snakemake-executor-plugin-slurm 0.6.0__tar.gz → 0.8.0__tar.gz

{snakemake_executor_plugin_slurm-0.6.0 → snakemake_executor_plugin_slurm-0.8.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: snakemake-executor-plugin-slurm
-Version: 0.6.0
+Version: 0.8.0
 Summary: A Snakemake executor plugin for submitting jobs to a SLURM cluster.
 Home-page: https://github.com/snakemake/snakemake-executor-plugin-slurm
 License: MIT

{snakemake_executor_plugin_slurm-0.6.0 → snakemake_executor_plugin_slurm-0.8.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "snakemake-executor-plugin-slurm"
-version = "0.6.0"
+version = "0.8.0"
 description = "A Snakemake executor plugin for submitting jobs to a SLURM cluster."
 authors = [
     "Christian Meesters <meesters@uni-mainz.de>",

{snakemake_executor_plugin_slurm-0.6.0 → snakemake_executor_plugin_slurm-0.8.0}/snakemake_executor_plugin_slurm/__init__.py

@@ -9,12 +9,16 @@ import os
 import re
 import subprocess
 import time
+from dataclasses import dataclass, field
 from datetime import datetime, timedelta
-from typing import List, Generator
+from typing import List, Generator, Optional
 import uuid
 from snakemake_interface_executor_plugins.executors.base import SubmittedJobInfo
 from snakemake_interface_executor_plugins.executors.remote import RemoteExecutor
-from snakemake_interface_executor_plugins.settings import CommonSettings
+from snakemake_interface_executor_plugins.settings import (
+    ExecutorSettingsBase,
+    CommonSettings,
+)
 from snakemake_interface_executor_plugins.jobs import (
     JobExecutorInterface,
 )
@@ -22,6 +26,21 @@ from snakemake_interface_common.exceptions import WorkflowError
 from snakemake_executor_plugin_slurm_jobstep import get_cpus_per_task
 
 
+@dataclass
+class ExecutorSettings(ExecutorSettingsBase):
+    init_seconds_before_status_checks: Optional[int] = field(
+        default=40,
+        metadata={
+            "help": """
+                    Defines the time in seconds before the first status
+                    check is performed after job submission.
+                    """,
+            "env_var": False,
+            "required": False,
+        },
+    )
+
+
 # Required:
 # Specify common settings shared by various executors.
 common_settings = CommonSettings(
@@ -50,10 +69,25 @@ common_settings = CommonSettings(
 # Implementation of your executor
 class Executor(RemoteExecutor):
     def __post_init__(self):
+        # run check whether we are running in a SLURM job context
+        self.warn_on_jobcontext()
         self.run_uuid = str(uuid.uuid4())
         self.logger.info(f"SLURM run ID: {self.run_uuid}")
         self._fallback_account_arg = None
         self._fallback_partition = None
+        # providing a short-hand, even if subsequent calls seem redundant
+        self.settings: ExecutorSettings = self.workflow.executor_settings
+
+    def warn_on_jobcontext(self, done=None):
+        if not done:
+            if "SLURM_JOB_ID" in os.environ:
+                self.logger.warning(
+                    "You are running snakemake in a SLURM job context. "
+                    "This is not recommended, as it may lead to unexpected behavior."
+                    "Please run Snakemake directly on the login node."
+                )
+                time.sleep(5)
+        done = True
 
     def additional_general_args(self):
         return "--executor slurm-jobstep --jobs 1"
@@ -127,7 +161,7 @@ class Executor(RemoteExecutor):
         if job.resources.get("nodes", False):
             call += f" --nodes={job.resources.get('nodes', 1)}"
 
-        # fixes #40 - set ntasks regarlless of mpi, because
+        # fixes #40 - set ntasks regardless of mpi, because
         # SLURM v22.05 will require it for all jobs
         call += f" --ntasks={job.resources.get('tasks', 1)}"
         # MPI job
@@ -182,7 +216,6 @@ class Executor(RemoteExecutor):
         self, active_jobs: List[SubmittedJobInfo]
     ) -> Generator[SubmittedJobInfo, None, None]:
         # Check the status of active jobs.
-
         # You have to iterate over the given list active_jobs.
         # For jobs that have finished successfully, you have to call
         # self.report_job_success(job).
@@ -393,6 +426,7 @@ class Executor(RemoteExecutor):
                 account = self.get_account()
                 if account:
                     self.logger.warning(f"Guessed SLURM account: {account}")
+                    self.test_account(f"{account}")
                     self._fallback_account_arg = f" -A {account}"
                 else:
                     self.logger.warning(
@@ -430,7 +464,7 @@ class Executor(RemoteExecutor):
             sacct_out = subprocess.check_output(
                 cmd, shell=True, text=True, stderr=subprocess.PIPE
             )
-            return sacct_out.strip()
+            return sacct_out.replace("(null)", "").strip()
         except subprocess.CalledProcessError as e:
             self.logger.warning(
                 f"No account was given, not able to get a SLURM account via sacct: "
@@ -495,10 +529,10 @@ class Executor(RemoteExecutor):
         jobname = re.compile(r"--job-name[=?|\s+]|-J\s?")
         if re.search(jobname, job.resources.slurm_extra):
             raise WorkflowError(
-                "The '--job-name' option is not allowed in the 'slurm_extra' "
+                "The --job-name option is not allowed in the 'slurm_extra' "
                 "parameter. The job name is set by snakemake and must not be "
-                "overwritten. It is internally used to check the stati of all "
-                "submitted jobs by this workflow."
+                "overwritten. It is internally used to check the stati of the "
+                "all submitted jobs by this workflow."
                 "Please consult the documentation if you are unsure how to "
                 "query the status of your jobs."
             )