Fix bugs related to the customized lmp task group submission (#161)

1. run customized command with dpgen run_command.
2. fix bug in run_command interface to dflow.utils.run_command: always
non-interactive. [reverted!`interactive` means the bashrc file would be
sourced, otherwise, not.]
3. optional parameters should be of type `Parameter`, `BigParameter`
cannot be indexed.
4. link plumed input file to lammps task dir. Output plumed if they
present.

---------

Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

dpgen2/exploration/task/customized_lmp_template_task_group.py

@@ -11,6 +11,10 @@
     Union,
 )
 
+from dflow.python import (
+    FatalError,
+)
+
 from dpgen2.constants import (
     lmp_conf_name,
     lmp_input_name,
@@ -173,11 +177,17 @@ def _make_customized_task_group(
                     Path(ff).write_text(cc)
                 # run all customized shell commands
                 for ss in self.custom_shell_commands:
-                    # run shell command with os.system
-                    ret = os.system(ss)
+                    # run shell command with dpgen2.utils.run_command
+                    ret, out, err = run_command(ss, shell=True)
                     if ret != 0:
-                        raise RuntimeError(
-                            f"execution of {ss} returns a non-zero value {ret}"
+                        raise FatalError(
+                            f"customized shell command {ss} failed with return code {ret}\n",
+                            "out msg",
+                            out,
+                            "\n",
+                            "err msg",
+                            err,
+                            "\n",
                         )
                 # loop over all pattern matched result dirs
                 for ff in [
@@ -191,7 +201,7 @@ def _make_customized_task_group(
                     # no matched continue
                     if matched_ff is None:
                         logging.info(
-                            "No output dir matches the patter {self.output_dir_pattern} "
+                            f"Dir {ff} does not matches the patter {self.output_dir_pattern} "
                         )
                         continue
                     with set_directory(Path(matched_ff)):

dpgen2/op/collect_data.py

@@ -41,7 +41,7 @@ def get_input_sign(cls):
             {
                 "name": str,
                 "type_map": List[str],
-                "optional_parameter": BigParameter(
+                "optional_parameter": Parameter(
                     dict,
                     default=CollectData.default_optional_parameter,
                 ),

dpgen2/op/run_dp_train.py

@@ -24,6 +24,7 @@
     BigParameter,
     FatalError,
     OPIOSign,
+    Parameter,
     TransientError,
 )
 
@@ -60,7 +61,7 @@ def get_input_sign(cls):
             {
                 "config": dict,
                 "task_name": BigParameter(str),
-                "optional_parameter": BigParameter(
+                "optional_parameter": Parameter(
                     dict,
                     default=RunDPTrain.default_optional_parameter,
                 ),

dpgen2/op/run_lmp.py

@@ -36,6 +36,7 @@
     lmp_traj_name,
     model_name_match_pattern,
     model_name_pattern,
+    plm_output_name,
 )
 from dpgen2.utils import (
     BinaryFileInput,
@@ -117,8 +118,9 @@ def execute(
         task_name = ip["task_name"]
         task_path = ip["task_path"]
         models = ip["models"]
-        input_files = [lmp_conf_name, lmp_input_name]
-        input_files = [(Path(task_path) / ii).resolve() for ii in input_files]
+        # input_files = [lmp_conf_name, lmp_input_name]
+        # input_files = [(Path(task_path) / ii).resolve() for ii in input_files]
+        input_files = [ii.resolve() for ii in Path(task_path).iterdir()]
         model_files = [Path(ii).resolve() for ii in models]
         work_dir = Path(task_name)
 
@@ -150,16 +152,30 @@ def execute(
             ret, out, err = run_command(command, shell=True)
             if ret != 0:
                 raise TransientError(
-                    "lmp failed\n", "out msg", out, "\n", "err msg", err, "\n"
+                    "lmp failed\n",
+                    "command was",
+                    command,
+                    "out msg",
+                    out,
+                    "\n",
+                    "err msg",
+                    err,
+                    "\n",
                 )
 
-        return OPIO(
-            {
-                "log": work_dir / lmp_log_name,
-                "traj": work_dir / lmp_traj_name,
-                "model_devi": work_dir / lmp_model_devi_name,
-            }
+        ret_dict = {
+            "log": work_dir / lmp_log_name,
+            "traj": work_dir / lmp_traj_name,
+            "model_devi": work_dir / lmp_model_devi_name,
+        }
+        plm_output = (
+            {"plm_output": work_dir / plm_output_name}
+            if (work_dir / plm_output_name).is_file()
+            else {}
         )
+        ret_dict.update(plm_output)
+
+        return OPIO(ret_dict)
 
     @staticmethod
     def lmp_args():