Remove preset environment variables from slurmSettings and mpirunSett…

…ings (#181)

Remove preset environment variables from slurmSettings and mpirunSettings since they are no longer needed.

Some other clean-ups:

- Check env var value types earlier in the process to ensure types are correct before launching any jobs
- Added a note to the `update_env` docs to inform users on how to have smartsim inherit the user environment
- Only throw `--export` flag if env_vars is not empty, otherwise we get an argument parsing error

Verified full testing passes on an HPC system with `SMARTSIM_TEST_LAUNCHER=slurm`.

Resolves #128

[ Commited by @ben-albrecht ]
[ Reviewed by @Spartee && @al-rigazzi ]

smartsim/_core/launcher/step/slurmStep.py

@@ -138,7 +138,9 @@ def get_launch_cmd(self):
                 env_var_str,
                 comma_separated_env_vars,
             ) = self.run_settings.format_comma_sep_env_vars()
-            srun_cmd += ["--export", env_var_str]
+
+            if len(env_var_str) > 0:
+                srun_cmd += ["--export", env_var_str]
 
             if comma_separated_env_vars:
                 srun_cmd = ["env"] + comma_separated_env_vars + srun_cmd
@@ -199,7 +201,8 @@ def _make_mpmd(self):
             cmd += mpmd.format_run_args()
             cmd += ["--job-name", self.name]
             (env_var_str, _) = mpmd.format_comma_sep_env_vars()
-            cmd += ["--export", env_var_str]
+            if len(env_var_str) > 0:
+                cmd += ["--export", env_var_str]
             cmd += mpmd.exe
             cmd += mpmd.exe_args
 

smartsim/settings/base.py

@@ -357,10 +357,23 @@ def run_command(self):
     def update_env(self, env_vars):
         """Update the job environment variables
 
+        To fully inherit the current user environment, add the
+        workload-manager-specific flag to the launch command through the
+        :meth:`add_exe_args` method. For example, ``--export=ALL`` for
+        slurm, or ``-V`` for PBS/aprun.
+
+
         :param env_vars: environment variables to update or add
-        :type env_vars: dict[str, str]
+        :type env_vars: dict[str, Union[str, int, float, bool]]
+        :raises TypeError: if env_vars values cannot be coerced to strings
         """
-        self.env_vars.update(env_vars)
+        val_types = (str, int, float, bool)
+        # Coerce env_vars values to str as a convenience to user
+        for (env, val) in env_vars.items():
+            if type(val) not in val_types:
+                raise TypeError(f"env_vars[{env}] was of type {type(val)}, not {val_types_union}")
+            else:
+                self.env_vars[env] = val
 
     def add_exe_args(self, args):
         """Add executable arguments to executable

smartsim/settings/mpirunSettings.py

@@ -224,16 +224,10 @@ def format_run_args(self):
     def format_env_vars(self):
         """Format the environment variables for mpirun
 
-        Automatically exports ``PYTHONPATH``, ``LD_LIBRARY_PATH``
-        and ``PATH``
-
         :return: list of env vars
         :rtype: list[str]
         """
         formatted = []
-        presets = ["PATH", "LD_LIBRARY_PATH", "PYTHONPATH"]
-        for preset in presets:
-            formatted.extend(["-x", preset])
 
         if self.env_vars:
             for name, value in self.env_vars.items():

smartsim/settings/slurmSettings.py

@@ -291,25 +291,10 @@ def format_comma_sep_env_vars(self):
         :returns: the formatted string of environment variables
         :rtype: tuple[str, list[str]]
         """
-        # TODO make these overridable by user
-        presets = ["PATH", "LD_LIBRARY_PATH", "PYTHONPATH"]
 
         comma_separated_format_str = []
-
-        def add_env_var(var, format_str):
-            try:
-                value = os.environ[var]
-                format_str += "=".join((var, value)) + ","
-                return format_str
-            except KeyError:
-                return format_str
-
         format_str = ""
 
-        # add env var presets due to slurm weirdness
-        for preset in presets:
-            format_str = add_env_var(preset, format_str)
-
         # add user supplied variables
         for k, v in self.env_vars.items():
             if "," in str(v):

tests/test_openmpi_settings.py

@@ -51,12 +51,6 @@ def test_format_env():
     settings.update_env({"OMP_NUM_THREADS": 10})
     formatted = settings.format_env_vars()
     result = [
-        "-x",
-        "PATH",
-        "-x",
-        "LD_LIBRARY_PATH",
-        "-x",
-        "PYTHONPATH",
         "-x",
         "OMP_NUM_THREADS=10",
         "-x",