From ab695310bfd3b02107104622ddfa1f0997e5dccb Mon Sep 17 00:00:00 2001
From: Xuan Gu <xuan.gu@liu.se>
Date: Tue, 9 May 2023 21:07:17 +0000
Subject: [PATCH] Update 2 files
- /scripts/benchmark_single_node.sbatch
- /scripts/benchmark_multi_node.sbatch
---
scripts/benchmark_multi_node.sbatch | 6 +++---
scripts/benchmark_single_node.sbatch | 6 +++---
2 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/scripts/benchmark_multi_node.sbatch b/scripts/benchmark_multi_node.sbatch
index 43eab69..0afae23 100644
--- a/scripts/benchmark_multi_node.sbatch
+++ b/scripts/benchmark_multi_node.sbatch
@@ -10,12 +10,12 @@ sbatch <<EOT
#SBATCH --time=0-00:10:00
#####SBATCH --reservation=bt-xuan_2nodes
-# For singularity
+# For apptainer
#rm -f results/benchmark_dim${1}_nodes${2}_gpus${3}_batchsize${4}_tf32_iteration${5}.json
-# srun singularity exec --nv -B ${PWD}/data:/data -B ${PWD}/results:/results nvidia_nnu-net_for_pytorch.sif 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""
+# srun apptainer exec --nv -B ${PWD}/data:/data -B ${PWD}/results:/results nvidia_nnu-net_for_pytorch.sif 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 singularity exec --nv -B ${PWD}/data:/data -B ${PWD}/results:/results nvidia_nnu-net_for_pytorch.sif 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""
+#srun apptainer exec --nv -B ${PWD}/data:/data -B ${PWD}/results:/results nvidia_nnu-net_for_pytorch.sif 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""
############## Running srun enroot ... stopped working at 20230220
# For enroot
diff --git a/scripts/benchmark_single_node.sbatch b/scripts/benchmark_single_node.sbatch
index accaf4d..55c8d1e 100644
--- a/scripts/benchmark_single_node.sbatch
+++ b/scripts/benchmark_single_node.sbatch
@@ -7,12 +7,12 @@
#####SBATCH --reservation=bt-xuan_1node_20221020_0900
-# For singularity
+# For apptainer
#rm -f results/benchmark_dim${1}_nodes${2}_gpus${3}_batchsize${4}_tf32_iteration${5}.json
-#singularity exec --nv -B ${PWD}/data:/data -B ${PWD}/results:/results nvidia_nnu-net_for_pytorch.sif 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""
+#apptainer exec --nv -B ${PWD}/data:/data -B ${PWD}/results:/results nvidia_nnu-net_for_pytorch.sif 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
-#singularity exec --nv -B ${PWD}/data:/data -B ${PWD}/results:/results nvidia_nnu-net_for_pytorch.sif 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"
+#apptainer exec --nv -B ${PWD}/data:/data -B ${PWD}/results:/results nvidia_nnu-net_for_pytorch.sif 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"
# For enroot
rm -f results/benchmark_dim${1}_nodes${2}_gpus${3}_batchsize${4}_tf32_iteration${5}.json
--
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