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isub: Job submitter for IDA OpenShift cluster

This is a basic system for submitting jobs to the IDA OpenShift GPU cluster. It sets up a job on the cluster using a Docker image and connects to the file system so that your files are accessible.

isub should be used on the head-node of the GPU cluster. You can SSH into the machine using tools such as PuTTY on Windows or the SSH client in the terminal on Mac.

Installation

You must log into the head node to run isub commands using SSH. You can install it using pip3 directly from this GitHub repo

pip3 install -U --user git+https://github.com/jakelever/isub.git

Important details

  • You cannot and should not run Python directly on the head-node of the cluster. Instead you should run isub commands that launch a job on the cluster which is then run on one of the nodes with a GPU
  • You can only run code inside your volume directory (something like /home/jakelever/jakelevervol1claim).
  • The directories which you write to must be write accessible to all. Use chmod a+w <DIRECTORY> with the directory you want to make write accessible to all

Example Usage

Let's show an example of running some HuggingFace Python code. Create a file called example.py with the five lines of Python below. And note the important details above about where you run it and write permissions.

from transformers import pipeline, set_seed
generator = pipeline('text-generation', model="distilgpt2")
set_seed(42)
generated = generator("Hello, I'm a language model,", max_length=30, num_return_sequences=5)
print(generated)

You can then run it on the cluster with the isub command below. It should create a job that will be visible through the cluster console (link on the cluster Moodle page) and save the output to a log file in the same directory.

isub --command "python3 example.py"

More controls

Run the help command to see all the options. This can give you controls over the resources requested (e.g. GPUs, CPUs, memory), the log file and other usefu 5E67 l things.

isub --help

Running a script instead of a command

The earlier example runs a Python3 command. You could also save the commands to a .sh shell script and use --script to run that.

Custom Docker images

The default Docker image used is jakelever/ml_gpu which is set up to work with the different machines and have a basic install of the standard machine learning and deep learning libraries. The Dockerfile for it is in the docker/ directory. You could create your own one, upload it to DockerHub and use --image to select it.

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