diff --git a/README.md b/README.md index 8a8402ff558b7a52a543d4ca35bbcf4e702513b9..1b56aff1ea078b6e630708ce073cc029edcc7306 100644 --- a/README.md +++ b/README.md @@ -14,6 +14,8 @@ cd ~/DeepLearningExamples/nnunet_for_pytorch_$VERSION/ - Build the nnU-Net PyTorch Docker container Change the pytorch-lightning version to 1.5.10 to avoid the `from torchmetrics.utilities.data import get_num_classes as _get_num_classes` error. + +Add `ENV PYTHONNOUSERSITE=True` to the `Dockerfile` to disable the user packages. ``` docker build -t nnunet . ``` diff --git a/scripts/benchmark_single_node.sbatch b/scripts/benchmark_single_node.sbatch index 0cdc3aac570e0148b567b980003e9faeb784b784..a4c124bf03a58ee175a9c2203e775d008b431f01 100644 --- a/scripts/benchmark_single_node.sbatch +++ b/scripts/benchmark_single_node.sbatch @@ -10,10 +10,10 @@ # This version does not run on multi-node # For apptainer rm -f results/benchmark_dim${1}_nodes${2}_gpus${3}_batchsize${4}_tf32_iteration${5}.json -apptainer exec --nv --no-home -B ${PWD}/data:/data -B ${PWD}/results:/results nvidia_nnu-net_for_pytorch_21.11.0.sif bash -c "cd /workspace/nnunet_pyt && python scripts/benchmark.py --mode train --gpus ${3} --dim ${1} --batch_size ${4} --logname='benchmark_dim${1}_nodes${2}_gpus${3}_batchsize${4}_tf32_iteration${5}.json'" +apptainer exec --nv -B ${PWD}/data:/data -B ${PWD}/results:/results nvidia_nnu-net_for_pytorch_21.11.0.sif bash -c "cd /workspace/nnunet_pyt && python scripts/benchmark.py --mode train --gpus ${3} --dim ${1} --batch_size ${4} --logname='benchmark_dim${1}_nodes${2}_gpus${3}_batchsize${4}_tf32_iteration${5}.json'" rm -f results/benchmark_dim${1}_nodes${2}_gpus${3}_batchsize${4}_amp_iteration${5}.json -apptainer exec --nv --no-home -B ${PWD}/data:/data -B ${PWD}/results:/results nvidia_nnu-net_for_pytorch_21.11.0.sif bash -c "cd /workspace/nnunet_pyt && python scripts/benchmark.py --mode train --gpus ${3} --dim ${1} --batch_size ${4} --amp --logname='benchmark_dim${1}_nodes${2}_gpus${3}_batchsize${4}_amp_iteration${5}.json'" +apptainer exec --nv -B ${PWD}/data:/data -B ${PWD}/results:/results nvidia_nnu-net_for_pytorch_21.11.0.sif bash -c "cd /workspace/nnunet_pyt && python scripts/benchmark.py --mode train --gpus ${3} --dim ${1} --batch_size ${4} --amp --logname='benchmark_dim${1}_nodes${2}_gpus${3}_batchsize${4}_amp_iteration${5}.json'" ###################22.11.0