snakemake-executor-plugin-slurm 0.15.0__py3-none-any.whl → 1.0.0__py3-none-any.whl

snakemake_executor_plugin_slurm/__init__.py

@@ -26,9 +26,9 @@ from snakemake_interface_executor_plugins.jobs import (
     JobExecutorInterface,
 )
 from snakemake_interface_common.exceptions import WorkflowError
-from snakemake_executor_plugin_slurm_jobstep import get_cpus_per_task
+from snakemake_executor_plugin_slurm_jobstep import get_cpu_setting
 
-from .utils import delete_slurm_environment, delete_empty_dirs
+from .utils import delete_slurm_environment, delete_empty_dirs, set_gres_string
 
 
 @dataclass
@@ -180,7 +180,9 @@ class Executor(RemoteExecutor):
         group_or_rule = f"group_{job.name}" if job.is_group() else f"rule_{job.name}"
 
         try:
-            wildcard_str = "_".join(job.wildcards) if job.wildcards else ""
+            wildcard_str = (
+                "_".join(job.wildcards).replace("/", "_") if job.wildcards else ""
+            )
         except AttributeError:
             wildcard_str = ""
 
@@ -208,7 +210,7 @@ class Executor(RemoteExecutor):
             f"--job-name {self.run_uuid} "
             f"--output '{slurm_logfile}' "
             f"--export=ALL "
-            f"--comment {comment_str}"
+            f"--comment '{comment_str}'"
         )
 
         call += self.get_account_arg(job)
@@ -217,6 +219,8 @@ class Executor(RemoteExecutor):
         if self.workflow.executor_settings.requeue:
             call += " --requeue"
 
+        call += set_gres_string(job)
+
         if job.resources.get("clusters"):
             call += f" --clusters {job.resources.clusters}"
 
@@ -247,7 +251,11 @@ class Executor(RemoteExecutor):
 
         # fixes #40 - set ntasks regardless of mpi, because
         # SLURM v22.05 will require it for all jobs
-        call += f" --ntasks={job.resources.get('tasks', 1)}"
+        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(
@@ -259,8 +267,9 @@ class Executor(RemoteExecutor):
                     "Probably not what you want."
                 )
 
-        call += f" --cpus-per-task={get_cpus_per_task(job)}"
-
+        # we need to set cpus-per-task OR cpus-per-gpu, the function
+        # will return a string with the corresponding value
+        call += f" {get_cpu_setting(job, gpu_job)}"
         if job.resources.get("slurm_extra"):
             self.check_slurm_extra(job)
             call += f" {job.resources.slurm_extra}"

snakemake_executor_plugin_slurm/utils.py

@@ -1,8 +1,14 @@
 # utility functions for the SLURM executor plugin
 
 import os
+import re
 from pathlib import Path
 
+from snakemake_interface_executor_plugins.jobs import (
+    JobExecutorInterface,
+)
+from snakemake_interface_common.exceptions import WorkflowError
+
 
 def delete_slurm_environment():
     """
@@ -40,3 +46,59 @@ def delete_empty_dirs(path: Path) -> None:
     except (OSError, FileNotFoundError) as e:
         # Provide more context in the error message
         raise OSError(f"Failed to remove empty directory {path}: {e}") from e
+
+
+def set_gres_string(job: JobExecutorInterface) -> str:
+    """
+    Function to set the gres string for the SLURM job
+    based on the resources requested in the job.
+    """
+    # generic resources (GRES) arguments can be of type
+    # "string:int" or "string:string:int"
+    gres_re = re.compile(r"^[a-zA-Z0-9_]+(:[a-zA-Z0-9_]+)?:\d+$")
+    # gpu model arguments can be of type "string"
+    gpu_model_re = re.compile(r"^[a-zA-Z0-9_]+$")
+    # The Snakemake resources can be only be of type "int",
+    # hence no further regex is needed.
+
+    gpu_string = None
+    if job.resources.get("gpu"):
+        gpu_string = str(job.resources.get("gpu"))
+
+    gpu_model = None
+    if job.resources.get("gpu_model"):
+        gpu_model = job.resources.get("gpu_model")
+
+    # ensure that gres is not set, if gpu and gpu_model are set
+    if job.resources.get("gres") and gpu_string:
+        raise WorkflowError(
+            "GRES and GPU are set. Please only set one of them.", rule=job.rule
+        )
+    elif not job.resources.get("gres") and not gpu_model and not gpu_string:
+        return ""
+
+    if job.resources.get("gres"):
+        # 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')"
+            )
+        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')"
+            )
+        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")
+    elif gpu_string:
+        # we assume here, that the validator ensures that the 'gpu_string'
+        # is an integer
+        return f" --gpus={gpu_string}"

