fix: cgroup confinement (#23)

fix #41

---------

Co-authored-by: meesters <meesters@uni-mainz.de>
Co-authored-by: Christian Meesters <cmeesters@users.noreply.github.com>

Author: johanneskoester

snakemake_executor_plugin_slurm_jobstep/__init__.py

@@ -13,6 +13,7 @@
     JobExecutorInterface,
 )
 from snakemake_interface_executor_plugins.settings import ExecMode, CommonSettings
+from snakemake_interface_common.exceptions import WorkflowError
 
 
 # Required:
@@ -111,7 +112,15 @@ def run_job(self, job: JobExecutorInterface):
             # The -n1 is important to avoid that srun executes the given command
             # multiple times, depending on the relation between
             # cpus per task and the number of CPU cores.
-            call = f"srun -n1 --cpu-bind=q {self.format_job_exec(job)}"
+
+            # as of v22.11.0, the --cpu-per-task flag is needed to ensure that
+            # the job can utilize the c-group's resources.
+            # We set the limitation accordingly, assuming the submit executor
+            # has set the resources correctly.
+
+            call = "srun -n1 --cpu-bind=q "
+            call += f"--cpus-per-task {get_cpus_per_task(job)} "
+            call += f"{self.format_job_exec(job)}"
 
         self.logger.debug(f"This job is a group job: {job.is_group()}")
         self.logger.debug(f"The call for this job is: {call}")
@@ -144,3 +153,16 @@ def cores(self):
 
     def get_exec_mode(self) -> ExecMode:
         return ExecMode.REMOTE
+
+
+def get_cpus_per_task(job: JobExecutorInterface):
+    cpus_per_task = job.threads
+    if job.resources.get("cpus_per_task"):
+        if not isinstance(cpus_per_task, int):
+            raise WorkflowError(
+                f"cpus_per_task must be an integer, but is {cpus_per_task}"
+            )
+        cpus_per_task = job.resources.cpus_per_task
+    # ensure that at least 1 cpu is requested
+    # because 0 is not allowed by slurm
+    return max(1, cpus_per_task)

tests/test_github_issue41/Snakefile

@@ -0,0 +1,10 @@
+rule all:
+     input: "1.out"
+
+rule test1:
+     output: "1.out"
+     #threads: 2
+     resources:
+        cpus_per_task=1
+     shell: "touch $SLURM_CPUS_PER_TASK.out"
+

tests/test_github_issue41/expected_results/1.out

@@ -12,3 +12,7 @@ def get_executor(self) -> str:
     def get_executor_settings(self) -> Optional[ExecutorSettingsBase]:
         # instatiate ExecutorSettings of this plugin as appropriate
         return None
+
+
+# def test_issue_41():
+#    run(dpath("test_github_issue41"))