Merge pull request #3474 from vkarak/bugfix/unset-sbatch-variables

[bugfix] Unset all `SBATCH_*` environment variables before submitting a job

Author: vkarak

docs/config_reference.rst

@@ -336,6 +336,17 @@ System Partition Configuration
  .. versionadded:: 4.4
  The ``ssh`` scheduler is added.
 
+ .. versionchanged:: 4.8.1
+ All ``SBATCH_*`` variables are unset before submitting a job through the Slurm-based backends.
+ See note below for information.
+
+ .. note::
+ The Slurm-based backends unset all ``SBATCH_*`` environment variables before submitting a job.
+ This is done to avoid environment variables bypassing ReFrame's configuration.
+ For example, if the :attr:`~config.systems.partitions.access` options for a partition used ``-A foo`` and ``SBATCH_ACCOUNT=bar`` was set, then the environment variable would override the configuration, as ReFrame emits those (by default) in the submission script.
+
+ Job submission in ReFrame is controlled exclusively by the system partition's :attr:`~config.systems.partitions.access` options, the test job's :attr:`~reframe.core.schedulers.Job.options` and the :option:`-J` command-line option.
+
  .. note::
 
  The way that multiple node jobs are submitted using the SGE scheduler can be very site-specific.

reframe/core/schedulers/slurm.py

@@ -6,6 +6,7 @@
 import functools
 import glob
 import itertools
+import os
 import re
 import shlex
 import time
@@ -260,17 +261,35 @@ def emit_preamble(self, job):
  # Filter out empty statements before returning
  return list(filter(None, preamble))
 
+ def sbatch(self, args):
+ '''Run sbatch using a clean environment
+
+ We unset all `SBATCH_*` environment variables before submitting;
+ submission should be controlled entirely by ReFrame through the
+ partition's `access` options, the test's `job.options` and the
+ command-line `-J` option
+ '''
+
+ with rt.temp_environment():
+ for var in [name for name in os.environ.keys()
+ if name.startswith('SBATCH_')]:
+ self.log(f'unsetting environment variable {var}',
+ logging.DEBUG)
+ del os.environ[var]
+
+ cmd = ' '.join(['sbatch'] + args)
+ return _run_strict(cmd, timeout=self._submit_timeout)
+
  def submit(self, job):
- cmd_parts = ['sbatch']
+ sbatch_args = []
  if self._sched_access_in_submit:
- cmd_parts += job.sched_access
+ sbatch_args += job.sched_access
 
- cmd_parts += [job.script_filename]
- cmd = ' '.join(cmd_parts)
+ sbatch_args += [job.script_filename]
  intervals = itertools.cycle([1, 2, 3])
  while True:
  try:
- completed = _run_strict(cmd, timeout=self._submit_timeout)
+ completed = self.sbatch(sbatch_args)
  break
  except SpawnedProcessError as e:
  error_match = re.search(

unittests/test_environments.py

@@ -139,6 +139,15 @@ def test_temp_environment(base_environ, user_runtime, modules_system):
  assert not rt.is_env_loaded(environ)
 
 
+def test_temp_environment_as_snapshot(base_environ):
+ with rt.temp_environment():
+ del os.environ['_var0']
+ os.environ['_var1'] = 'foo'
+
+ assert os.environ['_var0'] == 'val0'
+ assert os.environ['_var1'] == 'val1'
+
+
 def test_env_load_already_present(base_environ, user_runtime,
  modules_system, env0):
  modules_system.load_module('testmod_boo')