From 3c82f08fe8b83ebb3838d9492c841dc22b7c328d Mon Sep 17 00:00:00 2001
From: Xuan Gu <xuan.gu@liu.se>
Date: Thu, 28 Sep 2023 13:57:54 +0000
Subject: [PATCH] Update 2 files
- /PyTorch/Segmentation/nnUNet/submit_benchmark_sbatch.sh
- /PyTorch/Segmentation/nnUNet/run_benchmark_single_node.sh
---
PyTorch/Segmentation/nnUNet/run_benchmark_single_node.sh | 8 ++++----
PyTorch/Segmentation/nnUNet/submit_benchmark_sbatch.sh | 7 ++++---
2 files changed, 8 insertions(+), 7 deletions(-)
diff --git a/PyTorch/Segmentation/nnUNet/run_benchmark_single_node.sh b/PyTorch/Segmentation/nnUNet/run_benchmark_single_node.sh
index 8e7ba99..5e63266 100644
--- a/PyTorch/Segmentation/nnUNet/run_benchmark_single_node.sh
+++ b/PyTorch/Segmentation/nnUNet/run_benchmark_single_node.sh
@@ -4,9 +4,9 @@ MODULE_NAME=nnunet_for_pytorch
MODULE_VERSION=21.11.0
WORK_DIR=/proj/nsc_testing/xuan/berzelius-benchmarks/PyTorch/Segmentation/nnUNet
CONTAINER_DIR=/proj/nsc_testing/xuan/containers/${MODULE_NAME}_${MODULE_VERSION}.sif
-SBATCH_DIR=$WORK_DIR/sbatch_scripts/benchmark_dim${1}_nodes${2}_gpus${3}_batchsize${4}_iteration${5}.sbatch
-SBATCH_OUT_DIR=$WORK_DIR/sbatch_out/benchmark_dim${1}_nodes${2}_gpus${3}_batchsize${4}_iteration${5}.out
-LOG_DIR=benchmark_dim${1}_nodes${2}_gpus${3}_batchsize${4}_amp_iteration${5}.json
+SBATCH_DIR=$WORK_DIR/sbatch_scripts/benchmark_${5}_dim${1}_nodes${2}_gpus${3}_batchsize${4}.sbatch
+SBATCH_OUT_DIR=$WORK_DIR/sbatch_out/benchmark_${5}_dim${1}_nodes${2}_gpus${3}_batchsize${4}.out
+LOG_DIR=benchmark_${5}_dim${1}_nodes${2}_gpus${3}_batchsize${4}_amp.json
mkdir -p $WORK_DIR/sbatch_out $WORK_DIR/sbatch_scripts
cat <<EOT > $SBATCH_DIR
@@ -25,7 +25,7 @@ WORK_DIR=/proj/nsc_testing/xuan/berzelius-benchmarks/PyTorch/Segmentation/nnUNet
CONTAINER_DIR=/proj/nsc_testing/xuan/containers/${MODULE_NAME}_${MODULE_VERSION}.sif
rm -f $WORK_DIR/results/$LOG_DIR
-apptainer exec --nv -B ${WORK_DIR}/data:/data -B ${WORK_DIR}/results:/results --pwd /workspace/nnunet_pyt $CONTAINER_DIR python scripts/benchmark.py --mode train --gpus ${3} --dim ${1} --batch_size ${4} --amp --logname='$LOG_DIR'
+apptainer exec --nv -B ${WORK_DIR}/data:/data -B ${WORK_DIR}/results:/results --pwd /workspace/nnunet_pyt $CONTAINER_DIR python scripts/benchmark.py --mode ${5} --gpus ${3} --dim ${1} --batch_size ${4} --amp --logname='$LOG_DIR'
EOT
diff --git a/PyTorch/Segmentation/nnUNet/submit_benchmark_sbatch.sh b/PyTorch/Segmentation/nnUNet/submit_benchmark_sbatch.sh
index 2e5f89a..29a30d1 100644
--- a/PyTorch/Segmentation/nnUNet/submit_benchmark_sbatch.sh
+++ b/PyTorch/Segmentation/nnUNet/submit_benchmark_sbatch.sh
@@ -2,17 +2,18 @@
set -e
WORK_DIR=/proj/nsc_testing/xuan/berzelius-benchmarks/PyTorch/Segmentation/nnUNet
+benchmark_modes=("train" "predic")
dim=2
for nodes in {1..1}; do
for gpus in {1,8}; do
for batch_size in 256; do
- for iteration in {1..1}; do
+ for benchmark_mode in "${benchmark_modes[@]}"; do
- echo dim ${dim}, nodes ${nodes}, gpus ${gpus}, batch_size ${batch_size}, iteration ${iteration}
+ echo dim ${dim}, nodes ${nodes}, gpus ${gpus}, batch_size ${batch_size}, benchmark_mode ${benchmark_mode}
# For single node
- bash $WORK_DIR/run_benchmark_single_node.sh ${dim} ${nodes} ${gpus} ${batch_size} ${iteration}
+ bash $WORK_DIR/run_benchmark_single_node.sh ${dim} ${nodes} ${gpus} ${batch_size} ${benchmark_mode}
sleep 1
done
--
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