Merge branch 'main_dedup' into 'main'

Training data and task deduplication

See merge request ADLR/megatron-lm!252

tools/openwebtext/README.md

@@ -26,7 +26,8 @@ python blacklist_urls.py <path to the dowloaded deduplicated URLs> <filename for
 ```
 python cleanup_dataset.py <input data file> <output cleaned data filename>
 ```
-2. Using LSH, find possible duplicates and store then in a file for later processing. This step can NOT be sharded and usually takes 12 to 24 hours for OpenWebText dataset. The code supports saving and loading fingerprints for recurrent deduplications.
+Additional cleanup (e.g. remove documents less than 512 characters or dataset specific cleaning like stories, realnews datasets) can be done using `cleanup_fix_dataset.py`. More details can be found by running `python cleanup_fix_dataset.py --help`.
+2. Using LSH, find possible duplicates and store then in a file for later processing. The code supports saving and loading fingerprints for recurrent deduplications, and is also multithreaded for faster processing. More details are can be found by `python find_duplicate.py --help`.
 ```
 python find_duplicates.py --inputs <pairlist list of input cleaned data files and keys, e.g. cc.json cc_id news.json news_id> --output <output possible duplicate urls filename>
 ```
@@ -46,10 +47,13 @@ shuf <cleaned deduped data file> -o train_data.json
 
 # Deduplicating ngrams
 
-To deduplicate the downstream tasks from the training dataset, we run the following command.
+To deduplicate the downstream tasks (e.g. lambada, squad) from the training dataset, we run the following command.
 
 ```
-python filter_ngrams.py <down stream task dataset> <training dataset to deduplicate> <output training dataset>
+python filter_ngrams.py --tasks <name of he task, e.g. lambada, squad> --dedup-dataset <training dataset to deduplicate> <json key> --output <output training dataset>
 ```
+We use 13-grams by default for the deduplication. When we find a 13-gram match in a training document, we split the document into two pieces and remove the 13-gram along with 200 characters from the both side of the 13-gram. We also remove any splitted document with less than 200 characters or if a document got splitted more than 10 times. These parameters can be changed using corresponding arguments.
 
-We use 13-grams for the deduplication. When we find a 13-gram match in a training document, we split the document into two pieces and remove the 13-gram along with 200 characters from the both side of the 13-gram. We also remove any splitted document with less than 200 characters or if a document got splitted more than 10 times.
+Only for the lambada task, we need to provide the path, `--lambada-path <path of the lambada test data>`.
+
+Several other features (e.g. save and load dictionary) have been added, look at `python filter_ngrams.py --help` for details.

tools/openwebtext/add_id.py

+# coding=utf-8
+# Copyright (c) 2020, NVIDIA CORPORATION.  All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import argparse
+import json
+import os
+import time
+
+"""
+This code adds id to each json object in a json file. User can add prefix
+to the ids.
+"""
+
+if __name__ == '__main__':
+
+    print('parsing the arguments ...')
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--input-file', type=str, default=None, help='Input'\
+        ' json file where id needs to be added')
+    parser.add_argument('--output-file', type=str, default=None, help=\
+        'Output file name with id')
+    parser.add_argument('--id-prefix', type=str, default=None, help=\
+        'Id prefix')
+    parser.add_argument('--log-interval', type=int, default=100,
+                       help='Log interval')
+    args = parser.parse_args()
+
+    print('Adding ids to dataset ...')
+
+    f_input = open(args.input_file, 'r', encoding='utf-8')
+    f_output = open(args.output_file, 'wb')
+
+    unique_ids = 1
+    start_time = time.time()
+    for row in f_input:
+        each_row = json.loads(row)
+        adlr_id_string = args.id_prefix + '-{:010d}'.format(int(unique_ids))
+        each_row['adlr_id'] = adlr_id_string
+        myjson = json.dumps(each_row, ensure_ascii=False)
+
+        f_output.write(myjson.encode('utf-8'))
+        f_output.write('\n'.encode('utf-8'))
+
+        if unique_ids % args.log_interval == 0:
+            print('    processed {:9d} documents in {:.2f} seconds ...'.format( \
+                    unique_ids, time.time() - start_time), flush=True)
+
+        unique_ids += 1
+
+    # Close the file.
+    f_input.close()
+    f_output.close()
+    
+    print('done :-)', flush=True)

