nnU-Net for PyTorch | NVIDIA NGC

NVIDIA Deep Learning Examples

nnU-Net for PyTorch

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NVIDIA Deep Learning Examples

nnU-Net for PyTorch

An optimized, robust and self-adapting framework for U-Net based medical image segmentation

Benchmarking

The following section shows how to run benchmarks to measure the model performance in training and inference modes.

Training performance benchmark

To benchmark training, run the scripts/benchmark.py script with --mode train:

python scripts/benchmark.py --mode train --gpus <ngpus> --dim {2,3} --batch_size <bsize> [--amp] [--bind]

For example, to benchmark 3D U-Net training using mixed-precision on 8 GPUs with a batch size of 2, run:

python scripts/benchmark.py --mode train --gpus 8 --dim 3 --batch_size 2 --amp

Each of these scripts will by default run 1 warm-up epoch and start performance benchmarking during the second epoch.

At the end of the script, a line reporting the best train throughput and latency will be printed.

Inference performance benchmark

To benchmark inference, run the scripts/benchmark.py script with --mode predict:

python scripts/benchmark.py --mode predict --dim {2,3} --batch_size <bsize> [--amp]

For example, to benchmark inference using mixed-precision for 3D U-Net, with a batch size of 4, run:

python scripts/benchmark.py --mode predict --dim 3 --amp --batch_size 4

Each of these scripts will by default run a warm-up for 1 data pass and start inference benchmarking during the second pass.

At the end of the script, a line reporting the inference throughput and latency will be printed.

Note that this benchmark reports performance numbers for iterations over samples with fixed patch sizes. The real inference process uses sliding window for input images with arbitrary resolution and performance may vary for images with different resolutions.

Results

The following sections provide details on how to achieve the same performance and accuracy in training and inference.

Training accuracy results

Training accuracy: NVIDIA DGX A100 (8x A100 80G)

Our results were obtained by running the python scripts/train.py --gpus {1,8} --fold {0,1,2,3,4} --dim {2,3} [--amp] [--bind] --learning_rate lr --seed n training scripts and averaging results in the PyTorch 22.11 NGC container on NVIDIA DGX with (8x A100 80G) GPUs.

Note: We recommend using --bind flag for multi-GPU settings to increase the throughput. To launch multi-GPU with --bind use PyTorch distributed launcher, e.g., python -m torch.distributed.launch --use_env --nproc_per_node=8 scripts/benchmark.py --mode train --gpus 8 --dim 3 --amp --batch_size 2 --bind for the interactive session, or use regular command when launching with SLURM's sbatch.

Dimension	GPUs	Batch size / GPU	Dice - mixed precision	Dice - TF32	Time to train - mixed precision	Time to train - TF32	Time to train speedup (TF32 to mixed precision)
2	1	2	73.21	73.11	33 min	48 min	1.46
2	8	2	73.15	73.16	9 min	13 min	1.44
3	1	2	74.35	74.34	104 min	167 min	1.61
3	8	2	74.30	74.32	23min	36 min	1.57

Reported dice score is the average over 5 folds from the best run for grid search over learning rates {1e-4, 2e-4, ..., 9e-4} and seed {1, 3, 5}.

Training accuracy: NVIDIA DGX-1 (8x V100 32G)

Our results were obtained by running the python scripts/train.py --gpus {1,8} --fold {0,1,2,3,4} --dim {2,3} [--amp] [--bind] --seed n training scripts and averaging results in the PyTorch 22.11 NGC container on NVIDIA DGX-1 with (8x V100 32G) GPUs.

Dimension	GPUs	Batch size / GPU	Dice - mixed precision	Dice - FP32	Time to train - mixed precision	Time to train - FP32	Time to train speedup (FP32 to mixed precision)
2	1	2	73.18	73.22	60 min	114 min	1.90
2	8	2	73.15	73.18	13 min	19 min	1.46
3	1	2	74.31	74.33	201 min	680 min	3.38
3	8	2	74.35	74.39	41 min	153 min	3.73

Reported dice score is the average over 5 folds from the best run for grid search over learning rates {1e-4, 2e-4, ..., 9e-4} and seed {1, 3, 5}.

Training performance results

Training performance: NVIDIA DGX A100 (8x A100 80G)

Our results were obtained by running the python scripts/benchmark.py --mode train --gpus {1,8} --dim {2,3} --batch_size <bsize> [--amp] training script in the NGC container on NVIDIA DGX A100 (8x A100 80G) GPUs. Performance numbers (in volumes per second) were averaged over an entire training epoch.

Note: We recommend using --bind flag for multi-gpu settings to increase the througput. To launch multi-GPU with --bind use python -m torch.distributed.launch --use_env --nproc_per_node=<npgus> scripts/train.py --bind ... for the interactive session, or use regular command when launching with SLURM's sbatch.

