snakemake-executor-plugin-slurm 1.5.0__tar.gz → 1.6.0__tar.gz

{snakemake_executor_plugin_slurm-1.5.0 → snakemake_executor_plugin_slurm-1.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: snakemake-executor-plugin-slurm
-Version: 1.5.0
+Version: 1.6.0
 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: numpy (>=1.26.4,<2.0.0)
+Requires-Dist: numpy (>=1.26.4,<3)
 Requires-Dist: pandas (>=2.2.3,<3.0.0)
 Requires-Dist: snakemake-executor-plugin-slurm-jobstep (>=0.3.0,<0.4.0)
 Requires-Dist: snakemake-interface-common (>=1.13.0,<2.0.0)

{snakemake_executor_plugin_slurm-1.5.0 → snakemake_executor_plugin_slurm-1.6.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "snakemake-executor-plugin-slurm"
-version = "1.5.0"
+version = "1.6.0"
 description = "A Snakemake executor plugin for submitting jobs to a SLURM cluster."
 authors = [
     "Christian Meesters <meesters@uni-mainz.de>",
@@ -19,7 +19,7 @@ snakemake-interface-common = "^1.13.0"
 snakemake-interface-executor-plugins = "^9.1.1"
 snakemake-executor-plugin-slurm-jobstep = "^0.3.0"
 pandas = "^2.2.3"
-numpy = "^1.26.4"
+numpy = ">=1.26.4, <3"
 throttler = "^1.2.2"
 
 [tool.poetry.group.dev.dependencies]

{snakemake_executor_plugin_slurm-1.5.0 → snakemake_executor_plugin_slurm-1.6.0}/snakemake_executor_plugin_slurm/__init__.py

@@ -366,9 +366,15 @@ class Executor(RemoteExecutor):
                     process.returncode, call, output=err
                 )
         except subprocess.CalledProcessError as e:
-            raise WorkflowError(
-                f"SLURM sbatch failed. The error message was {e.output}"
+            self.report_job_error(
+                SubmittedJobInfo(job),
+                msg=(
+                    "SLURM sbatch failed. "
+                    f"The error message was '{e.output.strip()}'.\n"
+                    f"    sbatch call:\n        {call}\n"
+                ),
             )
+            return
         # any other error message indicating failure?
         if "submission failed" in err:
             raise WorkflowError(
@@ -445,7 +451,7 @@ class Executor(RemoteExecutor):
 
         # We use this sacct syntax for argument 'starttime' to keep it compatible
         # with slurm < 20.11
-        sacct_starttime = f"{datetime.now() - timedelta(days = 2):%Y-%m-%dT%H:00}"
+        sacct_starttime = f"{datetime.now() - timedelta(days=2):%Y-%m-%dT%H:00}"
         # previously we had
         # f"--starttime now-2days --endtime now --name {self.run_uuid}"
         # in line 218 - once v20.11 is definitively not in use any more,

{snakemake_executor_plugin_slurm-1.5.0 → snakemake_executor_plugin_slurm-1.6.0}/snakemake_executor_plugin_slurm/submit_string.py

@@ -50,12 +50,19 @@ def get_submit_command(job, params):
     if job.resources.get("nodes", False):
         call += f" --nodes={job.resources.get('nodes', 1)}"
 
-    # fixes #40 - set ntasks regardless of mpi, because
-    # SLURM v22.05 will require it 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)}"
+        # fixes #316 - allow unsetting of tasks per gpu
+        # apparently, python's internal process manangement interfers with SLURM
+        # e.g. for pytorch
+        ntasks_per_gpu = job.resources.get(
+            "tasks_per_gpu", job.resources.get("tasks", 1)
+        )
+        if ntasks_per_gpu >= 1:
+            call += f" --ntasks-per-gpu={ntasks_per_gpu}"
     else:
+        # 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)}"
 
     # we need to set cpus-per-task OR cpus-per-gpu, the function