tools/openwebtext/cleanup_fix_dataset.py

+# coding=utf-8
+# Copyright (c) 2020, NVIDIA CORPORATION.  All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""
+Filter and clean documents:
+Capable to clean docs with less than 512 characters, less than
+256 characters and contains javascript, fix text and dataset specific
+cleaning like stories and realnews datasets.
+Program arguments have the details.
+"""
+
+import argparse
+from functools import partial
+import glob
+import ftfy
+import json
+from langdetect import detect
+import multiprocessing
+import os
+from pathlib import Path
+import re
+import time
+
+def process_doc(json_line, args):
+
+    # Read the line.
+    document = json.loads(json_line)
+    text = document['text']
+
+    output = {'remove_512': False, 'remove_256_javascript': False, \
+        'remove_512_non_english': False, 'ftfy_fix_text': False, \
+        'general_cleaning': False}
+
+    try:
+        # Reomove all docs with less than 512 characters
+        if "remove_512" in args.tasks:
+            if len(text) < 512:
+                output['remove_512'] = True
+                return output, text, document, True
+
+        # Remove docs if less than 256 character length and contains Javascript
+        if "remove_256_javascript" in args.tasks:
+            if len(text) < 256 and 'javascript' in text.lower():
+                output['remove_256_javascript'] = True
+                return output, text, document, True
+
+        # Remove docs < 512 and nonenglish
+        if "remove_512_non_english" in args.tasks:
+            if len(text) < 512 and detect(text) != 'en':
+                output['remove_512_non_english'] = True
+                return output, text, document, True
+
+        # Fix the text using ftfy, don't remove the text, hence return False
+        if "ftfy_fix_text" in args.tasks:
+            fixed_text = ftfy.fix_text(text)
+            output['ftfy_fix_text'] = True
+            return output, fixed_text, document, False
+
+        # Cleaning extra spaces and newlines
+        if "general_cleaning" in args.tasks:
+            cleaned_text = re.sub(r"  +|\b\n+ |\b\n+", " ", text)
+            #cleaned_text = re.sub(r"\n\n+", "\n\n", text) # used this for Gutenberg dataset
+            #cleaned_text = re.sub(r"\n", "\n\n", text) # Used this for realnews
+
+            # stories datasets
+            #cleaned_text = re.sub(r" \'", "'", text)
+            #cleaned_text = re.sub(r" \!", "!", cleaned_text)
+            #cleaned_text = re.sub(r" \.", ".", cleaned_text)
+            #cleaned_text = re.sub(r" \?", "?", cleaned_text)
+            #cleaned_text = re.sub(r" - ", "-", cleaned_text)
+            ##cleaned_text = re.sub(r"\" ", "\"", cleaned_text)
+            #cleaned_text = re.sub(r" @ ", "@", cleaned_text)
+
+            output['general_cleaning'] = True
+            return output, cleaned_text, document, False
+
+    except Exception as e:
+        print('Error: *************************\n{}\ntext: {}'.format(e, \
+            text), flush=True)
+        return output, text, document, True
+
+    # don't remove
+    return output, text, document, False
+
+
+def process_set(args, input_file, output_f_cleaned, output_f_filtered):
+
+    print(' > working on {} ...'.format(input_file), flush=True)
+    
+    num_docs = num_remove_512 = num_remove_java = num_remove_512_non_english \
+        = num_ftfy_fix_text = num_general_cleaning = 0
+
+    # Output file and counters.
+    output_cleaned = open(output_f_cleaned, 'wb')
+    output_filtered = open(output_f_filtered, 'wb')
+
+    start_time = time.time()
+
+    # Setup multi-processing.
+    num_workers = 40
+    fin = open(input_file, 'r', encoding='utf-8')
+    pool = multiprocessing.Pool(num_workers)
+    process_doc_partial = partial(process_doc, args=args)
+    processed_docs = pool.imap(process_doc_partial, fin, 500)
+
+    # Process documents.
+    for output, text, document, to_filter in processed_docs:
+        num_docs += 1
+
+        num_remove_512 += 1 if output['remove_512'] else 0
+        num_remove_java += 1 if output['remove_256_javascript'] else 0
+        num_remove_512_non_english += 1 if output['remove_512_non_english'] \
+            else 0
+        num_ftfy_fix_text += 1 if output['ftfy_fix_text'] else 0
+        num_general_cleaning += 1 if output['general_cleaning'] else 0
+
+        document['text'] = text
+        myjson = json.dumps(document, ensure_ascii=False)
+
+        if to_filter:
+            output_filtered.write(myjson.encode('utf-8'))
+            output_filtered.write('\n'.encode('utf-8'))
+        else:
+            output_cleaned.write(myjson.encode('utf-8'))
+            output_cleaned.write('\n'.encode('utf-8'))
+
+        if num_docs % args.log_interval == 0:
+            print('    processed {:9d} documents in {:.2f} seconds ...'.format(
+                num_docs, time.time() - start_time), flush=True)
+
+    # Close the file.
+    output_cleaned.close()
+    output_filtered.close()
+    fin.close()
+
+    # Print stats.
+    print('  >> total docs: {} remove_512 {} remove_256_javascript {} '\
+        'remove_512_non_english {} ftfy_fix_text {} general_cleaning {}'.\
+        format(num_docs, num_remove_512, num_remove_java,\
+        num_remove_512_non_english, num_ftfy_fix_text, \
+        num_general_cleaning), flush=True)
+
+if __name__ == '__main__':
+
+
+    print('parsing the arguments ...')
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--input-files', nargs = '*', required=True, default=\
+                        None, help = 'Input json files that needs to be'\
+                        ' cleaned')
+    parser.add_argument('--tasks', nargs = '*', required=True, default=None,\
+                        help = 'Tasks to perform on the input files, ' \
+                        'such as remove_512, remove_256_javascript, ' \
+                        'remove_512_non_english, ftfy_fix_text, and ' \
+                        'general_cleaning. 256 or 512 means the number' \
+                        ' of characters.')
+
+    parser.add_argument('--output-path', type=str, default=None,
+                       help='Directory where the output should go')
+    parser.add_argument('--log-interval', type=int, default=100,
+                       help='Log interval')
+
+    args = parser.parse_args()
+
+    print('cleanup dataset ...')
+
+    for input_file in args.input_files:
+        input_filename, input_filename_ext = os.path.splitext(Path(input_file)\
+            .name)
+
+        output_f_cleaned = os.path.join(args.output_path, input_filename + \
+            "_cleaned" + input_filename_ext)
+        output_f_filtered = os.path.join(args.output_path, input_filename + \
+            "_filtered" + input_filename_ext)
+
+        process_set(args, input_file, output_f_cleaned, output_f_filtered)
+
+    print('done :-)', flush=True)

tools/openwebtext/filter_ngrams.py

@@ -19,10 +19,12 @@ All split documents with less than 200 characters got filtered. Any document
 with more than 10 splits got filtered as well.
 """
 
+import argparse
 from functools import partial
 import json
 import multiprocessing
 import nltk
+import pickle
 import re
 import string
 import sys
@@ -36,40 +38,20 @@ def get_words(text):
         positions.append(match.start())
     return words, positions
 
-def free_ngram(line, ngrams, ngram_size, filter_text_len, 
-    splits_count, split_window_each_size):
-    # remove all the ngrams
-
-    try:
-        myjson = json.loads(line)
-        text_buf = [myjson['text']]
-    except Exception as e:
-        print("Error: {}".format(e), flush=True)
-        text_buf = []
-
-    text_buf_ngram_free = []
-    while len(text_buf) > 0:
-
-        # get the first one from the buffer
-        text = text_buf.pop(0)
-        words, positions = get_words(text)
-        
-        not_ngram_free = True
-        punctuations = ".!?"
-        # find n-grams
-        for i in range(len(words) - ngram_size + 1):
-            seq = " ".join(words[i:i+ngram_size])
-            if seq in ngrams:
-
-                # splits the text
+# splits the text
+def split_text(text, start_position, remove_char_each_side, seq):
     # first part of the text
-                pos = positions[i] - split_window_each_size
+    punctuations = ".!?"
+    pos = start_position - remove_char_each_side
     text_first = ""
     while pos > 0 and not text[pos] in punctuations:
         pos -= 1
     if pos > 0:
         text_first = text[0:pos+1]
-                pos = positions[i] + split_window_each_size
+
+    # add length of seq and remove_char_each_side
+    pos = start_position + len(seq) + remove_char_each_side
+
     # last part of the text
     text_second = ""
     while pos < len(text) and not text[pos] in punctuations:
@@ -77,97 +59,434 @@ def free_ngram(line, ngrams, ngram_size, filter_text_len,
     if pos + 1 < len(text):
         text_second = text[pos+1:len(text)]
 
+    return text_first, text_second
+
+def check_and_clean_text(args, words, ngrams, text, start_position, \
+    text_buf_ngram_free, text_buf, local_ngram):
+
+    seq = " ".join(words)
+    if seq in ngrams:
+        print(" [matched]: {}".format(seq), flush=True)
+
+        if args.get_ngram_freq_only:
+            # increase freq of this seq and then only consider the later part
+            # of the text for further processing
+            if seq in local_ngram:
+                local_ngram[seq] += 1
+            else:
+                local_ngram[seq] = 1
+            #print(" [increased]: {} {}".format(seq, ngrams[seq]), flush=True)
+            if (start_position + len(seq) + 1) < len(text):
+                text_buf.append(text[start_position + len(seq) + 1:len(text)])
+            return False            
+
+        # split the text
+        text_first, text_second = split_text(text, start_position, \
+            args.remove_char_each_side, seq)
+
         # first part of ngrams free
-                if len(text_first) > filter_text_len:
+        if len(text_first) > args.filter_text_char_len:
             text_buf_ngram_free.append(text_first)
 
         # add second part for further processing
-                if len(text_second) > filter_text_len:
+        if len(text_second) > args.filter_text_char_len:
             text_buf.append(text_second)
-                not_ngram_free = False
+
+        return False # not ngram free
+
+    # ngram free
+    return True
+
+
+def free_ngram(line, args, key, ngrams, ngrams_freq_sorted):
+    # remove all the ngrams
+
+    try:
+        myjson = json.loads(line)
+        text_buf = [myjson[key]]
+    except Exception as e:
+        print("Error: {}".format(e), flush=True)
+        text_buf = []
+
+    text_buf_ngram_free = []
+    local_ngram = {}
+    while len(text_buf) > 0:
+
+        # get the first one from the buffer
+        text = text_buf.pop(0)
+        words, positions = get_words(text)
+        
+        ngram_free = True
+        # find each max n-grams and check dictionary
+        for i in range(len(words) - args.max_ngram_size + 1):
+            check_ngram_free = check_and_clean_text(args, words[i:\
+                i+args.max_ngram_size], ngrams, text, positions[i], \
+                text_buf_ngram_free, text_buf, local_ngram)
+
+            # the seq is ngram free? if yes, break
+            if not check_ngram_free:
+                ngram_free = False
                 break
 
-        # text are ngram free
-        if not_ngram_free:
+            # if max ngrams doesn't match, check if any other lower n-grams
+            # within max ngram macthes
+            for ngram_len, _ in ngrams_freq_sorted:
+                check_ngram_free = check_and_clean_text(args, words[i:\
+                    i+ngram_len], ngrams, text, positions[i], \
+                    text_buf_ngram_free, text_buf, local_ngram)
+
+                # same check as above
+                if not check_ngram_free:
+                    ngram_free = False
+                    break
+
+            # check break from lower than max ngram loop above
+            if not ngram_free:
+                break
+
+        # for the last max n-gram, check all the lower ngrams in it
+        if ngram_free and len(words) - args.max_ngram_size > 0:
+            # get the last words of the lax max ngram
+            last_seq_words = words[(len(words)-args.max_ngram_size):len(words)]
+            last_seq_start_position = len(words) - args.max_ngram_size
+
+            # check all n-grams lower than the max
+            for pos, (ngram_len, _) in enumerate(ngrams_freq_sorted):
+
+                # ignore the max ngram as has been considered already
+                if ngram_len == args.max_ngram_size:
+                    continue
+
+                # find each ngram of ngram_len in max n-grams and check
+                for i in range(len(last_seq_words) - ngram_len + 1):
+                    check_ngram_free = check_and_clean_text(args, \
+                        last_seq_words[i:i+ngram_len], ngrams, text,\
+                        positions[last_seq_start_position+i], \
+                        text_buf_ngram_free, text_buf, local_ngram)
+
+                    if not check_ngram_free:
+                        ngram_free = False
+                        break
+
+                if not ngram_free:
+                    break
+
+        # texts are ngram free
+        if ngram_free and not args.get_ngram_freq_only:
             text_buf_ngram_free.append(text)
 
-    return text_buf_ngram_free
+    # check if the text has only been trimmed
+    trimmed = 0
+    if not args.get_ngram_freq_only and len(text_buf_ngram_free) == 1 and \
+        len(text_buf_ngram_free[0]) < len(myjson[key]):
+        trimmed = 1
 
+    return text_buf_ngram_free, trimmed, myjson, local_ngram
 
-if __name__ == '__main__':
+# insert word sequence into dictionary
+def insert_dict(words, ngrams, pos):
+    seq = " ".join(words)
+    if seq not in ngrams:
+        ngrams[seq] = 0
+        #ngrams[seq] = pos
 
-    print('finding possible duplicate content ...')
-    main_file = sys.argv[1] # lambada file
-    dedup_file = sys.argv[2] # Book corpus
-    output_file = sys.argv[3] #Filtered book corpus
-    ngrams = {}
-    id_prefix = "lambada"
+# insert each ngram from text into the ngrams dictionary
+def compute_ngrams_insert_dict(args, text, ngrams):
+    words, positions = get_words(text)
+    if len(words) < args.min_ngram_size:
+        return
 
-    # we use 13-grams, any text less than 200 characters got removed
-    # any text splitted more than 10 got removed as well
-    ngram_size = 13
-    filter_text_len = 200
-    splits_count = 10
-    split_window_each_size = 200
+    if len(words) < args.max_ngram_size:
+        insert_dict(words, ngrams, positions[0])
+
+    for i in range(len(words) - args.max_ngram_size+1):
+        insert_dict(words[i:i+args.max_ngram_size], ngrams, positions[i])
 
-    print('Reading file {} and computing ngrams'.format(main_file))
-    with open(main_file, 'r') as f:
+
+# Build ngrams for the lambada dataset
+def process_task_lambda(args, task_file, ngrams):
+    print(' reading from {} and computing ngrams'.format(task_file))
+    with open(task_file, 'r') as f:
         for line in f:
             try:
                 myjson = json.loads(line)
-                words, positions = get_words(myjson['text'])
-                for i in range(len(words) - ngram_size+1):
-                    seq = " ".join(words[i:i+ngram_size])
-                    if seq not in ngrams:
-                        ngrams[seq] = positions[i]
+                text = myjson['text']
+                compute_ngrams_insert_dict(args, text, ngrams)
             except Exception as e:
                 print('Error:', e)
-    print("ngrams size {}".format(len(ngrams)))
+    print(" Entities in ngrams {}".format(len(ngrams)), flush=True)
+
+
+# Build ngrams for the dataset of the given task
+def process_task(args, task_name, ngrams):
+
+    print(' reading from {} and computing ngrams'.format('import datasets'))
+    print(" Current entities in ngrams {}".format(len(ngrams)), flush=True)
+    # using validation/test data from datasets
+    from datasets import load_dataset
+
+    entities_in_ngrams = len(ngrams)
+
+    # load the dataset
+    if task_name == 'squad':
+        dataset = load_dataset('squad_v2', split='validation')
+    elif task_name == 'natural_questions':
+        dataset = load_dataset('natural_questions', split='validation')
+    elif task_name == 'triviaqa':
+        dataset = load_dataset('trivia_qa', 'unfiltered', split='test')
+    elif task_name == 'webqa':
+        dataset = load_dataset('web_questions', split='test')
+    elif task_name == 'race':
+        dataset = load_dataset('race', 'all', split='test')
+    elif task_name == 'drop':
+        dataset = load_dataset('drop', split='validation')
+    elif task_name == 'coqa':
+        dataset = load_dataset('coqa', split='validation')
+    elif task_name == 'piqa':
+        dataset = load_dataset('piqa', split='test')
+    else:
+        print("Invalid task name: {}".format(task_name), flush=True)
+        return
+
+    # read the dataset and add to ngrams
+    for line in dataset:
+        try:
+            if task_name in ['squad', 'triviaqa', 'webqa', 'race', 'drop']:
+                text = line['question']
+                compute_ngrams_insert_dict(args, text, ngrams)
+            elif task_name == 'natural_questions':
+                text = line['question']['text']
+                compute_ngrams_insert_dict(args, text, ngrams)
+            elif task_name == 'coqa':
+                all_questions = line['questions']
+                for question in all_questions:
+                    compute_ngrams_insert_dict(args, question, ngrams)
+            elif task_name == 'piqa':
+                text = line['goal']
+                compute_ngrams_insert_dict(args, text, ngrams)
+        except Exception as e:
+            print('Error:', e)
+
+    print(" After task {} entities in ngrams {}, added {}".format(task_name, \
+            len(ngrams), len(ngrams) - entities_in_ngrams), flush=True)
+
+def compute_tasks_ngrams(args, ngrams):
+    start_time = time.time()
+    for _, task_name in enumerate(args.tasks):
+        print('Task: {}'.format(task_name), flush=True)
+        if task_name == 'lambada':
+            assert args.lambada_path is not None
+            process_task_lambda(args, args.lambada_path, ngrams)
+        else:
+            process_task(args, task_name, ngrams)
+    print(" Taken time to compute ngrams {:.2f}".format(time.time() - \
+        start_time), flush=True)
+
+def compute_ngram_freq_sorted(args, ngrams):
+    ngrams_freq = {}
+    for ngram_key in ngrams.keys():
+        length = len(ngram_key.split())
+        ngrams_freq[length] = ngrams_freq[length] + 1 if length in \
+            ngrams_freq else 1
+
+    ngrams_freq_sorted = sorted(ngrams_freq.items(), key=lambda item: item[0])
+    print(" Ngram frequencies: {}".format(ngrams_freq_sorted), flush=True)
+    print(" Entities in ngrams {} min_ngram_size {} max_ngram_size {}".format(\
+            len(ngrams), ngrams_freq_sorted[0][0], ngrams_freq_sorted[len(\
+            ngrams_freq_sorted) -1 ][0]), flush=True)
+    return ngrams_freq_sorted
+
+def get_ngrams_below_threshold(args, ngrams, ngrams_below_threshold, \
+    dedup_file, dedup_key, ngrams_freq_sorted):
 
