From 1719d76abef2487f9a9df8ac22a99b3ff8c8018a Mon Sep 17 00:00:00 2001
From: Xuan Gu <xuan.gu@liu.se>
Date: Wed, 11 Oct 2023 17:46:54 +0000
Subject: [PATCH] Update 2 files
- /MLPerf/training/image_segmentation/pytorch/U-Net3D.def
- /MLPerf/training/image_segmentation/pytorch/benchmark.txt
---
.../image_segmentation/pytorch/U-Net3D.def | 3 ++-
.../image_segmentation/pytorch/benchmark.txt | 18 +++++++++++++-----
2 files changed, 15 insertions(+), 6 deletions(-)
diff --git a/MLPerf/training/image_segmentation/pytorch/U-Net3D.def b/MLPerf/training/image_segmentation/pytorch/U-Net3D.def
index 7b4a50c..2ccbbac 100644
--- a/MLPerf/training/image_segmentation/pytorch/U-Net3D.def
+++ b/MLPerf/training/image_segmentation/pytorch/U-Net3D.def
@@ -26,4 +26,5 @@ pip install --disable-pip-version-check -r requirements.txt
git clone https://github.com/neheller/kits19
cd kits19
-pip3 install -r requirements.txt
\ No newline at end of file
+pip3 install -r requirements.txt
+rm -rf ../kits19
\ No newline at end of file
diff --git a/MLPerf/training/image_segmentation/pytorch/benchmark.txt b/MLPerf/training/image_segmentation/pytorch/benchmark.txt
index 716fc21..bdf3d44 100644
--- a/MLPerf/training/image_segmentation/pytorch/benchmark.txt
+++ b/MLPerf/training/image_segmentation/pytorch/benchmark.txt
@@ -5,10 +5,18 @@ MODLE_NAME=U-Net3D
CONTAINER_DIR=/proj/nsc_testing/xuan/containers/${MODLE_NAME}.sif
WORK_DIR=/proj/nsc_testing/xuan/berzelius-benchmarks/MLPerf/training/image_segmentation/pytorch
+
+
+mkdir -p $WORK_DIR/raw-data $WORK_DIR/data $WORK_DIR/results
+
+
cd $WORK_DIR
-mkdir raw-data-dir
-cd raw-data-dir
+
+To download the data please follow the instructions:
+
git clone https://github.com/neheller/kits19
-cd kits19
-pip3 install -r requirements.txt
-python3 -m starter_code.get_imaging
\ No newline at end of file
+apptainer exec $CONTAINER_DIR bash -c "cd kits19 && python3 -m starter_code.get_imaging"
+
+-B ${WORK_DIR}/data:/data -B ${WORK_DIR}/results:/results
+
+-B ${WORK_DIR}/raw-data:/raw-data
\ No newline at end of file
--
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