Clean up environment before each test

conftest.py

@@ -411,6 +411,13 @@ def db_cluster(fileutils, wlmutils, request):
     exp.stop(db)
 
 
+@pytest.fixture(scope="function", autouse=True)
+def environment_cleanup():
+    os.environ.pop("SSDB", "")
+    os.environ.pop("SSKEYIN", "")
+    os.environ.pop("SSKEYOUT", "")
+
+
 @pytest.fixture
 def dbutils():
     return DBUtils

smartsim/settings/slurmSettings.py

@@ -25,11 +25,16 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 import datetime
+import os
 from typing import List, Tuple
 
 from ..error import SSUnsupportedError
 from .base import BatchSettings, RunSettings
 
+from ..log import get_logger
+
+logger = get_logger(__name__)
+
 
 class SrunSettings(RunSettings):
     def __init__(
@@ -277,14 +282,32 @@ def format_run_args(self):
                     opts += ["=".join((prefix + opt, str(value)))]
         return opts
 
+    def check_env_vars(self):
+        """Warn a user trying to set a variable which is set in the environment
+
+        Given Slurm's env var precedence, trying to export a variable which is already
+        present in the environment will not work.
+        """
+        for k,v in self.env_vars.items():
+            if "," not in str(v):
+                # If a variable is defined, it will take precedence over --export
+                # we warn the user
+                preexisting_var = os.environ.get(k, None)
+                if preexisting_var:
+                    msg = f"Variable {k} is set to {preexisting_var} in current environment. "
+                    msg += f"If the job is running in an interactive allocation, the value {v} will not be set. "
+                    msg += "Please consider removing the variable from the environment and re-run the experiment."
+                    logger.warning(msg)
+
     def format_env_vars(self):
         """Build bash compatible environment variable string for Slurm
 
         :returns: the formatted string of environment variables
         :rtype: list[str]
         """
+        self.check_env_vars()
         return [f"{k}={v}" for k, v in self.env_vars.items() if "," not in str(v)]
-
+    
     def format_comma_sep_env_vars(self) -> Tuple[str, List[str]]:
         """Build environment variable string for Slurm
 
@@ -295,7 +318,7 @@ def format_comma_sep_env_vars(self) -> Tuple[str, List[str]]:
         :returns: the formatted string of environment variables
         :rtype: tuple[str, list[str]]
         """
-
+        self.check_env_vars()
         exportable_env, compound_env, key_only = [], [], []
 
         for k, v in self.env_vars.items():

tests/test_slurm_settings.py

@@ -24,6 +24,8 @@
 # OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
+import logging
+import os
 import pytest
 
 from smartsim.error import SSUnsupportedError
@@ -245,6 +247,40 @@ def test_format_env_vars():
     assert all("SSKEYIN" not in x for x in formatted)
 
 
+def test_catch_existing_env_var(caplog):
+    rs = SrunSettings(
+        "python",
+        env_vars={
+            "SMARTSIM_TEST_VAR": "B",
+        },
+    )
+    os.environ["SMARTSIM_TEST_VAR"] = "A"
+    os.environ["SMARTSIM_TEST_CSVAR"] = "A,B"
+    caplog.clear()
+    rs.format_env_vars()
+
+    msg = f"Variable SMARTSIM_TEST_VAR is set to A in current environment. "
+    msg += f"If the job is running in an interactive allocation, the value B will not be set. "
+    msg += "Please consider removing the variable from the environment and re-running the experiment."
+
+    for record in caplog.records:
+        assert record.levelname == "WARNING"
+        assert record.message == msg
+
+    caplog.clear()
+
+    env_vars = {"SMARTSIM_TEST_VAR": "B", "SMARTSIM_TEST_CSVAR": "C,D"}
+    settings = SrunSettings("python", env_vars=env_vars)
+    settings.format_comma_sep_env_vars()
+
+    for record in caplog.records:
+        assert record.levelname == "WARNING"
+        assert record.message == msg
+
+    os.environ.pop("SMARTSIM_TEST_VAR", None)
+    os.environ.pop("SMARTSIM_TEST_CSVAR", None)
+
+
 def test_format_comma_sep_env_vars():
     env_vars = {"OMP_NUM_THREADS": 20, "LOGGING": "verbose", "SSKEYIN": "name_0,name_1"}
     settings = SrunSettings("python", env_vars=env_vars)