Update file run_benchmark_single_node.sh

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