Merge e2ce039 into 4e7f0ac

.ci_support/environment.yml

@@ -10,3 +10,5 @@ dependencies:
   - jinja2 =3.1.2
   - paramiko =3.2.0
   - tqdm =4.65.0
+  - pympipool =0.5.4
+  - cloudpickle =2.2.1

pysqa/__init__.py

@@ -2,6 +2,7 @@
 __all__ = []
 
 from pysqa.queueadapter import QueueAdapter
+from pysqa.executor.executor import Executor
 
 from ._version import get_versions
 

pysqa/executor/__main__.py

@@ -0,0 +1,6 @@
+import sys
+from pysqa.executor.backend import command_line
+
+
+if __name__ == "__main__":
+    command_line(arguments_lst=sys.argv[1:])

pysqa/executor/backend.py

@@ -0,0 +1,65 @@
+import os
+import sys
+
+from pympipool import PoolExecutor
+from pysqa.executor.helper import (
+    read_from_file,
+    deserialize,
+    write_to_file,
+    serialize_result,
+)
+
+
+def execute_files_from_list(tasks_in_progress_dict, cache_directory, executor):
+    file_lst = os.listdir(cache_directory)
+    for file_name_in in file_lst:
+        key = file_name_in.split(".in.pl")[0]
+        file_name_out = key + ".out.pl"
+        if (
+            file_name_in.endswith(".in.pl")
+            and file_name_out not in file_lst
+            and file_name_out not in tasks_in_progress_dict.keys()
+        ):
+            funct_dict = read_from_file(
+                file_name=os.path.join(cache_directory, file_name_in)
+            )
+            apply_dict = deserialize(funct_dict=funct_dict)
+            for k, v in apply_dict.items():
+                tasks_in_progress_dict[k] = executor.submit(
+                    v["fn"], *v["args"], **v["kwargs"]
+                )
+    for k, v in tasks_in_progress_dict.items():
+        if v.done():
+            write_to_file(
+                funct_dict=serialize_result(result_dict={k: v.result()}),
+                state="out",
+                cache_directory=cache_directory,
+            )
+
+
+def execute_tasks(cores, cache_directory):
+    tasks_in_progress_dict = {}
+    with PoolExecutor(
+        max_workers=cores,
+        oversubscribe=False,
+        enable_flux_backend=False,
+        enable_slurm_backend=False,
+        init_function=None,
+        cwd=cache_directory,
+        queue_adapter=None,
+        queue_adapter_kwargs=None,
+    ) as exe:
+        while True:
+            execute_files_from_list(
+                tasks_in_progress_dict=tasks_in_progress_dict,
+                cache_directory=cache_directory,
+                executor=exe,
+            )
+
+
+def command_line(arguments_lst=None):
+    if arguments_lst is None:
+        arguments_lst = sys.argv[1:]
+    cores_arg = arguments_lst[arguments_lst.index("--cores") + 1]
+    path_arg = arguments_lst[arguments_lst.index("--path") + 1]
+    execute_tasks(cores=cores_arg, cache_directory=path_arg)

pysqa/executor/executor.py

@@ -0,0 +1,62 @@
+import os
+import queue
+from threading import Thread
+from concurrent.futures import Future, Executor as FutureExecutor
+
+from pympipool import cancel_items_in_queue
+from pysqa.executor.helper import (
+    reload_previous_futures,
+    find_executed_tasks,
+    serialize_funct,
+    write_to_file,
+)
+
+
+class Executor(FutureExecutor):
+    def __init__(self, cwd=None, queue_adapter=None, queue_adapter_kwargs=None):
+        self._task_queue = queue.Queue()
+        self._memory_dict = {}
+        self._cache_directory = os.path.abspath(os.path.expanduser(cwd))
+        self._queue_adapter = queue_adapter
+        reload_previous_futures(
+            future_queue=self._task_queue,
+            future_dict=self._memory_dict,
+            cache_directory=self._cache_directory,
+        )
+        command = (
+            "python -m pysqa.executor --cores "
+            + str(queue_adapter_kwargs["cores"])
+            + " --path "
+            + str(self._cache_directory)
+        )
+        self._queue_id = self._queue_adapter.submit_job(
+            working_directory=self._cache_directory,
+            command=command,
+            **queue_adapter_kwargs
+        )
+        self._process = Thread(
+            target=find_executed_tasks,
+            kwargs={
+                "future_queue": self._task_queue,
+                "cache_directory": self._cache_directory,
+            },
+        )
+        self._process.start()
+
+    def submit(self, fn, *args, **kwargs):
+        funct_dict = serialize_funct(fn, *args, **kwargs)
+        key = list(funct_dict.keys())[0]
+        if key not in self._memory_dict.keys():
+            self._memory_dict[key] = Future()
+            _ = write_to_file(
+                funct_dict=funct_dict, state="in", cache_directory=self._cache_directory
+            )[0]
+            self._task_queue.put({key: self._memory_dict[key]})
+        return self._memory_dict[key]
+
+    def shutdown(self, wait=True, *, cancel_futures=False):
+        if cancel_futures:
+            cancel_items_in_queue(que=self._task_queue)
+        self._task_queue.put({"shutdown": True, "wait": wait})
+        self._queue_adapter.delete_job(process_id=self._queue_id)
+        self._process.join()

