Update file README.md

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