Adding guided decoding option

scripts/run_benchmark_guided_decoding.sh

@@ -0,0 +1,220 @@
+#!/bin/bash
+
+# Runs an olmocr-bench run using the full pipeline (no fallback)
+#  Without model parameter (default behavior):, uses the default image from hugging face
+#   ./scripts/run_benchmark.sh
+#  With model parameter: for testing custom models
+#   ./scripts/run_benchmark.sh --model your-model-name
+
+set -e
+
+# Parse command line arguments
+MODEL=""
+while [[ $# -gt 0 ]]; do
+    case $1 in
+        --model)
+            MODEL="$2"
+            shift 2
+            ;;
+        *)
+            echo "Unknown option: $1"
+            echo "Usage: $0 [--model MODEL_NAME]"
+            exit 1
+            ;;
+    esac
+done
+
+# Check for uncommitted changes
+if ! git diff-index --quiet HEAD --; then
+    echo "Error: There are uncommitted changes in the repository."
+    echo "Please commit or stash your changes before running the benchmark."
+    echo ""
+    echo "Uncommitted changes:"
+    git status --short
+    exit 1
+fi
+
+# Use conda environment Python if available, otherwise use system Python
+if [ -n "$CONDA_PREFIX" ]; then
+    PYTHON="$CONDA_PREFIX/bin/python"
+    echo "Using conda Python from: $CONDA_PREFIX"
+else
+    PYTHON="python"
+    echo "Warning: No conda environment detected, using system Python"
+fi
+
+# Get version from version.py
+VERSION=$($PYTHON -c 'import olmocr.version; print(olmocr.version.VERSION)')
+echo "OlmOCR version: $VERSION"
+
+# Get first 10 characters of git hash
+GIT_HASH=$(git rev-parse HEAD | cut -c1-10)
+echo "Git hash: $GIT_HASH"
+
+# Get current git branch name
+GIT_BRANCH=$(git rev-parse --abbrev-ref HEAD)
+echo "Git branch: $GIT_BRANCH"
+
+# Create full image tag
+IMAGE_TAG="olmocr-benchmark-${VERSION}-${GIT_HASH}"
+echo "Building Docker image with tag: $IMAGE_TAG"
+
+# Build the Docker image
+echo "Building Docker image..."
+docker build --platform linux/amd64 -f ./Dockerfile -t $IMAGE_TAG .
+
+# Get Beaker username
+BEAKER_USER=$(beaker account whoami --format json | jq -r '.[0].name')
+echo "Beaker user: $BEAKER_USER"
+
+# Push image to beaker
+echo "Trying to push image to Beaker..."
+if ! beaker image create --workspace ai2/oe-data-pdf --name $IMAGE_TAG $IMAGE_TAG 2>/dev/null; then
+    echo "Warning: Beaker image with tag $IMAGE_TAG already exists. Using existing image."
+fi
+
+# Create Python script to run beaker experiment
+cat << 'EOF' > /tmp/run_benchmark_experiment.py
+import sys
+from beaker import Beaker, ExperimentSpec, TaskSpec, TaskContext, ResultSpec, TaskResources, ImageSource, Priority, Constraints, EnvVar
+
+# Get image tag, beaker user, git branch, git hash, and optional model from command line
+image_tag = sys.argv[1]
+beaker_user = sys.argv[2]
+git_branch = sys.argv[3]
+git_hash = sys.argv[4]
+model = sys.argv[5] if len(sys.argv) > 5 else None
+
+# Initialize Beaker client
+b = Beaker.from_env(default_workspace="ai2/olmocr")
+
+# Build the pipeline command with optional model parameter
+pipeline_cmd = "python -m olmocr.pipeline ./localworkspace --guided_decoding --markdown --pdfs ./olmOCR-bench/bench_data/pdfs/**/*.pdf"
+if model:
+    pipeline_cmd += f" --model {model}"
+
+# Check if AWS credentials secret exists
+aws_creds_secret = f"{beaker_user}-AWS_CREDENTIALS_FILE"
+try:
+    # Try to get the secret to see if it exists
+    b.secret.get(aws_creds_secret, workspace="ai2/olmocr")
+    has_aws_creds = True
+    print(f"Found AWS credentials secret: {aws_creds_secret}")
+except:
+    has_aws_creds = False
+    print(f"AWS credentials secret not found: {aws_creds_secret}")
+
+# First experiment: Original benchmark job
+commands = []
+if has_aws_creds:
+    commands.extend([
+        "mkdir -p ~/.aws",
