Multi-GPU and multi-node machine learning

This guide explains how to utilize multiple GPUs and multiple nodes for machine learning applications on CSC's supercomputers. It is part of our Machine learning guide.

First we will explain the general principles, such as single- and multi-node jobs and mechanisms for launching multiple processes. After that we discuss some common software frameworks how to use them on CSC's supercomputers: PyTorch DDP, DeepSpeed and briefly Horovod and TensorFlow's tf.distribute.Strategy.

Nodes and tasks

GPU Nodes

Each separate GPU node (i.e., a single computer in the cluster), has a fixed number of GPUs. Puhti and Mahti have 4 GPUs per node, and LUMI has 8 GPUs per node. (Technically a LUMI node has 4 GPUs cards, but 8 GPU dies.) The entire supercomputer may have tens or even thousands of GPU nodes. See GPU-accelerated machine learning for more details, in particular the table describing the different GPUs in CSC's various supercomputers might be of interest.

If you need 1-4 GPUs (or 1-8 in LUMI) you should always reserve a single node job. If you need more than 4 GPUs (or 8 in LUMI) you need to reserve a multi-node job. While it is technically possible to reserve, e.g., two GPUs in one node and two in another, this is not recommended except for testing purposes, as the communication across nodes is always slower than inside a node.

MPI tasks

When parallelizing to multiple GPUs it is common to allocate a separate CPU process for handling the communication to each GPU. This per GPU task division may be handled by the program itself, for example using Python's multiprocessing library to launch separate processes. Another method is to use Slurm's MPI facility to launch multiple MPI tasks. Whether MPI tasks are used or not often depends on the software framework used.

Slurm examples

In this section we provide Slurm batch script examples for launching single- or multi-node jobs, with or without MPI.

Note

Please make sure that your code can actually take advantage of multiple GPUs as this typically requires some changes to the program. Simply reserving more GPUs is not enough!

You can monitor that your program is using all the reserved GPUs with the same mechanisms described in our GPU-accelerated machine learning guide. The only difference is that you should now see statistics for more than one GPU.

Single node run using 2 GPUs, no MPI

PuhtiMahtiLUMI

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=gpu
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=20
#SBATCH --mem=160G
#SBATCH --time=1:00:00
#SBATCH --gres=gpu:v100:2

srun python3 myprog.py <options>

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=gpusmall
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=64
#SBATCH --time=1:00:00
#SBATCH --gres=gpu:a100:2

srun python3 myprog.py <options>

Note that on Mahti, the maximum for the gpusmall partition is 2 GPUs. For 3 or 4 GPUs or more you need to use the gpumedium partition.

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=small-g
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=14
#SBATCH --gpus-per-node=2
#SBATCH --mem=120G
#SBATCH --time=1:00:00

srun python3 myprog.py <options>

The example above can be easily changed to more than 2 GPUs by changing the number specified in the --gres option (Puhti and Mahti) or --gpus-per-node option (LUMI). The maximum for a single node job is 4 GPUs (Puhti and Mahti) or 8 GPUs (LUMI).

If you increase the number of GPUs you may also wish to increase the number of CPU cores and the amount of memory reserved. In our examples, we have used as a rule of thumb to reserve CPU cores and memory in the same proportion as the number of GPUs.

For example in Puhti there are 4 GPUs, 40 CPU cores, and 384 GBs of memory per node. For each GPU we would then reserve 10 CPU cores, and roughly 95G of memory (for memory we round down a bit as the units are not so exact).

On LUMI use a maximum of 7 CPU cores and 60GB per reserved GPU.

Single node using all GPUs, using MPI

PuhtiMahtiLUMI

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=gpu
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --cpus-per-task=10
#SBATCH --mem=320G
#SBATCH --time=1:00:00
#SBATCH --gres=gpu:v100:4

srun python3 myprog.py <options>

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=gpumedium
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --cpus-per-task=32
#SBATCH --time=1:00:00
#SBATCH --gres=gpu:a100:4

srun python3 myprog.py <options>

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=small-g
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --cpus-per-task=7
#SBATCH --gpus-per-node=8
#SBATCH --mem=480G
#SBATCH --time=1:00:00

srun python3 myprog.py <options>

Multi-node with 2 full nodes, no MPI

PuhtiMahtiLUMI

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=gpu
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=40
#SBATCH --mem=320G
#SBATCH --time=1:00:00
#SBATCH --gres=gpu:v100:4

srun python3 myprog.py <options>

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=gpumedium
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=128
#SBATCH --time=1:00:00
#SBATCH --gres=gpu:a100:4

srun python3 myprog.py <options>

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=small-g
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=56
#SBATCH --gpus-per-node=8
#SBATCH --mem=480G
#SBATCH --time=1:00:00

srun python3 myprog.py <options>

Note that the --gres option always specifies the number of GPUs on a single-node, even in the multi-node case. So if we are reserving 8 GPUs across 2 nodes in Puhti, that is 4 GPUs on each node, i.e, --gres=gpu:v100:4.

