snakemake-executor-plugin-slurm 1.2.0__py3-none-any.whl → 1.2.1__py3-none-any.whl

snakemake_executor_plugin_slurm/__init__.py

@@ -261,6 +261,13 @@ class Executor(RemoteExecutor):
                 "- submitting without. This might or might not work on your cluster."
             )
 
+            # fixes #40 - set ntasks regardless of mpi, because
+            # SLURM v22.05 introduced the requirement for all jobs
+            gpu_job = job.resources.get("gpu") or "gpu" in job.resources.get("gres", "")
+            if gpu_job:
+                call += f" --ntasks-per-gpu={job.resources.get('tasks', 1)}"
+            else:
+                call += f" --ntasks={job.resources.get('tasks', 1)}"
         # MPI job
         if job.resources.get("mpi", False):
             if not job.resources.get("tasks_per_node") and not job.resources.get(
@@ -627,12 +634,14 @@ We leave it to SLURM to resume your job(s)"""
         tries to deduce the acccount from recent jobs,
         returns None, if none is found
         """
-        cmd = f'sacct -nu "{os.environ["USER"]}" -o Account%256 | head -n1'
+        cmd = f'sacct -nu "{os.environ["USER"]}" -o Account%256 | tail -1'
         try:
             sacct_out = subprocess.check_output(
                 cmd, shell=True, text=True, stderr=subprocess.PIPE
             )
-            return sacct_out.replace("(null)", "").strip()
+            possible_account = sacct_out.replace("(null)", "").strip()
+            if possible_account == "none":  # some clusters may not use an account
+                return None
         except subprocess.CalledProcessError as e:
             self.logger.warning(
                 f"No account was given, not able to get a SLURM account via sacct: "

{snakemake_executor_plugin_slurm-1.2.0.dist-info → snakemake_executor_plugin_slurm-1.2.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: snakemake-executor-plugin-slurm
-Version: 1.2.0
+Version: 1.2.1
 Summary: A Snakemake executor plugin for submitting jobs to a SLURM cluster.
 License: MIT
 Keywords: snakemake,plugin,executor,cluster,slurm

snakemake_executor_plugin_slurm-1.2.1.dist-info/RECORD

@@ -0,0 +1,7 @@
+snakemake_executor_plugin_slurm/__init__.py,sha256=QFAmMAvEkBg6BuEtZIFFrh8IY0C0lxZksEd_WwiCyCU,31472
+snakemake_executor_plugin_slurm/submit_string.py,sha256=sXzMm5SVNQ4upIOcsIZjUqj7khnG-lieo5yJSSus5sc,2483
+snakemake_executor_plugin_slurm/utils.py,sha256=ZzXiXFDVLs15PLJnDP0eq98fNCtzlLbhtT03ec8Ou34,3578
+snakemake_executor_plugin_slurm-1.2.1.dist-info/LICENSE,sha256=YVc4xTLWMqGfFL36120k7rzXtsT6e4RkJsh68VVn12s,1076
+snakemake_executor_plugin_slurm-1.2.1.dist-info/METADATA,sha256=3l9RutnMcL44MmGTqKEOzfAkSMD8EJwyvRO3yYiGtPc,1360
+snakemake_executor_plugin_slurm-1.2.1.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
+snakemake_executor_plugin_slurm-1.2.1.dist-info/RECORD,,

snakemake_executor_plugin_slurm-1.2.0.dist-info/RECORD

@@ -1,7 +0,0 @@
-snakemake_executor_plugin_slurm/__init__.py,sha256=EqMKNkKYVFeDfw2pwCnFKYxgKOGJazlDm658wvFvQN0,30942
-snakemake_executor_plugin_slurm/submit_string.py,sha256=sXzMm5SVNQ4upIOcsIZjUqj7khnG-lieo5yJSSus5sc,2483
-snakemake_executor_plugin_slurm/utils.py,sha256=ZzXiXFDVLs15PLJnDP0eq98fNCtzlLbhtT03ec8Ou34,3578
-snakemake_executor_plugin_slurm-1.2.0.dist-info/LICENSE,sha256=YVc4xTLWMqGfFL36120k7rzXtsT6e4RkJsh68VVn12s,1076
-snakemake_executor_plugin_slurm-1.2.0.dist-info/METADATA,sha256=rOpk-4_-aw3w-2X0POSy6rAvFZnPfzArN6MT9CuUxwA,1360
-snakemake_executor_plugin_slurm-1.2.0.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
-snakemake_executor_plugin_slurm-1.2.0.dist-info/RECORD,,