6697 run default command formatting (#6698)

Fixes #6697 


### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Author: wyli

monai/apps/auto3dseg/auto_runner.py

@@ -525,7 +525,7 @@ def set_device_info(
         self.device_setting["MN_START_METHOD"] = mn_start_method
 
         if cmd_prefix is None:
-            cmd_prefix = os.environ.get("CMD_PREFIX")
+            cmd_prefix = os.environ.get("CMD_PREFIX", "")
         self.device_setting["CMD_PREFIX"] = cmd_prefix
 
         if cmd_prefix is not None:

monai/apps/auto3dseg/bundle_gen.py

@@ -251,7 +251,7 @@ def _run_cmd(self, cmd: str, devices_info: str = "") -> subprocess.CompletedProc
                 cmd, nnodes=1, nproc_per_node=self.device_setting["n_devices"], env=ps_environ, check=True
             )
         else:
-            return run_cmd(cmd.split(), env=ps_environ, check=True)
+            return run_cmd(cmd.split(), run_cmd_verbose=True, env=ps_environ, check=True)
 
     def train(
         self, train_params: None | dict = None, device_setting: None | dict = None

monai/apps/auto3dseg/ensemble_builder.py

@@ -453,7 +453,7 @@ def __init__(
             "n_devices": torch.cuda.device_count(),
             "NUM_NODES": int(os.environ.get("NUM_NODES", 1)),
             "MN_START_METHOD": os.environ.get("MN_START_METHOD", "bcprun"),
-            "CMD_PREFIX": os.environ.get("CMD_PREFIX"),  # type: ignore
+            "CMD_PREFIX": os.environ.get("CMD_PREFIX", ""),  # type: ignore
         }
 
     def set_ensemble_method(self, ensemble_method_name: str = "AlgoEnsembleBestByFold", **kwargs: Any) -> None:

monai/auto3dseg/utils.py

@@ -390,14 +390,14 @@ def list_to_python_fire_arg_str(args: list) -> str:
 
 
 def check_and_set_optional_args(params: dict) -> str:
-    """ """
+    """convert `params` into '--key_1=value_1 --key_2=value_2 ...'"""
     cmd_mod_opt = ""
     for k, v in params.items():
         if isinstance(v, dict):
             raise ValueError("Nested dict is not supported.")
         elif isinstance(v, list):
             v = list_to_python_fire_arg_str(v)
-        cmd_mod_opt += f" --{k} {str(v)}"
+        cmd_mod_opt += f" --{k}={v}"
     return cmd_mod_opt
 
 
@@ -422,7 +422,8 @@ def _prepare_cmd_default(cmd: str, cmd_prefix: str | None = None, **kwargs: Any)
     """
     params = kwargs.copy()
 
-    cmd_prefix = cmd_prefix or "python"
+    if not cmd_prefix or "None" in cmd_prefix:  # defaulting to 'python'
+        cmd_prefix = "python"
 
     if not cmd_prefix.endswith(" "):
         cmd_prefix += " "  # ensure a space after the command prefix so that the script can be appended
@@ -498,7 +499,7 @@ def _run_cmd_torchrun(cmd: str, **kwargs: Any) -> subprocess.CompletedProcess:
             raise ValueError(f"Missing required argument {arg} for torchrun.")
         torchrun_list += [f"--{arg}", str(params.pop(arg))]
     torchrun_list += cmd_list
-    return run_cmd(torchrun_list, **params)
+    return run_cmd(torchrun_list, run_cmd_verbose=True, **params)
 
 
 def _run_cmd_bcprun(cmd: str, **kwargs: Any) -> subprocess.CompletedProcess:
@@ -520,4 +521,4 @@ def _run_cmd_bcprun(cmd: str, **kwargs: Any) -> subprocess.CompletedProcess:
             raise ValueError(f"Missing required argument {arg} for bcprun.")
         cmd_list += [f"-{arg}", str(params.pop(arg))]
     cmd_list.extend(["-c", cmd])
-    return run_cmd(cmd_list, **params)
+    return run_cmd(cmd_list, run_cmd_verbose=True, **params)

monai/utils/misc.py

@@ -841,6 +841,10 @@ def run_cmd(cmd_list: list[str], **kwargs: Any) -> subprocess.CompletedProcess:
     debug = MONAIEnvVars.debug()
     kwargs["capture_output"] = kwargs.get("capture_output", debug)
 
+    if kwargs.pop("run_cmd_verbose", False):
+        import monai
+
+        monai.apps.utils.get_logger("run_cmd").info(f"{cmd_list}")
     try:
         return subprocess.run(cmd_list, **kwargs)
     except subprocess.CalledProcessError as e: