Merge pull request #194 from notoraptor/cw-521-cleanup-jobs

[CW-521] - Implémenter un script de "ménage des jobs"

scripts/cleanup_jobs.py

@@ -0,0 +1,230 @@
+"""
+Script to clean-up jobs in database.
+
+To evaluate job status, we check job["slurm"]["slurm_last_update"].
+"""
+
+import argparse
+import sys
+from datetime import datetime
+from slurm_state.mongo_client import get_mongo_client
+from slurm_state.config import get_config
+
+
+def main(arguments: list):
+    parser = argparse.ArgumentParser(description="Delete old jobs from database.")
+    group = parser.add_mutually_exclusive_group(required=True)
+    group.add_argument(
+        "-n",
+        "--jobs",
+        type=int,
+        help=(
+            "Number of most recent jobs to keep. If specified, script will delete all older jobs until N jobs remain. "
+            "If there were initially at most N jobs in database, nothing will be deleted."
+        ),
+    )
+    group.add_argument(
+        "-u",
+        "--jobs-per-user",
+        type=int,
+        help=(
+            "Number of most recent jobs to keep **PER USER**. "
+            "If specified, script will delete all older jobs until N Jobss remain for each user. "
+            "If a user initially had at most N jobs, all its jobs will remain."
+        ),
+    )
+    group.add_argument(
+        "-d",
+        "--date",
+        help=(
+            "Date of older job to keep. "
+            "Format 'YYYY-MM-DD-HH:MM:SS', or 'YYYY-MM-DD' (equivalent to 'YYYY-MM-DD-00:00:00'). "
+            "If specified, script will delete all jobs older than given date."
+        ),
+    )
+    parser.add_argument(
+        "--debug",
+        action="store_true",
+        help=(
+            "If specified, print info (job ID and slurm_last_update) "
+            "about all available jobs before and after cleanup."
+        ),
+    )
+    args = parser.parse_args(arguments)
+
+    if args.debug:
+        _debug_db_jobs()
+
+    if args.jobs is not None:
+        keep_n_most_recent_jobs(args.jobs)
+    elif args.jobs_per_user is not None:
+        keep_n_most_recent_jobs_per_user(args.jobs_per_user)
+    else:
+        if args.date.count("-") == 2:
+            date_format = "%Y-%m-%d"
+        else:
+            date_format = "%Y-%m-%d-%H:%M:%S"
+        date = datetime.strptime(args.date, date_format)
+        keep_jobs_from_date(date)
+
+    if args.debug:
+        _debug_db_jobs()
+
+
+def keep_n_most_recent_jobs(n: int):
+    print(f"Keeping {n} most recent jobs")
+    mc = _get_db()
+    db_jobs = mc["jobs"]
+    nb_total_jobs = db_jobs.count_documents({})
+
+    if nb_total_jobs <= n:
+        print(f"{nb_total_jobs} jobs in database, {n} to keep, nothing to do.")
+        return
+
+    # Find jobs to delete.
+    # Sort jobs by slurm_last_update ascending
+    # and keep only first jobs, excluding n last jobs.
+    jobs_to_delete = list(
+        db_jobs.find({}).sort([("cw.last_slurm_update", 1)]).limit(nb_total_jobs - n)
+    )
+    assert len(jobs_to_delete) == nb_total_jobs - n
+    # Delete jobs
+    filter_to_delete = {"_id": {"$in": [job["_id"] for job in jobs_to_delete]}}
+    result = db_jobs.delete_many(filter_to_delete)
+    nb_deleted_jobs = result.deleted_count
+    # Delete user props associated to deleted jobs
+    _delete_user_props(mc, jobs_to_delete)
+
+    nb_remaining_jobs = db_jobs.count_documents({})
+
+    print(
+        f"Jobs in database: initially {nb_total_jobs}, deleted {nb_deleted_jobs}, remaining {nb_remaining_jobs}"
+    )
+
+
+def keep_n_most_recent_jobs_per_user(n: int):
+    mc = _get_db()
+    db_jobs = mc["jobs"]
+    nb_total_jobs = db_jobs.count_documents({})
+
+    db_users = mc["users"]
+    nb_users = db_users.count_documents({})
+    print(f"Keeping {n} most recent jobs for each of {nb_users} users.")
+
+    jobs_to_delete = []
+    for user in db_users.find({}).sort([("mila_email_username", 1)]):
+        mila_email_username = user["mila_email_username"]
+        user_filter = {"cw.mila_email_username": mila_email_username}
+        nb_user_jobs = db_jobs.count_documents(user_filter)
+        if nb_user_jobs <= n:
+            # print(f"[{mila_email_username}] {nb_user_jobs} user jobs, nothing to do.")
