Merge branch 'main' into 1774-introduce-user-settings

CHANGELOG.md

@@ -1,5 +1,16 @@
 **Note**: Numbers like (\#1234) point to closed Pull Requests on the fractal-server repository.
 
+# 2.5.2
+
+* App:
+    * Replace `fractal_ssh` attribute with `fractal_ssh_list`, in `app.state` (\#1790).
+    * Move creation of SSH connections from app startup to endpoints (\#1790).
+* Internal
+    * Introduce `FractalSSHList`, in view of support for multiple SSH/Slurm service users (\#1790).
+    * Make `FractalSSH.close()` more aggressively close `Transport` attribute (\#1790).
+    * Set `look_for_keys=False` for paramiko/fabric connection (\#1790).
+* Testing:
+    * Add fixture to always test that threads do not accumulate during tests (\#1790).
 
 # 2.5.1
 

fractal_server/app/routes/api/v2/submit.py

@@ -231,6 +231,18 @@ async def apply_workflow(
     await db.merge(job)
     await db.commit()
 
+    # User appropriate FractalSSH object
+    if settings.FRACTAL_RUNNER_BACKEND == "slurm_ssh":
+        ssh_credentials = dict(
+            user=settings.FRACTAL_SLURM_SSH_USER,
+            host=settings.FRACTAL_SLURM_SSH_HOST,
+            key_path=settings.FRACTAL_SLURM_SSH_PRIVATE_KEY_PATH,
+        )
+        fractal_ssh_list = request.app.state.fractal_ssh_list
+        fractal_ssh = fractal_ssh_list.get(**ssh_credentials)
+    else:
+        fractal_ssh = None
+
     background_tasks.add_task(
         submit_workflow,
         workflow_id=workflow.id,
@@ -239,7 +251,7 @@ async def apply_workflow(
         worker_init=job.worker_init,
         slurm_user=user_settings.slurm_user,
         user_cache_dir=user_settings.cache_dir,
-        fractal_ssh=request.app.state.fractal_ssh,
+        fractal_ssh=fractal_ssh,
     )
     request.app.state.jobsV2.append(job.id)
     logger.info(

fractal_server/app/routes/api/v2/task_collection.py

@@ -129,11 +129,20 @@ async def collect_tasks_pip(
         db.add(state)
         await db.commit()
 
+        # User appropriate FractalSSH object
+        ssh_credentials = dict(
+            user=settings.FRACTAL_SLURM_SSH_USER,
+            host=settings.FRACTAL_SLURM_SSH_HOST,
+            key_path=settings.FRACTAL_SLURM_SSH_PRIVATE_KEY_PATH,
+        )
+        fractal_ssh_list = request.app.state.fractal_ssh_list
+        fractal_ssh = fractal_ssh_list.get(**ssh_credentials)
+
         background_tasks.add_task(
             background_collect_pip_ssh,
             state.id,
             task_pkg,
-            request.app.state.fractal_ssh,
+            fractal_ssh,
         )
 
         response.status_code = status.HTTP_201_CREATED

fractal_server/app/runner/executors/slurm/ssh/executor.py

@@ -163,17 +163,34 @@ def __init__(
         settings = Inject(get_settings)
         self.python_remote = settings.FRACTAL_SLURM_WORKER_PYTHON
         if self.python_remote is None:
+            self._stop_and_join_wait_thread()
             raise ValueError("FRACTAL_SLURM_WORKER_PYTHON is not set. Exit.")
 
