fix: partition cluster selection

snakemake_executor_plugin_slurm/__init__.py

@@ -868,10 +868,35 @@ def get_partition_arg(self, job: JobExecutorInterface):
         else raises an error - implicetly.
         """
         partition = None
+
+        # Check if a specific partition is requested
         if job.resources.get("slurm_partition"):
-            partition = job.resources.slurm_partition
-        elif self._partitions:
+            # But also check if there's a cluster requirement that might override it
+            job_cluster = (
+                job.resources.get("slurm_cluster")
+                or job.resources.get("cluster")
+                or job.resources.get("clusters")
+            )
+
+            if job_cluster and self._partitions:
+                # If a cluster is specified, verify the partition exists and matches
+                # Otherwise, use auto-selection to find a partition for that cluster
+                partition_obj = next(
+                    (p for p in self._partitions if p.name == job.resources.slurm_partition),
+                    None
+                )
+                if partition_obj and partition_obj.partition_cluster and partition_obj.partition_cluster != job_cluster:
+                    # Partition exists but is for a different cluster - use auto-selection
+                    partition = get_best_partition(self._partitions, job, self.logger)
+                else:
+                    partition = job.resources.slurm_partition
+            else:
+                partition = job.resources.slurm_partition
+
+        # If no partition was selected yet, try auto-selection
+        if not partition and self._partitions:
             partition = get_best_partition(self._partitions, job, self.logger)
+
         # we didnt get a partition yet so try fallback.
         if not partition:
             if self._fallback_partition is None:

snakemake_executor_plugin_slurm/partitions.py

@@ -39,12 +39,16 @@ def read_partition_file(partition_file: Path) -> List["Partition"]:
             raise KeyError("Partition name cannot be empty")
 
         # Extract optional cluster name from partition config
-        cluster = partition_config.pop("cluster", None)
+        cluster = None
+        for key in ("slurm_cluster", "cluster", "clusters"):
+            if key in partition_config:
+                cluster = partition_config.pop(key)
+                break
 
         out.append(
             Partition(
                 name=partition_name,
-                cluster=cluster,
+                partition_cluster=cluster,
                 limits=PartitionLimits(**partition_config),
             )
         )
@@ -241,7 +245,7 @@ class Partition:
 
     name: str
     limits: PartitionLimits
-    cluster: Optional[str] = None
+    partition_cluster: Optional[str] = None
 
     def score_job_fit(self, job: JobExecutorInterface) -> Optional[float]:
         """
@@ -269,14 +273,14 @@ def score_job_fit(self, job: JobExecutorInterface) -> Optional[float]:
         # Accept multiple possible resource names for cluster specification
         job_cluster = (
             job.resources.get("slurm_cluster")
-            or job.resources.get("clusters")
             or job.resources.get("cluster")
+            or job.resources.get("clusters")
         )
 
-        if job_cluster is not None:
-            # Job specifies a cluster - partition must match
-            if self.cluster is not None and self.cluster != job_cluster:
-                return None  # Partition is for a different cluster
+        # If either partition or job specifies a cluster, they must match for scoring
+        if self.partition_cluster is not None or job_cluster is not None:
+            if self.partition_cluster != job_cluster:
+                return 0  # Cluster mismatch: score is 0
 
         for resource_key, limit in numerical_resources.items():
             job_requirement = job.resources.get(resource_key, 0)

snakemake_executor_plugin_slurm/submit_string.py

@@ -42,8 +42,15 @@ def get_submit_command(job, params):
     # "- p '{partition_name}'"
     call += f" {params.partition}"
 
-    if job.resources.get("clusters"):
-        call += f" --clusters {safe_quote(job.resources.clusters)}"
+    # Add cluster specification if provided
+    # Check for cluster first (singular), then fall back to clusters (plural) for backwards compatibility
+    cluster_val = (
+        job.resources.get("cluster")
+        or job.resources.get("clusters")
+        or job.resources.get("slurm_cluster")
+    )
+    if cluster_val:
+        call += f" --cluster {safe_quote(cluster_val)}"
 
     if job.resources.get("runtime"):
         call += f" -t {safe_quote(job.resources.runtime)}"

snakemake_executor_plugin_slurm/validation.py

@@ -132,7 +132,7 @@ def validate_executor_settings(settings, logger=None):
     if settings.init_seconds_before_status_checks is not None:
         if (
             not isinstance(settings.init_seconds_before_status_checks, int)
-            or settings.init_seconds_before_status_checks > 0
+            or settings.init_seconds_before_status_checks < 1
         ):
             raise WorkflowError(
                 "init-seconds-before-status-checks must be a positive integer."