feat: allow to disable the memory array fudge

docs/further.md

@@ -356,6 +356,22 @@ When submitting array jobs, the `--slurm-array-limit` flag defines the
 maximum number of array tasks to be submitted in one job submission.
 If the number of tasks exceeds this limit, multiple array job submissions will be performed. This is useful to avoid hitting cluster limits on the maximum number of array tasks per job. Please obey your cluster limits and set this flag accordingly.
 
+##### Array memory adjustment
+
+By default, the plugin increases an explicit memory request for an array job to
+account for the encoded array-job payload. If a job has no memory constraint,
+the plugin adds a minimal `--mem` request so that this adjustment is not lost.
+
+Some clusters derive memory allocation from other requested resources and do
+not allow an explicit memory option. Disable the adjustment on such clusters:
+
+```console
+snakemake --slurm-disable-memory-fudge ...
+```
+
+The default is `false`, preserving the standard array submission behavior. In a
+Snakemake profile, use `slurm-disable-memory-fudge: true` instead.
+
 
 #### MPI-specific Resources
 

snakemake_executor_plugin_slurm/__init__.py

@@ -194,6 +194,18 @@ class ExecutorSettings(ExecutorSettingsBase):
         },
     )
 
+    disable_memory_fudge: bool = field(
+        default=False,
+        metadata={
+            "help": "Increase an explicit SLURM memory request for array jobs "
+            "to account for the encoded job payload. When no memory resource is "
+            "set, the executor adds a minimal --mem request. Disable this on "
+            "clusters whose memory allocation is derived from other resources.",
+            "env_var": False,
+            "required": False,
+        },
+    )
+
     logdir: Optional[Path] = field(
         default=None,
         metadata={
@@ -911,7 +923,8 @@ def run_array_jobs(self, jobs: List[JobExecutorInterface]):
                 # add memory fudge factor to the base call,
                 # to account for the extra memory needed by the
                 # jobstep process to hold and parse the array execs payload.
-                call = apply_mem_fudge(call, array_execs_payload)
+                if not self.workflow.executor_settings.disable_memory_fudge:
+                    call = apply_mem_fudge(call, array_execs_payload)
 
                 use_script_submission = (
                     self.workflow.executor_settings.pass_command_as_script

tests/test_array_jobs.py

@@ -100,6 +100,7 @@ def _make_executor_stub(array_jobs=None, array_limit=100):
             array_limit=array_limit,
             status_attempts=1,
             init_seconds_before_status_checks=40,
+            disable_memory_fudge=False,
             keep_successful_logs=False,
             requeue=False,
             no_requeue=False,
@@ -131,6 +132,11 @@ def test_array_limit_default_is_1000(self):
         settings = ExecutorSettings()
         assert settings.array_limit == 1000
 
+    def test_disable_memory_fudge_defaults_to_false(self):
+        """Existing array memory behavior remains enabled by default."""
+        settings = ExecutorSettings()
+        assert settings.disable_memory_fudge is False
+
     def test_array_jobs_none_yields_empty_set_on_executor(self):
         """Executor with array_jobs=None initialises self.array_jobs as empty set."""
         executor = _make_executor_stub(array_jobs=None)
@@ -396,6 +402,28 @@ def test_array_execs_task_1_absent_tasks_2_plus_present(
         assert "2" in array_execs
         assert "3" in array_execs
 
+    def test_memory_fudge_can_be_disabled(self, tmp_path, mock_popen_success):
+        executor = self._build_executor(tmp_path)
+        executor.workflow.executor_settings.disable_memory_fudge = True
+        jobs = self._make_jobs(n=2)
+
+        executor.run_array_jobs(jobs)
+
+        popen_call_str = mock_popen_success.call_args_list[0][0][0]
+        assert "--mem " not in popen_call_str
+        assert "--mem-per-cpu " not in popen_call_str
+
+    def test_memory_fudge_remains_enabled_by_default(
+        self, tmp_path, mock_popen_success
+    ):
+        executor = self._build_executor(tmp_path)
+        jobs = self._make_jobs(n=2)
+
+        executor.run_array_jobs(jobs)
+
+        popen_call_str = mock_popen_success.call_args_list[0][0][0]
+        assert "--mem 1" in popen_call_str
+
     def test_array_execs_omits_first_task_of_each_chunk(self, tmp_path):
         """For each chunk, first task uses base exec command and is absent from map."""
         executor = self._build_executor(tmp_path, array_limit=3)

tests/test_cli.py

@@ -6,13 +6,31 @@
 executor functionality.
 """
 
+from argparse import ArgumentParser
 from unittest.mock import MagicMock, patch
 import uuid
 
 import pytest
 
 from snakemake_executor_plugin_slurm import Executor, ExecutorSettings
 from snakemake_interface_common.exceptions import WorkflowError
+from snakemake_interface_common.plugin_registry.plugin import PluginBase
+
+
+class _SlurmSettingsPlugin(PluginBase[ExecutorSettings]):
+    """Minimal plugin wrapper for exercising the settings resolution path."""
+
+    @property
+    def name(self) -> str:
+        return "slurm"
+
+    @property
+    def cli_prefix(self) -> str:
+        return "slurm"
+
+    @property
+    def settings_cls(self):
+        return ExecutorSettings
 
 
 def _make_executor(jobname_prefix: str):
@@ -50,6 +68,18 @@ def test_jobname_prefix_validation():
         executor.__post_init__(test_mode=True)
 
 
+def test_disable_memory_fudge_flag_resolves_from_cli():
+    """CLI flag is a no-argument switch that sets disable_memory_fudge=True."""
+    plugin = _SlurmSettingsPlugin()
+    parser = ArgumentParser()
+    plugin.register_cli_args(parser, "executor")
+
+    args = parser.parse_args(["--slurm-disable-memory-fudge"])
+    settings = plugin.get_settings(args)
+
+    assert settings.disable_memory_fudge is True
+
+
 def test_requeue_options_are_mutually_exclusive():
     with pytest.raises(WorkflowError, match="mutually exclusive"):
         ExecutorSettings(requeue=True, no_requeue=True)