pysqa/executor/helper.py

@@ -0,0 +1,99 @@
+import os
+import re
+import queue
+from concurrent.futures import Future
+
+import hashlib
+import cloudpickle
+
+
+def deserialize(funct_dict):
+    try:
+        return {k: cloudpickle.loads(v) for k, v in funct_dict.items()}
+    except EOFError:
+        return {}
+
+
+def find_executed_tasks(future_queue, cache_directory):
+    task_memory_dict = {}
+    while True:
+        task_dict = {}
+        try:
+            task_dict = future_queue.get_nowait()
+        except queue.Empty:
+            pass
+        _update_task_dict(
+            task_dict=task_dict,
+            task_memory_dict=task_memory_dict,
+            cache_directory=cache_directory,
+        )
+
+
+def read_from_file(file_name):
+    name = file_name.split("/")[-1].split(".")[0]
+    with open(file_name, "rb") as f:
+        return {name: f.read()}
+
+
+def reload_previous_futures(future_queue, future_dict, cache_directory):
+    file_lst = os.listdir(cache_directory)
+    for f in file_lst:
+        if f.endswith(".in.pl"):
+            key = f.split(".in.pl")[0]
+            future_dict[key] = Future()
+            file_name_out = key + ".out.pl"
+            if file_name_out in file_lst:
+                _set_future(
+                    file_name=os.path.join(cache_directory, file_name_out),
+                    future=future_dict[key],
+                )
+            else:
+                future_queue.put({key: future_dict[key]})
+
+
+def serialize_result(result_dict):
+    return {k: cloudpickle.dumps(v) for k, v in result_dict.items()}
+
+
+def serialize_funct(fn, *args, **kwargs):
+    binary = cloudpickle.dumps({"fn": fn, "args": args, "kwargs": kwargs})
+    return {fn.__name__ + _get_hash(binary=binary): binary}
+
+
+def write_to_file(funct_dict, state, cache_directory):
+    file_name_lst = []
+    for k, v in funct_dict.items():
+        file_name = _get_file_name(name=k, state=state)
+        file_name_lst.append(file_name)
+        with open(os.path.join(cache_directory, file_name), "wb") as f:
+            f.write(v)
+    return file_name_lst
+
+
+def _get_file_name(name, state):
+    return name + "." + state + ".pl"
+
+
+def _get_hash(binary):
+    # Remove specification of jupyter kernel from hash to be deterministic
+    binary_no_ipykernel = re.sub(b"(?<=/ipykernel_)(.*)(?=/)", b"", binary)
+    return str(hashlib.md5(binary_no_ipykernel).hexdigest())
+
+
+def _set_future(file_name, future):
+    values = deserialize(funct_dict=read_from_file(file_name=file_name)).values()
+    if len(values) == 1:
+        future.set_result(list(values)[0])
+
+
+def _update_task_dict(task_dict, task_memory_dict, cache_directory):
+    file_lst = os.listdir(cache_directory)
+    for key, future in task_dict.items():
+        task_memory_dict[key] = future
+    for key, future in task_memory_dict.items():
+        file_name_out = _get_file_name(name=key, state="out")
+        if not future.done() and file_name_out in file_lst:
+            _set_future(
+                file_name=os.path.join(cache_directory, file_name_out),
+                future=future,
+            )

setup.py

@@ -33,11 +33,13 @@
     extras_require={
         "sge": ['defusedxml==0.7.1'],
         "remote": ['paramiko==3.2.0', 'tqdm==4.65.0'],
+        "executor": ['pympipool==0.5.4', 'cloudpickle==2.2.1'],
     },
     cmdclass=versioneer.get_cmdclass(),
     entry_points={
             "console_scripts": [
-                'pysqa=pysqa:main'
+                'pysqa=pysqa.cmd:command_line',
+                'pysqa-executor=pysqa.executor.backend:command_line'
             ]
     }
 )