         # Initialize connection and perform handshake
         self.fractal_ssh = fractal_ssh
         logger.warning(self.fractal_ssh)
-        self.handshake()
+        try:
+            self.handshake()
+        except Exception as e:
+            logger.warning(
+                "Stop/join waiting thread and then "
+                f"re-raise original error {str(e)}"
+            )
+            self._stop_and_join_wait_thread()
+            raise e
 
         # Set/validate parameters for SLURM submission scripts
         self.slurm_account = slurm_account
         self.common_script_lines = common_script_lines or []
-        self._validate_common_script_lines()
+        try:
+            self._validate_common_script_lines()
+        except Exception as e:
+            logger.warning(
+                "Stop/join waiting thread and then "
+                f"re-raise original error {str(e)}"
+            )
+            self._stop_and_join_wait_thread()
+            raise e
 
         # Set/initialize some more options
         self.keep_pickle_files = keep_pickle_files
@@ -1385,6 +1402,10 @@ def shutdown(self, wait=True, *, cancel_futures=False):
             self.fractal_ssh.run_command(cmd=scancel_command)
         logger.debug("Executor shutdown: end")
 
+    def _stop_and_join_wait_thread(self):
+        self.wait_thread.stop()
+        self.wait_thread.join()
+
     def __exit__(self, *args, **kwargs):
         """
         See
@@ -1393,8 +1414,7 @@ def __exit__(self, *args, **kwargs):
         logger.debug(
             "[FractalSlurmSSHExecutor.__exit__] Stop and join `wait_thread`"
         )
-        self.wait_thread.stop()
-        self.wait_thread.join()
+        self._stop_and_join_wait_thread()
         logger.debug("[FractalSlurmSSHExecutor.__exit__] End")
 
     def run_squeue(self, job_ids):

fractal_server/app/runner/executors/slurm/sudo/executor.py

@@ -259,6 +259,7 @@ def __init__(
                 for line in self.common_script_lines
                 if line.startswith("#SBATCH --account=")
             )
+            self._stop_and_join_wait_thread()
             raise RuntimeError(
                 "Invalid line in `FractalSlurmExecutor.common_script_lines`: "
                 f"'{invalid_line}'.\n"
@@ -1287,6 +1288,10 @@ def shutdown(self, wait=True, *, cancel_futures=False):
 
         logger.debug("Executor shutdown: end")
 
+    def _stop_and_join_wait_thread(self):
+        self.wait_thread.stop()
+        self.wait_thread.join()
+
     def __exit__(self, *args, **kwargs):
         """
         See
@@ -1295,6 +1300,5 @@ def __exit__(self, *args, **kwargs):
         logger.debug(
             "[FractalSlurmExecutor.__exit__] Stop and join `wait_thread`"
         )
-        self.wait_thread.stop()
-        self.wait_thread.join()
+        self._stop_and_join_wait_thread()
         logger.debug("[FractalSlurmExecutor.__exit__] End")

fractal_server/main.py

@@ -92,32 +92,34 @@ async def lifespan(app: FastAPI):
     settings = Inject(get_settings)
 
     if settings.FRACTAL_RUNNER_BACKEND == "slurm_ssh":
-        from fractal_server.ssh._fabric import get_ssh_connection
-        from fractal_server.ssh._fabric import FractalSSH
 
-        connection = get_ssh_connection()
-        app.state.fractal_ssh = FractalSSH(connection=connection)
+        from fractal_server.ssh._fabric import FractalSSHList
+
+        app.state.fractal_ssh_list = FractalSSHList()
+
         logger.info(
-            f"Created SSH connection "
-            f"({app.state.fractal_ssh.is_connected=})."
+            "Added empty FractalSSHList to app.state "
+            f"(id={id(app.state.fractal_ssh_list)})."
         )
     else:
-        app.state.fractal_ssh = None
+        app.state.fractal_ssh_list = None
 
     config_uvicorn_loggers()
     logger.info("End application startup")
     reset_logger_handlers(logger)
+
     yield
+
     logger = get_logger("fractal_server.lifespan")
     logger.info("Start application shutdown")
 
     if settings.FRACTAL_RUNNER_BACKEND == "slurm_ssh":
         logger.info(
-            f"Closing SSH connection "
-            f"(current: {app.state.fractal_ssh.is_connected=})."
+            "Close FractalSSH connections "
+            f"(current size: {app.state.fractal_ssh_list.size})."
         )
 
-        app.state.fractal_ssh.close()
+        app.state.fractal_ssh_list.close_all()
 
     logger.info(
         f"Current worker with pid {os.getpid()} is shutting down. "