From 18096f625186969251b878939e155195f7fa16fd Mon Sep 17 00:00:00 2001
From: Xuan Gu <xuan.gu@liu.se>
Date: Wed, 11 Oct 2023 20:55:54 +0000
Subject: [PATCH] Update 2 files
- /MLPerf/training/image_segmentation/pytorch/benchmark.txt
- /MLPerf/training/image_segmentation/pytorch/U-Net3D.def
---
MLPerf/training/image_segmentation/pytorch/U-Net3D.def | 6 +++---
MLPerf/training/image_segmentation/pytorch/benchmark.txt | 8 ++++++--
2 files changed, 9 insertions(+), 5 deletions(-)
diff --git a/MLPerf/training/image_segmentation/pytorch/U-Net3D.def b/MLPerf/training/image_segmentation/pytorch/U-Net3D.def
index 2ccbbac..c145a55 100644
--- a/MLPerf/training/image_segmentation/pytorch/U-Net3D.def
+++ b/MLPerf/training/image_segmentation/pytorch/U-Net3D.def
@@ -17,9 +17,9 @@ apt-get update && \
apt-get install -y git
apt-get install -y vim
-git clone https://github.com/mlperf/training.git
-mv training/image_segmentation/pytorch/* /workspace/unet3d/
-rm -rf training
+git clone https://github.com/xuagu37/mlperf-training.git
+mv mlperf-training/image_segmentation/pytorch/* /workspace/unet3d/
+rm -rf mlperf-training
pip install --upgrade pip
pip install --disable-pip-version-check -r requirements.txt
diff --git a/MLPerf/training/image_segmentation/pytorch/benchmark.txt b/MLPerf/training/image_segmentation/pytorch/benchmark.txt
index bdf3d44..65953d5 100644
--- a/MLPerf/training/image_segmentation/pytorch/benchmark.txt
+++ b/MLPerf/training/image_segmentation/pytorch/benchmark.txt
@@ -16,7 +16,11 @@ To download the data please follow the instructions:
git clone https://github.com/neheller/kits19
apptainer exec $CONTAINER_DIR bash -c "cd kits19 && python3 -m starter_code.get_imaging"
+mv kits19/data/* raw-data/
+rm -rf kits19
--B ${WORK_DIR}/data:/data -B ${WORK_DIR}/results:/results
--B ${WORK_DIR}/raw-data:/raw-data
\ No newline at end of file
+apptainer exec -B ${WORK_DIR}/raw-data:/raw-data -B ${WORK_DIR}/data:/data -B ${WORK_DIR}/results:/results $CONTAINER_DIR bash -c "cd /workspace/unet3d && python3 preprocess_dataset.py --data_dir /raw-data --results_dir /data"
+
+apptainer exec -B ${WORK_DIR}/raw-data:/raw-data -B ${WORK_DIR}/data:/data -B ${WORK_DIR}/results:/results $CONTAINER_DIR bash -c "bash /workspace/unet3d/run_and_time.sh 1"
+
--
GitLab