snakemake-executor-plugin-slurm 0.3.1__py3-none-any.whl → 0.4.0__py3-none-any.whl

snakemake_executor_plugin_slurm/__init__.py

@@ -67,7 +67,14 @@ class Executor(RemoteExecutor):
 
         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")
+        try:
+            wildcard_str = f"_{'_'.join(job.wildcards)}" if job.wildcards else ""
+        except AttributeError:
+            wildcard_str = ""
+
+        slurm_logfile = os.path.abspath(
+            f".snakemake/slurm_logs/{log_folder}/%j{wildcard_str}.log"
+        )
         os.makedirs(os.path.dirname(slurm_logfile), exist_ok=True)
 
         # generic part of a submission string:
@@ -199,6 +206,7 @@ class Executor(RemoteExecutor):
 
         active_jobs_ids = {job_info.external_jobid for job_info in active_jobs}
         active_jobs_seen_by_sacct = set()
+        missing_sacct_status = set()
 
         # We use this sacct syntax for argument 'starttime' to keep it compatible
         # with slurm < 20.11
@@ -245,53 +253,55 @@ class Executor(RemoteExecutor):
                 self.logger.debug(f"missing_sacct_status are: {missing_sacct_status}")
                 if not missing_sacct_status:
                     break
-            if i >= status_attempts - 1:
-                self.logger.warning(
-                    f"Unable to get the status of all active_jobs that should be "
-                    f"in slurmdbd, even after {status_attempts} attempts.\n"
-                    f"The jobs with the following slurm job ids were previously seen "
-                    "by sacct, but sacct doesn't report them any more:\n"
-                    f"{missing_sacct_status}\n"
-                    f"Please double-check with your slurm cluster administrator, that "
-                    "slurmdbd job accounting is properly set up.\n"
-                )
 
-        any_finished = False
-        for j in active_jobs:
-            # the job probably didn't make it into slurmdbd yet, so
-            # `sacct` doesn't return it
-            if j.external_jobid not in status_of_jobs:
-                # but the job should still be queueing or running and
-                # appear in slurmdbd (and thus `sacct` output) later
-                yield j
-                continue
-            status = status_of_jobs[j.external_jobid]
-            if status == "COMPLETED":
-                self.report_job_success(j)
-                any_finished = True
-                active_jobs_seen_by_sacct.remove(j.external_jobid)
-            elif status == "UNKNOWN":
-                # the job probably does not exist anymore, but 'sacct' did not work
-                # so we assume it is finished
-                self.report_job_success(j)
-                any_finished = True
-                active_jobs_seen_by_sacct.remove(j.external_jobid)
-            elif status in fail_stati:
-                msg = (
-                    f"SLURM-job '{j.external_jobid}' failed, SLURM status is: "
-                    f"'{status}'"
-                )
-                self.report_job_error(j, msg=msg, aux_logs=[j.aux["slurm_logfile"]])
-                active_jobs_seen_by_sacct.remove(j.external_jobid)
-            else:  # still running?
-                yield j
-
-        if not any_finished:
-            self.next_seconds_between_status_checks = min(
-                self.next_seconds_between_status_checks + 10, max_sleep_time
+        if missing_sacct_status:
+            self.logger.warning(
+                f"Unable to get the status of all active jobs that should be "
+                f"in slurmdbd, even after {status_attempts} attempts.\n"
+                f"The jobs with the following slurm job ids were previously seen "
+                "by sacct, but sacct doesn't report them any more:\n"
+                f"{missing_sacct_status}\n"
+                f"Please double-check with your slurm cluster administrator, that "
+                "slurmdbd job accounting is properly set up.\n"
             )
-        else:
-            self.next_seconds_between_status_checks = None
+
+        if status_of_jobs is not None:
+            any_finished = False
+            for j in active_jobs:
+                # the job probably didn't make it into slurmdbd yet, so
+                # `sacct` doesn't return it
+                if j.external_jobid not in status_of_jobs:
+                    # but the job should still be queueing or running and
+                    # appear in slurmdbd (and thus `sacct` output) later
+                    yield j
+                    continue
+                status = status_of_jobs[j.external_jobid]
+                if status == "COMPLETED":
+                    self.report_job_success(j)
+                    any_finished = True
+                    active_jobs_seen_by_sacct.remove(j.external_jobid)
+                elif status == "UNKNOWN":
+                    # the job probably does not exist anymore, but 'sacct' did not work
+                    # so we assume it is finished
+                    self.report_job_success(j)
+                    any_finished = True
+                    active_jobs_seen_by_sacct.remove(j.external_jobid)
+                elif status in fail_stati:
+                    msg = (
+                        f"SLURM-job '{j.external_jobid}' failed, SLURM status is: "
+                        f"'{status}'"
+                    )
+                    self.report_job_error(j, msg=msg, aux_logs=[j.aux["slurm_logfile"]])
+                    active_jobs_seen_by_sacct.remove(j.external_jobid)
+                else:  # still running?
+                    yield j
+
+            if not any_finished:
+                self.next_seconds_between_status_checks = min(
+                    self.next_seconds_between_status_checks + 10, max_sleep_time
+                )
+            else:
+                self.next_seconds_between_status_checks = None
 
     def cancel_jobs(self, active_jobs: List[SubmittedJobInfo]):
         # Cancel all active jobs.

{snakemake_executor_plugin_slurm-0.3.1.dist-info → snakemake_executor_plugin_slurm-0.4.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: snakemake-executor-plugin-slurm
-Version: 0.3.1
+Version: 0.4.0
 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-0.4.0.dist-info/RECORD

@@ -0,0 +1,5 @@
+snakemake_executor_plugin_slurm/__init__.py,sha256=KNJtszoEJIcRiO_2QPFhWSjfMj7CiUoPZeiHF8-Qus8,19939
+snakemake_executor_plugin_slurm-0.4.0.dist-info/LICENSE,sha256=YVc4xTLWMqGfFL36120k7rzXtsT6e4RkJsh68VVn12s,1076
+snakemake_executor_plugin_slurm-0.4.0.dist-info/METADATA,sha256=B3GYo_kbEAZJuPri9F4PYKu94HUREHs2uS4KoFUP6F0,1233
+snakemake_executor_plugin_slurm-0.4.0.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+snakemake_executor_plugin_slurm-0.4.0.dist-info/RECORD,,

{snakemake_executor_plugin_slurm-0.3.1.dist-info → snakemake_executor_plugin_slurm-0.4.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.8.1
+Generator: poetry-core 1.9.0
 Root-Is-Purelib: true
 Tag: py3-none-any

snakemake_executor_plugin_slurm-0.3.1.dist-info/RECORD

@@ -1,5 +0,0 @@
-snakemake_executor_plugin_slurm/__init__.py,sha256=xOWNu2sEs95P-k0VD9HzzlsuLoa-MosARD0amev8y_0,19573
-snakemake_executor_plugin_slurm-0.3.1.dist-info/LICENSE,sha256=YVc4xTLWMqGfFL36120k7rzXtsT6e4RkJsh68VVn12s,1076
-snakemake_executor_plugin_slurm-0.3.1.dist-info/METADATA,sha256=cFmErk1uq995V5M7ePFsFF5dpS1ob69wxxjtitFA1pY,1233
-snakemake_executor_plugin_slurm-0.3.1.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-snakemake_executor_plugin_slurm-0.3.1.dist-info/RECORD,,