-    print('Reading file {} and deduping n-grams'.format(dedup_file))
-    counter = 0
     start_time = time.time()
-    out_f = open(output_file, 'wb')
-    splitted, ignored, split_mt_thld = 0, 0, 0
+    # get the ngrams frequency
+    args.get_ngram_freq_only = True
  
-    # Setup multi-processing.
-    num_workers = 40
+    # Open the large file to process in parallel
+    num_workers = args.num_threads 
+    pool = multiprocessing.Pool(num_workers)
     fin = open(dedup_file, 'r', encoding='utf-8')
+    free_ngram_abt_partial=partial(free_ngram, args=args, key=dedup_key, \
+        ngrams=ngrams, ngrams_freq_sorted=ngrams_freq_sorted)
+    free_ngrams_abt = pool.imap(free_ngram_abt_partial, fin, 500)
+ 
+    counter = 0
+    for _, _, _, local_ngram in free_ngrams_abt:
+        counter += 1
+        if counter % 1000 == 0:
+            print(' [compute_stat]> processed {} documents in {:.2f} seconds ...'.
+                    format(counter, time.time() - start_time), flush=True)
+        for local_key in local_ngram:
+            if local_key in ngrams:
+                ngrams[local_key] += 1
+        local_ngram = {}
+
+    print(' Time taken to compute statistics {:.2f} seconds'.format(time.time() - \
+        start_time), flush=True)
+    pool.close()
+    pool.join()
+
+    start_time = time.time()
+    counter_threshold = 0
+    # Get ngram below theadhold
+    for local_key, local_val in ngrams.items():
+        if ngrams[local_key] < args.key_threshold:
+            print(" [threshold] {} {}".format(local_key, local_val), flush=True)
+            counter_threshold += 1
+            ngrams_below_threshold[local_key] = 1
+            
+    print(' Ngrams below threshold {}'.format(counter_threshold), flush=True)
+    fin.close()
+
+def clean_ngrams_below_threshold(args, ngrams_below_threshold, dedup_file, \
+    dedup_key):
+
+    start_time = time.time()
+    # Now actually filter the dataset
+    args.get_ngram_freq_only = False
+    #id_prefix = '-'.join(args.tasks[::2])
+    id_prefix = '-'.join(args.tasks[::1])
+
+    # get the range of the size of the ngrams
+    ngrams_freq_sorted = compute_ngram_freq_sorted(args, ngrams_below_threshold)
+
+    # Open the large file to process in parallel
+    counter = splitted = ignored = split_mt_thld = trimmed_count = 0
+    num_workers = args.num_threads
     pool = multiprocessing.Pool(num_workers)
-    free_ngram_x=partial(free_ngram, ngrams=ngrams, ngram_size=ngram_size, 
-        filter_text_len=filter_text_len, splits_count=splits_count,
-        split_window_each_size=split_window_each_size)
-    free_ngrams = pool.imap(free_ngram_x, fin, 25)
+    fin = open(dedup_file, 'r', encoding='utf-8')
+    free_ngram_clean_partial=partial(free_ngram, args=args, key=dedup_key, \
+        ngrams=ngrams_below_threshold, ngrams_freq_sorted=ngrams_freq_sorted)
+    free_ngrams_clean = pool.imap(free_ngram_clean_partial, fin, 500)
+ 
+    out_f = open(args.output, 'wb')
 
-    for text_buf_ngram_free in free_ngrams:
+    for text_buf_ngram_free, trimmed, myjson, _ in free_ngrams_clean:
         counter += 1
         try:
 
+            trimmed_count += trimmed
+
             if len(text_buf_ngram_free) > 1:
-                splitted += (len(text_buf_ngram_free) - 1)
+                splitted += 1
             if len(text_buf_ngram_free) == 0:
                 ignored += 1
             # more than 10 splits ignored
-            if len(text_buf_ngram_free) > splits_count:
+            if len(text_buf_ngram_free) > args.splits_count:
                 text_buf_ngram_free = []
                 split_mt_thld += 1
 
+            if args.output is not None:
+                if "split_id" in myjson:
+                    use_prefix = myjson["split_id"] + "-"
+                else:
+                    use_prefix = ""
+
                 for i in range(len(text_buf_ngram_free)):
-                split_id_string = id_prefix + '-{:010d}'.format(int(counter)) \
-                    + '-{:010d}'.format(int(i))
-                outjson = json.dumps({"text":text_buf_ngram_free[i], 
-                    id_prefix+"_split_id":split_id_string},
-                    ensure_ascii=False)
+                    split_id_string = id_prefix + '-{:010d}'.format(int(\
+                        counter)) + '-{:04d}'.format(int(i))
+                    myjson[dedup_key] = text_buf_ngram_free[i]
+                    myjson["split_id"] = use_prefix + split_id_string
+                    outjson = json.dumps(myjson, ensure_ascii=False)
+                    #outjson = json.dumps({"text":text_buf_ngram_free[i],
+                    #    id_prefix+"_split_id":split_id_string},
+                    #    ensure_ascii=False)
                     out_f.write(outjson.encode('utf-8'))
                     out_f.write('\n'.encode('utf-8'))
 
             if counter % 1000 == 0:
-                print(' [search]> processed {} documents in {:.2f} seconds ...'.
+                print(' [final]> processed {} documents in {:.2f} seconds ...'.
                     format(counter, time.time() - start_time), flush=True)
         except Exception as e:
             print('Error:', e)
 