Dimension	GPUs	Batch size / GPU	Throughput - mixed precision [img/s]	Throughput - TF32 [img/s]	Throughput speedup (TF32 - mixed precision)	Weak scaling - mixed precision	Weak scaling - TF32
2	1	32	1040.58	732.22	1.42	-	-
2	1	64	1238.68	797.37	1.55	-	-
2	1	128	1345.29	838.38	1.60	-	-
2	8	32	7747.27	5588.2	1.39	7.45	7.60
2	8	64	9417.27	6246.95	1.51	7.60	8.04
2	8	128	10694.1	6631.08	1.61	7.95	7.83
3	1	1	24.61	9.66	2.55	-	-
3	1	2	27.48	11.27	2.44	-	-
3	1	4	29.96	12.22	2.45	-	-
3	8	1	187.07	76.44	2.45	7.63	7.91
3	8	2	220.83	88.67	2.49	7.83	7.87
3	8	4	234.5	96.61	2.43	7.91	7.91

To achieve these same results, follow the steps in the Quick Start Guide.

Training performance: NVIDIA DGX-1 (8x V100 32G)

Our results were obtained by running the python scripts/benchmark.py --mode train --gpus {1,8} --dim {2,3} --batch_size <bsize> [--amp] [--bind] training script in the PyTorch 22.11 NGC container on NVIDIA DGX-1 with (8x V100 32G) GPUs. Performance numbers (in volumes per second) were averaged over an entire training epoch.

Dimension	GPUs	Batch size / GPU	Throughput - mixed precision [img/s]	Throughput - FP32 [img/s]	Throughput speedup (FP32 - mixed precision)	Weak scaling - mixed precision	Weak scaling - FP32
2	1	32	561.6	310.21	1.81	-	-
2	1	64	657.91	326.02	2.02	-	-
2	1	128	706.92	332.81	2.12	-	-
2	8	32	3903.88	2396.88	1.63	6.95	7.73
2	8	64	4922.76	2590.66	1.90	7.48	7.95
2	8	128	5597.87	2667.56	2.10	7.92	8.02
3	1	1	11.38	2.07	5.50	-	-
3	1	2	12.34	2.51	4.92	-	-
3	8	1	84.38	16.55	5.10	7.41	8.00
3	8	2	98.17	20.15	4.87	7.96	8.03

To achieve these same results, follow the steps in the Quick Start Guide.

Inference performance results

Inference performance: NVIDIA DGX A100 (1x A100 80G)

Our results were obtained by running the python scripts/benchmark.py --mode predict --dim {2,3} --batch_size <bsize> [--amp] inferencing benchmarking script in the PyTorch 22.11 NGC container on NVIDIA DGX A100 (1x A100 80G) GPU.

FP16

Dimension	Batch size	Resolution	Throughput Avg [img/s]	Latency Avg [ms]	Latency 90% [ms]	Latency 95% [ms]	Latency 99% [ms]
2	32	192x160	1818.05	17.6	19.86	20.38	20.98
2	64	192x160	3645.16	17.56	19.86	20.82	23.66
2	128	192x160	3850.35	33.24	34.72	61.4	63.58
3	1	128x128x128	68.45	14.61	17.02	17.41	19.27
3	2	128x128x128	56.9	35.15	40.9	43.15	57.94
3	4	128x128x128	76.39	52.36	57.9	59.52	70.24

TF32

Dimension	Batch size	Resolution	Throughput Avg [img/s]	Latency Avg [ms]	Latency 90% [ms]	Latency 95% [ms]	Latency 99% [ms]
2	32	192x160	1868.56	17.13	51.75	53.07	54.92
2	64	192x160	2508.57	25.51	56.83	90.08	96.87
2	128	192x160	2609.6	49.05	191.48	201.8	205.29
3	1	128x128x128	35.02	28.55	51.75	53.07	54.92
3	2	128x128x128	39.88	50.15	56.83	90.08	96.87
3	4	128x128x128	41.32	96.8	191.48	201.8	205.29

Throughput is reported in images per second. Latency is reported in milliseconds per batch. To achieve these same results, follow the steps in the Quick Start Guide.

Inference performance: NVIDIA DGX-1 (1x V100 32G)

FP16

Dimension	Batch size	Resolution	Throughput Avg [img/s]	Latency Avg [ms]	Latency 90% [ms]	Latency 95% [ms]	Latency 99% [ms]
2	32	192x160	1254.38	25.51	29.07	30.07	31.23
2	64	192x160	2024.13	31.62	71.51	71.78	72.44
2	128	192x160	2136.95	59.9	61.23	61.63	110.13
3	1	128x128x128	36.93	27.08	28.6	31.43	48.3
3	2	128x128x128	38.86	51.47	53.3	54.77	92.49
3	4	128x128x128	39.15	102.18	104.62	112.17	180.47

FP32

Dimension	Batch size	Resolution	Throughput Avg [img/s]	Latency Avg [ms]	Latency 90% [ms]	Latency 95% [ms]	Latency 99% [ms]
2	32	192x160	1019.97	31.37	32.93	55.58	69.14
2	64	192x160	1063.59	60.17	62.32	63.11	111.01
2	128	192x160	1069.81	119.65	123.48	123.83	225.46
3	1	128x128x128	9.92	100.78	103.2	103.62	111.97
3	2	128x128x128	10.14	197.33	201.05	201.4	201.79
3	4	128x128x128	10.25	390.33	398.21	399.34	401.05

Throughput is reported in images per second. Latency is reported in milliseconds per batch. To achieve these same results, follow the steps in the Quick Start Guide.