diff --git a/MLPerf/training/image_segmentation/pytorch/U-Net3D.def b/MLPerf/training/image_segmentation/pytorch/U-Net3D.def index 7b4a50c605bb708386d1950f47b4d208a58b21db..2ccbbac65052924f53ee614af7a42b5ac26837e5 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 716fc2139be5ca67b45d17823683108ea0374b38..bdf3d4404651075b30eb27736525f3127d5025b3 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