-    print("Deduped file written to: {}".format(output_file), flush=True)
-    print("Total docs {} splitted {} ignored {} docs with many splits {}".\
-        format(counter, splitted, ignored, split_mt_thld), flush=True)
+    print(' [final]> processed {} documents in {:.2f} seconds ...'.
+        format(counter, time.time() - start_time), flush=True)
+    
+    print(' Total docs {} splitted {} ignored {} splits > theshold {} trimmed'\
+        ' {}'.format(counter, splitted, ignored, split_mt_thld, trimmed_count)\
+        , flush=True)
+
+    pool.close()
+    pool.join()
+
+    out_f.close()
+    fin.close()
+
+if __name__ == '__main__':
+
+    # we use 13-grams, any text less than 200 characters got removed
+    # any text splitted more than 10 got removed as well
+
+    print('parsing the arguments ...')
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--tasks', nargs = '*', required=True, default=None, \
+                        help = 'Tasks to use for deduplication: currently '
+                        ' suuport [lambada, squad, natural_questions,'
+                        ' triviaqa, webqa, race, drop, coqa, and piqa]')
+    parser.add_argument('--lambada-path', type=str, default=None,
+                       help='Only Lambada task needs the path')
+    parser.add_argument('--dedup-dataset', nargs = '*', default=None,
+                       help='Dataset to deduplicate with the key to use'
+                        ' e.g. cc.json text')
+    parser.add_argument('--output', type=str, default=None,
+                       help='Output file name to save dedup dataset')
+    parser.add_argument('--num-threads', type=int, default=40,
+                       help='Number of threads to use')
+    # Default dedup values
+    parser.add_argument('--max-ngram-size', type=int, default=13,
+                       help='Maximum size of ngram to use.')
+    parser.add_argument('--min-ngram-size', type=int, default=8,
+                       help='Minimum size of ngram to use.')
+    parser.add_argument('--filter-text-char-len', type=int, default=200,
+                       help='Remove any text below this length.')
+    parser.add_argument('--key-threshold', type=int, default=10,
+                       help='Number of keys to consider as threshold')
+    parser.add_argument('--save-dictionary', type=str, default=None,
+                       help='Save the dictionary')
+    parser.add_argument('--load-dictionary', type=str, default=None,
+                       help='Load the dictionary')
+    parser.add_argument('--splits-count', type=int, default=10,
+                       help='Remove any documents more than this many splits')
+    parser.add_argument('--remove-char-each-side', type=int, default=200,
+                       help='Maximum size of ngram to use.')
+
+    args = parser.parse_args()
+
+    assert len(args.dedup_dataset) == 2
+    dedup_file = args.dedup_dataset[0]
+    dedup_key = args.dedup_dataset[1]
+
+    # Setup multi-processing
+    num_workers = args.num_threads
+    if args.load_dictionary is None:
+
+        # Build ngrams
+        ngrams = {}
+        compute_tasks_ngrams(args, ngrams)
+
+        # get the range of the size of the ngrams
+        ngrams_freq_sorted = compute_ngram_freq_sorted(args, ngrams)
+
+        # get ngram freq from large file in parallel
+        # get ngrams below threshold
+        ngrams_below_threshold = {}
+        get_ngrams_below_threshold(args, ngrams, ngrams_below_threshold, \
+            dedup_file, dedup_key, ngrams_freq_sorted)
+
+        # save the dictionary if needed
+        if args.save_dictionary is not None:
+            with open(args.save_dictionary, 'wb') as save_dict_handle:
+                pickle.dump(ngrams_below_threshold, save_dict_handle)
+    else:
+        with open(args.load_dictionary, 'rb') as load_dict_handle:
+            ngrams_below_threshold = pickle.load(load_dict_handle)
+
+    # filter the large file
+    if args.output is not None:
+        clean_ngrams_below_threshold(args, ngrams_below_threshold, \
+            dedup_file, dedup_key)
+
     print('done :-)')

tools/openwebtext/find_duplicates.py

@@ -14,13 +14,16 @@
 # limitations under the License.
 
 import argparse
+from functools import partial
 import itertools
 import json
 from lsh import cache, minhash
+import multiprocessing
 import numpy as np
 import time
 import pickle
 import sys
+import os
 
 # This function is adapted from:
 #   https://github.com/mattilyra/LSH/blob/master/examples/Introduction.ipynb
@@ -31,11 +34,158 @@ def shingles(text, char_ngram=5):
 
 # This function is adapted from:
 #  https://github.com/mattilyra/LSH/blob/master/examples/Introduction.ipynb
-def jaccard(set_a, set_b):
+def jaccard(set_a, set_b, args):
+    if len(set_a) < 1 or len(set_b) < 1:
+        return 0.0
+
     intersection = set_a & set_b
     union = set_a | set_b
+
+    if args.jaccard == 'min':
+        return len(intersection) / min(len(set_a), len(set_b))
+    elif args.jaccard == 'max':
+        return len(intersection) / max(len(set_a), len(set_b))
+    else:
         return len(intersection) / len(union)
 
