diff --git a/PyTorch/Segmentation/nnUNet/run_benchmark_single_node.sh b/PyTorch/Segmentation/nnUNet/run_benchmark_single_node.sh index 029185764e9fe290d4d288cf2ca8adfc108b5186..1834e9d2a4ed0d02d92f912487f13abbae682eb7 100644 --- a/PyTorch/Segmentation/nnUNet/run_benchmark_single_node.sh +++ b/PyTorch/Segmentation/nnUNet/run_benchmark_single_node.sh @@ -3,8 +3,10 @@ MODULE_NAME=nnunet_for_pytorch MODULE_VERSION=21.11.0 WORK_DIR=/proj/nsc_testing/xuan/berzelius-benchmarks/PyTorch/Segmentation/nnUNet +SBATCH_DIR=$WORK_DIR/benchmark_dim${1}_nodes${2}_gpus${3}_batchsize${4}_iteration${5}.sbatch +LOG_DIR=benchmark_dim${1}_nodes${2}_gpus${3}_batchsize${4}_amp_iteration${5}.json -cat <<EOT > $WORK_DIR/benchmark_dim${1}_nodes${2}_gpus${3}_batchsize${4}_iteration${5}.sbatch +cat <<EOT > $SBATCH_DIR #!/bin/bash @@ -23,13 +25,11 @@ CONTAINER_DIR=/proj/nsc_testing/xuan/containers/${MODULE_NAME}_${MODULE_VERSION} mkdir -p $WORK_DIR/sbatch_out cd $WORK_DIR -rm -f results/benchmark_dim${1}_nodes${2}_gpus${3}_batchsize${4}_tf32_iteration${5}.json -srun apptainer exec --nv -B ${PWD}/data:/data -B ${PWD}/results:/results $CONTAINER_DIR bash -c "cd /workspace/nnunet_pyt && python scripts/benchmark.py --mode train --gpus ${3} --dim ${1} --batch_size ${4} --nodes ${2} --logname='benchmark_dim${1}_nodes${2}_gpus${3}_batchsize${4}_tf32_iteration${5}.json'" -rm -f results/benchmark_dim${1}_nodes${2}_gpus${3}_batchsize${4}_amp_iteration${5}.json -srun apptainer exec --nv -B ${PWD}/data:/data -B ${PWD}/results:/results $CONTAINER_DIR bash -c "cd /workspace/nnunet_pyt && python scripts/benchmark.py --mode train --gpus ${3} --dim ${1} --batch_size ${4} --nodes ${2} --amp --logname='benchmark_dim${1}_nodes${2}_gpus${3}_batchsize${4}_amp_iteration${5}.json'" +rm -f results/$LOG_DIR +srun apptainer exec --nv -B ${PWD}/data:/data -B ${PWD}/results:/results $CONTAINER_DIR bash -c "cd /workspace/nnunet_pyt && python scripts/benchmark.py --mode train --gpus ${3} --dim ${1} --batch_size ${4} --nodes ${2} --amp --logname='$LOG_DIR'" EOT -sbatch scripts/benchmark_dim${1}_nodes${2}_gpus${3}_batchsize${4}_iteration${5}.sbatch \ No newline at end of file +sbatch $SBATCH_DIR \ No newline at end of file