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Computing cluster

With Lightning it is easy to run your training script on a computing cluster without almost any modifications to the script. In this guide, we cover

  1. General purpose cluster (not managed)

  2. SLURM cluster

  3. Custom cluster environment

  4. General tips for multi-node training


1. General purpose cluster

This guide shows how to run a training job on a general purpose cluster. We recommend beginners to try this method first because it requires the least amount of configuration and changes to the code. To setup a multi-node computing cluster you need:

  1. Multiple computers with PyTorch Lightning installed

  2. A network connectivity between them with firewall rules that allow traffic flow on a specified MASTER_PORT.

  3. Defined environment variables on each node required for the PyTorch Lightning multi-node distributed training

PyTorch Lightning follows the design of PyTorch distributed communication package. and requires the following environment variables to be defined on each node:

  • MASTER_PORT - required; has to be a free port on machine with NODE_RANK 0

  • MASTER_ADDR - required (except for NODE_RANK 0); address of NODE_RANK 0 node

  • WORLD_SIZE - required; how many nodes are in the cluster

  • NODE_RANK - required; id of the node in the cluster

Training script setup

To train a model using multiple nodes, do the following:

  1. Design your LightningModule (no need to add anything specific here).

  2. Enable DDP in the trainer

    # train on 32 GPUs across 4 nodes
    trainer = Trainer(gpus=8, num_nodes=4, accelerator='ddp')
    

Submit a job to the cluster

To submit a training job to the cluster you need to run the same training script on each node of the cluster. This means that you need to:

  1. Copy all third-party libraries to each node (usually means - distribute requirements.txt file and install it).

  2. Copy all your import dependencies and the script itself to each node.

  3. Run the script on each node.


2. SLURM managed cluster

Lightning automates the details behind training on a SLURM-powered cluster. In contrast to the general purpose cluster above, the user does not start the jobs manually on each node and instead submits it to SLURM which schedules the resources and time for which the job is allowed to run.

Training script design

To train a model using multiple nodes, do the following:

  1. Design your LightningModule (no need to add anything specific here).

  2. Enable DDP in the trainer

    # train on 32 GPUs across 4 nodes
    trainer = Trainer(gpus=8, num_nodes=4, accelerator='ddp')
    
  3. It’s a good idea to structure your training script like this:

    # train.py
    def main(hparams):
        model = LightningTemplateModel(hparams)
    
        trainer = Trainer(
            gpus=8,
            num_nodes=4,
            accelerator='ddp'
        )
    
        trainer.fit(model)
    
    
    if __name__ == '__main__':
        root_dir = os.path.dirname(os.path.realpath(__file__))
        parent_parser = ArgumentParser(add_help=False)
        hyperparams = parser.parse_args()
    
        # TRAIN
        main(hyperparams)
    
  4. Create the appropriate SLURM job:

    # (submit.sh)
    #!/bin/bash -l
    
    # SLURM SUBMIT SCRIPT
    #SBATCH --nodes=4
    #SBATCH --gres=gpu:8
    #SBATCH --ntasks-per-node=8
    #SBATCH --mem=0
    #SBATCH --time=0-02:00:00
    
    # activate conda env
    source activate $1
    
    # debugging flags (optional)
    export NCCL_DEBUG=INFO
    export PYTHONFAULTHANDLER=1
    
    # on your cluster you might need these:
    # set the network interface
    # export NCCL_SOCKET_IFNAME=^docker0,lo
    
    # might need the latest CUDA
    # module load NCCL/2.4.7-1-cuda.10.0
    
    # run script from above
    srun python3 train.py
    
  5. If you want auto-resubmit (read below), add this line to the submit.sh script

    #SBATCH --signal=SIGUSR1@90
    
  6. Submit the SLURM job

    sbatch submit.sh
    

Wall time auto-resubmit

When you use Lightning in a SLURM cluster, it automatically detects when it is about to run into the wall time and does the following:

  1. Saves a temporary checkpoint.

  2. Requeues the job.

  3. When the job starts, it loads the temporary checkpoint.

To get this behavior make sure to add the correct signal to your SLURM script

# 90 seconds before training ends
SBATCH --signal=SIGUSR1@90

Building SLURM scripts

Instead of manually building SLURM scripts, you can use the SlurmCluster object to do this for you. The SlurmCluster can also run a grid search if you pass in a HyperOptArgumentParser.

Here is an example where you run a grid search of 9 combinations of hyperparameters. See also the multi-node examples here.

# grid search 3 values of learning rate and 3 values of number of layers for your net
# this generates 9 experiments (lr=1e-3, layers=16), (lr=1e-3, layers=32),
# (lr=1e-3, layers=64), ... (lr=1e-1, layers=64)
parser = HyperOptArgumentParser(strategy='grid_search', add_help=False)
parser.opt_list('--learning_rate', default=0.001, type=float,
                options=[1e-3, 1e-2, 1e-1], tunable=True)
parser.opt_list('--layers', default=1, type=float, options=[16, 32, 64], tunable=True)
hyperparams = parser.parse_args()

# Slurm cluster submits 9 jobs, each with a set of hyperparams
cluster = SlurmCluster(
    hyperparam_optimizer=hyperparams,
    log_path='/some/path/to/save',
)

# OPTIONAL FLAGS WHICH MAY BE CLUSTER DEPENDENT
# which interface your nodes use for communication
cluster.add_command('export NCCL_SOCKET_IFNAME=^docker0,lo')

# see the output of the NCCL connection process
# NCCL is how the nodes talk to each other
cluster.add_command('export NCCL_DEBUG=INFO')

# setting a master port here is a good idea.
cluster.add_command('export MASTER_PORT=%r' % PORT)

# ************** DON'T FORGET THIS ***************
# MUST load the latest NCCL version
cluster.load_modules(['NCCL/2.4.7-1-cuda.10.0'])

# configure cluster
cluster.per_experiment_nb_nodes = 12
cluster.per_experiment_nb_gpus = 8

cluster.add_slurm_cmd(cmd='ntasks-per-node', value=8, comment='1 task per gpu')

# submit a script with 9 combinations of hyper params
# (lr=1e-3, layers=16), (lr=1e-3, layers=32), (lr=1e-3, layers=64), ... (lr=1e-1, layers=64)
cluster.optimize_parallel_cluster_gpu(
    main,
    nb_trials=9, # how many permutations of the grid search to run
    job_name='name_for_squeue'
)

The other option is that you generate scripts on your own via a bash command or use our native solution.


3. Custom cluster

Lightning provides an interface for providing your own definition of a cluster environment. It mainly consists of parsing the right environment variables to access information such as world size, global and local rank (process id), and node rank (node id). Here is an example of a custom ClusterEnvironment:

import os
from pytorch_lightning.plugins.environments import ClusterEnvironment

class MyClusterEnvironment(ClusterEnvironment):

    def creates_children(self) -> bool:
        # return True if the cluster is managed (you don't launch processes yourself)
        return True

    def world_size(self) -> int:
        return int(os.environ["WORLD_SIZE"])

    def global_rank(self) -> int:
        return int(os.environ["RANK"])

    def local_rank(self) -> int:
        return int(os.environ["LOCAL_RANK"])

    def node_rank(self) -> int:
        return int(os.environ["NODE_RANK"])

    def master_address(self) -> str:
        return os.environ["MASTER_ADDRESS"]

    def master_port(self) -> int:
        return int(os.environ["MASTER_PORT"])


trainer = Trainer(plugins=[MyClusterEnvironment()])

4. General tips for multi-node training

Debugging flags

When running in DDP mode, some errors in your code can show up as an NCCL issue. Set the NCCL_DEBUG=INFO environment variable to see the ACTUAL error.

python NCCL_DEBUG=INFO train.py ...

Distributed sampler

Normally now you would need to add a DistributedSampler to your dataset, however Lightning automates this for you. But if you still need to set a sampler set the Trainer flag replace_sampler_ddp to False.

Here’s an example of how to add your own sampler (again, not needed with Lightning).

# in your LightningModule
def train_dataloader(self):
    dataset = MyDataset()
    dist_sampler = torch.utils.data.distributed.DistributedSampler(dataset)
    dataloader = Dataloader(dataset, sampler=dist_sampler)
    return dataloader

# in your training script
trainer = Trainer(replace_sampler_ddp=False)
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