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

@@ -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

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