From: Nate E TeBlunthuis Date: Sun, 9 Aug 2020 07:21:50 +0000 (-0700) Subject: Use groupby - joins instead of windows X-Git-Url: https://code.communitydata.science/cdsc_reddit.git/commitdiff_plain/2d1c8013f2a59cde10b5169ee61edea3a4f35aca?hp=-c Use groupby - joins instead of windows --- 2d1c8013f2a59cde10b5169ee61edea3a4f35aca diff --git a/checkpoint_parallelsql.sbatch b/checkpoint_parallelsql.sbatch new file mode 100644 index 0000000..a54aab1 --- /dev/null +++ b/checkpoint_parallelsql.sbatch @@ -0,0 +1,24 @@ +#!/bin/bash +## parallel_sql_job.sh +#SBATCH --job-name=tf_subreddit_comments +## Allocation Definition +#SBATCH --account=comdata-ckpt +#SBATCH --partition=ckpt +## Resources +## Nodes. This should always be 1 for parallel-sql. +#SBATCH --nodes=1 +## Walltime (12 hours) +#SBATCH --time=12:00:00 +## Memory per node +#SBATCH --mem=100G +#SBATCH --cpus-per-task=4 +#SBATCH --ntasks=1 + + +module load parallel_sql + +#Put here commands to load other modules (e.g. matlab etc.) +#Below command means that parallel_sql will get tasks from the database +#and run them on the node (in parallel). So a 16 core node will have +#16 tasks running at one time. +parallel-sql --sql -a parallel --exit-on-term --jobs 4 diff --git a/run_tf_jobs.sh b/run_tf_jobs.sh new file mode 100755 index 0000000..fc191d4 --- /dev/null +++ b/run_tf_jobs.sh @@ -0,0 +1,8 @@ +#!/usr/bin/env bash +module load parallel_sql +source ../bin/activate +python3 tf_comments.py gen_task_list +psu --del --Y +cat tf_task_list | psu --load + +for job in $(seq 1 50); do sbatch checkpoint_parallelsql.sbatch; done; diff --git a/tf_comments.py b/tf_comments.py index 85eebec..277b76f 100644 --- a/tf_comments.py +++ b/tf_comments.py @@ -64,7 +64,15 @@ def weekly_tf(partition, mwe_pass = 'first'): subreddit_weeks = groupby(rows, lambda r: (r.subreddit, r.week)) - mwe_tokenize = MWETokenizer().tokenize + if mwe_pass != 'first': + mwe_dataset = ds.dataset(f'/gscratch/comdata/users/nathante/reddit_comment_ngrams_pwmi.parquet',format='parquet') + mwe_dataset = mwe_dataset.to_pandas(columns=['phrase','phraseCount','phrasePWMI']) + mwe_dataset = mwe_dataset.sort_values(['phrasePWMI'],ascending=False) + mwe_phrases = list(mwe_dataset.phrase[0:1000]) + + + mwe_tokenize = MWETokenizer(mwe_phrases).tokenize + def remove_punct(sentence): new_sentence = [] @@ -119,6 +127,7 @@ def weekly_tf(partition, mwe_pass = 'first'): else: # remove stopWords + sentences = map(mwe_tokenize, sentences) sentences = map(lambda s: filter(lambda token: token not in stopWords, s), sentences) return chain(* sentences) @@ -142,19 +151,17 @@ def weekly_tf(partition, mwe_pass = 'first'): outchunksize = 10000 - with pq.ParquetWriter("/gscratch/comdata/users/nathante/reddit_tfidf_test.parquet_temp/{partition}",schema=schema,compression='snappy',flavor='spark') as writer, pq.ParquetWriter("/gscratch/comdata/users/nathante/reddit_tfidf_test_authors.parquet_temp/{partition}",schema=author_schema,compression='snappy',flavor='spark') as author_writer: + with pq.ParquetWriter(f"/gscratch/comdata/users/nathante/reddit_tfidf_test.parquet_temp/{partition}",schema=schema,compression='snappy',flavor='spark') as writer, pq.ParquetWriter(f"/gscratch/comdata/users/nathante/reddit_tfidf_test_authors.parquet_temp/{partition}",schema=author_schema,compression='snappy',flavor='spark') as author_writer: while True: chunk = islice(outrows,outchunksize) pddf = pd.DataFrame(chunk, columns=["is_token"] + schema.names) - print(pddf) - author_pddf = pddf.loc[pddf.is_token == False] + + author_pddf = pddf.loc[pddf.is_token == False, schema.names] + pddf = pddf.loc[pddf.is_token == True, schema.names] + author_pddf = author_pddf.rename({'term':'author'}, axis='columns') author_pddf = author_pddf.loc[:,author_schema.names] - - pddf = pddf.loc[pddf.is_token == True, schema.names] - print(pddf) - print(author_pddf) table = pa.Table.from_pandas(pddf,schema=schema) author_table = pa.Table.from_pandas(author_pddf,schema=author_schema) if table.shape[0] == 0: @@ -171,7 +178,7 @@ def gen_task_list(): with open("tf_task_list",'w') as outfile: for f in files: if f.endswith(".parquet"): - outfile.write(f"source python3 tf_comments.py weekly_tf {f}\n") + outfile.write(f"python3 tf_comments.py weekly_tf {f}\n") if __name__ == "__main__": fire.Fire({"gen_task_list":gen_task_list,