+            continue
+
+        # Find user jobs to delete.
+        # Sort jobs by slurm_last_update ascending
+        # and keep only first jobs, excluding n last jobs.
+        user_jobs_to_delete = list(
+            db_jobs.find(user_filter)
+            .sort([("cw.last_slurm_update", 1)])
+            .limit(nb_user_jobs - n)
+        )
+        assert len(user_jobs_to_delete) == nb_user_jobs - n
+        jobs_to_delete.extend(user_jobs_to_delete)
+        # print(f"[{mila_email_username}] {nb_user_jobs} user jobs, {len(user_jobs_to_delete)} to delete.")
+
+    if not jobs_to_delete:
+        print(f"Each user has at most {n} jobs, nothing to do.")
+        return
+
+    filter_to_delete = {"_id": {"$in": [job["_id"] for job in jobs_to_delete]}}
+    result = db_jobs.delete_many(filter_to_delete)
+    nb_deleted_jobs = result.deleted_count
+    # Delete user props associated to deleted jobs
+    _delete_user_props(mc, jobs_to_delete)
+
+    nb_remaining_jobs = db_jobs.count_documents({})
+
+    print(
+        f"Jobs in database: initially {nb_total_jobs}, deleted {nb_deleted_jobs}, remaining {nb_remaining_jobs}"
+    )
+
+
+def keep_jobs_from_date(date: datetime):
+    print(f"Keeping jobs starting from: {date}")
+    mc = _get_db()
+    db_jobs = mc["jobs"]
+    nb_total_jobs = db_jobs.count_documents({})
+
+    # Find jobs to delete
+
+    jobs_to_delete = list(
+        db_jobs.find({"cw.last_slurm_update": {"$lt": date.timestamp()}})
+    )
+    if not jobs_to_delete:
+        print(f"No job found before {date}, nothing to do.")
+        return
+
+    # Delete jobs
+    filter_to_delete = {"_id": {"$in": [job["_id"] for job in jobs_to_delete]}}
+    result = db_jobs.delete_many(filter_to_delete)
+    nb_deleted_jobs = result.deleted_count
+    # Delete user props associated to deleted jobs
+    _delete_user_props(mc, jobs_to_delete)
+
+    nb_remaining_jobs = db_jobs.count_documents({})
+
+    print(
+        f"Jobs in database: initially {nb_total_jobs}, deleted {nb_deleted_jobs}, remaining {nb_remaining_jobs}"
+    )
+
+
+def _delete_user_props(mc, jobs: list):
+    """Delete user props associated to given jobs."""
+    # Build filter.
+    # Use OR, to delete any of given jobs.
+    filter_jobs = {
+        "$or": [
+            # For each job, find user prop with same job ID and cluster name.
+            {
+                "$and": [
+                    {"job_id": job["slurm"]["job_id"]},
+                    {"cluster_name": job["slurm"]["cluster_name"]},
+                ]
+            }
+            for job in jobs
+        ]
+    }
+
+    result = mc["job_user_props"].delete_many(filter_jobs)
+    return result.deleted_count
+
+
+def _get_db():
+    client = get_mongo_client()
+    mc = client[get_config("mongo.database_name")]
+    return mc
+
+
+def _debug_db_jobs():
+    """Debug function. Print job ID and `last_slurm_update` for each job in database."""
+    mc = _get_db()
+    db_jobs = mc["jobs"]
+    jobs = list(db_jobs.find({}).sort([("cw.last_slurm_update", 1)]))
+    nb_jobs = len(jobs)
+    print(f"[JOBS: {nb_jobs}]")
+    for i, job in enumerate(jobs):
+        print(
+            f"\t[{i + 1}/{nb_jobs}] job_id={job['slurm']['job_id']} cw.last_slurm_update={_fmt_last_slurm_update(job)}"
+        )
+
+
+def _fmt_last_slurm_update(job):
+    """Pretty print last_slurm_update (None if None, else as a date time)."""
+    v = job["cw"].get("last_slurm_update")
+    if v is None:
+        return v
+    return datetime.fromtimestamp(v)
+
+
+if __name__ == "__main__":
+    main(sys.argv[1:])

scripts_test/Dockerfile

@@ -15,4 +15,8 @@ RUN pip install -r /requirements_scripts.txt && rm -rf /root/.cache
 COPY scripts_test/requirements.txt /requirements_scripts_test.txt
 RUN pip install -r /requirements_scripts_test.txt && rm -rf /root/.cache
 
+# Add folder `slurm_state` so that `slurm_state` symbols are available during tests.
+# `slurm_state` symbols get_mongo_client() and get_config() are used in script `cleanup_jobs`.
+ADD slurm_state slurm_state
+
 CMD ["coverage", "run", "--source=scripts", "--rcfile=scripts_test/.coveragerc", "-m", "pytest", "scripts_test"]