+def compute_fingerprint(line, key):
+    try:
+        myjson = json.loads(line)
+        url = myjson[key]
+        text = myjson['text']
+        fingerprint = hasher.fingerprint(text)
+    except Exception as e:
+        print('Error:', e)
+        return None, None, None, False
+
+    return url, text, fingerprint, True
+
+def url_pairs_to_remove(args, bucket_urls, url_doc):
+    remove_urls_list = []
+    deduped_local, counter_local = 0, 0
+    iteration = 0
+    while len(bucket_urls) > 1:
+        if args.heuristic_iter != -1 and \
+            iteration == args.heuristic_iter:
+            break
+
+        items = list(bucket_urls)
+        remove_urls = []
+        main_url = items[np.random.randint(0, len(items))]
+        main_dhingles = shingles(url_doc[main_url])
+
+        for i in range(0, len(items)):
+            counter_local += 1
+            other_url = items[i]
+            if other_url == main_url:
+                continue
+            other_shingles = shingles(url_doc[other_url])
+            try:
+                jaccard_sim = jaccard(main_dhingles, other_shingles, args)
+            except Exception as e:
+                print('Error:', e)
+                jaccard_sim = 0.0
+            if jaccard_sim > 0.5:
+                remove_urls.append({other_url: jaccard_sim})
+                deduped_local += 1
+                bucket_urls.remove(other_url)
+
+        bucket_urls.remove(main_url)
+        if len(remove_urls) > 0:
+            remove_urls_list.append({main_url: remove_urls})
+        iteration += 1
+    return remove_urls_list, deduped_local, counter_local
+
+def write_remove_urls_list(remove_urls_list, f_out):
+    if len(remove_urls_list) > 0:
+        for each_url_remove in remove_urls_list:
+            myjson = json.dumps(each_url_remove, ensure_ascii=False)
+            f_out.write(myjson.encode('utf-8'))
+            f_out.write('\n'.encode('utf-8'))
+
+def compute_jaccard(each_bin, num_bins, start_time_local):
+
+    remove_urls_list = []
+    deduped_local, counter_local, bucket_local = 0, 0, 0
+
+    for bucket_id in each_bin:
+        bucket_local += 1
+        if os.getpid() % num_bins == 0 and bucket_local % 100000 == 0:
+            print("Counter {}, progress {:.2f} time {:.2f}".\
+                format(bucket_local, float(bucket_local)/float(len(each_bin)),\
+                time.time() - start_time_local), flush=True)
+
+        if len(each_bin[bucket_id]) <= 1:
+            continue
+
+        bucket_urls = each_bin[bucket_id].copy()
+        remove_urls_list_sub, deduped_local_sub, counter_local_sub = \
+            url_pairs_to_remove(args, bucket_urls, url_doc)
+
+        deduped_local += deduped_local_sub
+        counter_local += counter_local_sub
+        if len(remove_urls_list_sub) > 0:
+            remove_urls_list.extend(remove_urls_list_sub)
+
+    return remove_urls_list, deduped_local, counter_local
+
+def find_pair_urls_parallel(args, lshcache, url_doc):
+    start_time = time.time()
+    f_out = open(args.output, 'wb')
+    deduped, counter = 0, 0
+
+    # compute jaccards of buckets in bin in parallel (parallelism
+    # limited to # of bins)
+    num_bins = len(lshcache.bins)
+    pool = multiprocessing.Pool(num_bins)
+    compute_jaccard_partial = partial(compute_jaccard, num_bins=num_bins, \
+        start_time_local=start_time)
+    # don't need to pass args and url_doc as they are already shared
+    compute_jaccard_iter = pool.imap(compute_jaccard_partial, lshcache.bins)
+
+    print("multiprocessing init took {:.2f}".format(time.time() - start_time),\
+        flush=True)
+    for remove_urls_list, deduped_local, counter_local in compute_jaccard_iter:
+        deduped += deduped_local
+        counter += counter_local
+        write_remove_urls_list(remove_urls_list, f_out)
+        print(' [write]> processed {} documents in {:.2f} '
+            'seoncds and deduped {} documents ...'.format(counter, time.time()\
+            - start_time, deduped), flush=True)
+
+    pool.close()
+    pool.join()
+    f_out.close()
+
+    print(' Taken time for jaccard similariries {:.2f} seconds'.format(\
+        time.time() - start_time), flush=True)
+
+def find_pair_urls_sequential(args, lshcache, url_doc):
+    start_time = time.time()
+    f_out = open(args.output, 'wb')
+    deduped, counter = 0, 0
+    for b in lshcache.bins:
+        for bucket_id in b:
+            if len(b[bucket_id]) <= 1:
+                continue
+
+            bucket_urls = b[bucket_id].copy()
+            remove_urls_list_sub, deduped_local_sub, counter_local_sub = \
+                url_pairs_to_remove(args, bucket_urls, url_doc)
+
+            deduped += deduped_local_sub
+            counter += counter_local_sub
+            write_remove_urls_list(remove_urls_list_sub, f_out)
+            if counter % 10000 == 0:
+                print(' [write]> processed {} documents in {:.2f} '
+                    'seoncds and deduped {} documents ...'.
+                    format(counter, time.time() - start_time,
+                    deduped), flush=True)
+    f_out.close()
+    print(' [write]> processed {} documents in {:.2f} '
+        'seoncds and deduped {} documents ...'.
+        format(counter, time.time() - start_time,
+        deduped), flush=True)
 
 if __name__ == '__main__':
 
@@ -55,17 +205,30 @@ if __name__ == '__main__':
     parser.add_argument('--output', type=str, default=None,
                        help='Output file name that consists of all ids'
                         ' with matching similarities')
+    parser.add_argument('--jaccard', type=str, default='union',
+                        choices=['union', 'min', 'max'], help='Jaccard'\
+                        ' similarity computation')
+    parser.add_argument('--heuristic-iter', type=int, default=1,
+                       help='Number of iterations to run the heuristics'
+                        ': use -1 for exact')
+    parser.add_argument('--num-bands', type=int, default=10,
+                       help='Number of bands to use in cache')
+    parser.add_argument('--num-seeds', type=int, default=100,
+                       help='Number of seeds to use for minhash. Note that'
+                        ' this value should be divisible by num-bands')
+    parser.add_argument('--jaccard-parallel', action='store_true',
+                       help='Use this to process large number of documents.')
     args = parser.parse_args()
 
     print('finding possible duplicate content ...')
 
