From e99f0b002a4cf5eea6c79ba0890b610f06c2da48 Mon Sep 17 00:00:00 2001
From: Jan Trienes <jantrienes@users.noreply.github.com>
Date: Thu, 16 Jul 2020 15:49:04 +0200
Subject: [PATCH] Add efficiency benchmark (#18)

* Add efficiency benchmark script

* Set better defaults for number of repetitions and sentences

* Use human readable tagger names in statistics table

* Add wrapper script to start cpu/gpu benchmarks

* Change benchmark wrapper to fail on non-zero exit codes

* Increase number of sentences in benchmark

* Explicitly save number of docs and number of tokens

* Add parameters to configure batch size of BiLSTM-CRF

* Correctly apply parameters

* Fix typo

* Clear cuda cache in between repetitions
---
 scripts/benchmark.py | 111 +++++++++++++++++++++++++++++++++++++++++++
 scripts/benchmark.sh |  21 ++++++++
 2 files changed, 132 insertions(+)
 create mode 100644 scripts/benchmark.py
 create mode 100755 scripts/benchmark.sh

diff --git a/scripts/benchmark.py b/scripts/benchmark.py
new file mode 100644
index 0000000..b51bd03
--- /dev/null
+++ b/scripts/benchmark.py
@@ -0,0 +1,111 @@
+import argparse
+from timeit import default_timer as timer
+from typing import List
+
+import numpy as np
+import pandas as pd
+import torch
+from flair.datasets import CONLL_03_DUTCH
+from loguru import logger
+from tqdm import tqdm
+
+from deidentify.base import Document
+from deidentify.taggers import CRFTagger, DeduceTagger, FlairTagger, TextTagger
+from deidentify.tokenizer import TokenizerFactory
+
+N_REPETITIONS = 5
+N_SENTS = 5000
+
+
+def load_data():
+    corpus = CONLL_03_DUTCH()
+    sentences = corpus.train[:N_SENTS]
+    tokens = sum(len(sent) for sent in sentences)
+    docs = [Document(name='', text=sent.to_plain_string(), annotations=[]) for sent in sentences]
+    return docs, tokens
+
+
+def benchmark_tagger(tagger: TextTagger, docs: List[Document], num_tokens: int):
+    durations = []
+
+    for _ in tqdm(range(0, N_REPETITIONS), desc='Repetitions'):
+        start = timer()
+        tagger.annotate(docs)
+        end = timer()
+        durations.append(end - start)
+
+        if isinstance(tagger, FlairTagger) and torch.cuda.is_available():
+            torch.cuda.empty_cache()
+
+    return {
+        'mean': np.mean(durations),
+        'std': np.std(durations),
+        'tokens/s': num_tokens / np.mean(durations),
+        'docs/s': len(docs) / np.mean(durations),
+        'num_docs': len(docs),
+        'num_tokens': num_tokens
+    }
+
+
+def main(args):
+    logger.info('Load data...')
+    documents, num_tokens = load_data()
+
+    logger.info('Initialize taggers...')
+    tokenizer_crf = TokenizerFactory().tokenizer(corpus='ons', disable=())
+    tokenizer_bilstm = TokenizerFactory().tokenizer(corpus='ons', disable=("tagger", "ner"))
+
+    taggers = [
+        ('DEDUCE', DeduceTagger(verbose=True)),
+        ('CRF', CRFTagger(
+            model='model_crf_ons_tuned-v0.1.0',
+            tokenizer=tokenizer_crf,
+            verbose=True
+        )),
+        ('BiLSTM-CRF (large)', FlairTagger(
+            model='model_bilstmcrf_ons_large-v0.1.0',
+            tokenizer=tokenizer_bilstm,
+            mini_batch_size=args.bilstmcrf_large_batch_size,
+            verbose=True
+        )),
+        ('BiLSTM-CRF (fast)', FlairTagger(
+            model='model_bilstmcrf_ons_fast-v0.1.0',
+            tokenizer=tokenizer_bilstm,
+            mini_batch_size=args.bilstmcrf_fast_batch_size,
+            verbose=True
+        ))
+    ]
+
+    benchmark_results = []
+    tagger_names = []
+    for tagger_name, tagger in taggers:
+        logger.info(f'Benchmark inference for tagger: {tagger_name}')
+        scores = benchmark_tagger(tagger, documents, num_tokens)
+        benchmark_results.append(scores)
+        tagger_names.append(tagger_name)
+
+    df = pd.DataFrame(data=benchmark_results, index=tagger_names)
+    df.to_csv(f'{args.benchmark_name}.csv')
+    logger.info('\n{}', df)
+
+
+def arg_parser():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("benchmark_name", type=str, help="Name of the benchmark.")
+    parser.add_argument(
+        "--bilstmcrf_large_batch_size",
+        type=int,
+        help="Batch size to use with the large model.",
+        default=256
+    )
+    parser.add_argument(
+        "--bilstmcrf_fast_batch_size",
+        type=int,
+        help="Batch size to use with the fast model.",
+        default=256
+    )
+    return parser.parse_args()
+
+
+if __name__ == '__main__':
+    main(arg_parser())
diff --git a/scripts/benchmark.sh b/scripts/benchmark.sh
new file mode 100755
index 0000000..60e2982
--- /dev/null
+++ b/scripts/benchmark.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+set -e
+
+export CUDA_VISIBLE_DEVICES=0
+# Smaller batch size so that sequences with Flair embeddings fit in GPU memory.
+python -m scripts.benchmark benchmark_gpu \
+    --bilstmcrf_large_batch_size 64 \
+    --bilstmcrf_fast_batch_size 64
+
+export CUDA_VISIBLE_DEVICES=""
+export MKL_NUM_THREADS=32
+python -m scripts.benchmark benchmark_cpu_32_threads
+
+export CUDA_VISIBLE_DEVICES=""
+export MKL_NUM_THREADS=16
+python -m scripts.benchmark benchmark_cpu_16_threads
+
+export CUDA_VISIBLE_DEVICES=""
+export MKL_NUM_THREADS=8
+python -m scripts.benchmark benchmark_cpu_8_threads