc-11.3.1/sage-container-10.3-avpqipfsnbneig726l72jrgdmlrivg4m/sage.sif to load Sage version 9.5.

5. Once inside the container's shell use sage to launch the Sage console within your Terminal window.console.

Sage on VNCOscar OnDemand

The Sage install may not always work properly on Oscar's VNC nodes due to the VNC nodes running older chipsets. The easiest way to remedyrun thisSage issueon Oscar OcDemand is to run sage in an interactive job via the terminal in your VNCOnDemand session.

Use the interact command with parameters for your specific job to start the interactive session, then load your modules and run the sage binary (steps 2-4 above).

interact -n 2 -m 32g -t 04:00:00 -f 'haswell|broadwell|skylake'

Installing Sage Packages Locally with --user

It is possible to install most Sage packages locally to your home folder by passing the –user parameter at the end of your install command. See below for example steps to install the Sage packages “surface_dynamics” and “sage-flatsurf”. In this example, we are loading both packages from git repositories, so we need to load the git module.

1. module load git

2. sage -pip install git+https://gitlab.com/videlec/surface_dynamics –user

3. sage -pip install git+https://github.com/videlec/sage-flatsurf –user

Using Sage with Batch Scripts

Thanks to Trevor Hyde from Summer@ICERM 2019 for these instructions.

One method for running computations with Sage on Oscar is to write a script and use the slurm batch scheduler to have Oscar run your script. This requires two pieces:

Example Batch Script

sage-batch.sh

#!/bin/bash
 
#SBATCH -J test_program
#SBATCH --array=0-9
#SBATCH -t 1:00:00
#SBATCH --mem=8G
 
#SBATCH -e data/<oscar-username>/test_output/test%a.err
#SBATCH -o data/<oscar-username>/test_output/test%a.out
 
module load sagesage-container/10.3

apptainer shell /oscar/rt/9.2/software/0.20-generic/0.20.1/opt/spack/linux-rhel9-x86_64_v3/gcc-11.3.1/sage-container-10.3-avpqipfsnbneig726l72jrgdmlrivg4m/sage.sif
 
sage test_program.sage $SLURM_ARRAY_TASK_ID

Everything after this in the script happens as if you typed it yourself onto the command line.

Example Sage Program

test_program.sage

import sys
 
def fun_math(message):
    print message
    sys.stdout.flush()
 
job_id = int(sys.argv[1])
fun_math('hi this is a test')
fun_math('my job id is' + str(job_id))

• In the Sage program, you first define all of your functions and then you include the code you want to run.

• Import sys so you can access the array parameter passed to your function from the node. This is accessed in this case by sys.argv[1]. Make sure you explicitly coerce to be an integer if you want to use it as an integer; it's a string by default.

• The output of the print command is appended to the .out file for this node as a new line.

• Notice the line sys.stdout.flush() included in the function. This makes the program immediately send whatever output it has to the output file when called. Otherwise the program won’t output anything until it has completely finished running. If each node is running 100 potentially long computations and it finishes the first 99 but then times out on the 100th computation, and you don’t include any sys.stdout.flush() commands, everything will be lost when time runs out.

Submitting the Batch Job