From fdda6dd3239d2b28736f53ea8cd34a31caf29e56 Mon Sep 17 00:00:00 2001
From: Xuan Gu <xuan@nsc.liu.se>
Date: Wed, 11 Oct 2023 12:31:05 +0200
Subject: [PATCH] Updated
---
.../PyTorch/Segmentation/nnUNet/benchmark.txt | 3 +++
.../PyTorch/Segmentation/nnUNet/generate_benchmark_jobs.sh | 2 +-
.../PyTorch/Segmentation/nnUNet/submit_benchmark_jobs.sh | 4 ++--
3 files changed, 6 insertions(+), 3 deletions(-)
diff --git a/NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet/benchmark.txt b/NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet/benchmark.txt
index 4fd7ff9..b7d5604 100644
--- a/NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet/benchmark.txt
+++ b/NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet/benchmark.txt
@@ -20,6 +20,9 @@ apptainer exec --nv -B ${WORK_DIR}/data:/data -B ${WORK_DIR}/results:/results --
apptainer exec --nv -B ${WORK_DIR}/data:/data -B ${WORK_DIR}/results:/results --pwd /workspace/nnunet_pyt $CONTAINER_DIR python scripts/benchmark.py --mode predict --gpus 1 --dim 2 --batch_size 256 --amp
+
+
+
################# Issues #################
# Known issue https://github.com/NVIDIA/DeepLearningExamples/issues/1113
ImportError: cannot import name 'get_num_classes' from 'torchmetrics.utilities.data' (/opt/conda/lib/python3.8/site-packages/torchmetrics/utilities/data.py)
diff --git a/NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet/generate_benchmark_jobs.sh b/NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet/generate_benchmark_jobs.sh
index d2175c1..b4b874e 100644
--- a/NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet/generate_benchmark_jobs.sh
+++ b/NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet/generate_benchmark_jobs.sh
@@ -23,7 +23,7 @@ EOT
if [ "${6}" = "thin" ]; then
cat <<EOT >> $SBATCH_DIR
#SBATCH -C "thin"
-##SBATCH --reservation=devel
+#SBATCH --reservation=nodeimage
EOT
else
cat <<EOT >> $SBATCH_DIR
diff --git a/NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet/submit_benchmark_jobs.sh b/NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet/submit_benchmark_jobs.sh
index a28efd6..e596871 100644
--- a/NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet/submit_benchmark_jobs.sh
+++ b/NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet/submit_benchmark_jobs.sh
@@ -1,13 +1,13 @@
#!/bin/bash
set -e
-WORK_DIR=/proj/nsc_testing/xuan/berzelius-benchmarks/PyTorch/Segmentation/nnUNet
+WORK_DIR=/proj/nsc_testing/xuan/berzelius-benchmarks/NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet
benchmark_modes=("train" "predict")
node_types=("thin" "fat")
dim=2
for nodes in {1..1}; do
- for gpus in {1,8}; do
+ for gpus in {1..8}; do
for benchmark_mode in "${benchmark_modes[@]}"; do
for node_type in "${node_types[@]}"; do
--
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