From 08abacbd20bfa5d1bcee8d1641faef57060d9d78 Mon Sep 17 00:00:00 2001
From: Xuan Gu <xuan.gu@liu.se>
Date: Wed, 27 Sep 2023 20:41:08 +0000
Subject: [PATCH] Update 3 files
- /PyTorch/Segmentation/nnUNet/nnunet_for_pytorch.def
- /PyTorch/Segmentation/nnUNet/build.txt
- /PyTorch/Segmentation/nnUNet/nnunet_for_pytorch_21.11.0.def
---
PyTorch/Segmentation/nnUNet/build.txt | 9 ++++++---
...et_for_pytorch.def => nnunet_for_pytorch_21.11.0.def} | 0
2 files changed, 6 insertions(+), 3 deletions(-)
rename PyTorch/Segmentation/nnUNet/{nnunet_for_pytorch.def => nnunet_for_pytorch_21.11.0.def} (100%)
diff --git a/PyTorch/Segmentation/nnUNet/build.txt b/PyTorch/Segmentation/nnUNet/build.txt
index 8adaefb..83c84fd 100644
--- a/PyTorch/Segmentation/nnUNet/build.txt
+++ b/PyTorch/Segmentation/nnUNet/build.txt
@@ -8,7 +8,7 @@ gotesting
MODULE_NAME=nnunet_for_pytorch
MODULE_VERSION=21.11.0
-apptainer build ./containers/${MODULE_NAME}_${MODULE_VERSION}.sif ./berzelius-benchmarks/${MODULE_NAME}.def
+apptainer build ./containers/${MODULE_NAME}_${MODULE_VERSION}.sif ./berzelius-benchmarks/PyTorch/Segmentation/nnUNet/${MODULE_NAME}.def
WORK_DIR=/proj/nsc_testing/xuan/berzelius-benchmarks/PyTorch/Segmentation/nnUNet
@@ -18,11 +18,14 @@ cd $WORK_DIR
mkdir -p data results
+export APPTAINER_BINDPATH=$WORK_DIR/data:/data,$WORK_DIR/results:/results
+
+
To download and preprocess the data run:
-apptainer exec --nv --pwd /workspace/nnunet_pyt $CONTAINER_DIR python download.py --task 01 --results $WORK_DIR/data
+apptainer exec --nv --pwd /workspace/nnunet_pyt $CONTAINER_DIR python download.py --task 01
-apptainer exec --nv --pwd /workspace/nnunet_pyt $CONTAINER_DIR python /workspace/nnunet_pyt/preprocess.py --task 01 --data $WORK_DIR/data --results $WORK_DIR/results
+apptainer exec --nv --pwd /workspace/nnunet_pyt $CONTAINER_DIR python /workspace/nnunet_pyt/preprocess.py --task 01 --dim 2
apptainer exec --nv --pwd /workspace/nnunet_pyt $CONTAINER_DIR python scripts/benchmark.py --mode train --gpus 1 --dim 2 --batch_size 128 --amp
diff --git a/PyTorch/Segmentation/nnUNet/nnunet_for_pytorch.def b/PyTorch/Segmentation/nnUNet/nnunet_for_pytorch_21.11.0.def
similarity index 100%
rename from PyTorch/Segmentation/nnUNet/nnunet_for_pytorch.def
rename to PyTorch/Segmentation/nnUNet/nnunet_for_pytorch_21.11.0.def
--
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