now using multiprocessing style

openfold/data/data_pipeline.py

@@ -21,7 +21,8 @@ import dataclasses
 from multiprocessing import cpu_count
 import tempfile
 from typing import Mapping, Optional, Sequence, Any, MutableMapping, Union
-import asyncio
+import asyncio, multiprocessing
+import concurrent.futures
 import numpy as np
 import torch
 
@@ -738,36 +739,51 @@ class DataPipeline:
             fp.close()
         else:
             # Now will split the following steps into multiple processes 
-            async def parse_stockholm_file(alignment_dir: str, stockholm_file: str):
+            def parse_stockholm_file(alignment_dir: str, stockholm_file: str, queue: multiprocessing.Queue):
                 path = os.path.join(alignment_dir, stockholm_file)
                 file_name,_ = os.path.splitext(stockholm_file)
                 with open(path, "r") as infile:
                     msa = parsers.parse_stockholm(infile.read())
                     infile.close()
-                return {file_name: msa}
+                queue.put({file_name: msa})
             
-            async def parse_a3m_file(alignment_dir: str, a3m_file: str):
+            def parse_a3m_file(alignment_dir: str, a3m_file: str,queue: multiprocessing.Queue):
                 path = os.path.join(alignment_dir, a3m_file)
                 file_name,_ = os.path.splitext(a3m_file)
                 with open(path, "r") as infile:
                     msa = parsers.parse_a3m(infile.read())
                     infile.close()
-                return {file_name: msa}
-
-            async def run_parse_all_msa_files(stockholm_files: list, a3m_files: list, alignment_dir:str):
-                all_tasks = [asyncio.create_task(parse_stockholm_file(alignment_dir, sto)) for sto in stockholm_files]
-                all_tasks += [asyncio.create_task(parse_a3m_file(alignment_dir, a3m)) for a3m in a3m_files]
-                results = await asyncio.gather(*all_tasks)
-                return results 
+                queue.put({file_name: msa})
+
+            def run_parse_all_msa_files_multiprocessing(stockholm_files: list, a3m_files: list, alignment_dir:str):
+                print(f"#### line 764 start running in multiprocessing way")
+                msa_results={}
+                processes = []
+                queue = multiprocessing.Queue()
+                for f in stockholm_files: 
+                    process = multiprocessing.Process(target = parse_stockholm_file, args=(alignment_dir, f, queue))
+                    processes.append(process)
+                    process.start()
+                for f in a3m_files:
+                    process = multiprocessing.Process(target = parse_a3m_file, args=(alignment_dir, f, queue))
+                    processes.append(process)
+                    process.start()
+                
+                for p in processes:
+                    res = queue.get()
+                    msa_results.update(res)
+                    p.join()
+                    
+                return msa_results
+                        
             stockholm_files = [i for i in os.listdir(alignment_dir) if (i.endswith('.sto') and ("hmm_output" not in i))]
             a3m_files = [i for i in os.listdir(alignment_dir) if i.endswith('.a3m')]
             import time
             start = time.time()
-            msa_results = asyncio.run(run_parse_all_msa_files(stockholm_files, a3m_files, alignment_dir))
+            # msa_data = asyncio.run(run_parse_all_msa_files(stockholm_files, a3m_files, alignment_dir))
+            msa_data = run_parse_all_msa_files_multiprocessing(stockholm_files, a3m_files, alignment_dir)
             end = time.time()
             calculate_elapse(start, end, "asynchronised version")
-            for i in msa_results:
-                msa_data.update({k:v for k,v in i.items()})
 
         return msa_data