diff --git a/README.md b/README.md index bc01bf12d38709cdaa33a8215ff1ecb416e5ea0a..14dff974dcde2a7c458640dc8388d1e16435f7e6 100644 --- a/README.md +++ b/README.md @@ -42,21 +42,22 @@ Docker is not available on Berzelius. We use Apptainer or Enroot. With Apptainer ``` -apptainer pull nvidia_nnu-net_for_pytorch.sif docker://berzeliushub/nvidia_nnu-net_for_pytorch:$VERSION -apptainer exec --nv -B ${PWD}/data:/data -B ${PWD}/results:/results --nv nvidia_nnu-net_for_pytorch.sif bash -c "cd /workspace/nnunet_pyt && python download.py --task 01 && python preprocess.py --task 01 --dim 2" +apptainer pull nvidia_nnu-net_for_pytorch_$VERSION.sif docker://berzeliushub/nvidia_nnu-net_for_pytorch:$VERSION +apptainer exec --nv -B ${PWD}/data:/data -B ${PWD}/results:/results --nv nvidia_nnu-net_for_pytorch_$VERSION.sif bash -c "cd /workspace/nnunet_pyt && python download.py --task 01" +apptainer exec --nv -B ${PWD}/data:/data -B ${PWD}/results:/results --nv nvidia_nnu-net_for_pytorch_$VERSION.sif bash -c "cd /workspace/nnunet_pyt && python preprocess.py --task 01 --dim 2" ``` -With Enroot +<!-- With Enroot ``` enroot import 'docker://berzeliushub/nvidia_nnu-net_for_pytorch:$VERSION' enroot create --name nnunet berzeliushub+nvidia_nnu-net_for_pytorch+$VERSION.sqsh -enroot start --rw --mount ${PWD}/data:/data --mount ${PWD}/results:/results nnunet bash -c "cd /workspace/nnunet_pyt && python download.py --task 01 && python preprocess.py --task 01 --dim 2" +enroot start --rw --mount ${PWD}/data:/data --mount ${PWD}/results:/results nnunet bash -c "cd /workspace/nnunet_pyt && python download.py --task 01 && python preprocess.py --task 01 --dim 2" --> ``` -- For benchmarking purpose, we use copied of a single image +<!-- - For benchmarking purpose, we use copied of a single image ``` bash scripts/copy_data_for_benchmark.sh -``` +``` --> - Submit the job to Berzelius You can choose either singularity or enroot in the scripts ```benchmark_single_node.sbatch``` and ```benchmark_multi_node.sbatch```. @@ -64,7 +65,7 @@ You can choose either singularity or enroot in the scripts ```benchmark_single_n Chnage the following settings in `benchmark_sbatch_submit.sh`: 1. Data dimention, 2. Number of nodes, -3. Number of gpus per node, +3. Number of gpus used per node, 4. Number of iterations for each parameter setting. 5. Batch size