snakemake-executor-plugin-slurm 1.2.0__tar.gz → 1.2.2__tar.gz

{snakemake_executor_plugin_slurm-1.2.0 → snakemake_executor_plugin_slurm-1.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: snakemake-executor-plugin-slurm
-Version: 1.2.0
+Version: 1.2.2
 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-1.2.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "snakemake-executor-plugin-slurm"
-version = "1.2.0"
+version = "1.2.2"
 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-1.2.2}/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: "
@@ -644,7 +653,7 @@ We leave it to SLURM to resume your job(s)"""
         """
         tests whether the given account is registered, raises an error, if not
         """
-        cmd = "sshare -U --format Account --noheader"
+        cmd = "sshare -U --format Account%256 --noheader"
         try:
             accounts = subprocess.check_output(
                 cmd, shell=True, text=True, stderr=subprocess.PIPE

{snakemake_executor_plugin_slurm-1.2.0 → snakemake_executor_plugin_slurm-1.2.2}/snakemake_executor_plugin_slurm/utils.py

@@ -58,6 +58,9 @@ def set_gres_string(job: JobExecutorInterface) -> str:
     gres_re = re.compile(r"^[a-zA-Z0-9_]+(:[a-zA-Z0-9_]+)?:\d+$")
     # gpu model arguments can be of type "string"
     gpu_model_re = re.compile(r"^[a-zA-Z0-9_]+$")
+    # any arguments should not start and end with ticks or
+    # quotation marks:
+    string_check = re.compile(r"^[^'\"].*[^'\"]$")
     # The Snakemake resources can be only be of type "int",
     # hence no further regex is needed.
 
@@ -81,20 +84,36 @@ def set_gres_string(job: JobExecutorInterface) -> str:
         # Validate GRES format (e.g., "gpu:1", "gpu:tesla:2")
         gres = job.resources.gres
         if not gres_re.match(gres):
-            raise WorkflowError(
-                f"Invalid GRES format: {gres}. Expected format: "
-                "'<name>:<number>' or '<name>:<type>:<number>' "
-                "(e.g., 'gpu:1' or 'gpu:tesla:2')"
-            )
+            if not string_check.match(gres):
+                raise WorkflowError(
+                    "GRES format should not be a nested string (start "
+                    "and end with ticks or quotation marks). "
+                    "Expected format: "
+                    "'<name>:<number>' or '<name>:<type>:<number>' "
+                    "(e.g., 'gpu:1' or 'gpu:tesla:2')"
+                )
+            else:
+                raise WorkflowError(
+                    f"Invalid GRES format: {gres}. Expected format: "
+                    "'<name>:<number>' or '<name>:<type>:<number>' "
+                    "(e.g., 'gpu:1' or 'gpu:tesla:2')"
+                )
         return f" --gres={job.resources.gres}"
 
     if gpu_model and gpu_string:
         # validate GPU model format
         if not gpu_model_re.match(gpu_model):
-            raise WorkflowError(
-                f"Invalid GPU model format: {gpu_model}."
-                " Expected format: '<name>' (e.g., 'tesla')"
-            )
+            if not string_check.match(gpu_model):
+                raise WorkflowError(
+                    "GPU model format should not be a nested string (start "
+                    "and end with ticks or quotation marks). "
+                    "Expected format: '<name>' (e.g., 'tesla')"
+                )
+            else:
+                raise WorkflowError(
+                    f"Invalid GPU model format: {gpu_model}."
+                    " Expected format: '<name>' (e.g., 'tesla')"
+                )
         return f" --gpus={gpu_model}:{gpu_string}"
     elif gpu_model and not gpu_string:
         raise WorkflowError("GPU model is set, but no GPU number is given")