Multi-node with 2 full nodes, using MPI

PuhtiMahtiLUMI

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=gpu
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=4
#SBATCH --cpus-per-task=10
#SBATCH --mem=320G
#SBATCH --time=1:00:00
#SBATCH --gres=gpu:v100:4

srun python3 myprog.py <options>

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=gpumedium
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=4
#SBATCH --cpus-per-task=32
#SBATCH --time=1:00:00
#SBATCH --gres=gpu:a100:4

srun python3 myprog.py <options>

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=small-g
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=8
#SBATCH --cpus-per-task=7
#SBATCH --gpus-per-node=8
#SBATCH --mem=480G
#SBATCH --time=1:00:00

srun python3 myprog.py <options>

Available frameworks

There are many frameworks for doing multi-GPU and multi-node machine learning. Some frameworks are tightly coupled to a specific framework, such as PyTorch DistributedDataParallel, DeepSpeed or TensorFlow's tf.distribute.Strategy, while others are more general, for example Horovod.

Independent of which framework you pick, pay attention to the approach used to launch jobs. For example with Horovod it is common to use MPI, while DeepSpeed can be configured to use MPI or its own parallel launcher. In some frameworks, the launching mechanism may also vary depending on if you are running a single- or multi-node job.

All frameworks should use NCCL (NVIDIA) or RCCL (AMD) for fast inter-GPU communication, even if MPI is used to set up the connections.

PyTorch DDP

PyTorch distributed, and in particular DistributedDataParallel (DDP), offers a nice way of running multi-GPU and multi-node PyTorch jobs. Unfortunately, the PyTorch documentation has been a bit lacking in this area, and examples found online can often be out-of-date. Hence, to make usage of DDP on CSC's supercomputers easier, we have created a set of examples on how to run simple DDP jobs in the cluster. In the examples we use the rendezvous mechanism to set up communcations across nodes, not MPI.

Example Slurm batch job for running PyTorch DDP on a single full node:

PuhtiMahtiLUMI

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=gpu
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=40
#SBATCH --mem=320G
#SBATCH --time=1:00:00
#SBATCH --gres=gpu:v100:4

module purge
module load pytorch

srun python3 -m torch.distributed.run --standalone --nnodes=1 --nproc_per_node=4 \
    myprog.py <options>

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=gpumedium
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=128
#SBATCH --time=1:00:00
#SBATCH --gres=gpu:a100:4

module purge
module load pytorch

srun python3 -m torch.distributed.run --standalone --nnodes=1 --nproc_per_node=4 \
    myprog.py <options>

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=small-g
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=56
#SBATCH --gpus-per-node=8
#SBATCH --mem=480G
#SBATCH --time=1:00:00

module purge
module use /appl/local/csc/modulefiles
module load pytorch

srun python3 -m torch.distributed.run --standalone --nnodes=1 --nproc_per_node=8 \
    myprog.py <options>

Example of running PyTorch DDP on 2 full nodes:

PuhtiMahtiLUMI

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=gpu
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=40
#SBATCH --mem=320G
#SBATCH --time=1:00:00
#SBATCH --gres=gpu:v100:4

export RDZV_HOST=$(hostname)
export RDZV_PORT=29400

module purge
module load pytorch

srun python3 -m torch.distributed.run \
    --nnodes=$SLURM_JOB_NUM_NODES \
    --nproc_per_node=4 \
    --rdzv_id=$SLURM_JOB_ID \
    --rdzv_backend=c10d \
    --rdzv_endpoint="$RDZV_HOST:$RDZV_PORT" \
    myprog.py <options>

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=gpumedium
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=128
#SBATCH --time=1:00:00
#SBATCH --gres=gpu:a100:4

export RDZV_HOST=$(hostname)
export RDZV_PORT=29400

module purge
module load pytorch

srun python3 -m torch.distributed.run \
    --nnodes=$SLURM_JOB_NUM_NODES \
    --nproc_per_node=4 \
    --rdzv_id=$SLURM_JOB_ID \
    --rdzv_backend=c10d \
    --rdzv_endpoint="$RDZV_HOST:$RDZV_PORT" \
    myprog.py <options>

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=small-g
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=56
#SBATCH --gpus-per-node=8
#SBATCH --mem=480G
#SBATCH --time=1:00:00

export RDZV_HOST=$(hostname)
export RDZV_PORT=29400

module purge
module use /appl/local/csc/modulefiles
module load pytorch

srun python3 -m torch.distributed.run \
    --nnodes=$SLURM_JOB_NUM_NODES \
    --nproc_per_node=8 \
    --rdzv_id=$SLURM_JOB_ID \
    --rdzv_backend=c10d \
    --rdzv_endpoint="$RDZV_HOST:$RDZV_PORT" \
    myprog.py <options>

If you are not using our PyTorch module on LUMI, you might need to set environment variable NCCL_SOCKET_IFNAME=hsn and some other settings to get optimal performance. See the PyTorch example in the LUMI documentation for all the environment variables. These are set automatically in the CSC PyTorch module.