+        'echo "$AWS_CREDENTIALS_FILE" > ~/.aws/credentials'
+    ])
+commands.extend([
+    "git clone https://huggingface.co/datasets/allenai/olmOCR-bench",
+    "cd olmOCR-bench && git lfs pull && cd ..",
+    pipeline_cmd,
+    "python olmocr/bench/scripts/workspace_to_bench.py localworkspace/ olmOCR-bench/bench_data/olmocr --bench-path ./olmOCR-bench/",
+    "python -m olmocr.bench.benchmark --dir ./olmOCR-bench/bench_data"
+])
+
+# Build task spec with optional env vars
+task_spec_args = {
+    "name": "olmocr-benchmark",
+    "image": ImageSource(beaker=f"{beaker_user}/{image_tag}"),
+    "command": [
+        "bash", "-c",
+        " && ".join(commands)
+    ],
+    "context": TaskContext(
+        priority=Priority.normal,
+        preemptible=True,
+    ),
+    "resources": TaskResources(gpu_count=1),
+    "constraints": Constraints(cluster=["ai2/ceres-cirrascale", "ai2/jupiter-cirrascale-2"]),
+    "result": ResultSpec(path="/noop-results"),
+}
+
+# Add env vars if AWS credentials exist
+if has_aws_creds:
+    task_spec_args["env_vars"] = [
+        EnvVar(name="AWS_CREDENTIALS_FILE", secret=aws_creds_secret)
+    ]
+
+# Create first experiment spec
+experiment_spec = ExperimentSpec(
+    description=f"OlmOCR Benchmark Run - Branch: {git_branch}, Commit: {git_hash}",
+    budget="ai2/oe-data",
+    tasks=[TaskSpec(**task_spec_args)],
+)
+
+# Create the first experiment
+experiment = b.experiment.create(spec=experiment_spec, workspace="ai2/olmocr")
+print(f"Created benchmark experiment: {experiment.id}")
+print(f"View at: https://beaker.org/ex/{experiment.id}")
+print("-------")
+print("")
+
+# Second experiment: Performance test job
+perf_pipeline_cmd = "python -m olmocr.pipeline ./localworkspace --guided_decoding --markdown --pdfs s3://ai2-oe-data/jakep/olmocr/olmOCR-mix-0225/benchmark_set/*.pdf"
+if model:
+    perf_pipeline_cmd += f" --model {model}"
+
+perf_commands = []
+if has_aws_creds:
+    perf_commands.extend([
+        "mkdir -p ~/.aws",
+        'echo "$AWS_CREDENTIALS_FILE" > ~/.aws/credentials'
+    ])
+perf_commands.append(perf_pipeline_cmd)
+
+# Build performance task spec
+perf_task_spec_args = {
+    "name": "olmocr-performance",
+    "image": ImageSource(beaker=f"{beaker_user}/{image_tag}"),
+    "command": [
+        "bash", "-c",
+        " && ".join(perf_commands)
+    ],
+    "context": TaskContext(
+        priority=Priority.normal,
+        preemptible=True,
+    ),
+    "resources": TaskResources(gpu_count=1),
+    "constraints": Constraints(cluster=["ai2/ceres-cirrascale", "ai2/jupiter-cirrascale-2"]),
+    "result": ResultSpec(path="/noop-results"),
+}
+
+# Add env vars if AWS credentials exist
+if has_aws_creds:
+    perf_task_spec_args["env_vars"] = [
+        EnvVar(name="AWS_CREDENTIALS_FILE", secret=aws_creds_secret)
+    ]
+
+# Create performance experiment spec
+perf_experiment_spec = ExperimentSpec(
+    description=f"OlmOCR Performance Test - Branch: {git_branch}, Commit: {git_hash}",
+    budget="ai2/oe-data",
+    tasks=[TaskSpec(**perf_task_spec_args)],
+)
+
+# Create the performance experiment
+perf_experiment = b.experiment.create(spec=perf_experiment_spec, workspace="ai2/olmocr")
+print(f"Created performance experiment: {perf_experiment.id}")
+print(f"View at: https://beaker.org/ex/{perf_experiment.id}")
+EOF
+
+# Run the Python script to create the experiments
+echo "Creating Beaker experiments..."
+if [ -n "$MODEL" ]; then
+    echo "Using model: $MODEL"
+    $PYTHON /tmp/run_benchmark_experiment.py $IMAGE_TAG $BEAKER_USER $GIT_BRANCH $GIT_HASH "$MODEL"
+else
+    $PYTHON /tmp/run_benchmark_experiment.py $IMAGE_TAG $BEAKER_USER $GIT_BRANCH $GIT_HASH
+fi
+
+# Clean up temporary file
+rm /tmp/run_benchmark_experiment.py
+
+echo "Benchmark experiments submitted successfully!"