     # set seed and get an array of seeds of 100 integers
     np.random.seed(args.seed)
-    seeds = np.random.randint(0, 1e6, size=100)
+    seeds = np.random.randint(0, 1e6, size=args.num_seeds)
 
     # initialize minhash and lsh cache
     hasher = minhash.MinHasher(seeds=seeds, char_ngram=5, hashbytes=4)
-    lshcache = cache.Cache(bands=10, hasher=hasher)
+    lshcache = cache.Cache(num_bands=args.num_bands, hasher=hasher)
 
     url_doc = {}
 
@@ -91,32 +254,37 @@ if __name__ == '__main__':
     counter = 0
     start_time = time.time()
 
-    print("Computing fingerprints", flush=True)
-
     # compute finger prints of the inputs if any
     # input file and the key to use as id
     if args.inputs is not None:
+        print("Computing fingerprints", flush=True)
         assert len(args.inputs) % 2 == 0
         for input_file, key in zip(args.inputs[::2], args.inputs[1::2]):
             print(' document processing {} with key {}'.format(input_file, key),
                 flush=True)
+
+            # compute fingerprints in parallel
+            num_workers = 40
+            pool = multiprocessing.Pool(num_workers)
+            fin = open(input_file, 'r', encoding='utf-8')
+            compute_fingerprint_partial = partial(compute_fingerprint, key=key)
+            compute_fingerprint_iter = pool.imap(compute_fingerprint_partial,
+                                                    fin, 512)
             # traverse all the texts and add fingerprints
-            with open(input_file, 'r') as f_input:
-                for line in f_input:
-                    try:
-                        myjson = json.loads(line)
-                        url = myjson[key]
-                        text = myjson['text']
+            for url, text, fingerprint, flag in compute_fingerprint_iter:
                 counter += 1
+                if flag:
                     url_doc[url] = text
-                        lshcache.add_fingerprint(hasher.fingerprint(text), url)
-                    except Exception as e:
-                        print('Error:', e)
+                    lshcache.add_fingerprint(fingerprint, url)
                 if counter % 10000 == 0:
                     print(' [read]> processed {} documents in {:.2f} '
                         'seconds ...'.format(counter, time.time() - \
                         start_time), flush=True)
 
+            fin.close()
+            pool.close()
+            pool.join()
+
     # Save the fingerprints if needed
     if args.save_fingerprints is not None:
         print("Saving fingerprints to pickle file {}".format(
@@ -125,40 +293,13 @@ if __name__ == '__main__':
             pickle.dump(lshcache, f_save)
             pickle.dump(url_doc, f_save)
 
-    counter = 0
-    start_time = time.time()
-    deduped = 0
     # compute jaccard index of the input texts and write to file if needed
     if args.output is not None:
-        f_out = open(args.output, 'wb')
-        for b in lshcache.bins:
-            for bucket_id in b:
-                if len(b[bucket_id]) > 1:
-                    items = list(b[bucket_id])
-                    main_url = items[0]
-                    main_dhingles = shingles(url_doc[main_url])
-                    remove_urls = []
-                    for i in range(1, len(items)):
-                        counter += 1
-                        other_url= items[i]
-                        other_shingles = shingles(url_doc[other_url])
-                        try:
-                            jaccard_sim = jaccard(main_dhingles, other_shingles)
-                        except Exception as e:
-                            print('Error:', e)
-                        if jaccard_sim > 0.5:
-                            remove_urls.append({other_url: jaccard_sim})
-                            deduped += 1
-                        if counter % 10000 == 0:
-                            print(' [write]> processed {} documents in {:.2f} '
-                                  'seoncds and deduped {} documents ...'.
-                                  format(counter, time.time() - start_time,
-                                         deduped), flush=True)
-                    if len(remove_urls) > 0:
-                        myjson = json.dumps({main_url: remove_urls},
-                                            ensure_ascii=False)
-                        f_out.write(myjson.encode('utf-8'))
-                        f_out.write('\n'.encode('utf-8'))
-        f_out.close()
+        print("Compute jaccard similarity", flush=True)
+        if args.jaccard_parallel:
+            find_pair_urls_parallel(args, lshcache, url_doc)
+        else:
+            find_pair_urls_sequential(args, lshcache, url_doc)
 
     print('done :-)')
+ 

tools/openwebtext/group_duplicate_url.py

@@ -18,10 +18,6 @@ import time
 import sys
 
 
-def is_similar(jaccard_similarity):
-    return (jaccard_similarity >= 0.7)
-
-
 if __name__ == '__main__':
 
 
@@ -29,6 +25,10 @@ if __name__ == '__main__':
 
     input = sys.argv[1]
     output = sys.argv[2]
+    if len(sys.argv) > 3:
+        jaccard_similarity_threshold = float(sys.argv[3])
+    else:
+        jaccard_similarity_threshold = 0.7
 
     url_to_index = {}
     index_to_urls = []
@@ -43,7 +43,7 @@ if __name__ == '__main__':
                 urls.append(main_url)
                 for value in myjson[main_url]:
                     for other_url, js in value.items():
-                        if is_similar(js):
+                        if js >= jaccard_similarity_threshold:
                             urls.append(other_url)
             current_index = -1
             other_indices = set()