snakemake-executor-plugin-slurm 1.2.0__tar.gz → 1.2.1__tar.gz

{snakemake_executor_plugin_slurm-1.2.0 → snakemake_executor_plugin_slurm-1.2.1}/PKG-INFO

@@ -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-1.2.0 → snakemake_executor_plugin_slurm-1.2.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "snakemake-executor-plugin-slurm"
-version = "1.2.0"
+version = "1.2.1"
 description = "A Snakemake executor plugin for submitting jobs to a SLURM cluster."
 authors = [
     "Christian Meesters <meesters@uni-mainz.de>",

{snakemake_executor_plugin_slurm-1.2.0 → snakemake_executor_plugin_slurm-1.2.1}/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: "