If you are converting an old PyTorch script there are a few steps that you need to do:

1. Initialize with init_process_group(), for example:

   import torch.distributed as dist
   
   dist.init_process_group(backend='nccl')
   
   local_rank = int(os.environ['LOCAL_RANK'])
   torch.cuda.set_device(local_rank)
   

2. Wrap your model with DistributedDataParallel:

   from torch.nn.parallel import DistributedDataParallel
   
   model = DistributedDataParallel(model, device_ids=[local_rank])
   

3. Use DistributedSampler in your DataLoader:

   from torch.utils.data.distributed import DistributedSampler
   
   train_sampler = DistributedSampler(train_dataset)
   train_loader = DataLoader(dataset=train_dataset, sampler=train_sampler, ...)
   

A fully working example for Puhti can be found in our pytorch-ddp-examples repository:

• mnist_ddp.py shows the Python code for training a simple CNN model on MNIST data using PyTorch DDP
• run-ddp-gpu4.sh contains the Slurm script to run the training on 4 GPUs on a single node
• run-ddp-gpu8.sh shows the same for two full nodes, with a total of 8 GPUs

PyTorch Lightning with DDP

PyTorch Lightning is a popular higher-level framework designed to make using PyTorch easier. Running multi-GPU and multi-node jobs with Lightning is quite easy. If you wish to convert your existing PyTorch script to Lightning, we will refer you to the official PyTorch Lightning documentation.

We recommend using DistributedDataParallel (DDP) for multi-GPU and multi-node usage. You just need to add these options to your Lightning Trainer:

trainer = pl.Trainer(devices=args.gpus,
                     num_nodes=args.nodes,
                     accelerator='gpu',
                     strategy='ddp',
                     ...)

You need to give appropriate values for devices (number of GPUs per node) and num_nodes. We suggest giving these are command line arguments:

def main():
    parser = argparse.ArgumentParser()

    parser.add_argument('--gpus', default=1, type=int,
                        help='number of GPUs per node')
    parser.add_argument('--nodes', default=1, type=int,
                        help='number of nodes')
    # any other command line arguments here
    args = parser.parse_args()

PyTorch Lightning Slurm script for single node using all GPUs:

PuhtiMahtiLUMI

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=gpu
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --cpus-per-task=10
#SBATCH --mem=320G
#SBATCH --time=1:00:00
#SBATCH --gres=gpu:v100:4

module purge
module load pytorch

srun python3 myprog.py --gpus=4 --nodes=1 <options>

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=gpumedium
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --cpus-per-task=32
#SBATCH --time=1:00:00
#SBATCH --gres=gpu:a100:4

module purge
module load pytorch

srun python3 myprog.py --gpus=4 --nodes=1 <options>

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=small-g
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --cpus-per-task=7
#SBATCH --gpus-per-node=8
#SBATCH --mem=480G
#SBATCH --time=1:00:00

module purge
module use /appl/local/csc/modulefiles
module load pytorch

srun python3 myprog.py --gpus=8 --nodes=1 <options>

PyTorch Lightning Slurm script for two full nodes using all GPUs:

PuhtiMahtiLUMI

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=gpu
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=4
#SBATCH --cpus-per-task=10
#SBATCH --mem=320G
#SBATCH --time=1:00:00
#SBATCH --gres=gpu:v100:4

module purge
module load pytorch

srun python3 myprog.py --gpus=4 --nodes=2 <options>

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=gpumedium
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=4
#SBATCH --cpus-per-task=32
#SBATCH --time=1:00:00
#SBATCH --gres=gpu:a100:4

module purge
module load pytorch

srun python3 myprog.py --gpus=4 --nodes=2 <options>

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=small-g
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=8
#SBATCH --cpus-per-task=7
#SBATCH --gpus-per-node=8
#SBATCH --mem=480G
#SBATCH --time=1:00:00

module purge
module use /appl/local/csc/modulefiles
module load pytorch

srun python3 myprog.py --gpus=8 --nodes=2 <options>

DeepSpeed

DeepSpeed is an optimization software suite for PyTorch that helps in scaling both training and inference for large deep learning models. DeepSpeed is supported in the PyTorch modules in Puhti and Mahti since version 1.10. DeepSpeed is not yet fully supported on LUMI.

Example of running DeepSpeed on a single full node using the deepspeed launcher:

PuhtiMahtiLUMI

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=gpu
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=40
#SBATCH --mem=320G
#SBATCH --time=1:00:00
#SBATCH --gres=gpu:v100:4

module purge
module load pytorch

srun apptainer_wrapper exec deepspeed myprog.py \
    --deepspeed --deepspeed_config my_ds_config.json \
    <further options>

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=gpumedium
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=128
#SBATCH --time=1:00:00
#SBATCH --gres=gpu:a100:4

module purge
module load pytorch

srun apptainer_wrapper exec deepspeed myprog.py \
    --deepspeed --deepspeed_config my_ds_config.json \
    <further options>

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=small-g
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=56
#SBATCH --gpus-per-node=8
#SBATCH --mem=480G
#SBATCH --time=1:00:00

module purge
module use /appl/local/csc/modulefiles
module load pytorch

srun singularity_wrapper exec deepspeed myprog.py \
    --deepspeed --deepspeed_config my_ds_config.json \
    <further options>

Example of running DeepSpeed on 2 full nodes using MPI for launching a separate task for each GPU:

PuhtiMahtiLUMI

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=gpu
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=4
#SBATCH --cpus-per-task=10
#SBATCH --mem=320G
#SBATCH --time=1:00:00
#SBATCH --gres=gpu:v100:4

module purge
module load pytorch

srun python3 myprog.py \
    --deepspeed --deepspeed_config my_ds_config.json \
    <further options>

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=gpumedium
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=4
#SBATCH --cpus-per-task=32
#SBATCH --time=1:00:00
#SBATCH --gres=gpu:a100:4

module purge
module load pytorch

srun python3 myprog.py \
    --deepspeed --deepspeed_config my_ds_config.json \
    <further options>

#!/bin/bash
#SBATCH --account=<project>
#SBATCH --partition=small-g
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=8
#SBATCH --cpus-per-task=7
#SBATCH --gpus-per-node=8
#SBATCH --mem=480G
#SBATCH --time=1:00:00

module purge
module use /appl/local/csc/modulefiles
module load pytorch

srun python3 myprog.py \
    --deepspeed --deepspeed_config my_ds_config.json \
    <further options>

If you are converting an old PyTorch script there are a few steps that you need to do:

1. Make sure it handles the DeepSpeed command line arguments, for example:

   import argparse
   
   parser = argparse.ArgumentParser()
   # handle any own command line arguments here
   parser = deepspeed.add_config_arguments(parser)
   
   args = parser.parse_args()
   

2. Initialize the distributed environment, for example:

   import deepspeed
   
   deepspeed.init_distributed()
   

3. Initialize the DeepSpeed engine:

   model = # defined in normal way
   train_dataset = # defined normally
   
   model_engine, optimizer, train_loader, __ = deepspeed.initialize(
       args=args, model=model, model_parameters=model.parameters(),
       training_data=train_dataset)
   

4. Modify the training loop to use the DeepSpeed engine:

   for batch in train_loader:
       data = batch[0].to(model_engine.local_rank)
       labels = batch[1].to(model_engine.local_rank)
   
       outputs = model_engine(data)
       loss = criterion(outputs, labels)
   
       model_engine.backward(loss)
       model_engine.step()
   

See the DeepSpeed Getting started guide for the full details. In particular you also need to create a DeepSpeed configuration file.

A fully working example can be found in our pytorch-ddp-examples repository:

• mnist_deepspeed.py shows the Python code for training a simple CNN model on MNIST data using PyTorch DeepSpeed
• run-deepspeed-gpu4.sh contains the Slurm script to run the training on 4 GPUs on a single node
• run-deepspeed-gpu8.sh shows the same for two full nodes, with a total of 8 GPUs
• ds_config.json shows the DeepSpeed configuration file used for this example

Horovod

Horovod is a general library that supports PyTorch and TensorFlow among other frameworks. With Horovod you should use MPI for launching jobs. Horovod can be used both with single- and multi-node jobs.

In CSC's supercomputers Horovod is supported only for some specific versions of TensorFlow and PyTorch. Please check the application pages for further information. To take Horovod into use, just load the appropriate module, and modify your program according to the instructions in Horovod's documentation, for example:

• Horovod with PyTorch
• Horovod with TensorFlow and Keras

TensorFlow's tf.distribute.Strategy

TensorFlow also has its own built-in mechanisms for distributed training in the tf.distribute.Strategy API.

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