{snakemake_executor_plugin_slurm-0.15.0.dist-info → snakemake_executor_plugin_slurm-1.0.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: snakemake-executor-plugin-slurm
-Version: 0.15.0
+Version: 1.0.0
 Summary: A Snakemake executor plugin for submitting jobs to a SLURM cluster.
 License: MIT
 Keywords: snakemake,plugin,executor,cluster,slurm
@@ -12,7 +12,7 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Requires-Dist: snakemake-executor-plugin-slurm-jobstep (>=0.2.0,<0.3.0)
+Requires-Dist: snakemake-executor-plugin-slurm-jobstep (>=0.3.0,<0.4.0)
 Requires-Dist: snakemake-interface-common (>=1.13.0,<2.0.0)
 Requires-Dist: snakemake-interface-executor-plugins (>=9.1.1,<10.0.0)
 Requires-Dist: throttler (>=1.2.2,<2.0.0)
@@ -25,3 +25,4 @@ Description-Content-Type: text/markdown
 [![Open in Gitpod](https://gitpod.io/button/open-in-gitpod.svg)](https://gitpod.io/#https://github.com/snakemake/snakemake-executor-plugin-slurm)
 
 For documentation, see the [Snakemake plugin catalog](https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/slurm.html).
+

snakemake_executor_plugin_slurm-1.0.0.dist-info/RECORD

@@ -0,0 +1,6 @@
+snakemake_executor_plugin_slurm/__init__.py,sha256=Bpro_L6Ca3kjnYXbpjpDKWFYE-fgZCW0sW41claGpp4,30090
+snakemake_executor_plugin_slurm/utils.py,sha256=ZzXiXFDVLs15PLJnDP0eq98fNCtzlLbhtT03ec8Ou34,3578
+snakemake_executor_plugin_slurm-1.0.0.dist-info/LICENSE,sha256=YVc4xTLWMqGfFL36120k7rzXtsT6e4RkJsh68VVn12s,1076
+snakemake_executor_plugin_slurm-1.0.0.dist-info/METADATA,sha256=3wsaiJjVQrZXR5rcgtSqCU-HMWesfEqwtECI8COdeq0,1360
+snakemake_executor_plugin_slurm-1.0.0.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
+snakemake_executor_plugin_slurm-1.0.0.dist-info/RECORD,,

{snakemake_executor_plugin_slurm-0.15.0.dist-info → snakemake_executor_plugin_slurm-1.0.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.0.1
+Generator: poetry-core 2.1.1
 Root-Is-Purelib: true
 Tag: py3-none-any

snakemake_executor_plugin_slurm-0.15.0.dist-info/RECORD

@@ -1,6 +0,0 @@
-snakemake_executor_plugin_slurm/__init__.py,sha256=FftjPVxYHcMNFvjq63D5xrlCZHNYBDNOEynfsoD5v1s,29670
-snakemake_executor_plugin_slurm/utils.py,sha256=JOpQaUviGz6SORrMUsVDrSHc0lH6qX_SM0eUjVbWgp0,1282
-snakemake_executor_plugin_slurm-0.15.0.dist-info/LICENSE,sha256=YVc4xTLWMqGfFL36120k7rzXtsT6e4RkJsh68VVn12s,1076
-snakemake_executor_plugin_slurm-0.15.0.dist-info/METADATA,sha256=3swzWD9uoemx6bXSrpEEVEeKkDiBEJm_Q-mTED35UsA,1360
-snakemake_executor_plugin_slurm-0.15.0.dist-info/WHEEL,sha256=IYZQI976HJqqOpQU6PHkJ8fb3tMNBFjg-Cn-pwAbaFM,88
-snakemake_executor_plugin_slurm-0.15.0.dist-info/RECORD,,