useful scripts

chestagentbench_script.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+#SBATCH --job-name=chestagentbench
+#SBATCH -c 4
+#SBATCH --gres=gpu:l40s:1
+#SBATCH --time=16:00:00
+#SBATCH --mem=50G
+#SBATCH --output=chestagentbench-%j.out
+#SBATCH --error=chestagentbench-%j.err
+
+module load arrow clang/18.1.8 scipy-stack
+
+source venv/bin/activate
+
+/scratch/lijunzh3/MedRAX2/venv/bin/python -m benchmarking.cli run --benchmark chestagentbench --provider google --model gemini-2.5-pro --system-prompt CHESTAGENTBENCH_PROMPT --data-dir benchmarking/data/chestagentbench --output-dir temp --max-questions 20 --temperature 0.7 --top-p 0.95 --max-tokens 5000 --concurrency 4 --random-seed 42

medgemma_script.sh

@@ -2,13 +2,14 @@
 
 #SBATCH --job-name=medgemma
 #SBATCH -c 4
-#SBATCH --gres=gpu:rtx6000:1
-#SBATCH --exclude=gpu138
+#SBATCH --gres=gpu:l40s:1
 #SBATCH --time=16:00:00
 #SBATCH --mem=50G
 #SBATCH --output=medgemma-%j.out
 #SBATCH --error=medgemma-%j.err
 
+cd medrax/tools/vqa/medgemma
+
 source medgemma/bin/activate
 
-cd medrax/tools/vqa/medgemma && python medgemma.py
+python medgemma.py

rexvqa_script.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+#SBATCH --job-name=rexvqa
+#SBATCH -c 4
+#SBATCH --gres=gpu:l40s:1
+#SBATCH --time=16:00:00
+#SBATCH --mem=50G
+#SBATCH --output=rexvqa-%j.out
+#SBATCH --error=rexvqa-%j.err
+
+module load arrow clang/18.1.8 scipy-stack
+
+source venv/bin/activate
+
+/scratch/lijunzh3/MedRAX2/venv/bin/python -m benchmarking.cli run --benchmark rexvqa --provider medrax --model gemini-2.5-pro --system-prompt CHESTAGENTBENCH_PROMPT --data-dir benchmarking/data/rexvqa --output-dir temp --max-questions 20 --temperature 0.7 --top-p 0.95 --max-tokens 5000 --concurrency 4 --random-seed 42