From b7da791b9a433c56265a16f0781e596cacd6dc75 Mon Sep 17 00:00:00 2001
From: Xuan Gu <xuan.gu@liu.se>
Date: Tue, 30 May 2023 11:32:10 +0000
Subject: [PATCH] Update 2 files
- /README.md
- /scripts/benchmark_single_node.sbatch
---
README.md | 2 ++
scripts/benchmark_single_node.sbatch | 4 ++--
2 files changed, 4 insertions(+), 2 deletions(-)
diff --git a/README.md b/README.md
index 8a8402f..1b56aff 100644
--- a/README.md
+++ b/README.md
@@ -14,6 +14,8 @@ cd ~/DeepLearningExamples/nnunet_for_pytorch_$VERSION/
- Build the nnU-Net PyTorch Docker container
Change the pytorch-lightning version to 1.5.10 to avoid the `from torchmetrics.utilities.data import get_num_classes as _get_num_classes` error.
+
+Add `ENV PYTHONNOUSERSITE=True` to the `Dockerfile` to disable the user packages.
```
docker build -t nnunet .
```
diff --git a/scripts/benchmark_single_node.sbatch b/scripts/benchmark_single_node.sbatch
index 0cdc3aa..a4c124b 100644
--- a/scripts/benchmark_single_node.sbatch
+++ b/scripts/benchmark_single_node.sbatch
@@ -10,10 +10,10 @@
# This version does not run on multi-node
# For apptainer
rm -f results/benchmark_dim${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
--
GitLab