Reading HPC with Python

Do not run code that displays plots on screen. Instead, have them written to files.

Interactive jobs are useful for code testing and development. They are not however the most efficient way to run code, so you should limit their use to testing and development.

You start an interactive job with:

$ salloc --account=def-<account> --cpus-per-task=<n> --gres=gpu:<n> --mem=<mem> --time=<time>

Our training cluster does not have GPUs, so for this workshop, do not use the --gres=gpu:<n> option.

For the workshop, you also don't have to worry about the --account=def-<account> option (or, if you want, you can use --account=def-sponsor00).

Our training cluster has a total of 60 CPUs on 5 compute nodes. Since there are many of you in this workshop, please be very mindful when running interactive jobs: if you request a lot of CPUs for a long time, the other workshop attendees won't be able to use the cluster anymore until your interactive job requested time ends (even if you aren't running any code).

Here are my suggestions so that we don't run into this problem:

• Only start interactive jobs when you need to understand what Python is doing at every step, or to test, explore, and develop code (so where an interactive Python shell is really beneficial). Once you have a model, submit a batch job to Slurm instead
• When running interactive jobs on this training cluster, only request 1 CPU (so --cpus-per-task=1)
• Only request the time that you will really use (e.g. for the lesson on Python tensors, maybe 30 min to 1 hour seems reasonable)
• If you don't need your job allocation anymore before it runs out, you can relinquish it with Ctrl+d

As soon as you have a working Python script, you want to submit a batch job instead of running an interactive job. To do that, you need to write an sbatch script.

#!/bin/bash
#SBATCH --job-name=<name>*			  # job name
#SBATCH --account=def-<account>
#SBATCH --time=<time>				  # max walltime in D-HH:MM or HH:MM:SS
#SBATCH --cpus-per-task=<number>      # number of cores
#SBATCH --gres=gpu:<type>:<number>    # type and number of GPU(s) per node
#SBATCH --mem=<mem>					  # max memory (default unit is MB) per node
#SBATCH --output=%x_%j.out*		  # file name for the output
#SBATCH --error=%x_%j.err*		  # file name for errors
#SBATCH --mail-user=<email_address>*
#SBATCH --mail-type=ALL*

# Load modules
# (Do not use this in our workshop since we aren't using GPUs)
# (Note: loading the Python module is not necessary
# when you activate a Python virtual environment)
# module load cudacore/.10.1.243 cuda/10 cudnn/7.6.5

# Create a variable with the directory for your ML project
SOURCEDIR=~/<path/project/dir>

# Activate your Python virtual environment
source ~/env/bin/activate

# Transfer and extract data to a compute node
mkdir $SLURM_TMPDIR/data
tar xf ~/projects/def-<user>/<data>.tar -C $SLURM_TMPDIR/data

# Run your Python script on the data
python $SOURCEDIR/<script>.py $SLURM_TMPDIR/data

$ mkdir $SLURM_TMPDIR/data

$ tar xf ~/projects/def-<user>/<data>.tar -C $SLURM_TMPDIR/data

$ cp -r ~/projects/def-<user>/<data> $SLURM_TMPDIR/data

$ cd </dir/containing/job>
$ sbatch <jobscript>.sh

$ sq

$ scancel <jobid>

$ seff <jobid>

It might be wise to test your code in an interactive job before submitting a really big batch job to Slurm.

$ source ~/env/bin/activate

$ salloc --account=def-<account> --gres=gpu:1 --cpus-per-task=6 --mem=32000 --time=0:30:0

(env) $ mkdir $SLURM_TMPDIR/data

(env) $ tar xf ~/projects/def-<user>/<data>.tar -C $SLURM_TMPDIR/data

(env) $ python

>>> import torch
>>> ...

(env) $ deactivate

Long jobs should have a checkpoint at least every 24 hours. This ensures that an outage won't lead to days of computation lost and it will help get the job started by the scheduler sooner.

For instance, you might want to have checkpoints every n epochs (choose n so that n epochs take less than 24 hours to run).

In PyTorch, you can create dictionaries with all the information necessary and save them as .tar files with torch.save() . You can then load them back with torch.load() .

The information you want to save in each checkpoint includes the model’s state_dict , the optimizer’s state_dict , the epoch at which you stopped, the latest training loss , and anything else needed to restart training where you left off.

torch.save({
    'epoch': <last epoch run>,
    'model_state_dict': net.state_dict(),
    'optimizer_state_dict': optimizer.state_dict(),
    'loss': <latest loss>,
}, <path/to/checkpoint-file.tar>)

To restart, initialize the model and optimizer, load the dictionary, and resume training:

# Initialize the model and optimizer
model = <your model>
optimizer = <your optimizer>

# Load the dictionary
checkpoint = torch.load(<path/to/checkpoint-file.tar>)
model.load_state_dict(checkpoint['model_state_dict'])
optimizer.load_state_dict(checkpoint['optimizer_state_dict'])
epoch = checkpoint['epoch']
loss = checkpoint['loss']

# Resume training
model.train()

TensorBoard allows to visually track your model metrics (e.g. loss, accuracy, model graph, etc.). It requires a lot of processing power however, so if you want to use it on a Compute Canada cluster, do not run it from the login node. Instead, run it as part of your job. This section guides you through the whole workflow.

tensorboard --logdir=/tmp/<your log dir> --host 0.0.0.0 &

#!/bin/bash
#SBATCH ...
...

tensorboard --logdir=/tmp/<your log dir> --host 0.0.0.0 &
python $SOURCEDIR/<script>.py $SLURM_TMPDIR/data

$ sq

[local]$ ssh -N -f -L localhost:6006:<node hostname>:6006 <user>@<cluster>.computecanada.ca

A number of ML tasks (e.g. hyperparameter optimization) require running several instances of similar jobs. Grouping them into a single job with GLOST or GNU Parallel reduces the stress on the scheduler.