snakemake-executor-plugin-slurm 0.1.4__tar.gz → 0.2.0__tar.gz

{snakemake_executor_plugin_slurm-0.1.4 → snakemake_executor_plugin_slurm-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: snakemake-executor-plugin-slurm
-Version: 0.1.4
+Version: 0.2.0
 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-0.1.4 → snakemake_executor_plugin_slurm-0.2.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "snakemake-executor-plugin-slurm"
-version = "0.1.4"
+version = "0.2.0"
 description = "A Snakemake executor plugin for submitting jobs to a SLURM cluster."
 authors = [
     "Christian Meesters <meesters@uni-mainz.de>",

{snakemake_executor_plugin_slurm-0.1.4 → snakemake_executor_plugin_slurm-0.2.0}/snakemake_executor_plugin_slurm/__init__.py

@@ -68,8 +68,6 @@ class Executor(RemoteExecutor):
         # with job_info being of type
         # snakemake_interface_executor_plugins.executors.base.SubmittedJobInfo.
 
-        jobid = job.jobid
-
         log_folder = f"group_{job.name}" if job.is_group() else f"rule_{job.name}"
 
         slurm_logfile = os.path.abspath(f".snakemake/slurm_logs/{log_folder}/%j.log")
@@ -78,7 +76,10 @@ class Executor(RemoteExecutor):
         # generic part of a submission string:
         # we use a run_uuid as the job-name, to allow `--name`-based
         # filtering in the job status checks (`sacct --name` and `squeue --name`)
-        call = f"sbatch --job-name {self.run_uuid} -o {slurm_logfile} --export=ALL"
+        call = (
+            f"sbatch --job-name {self.run_uuid} --output {slurm_logfile} --export=ALL "
+            f"--comment {job.name}"
+        )
 
         call += self.get_account_arg(job)
         call += self.get_partition_arg(job)
@@ -149,7 +150,7 @@ class Executor(RemoteExecutor):
         slurm_jobid = out.split(" ")[-1]
         slurm_logfile = slurm_logfile.replace("%j", slurm_jobid)
         self.logger.info(
-            f"Job {jobid} has been submitted with SLURM jobid {slurm_jobid} "
+            f"Job {job.jobid} has been submitted with SLURM jobid {slurm_jobid} "
             f"(log: {slurm_logfile})."
         )
         self.report_job_submission(
@@ -209,7 +210,7 @@ class Executor(RemoteExecutor):
                 (status_of_jobs, sacct_query_duration) = await self.job_stati(
                     # -X: only show main job, no substeps
                     f"sacct -X --parsable2 --noheader --format=JobIdRaw,State "
-                    f"--name {self.run_uuid}"
+                    f"--starttime now-2days --endtime now --name {self.run_uuid}"
                 )
                 if status_of_jobs is None and sacct_query_duration is None:
                     self.logger.debug(f"could not check status of job {self.run_uuid}")
@@ -220,6 +221,10 @@ class Executor(RemoteExecutor):
                 active_jobs_ids_with_current_sacct_status = (
                     set(status_of_jobs.keys()) & active_jobs_ids
                 )
+                self.logger.debug(
+                    f"active_jobs_ids_with_current_sacct_status are: "
+                    f"{active_jobs_ids_with_current_sacct_status}"
+                )
                 active_jobs_seen_by_sacct = (
                     active_jobs_seen_by_sacct
                     | active_jobs_ids_with_current_sacct_status
@@ -231,6 +236,7 @@ class Executor(RemoteExecutor):
                     active_jobs_seen_by_sacct
                     - active_jobs_ids_with_current_sacct_status
                 )
+                self.logger.debug(f"missing_sacct_status are: {missing_sacct_status}")
                 if not missing_sacct_status:
                     break
             if i >= status_attempts - 1: