Add command line input argument to set log file (#163)

* Add command line input argument to set log file

* Make command line argument log_file optional

* Add log file option to docs

* Add Changelog entry

Author: IshaanDesai

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ## latest
 
+- Add command line input argument to set log file https://github.com/precice/micro-manager/pull/163
 - Fix adaptivity metrics logging and add logging documentation https://github.com/precice/micro-manager/pull/160
 - Checkpoint lazily created simulation only if a checkpoint is necessary https://github.com/precice/micro-manager/pull/161
 

docs/logging.md

@@ -19,6 +19,14 @@ For example
 
 The information (`INFO` level) message `Time window 1 converged.` from the file `micro_manager/micro_manager.py` is logged by rank `0` at `02:54:02 PM` on `04/17/2025`.
 
+## Parsing log output
+
+By default, the Micro Manager parses the log output to the terminal (`sys.out`). A log file, for example `micro-manager.log`, can be passed as a command line input in the following way
+
+```bash
+micro-manager-precice micro-manager-precice.json micro-manager.log
+```
+
 ## Logging adaptivity metrics
 
 If the Micro Manager is run with adaptivity, rank-wise and global metrics are written to CSV files. By default, the files are created in the working directory. To create the files in a specific folder, provide the folder path via the configuration parameter `output_dir`. More information is in the [configuration section](tooling-micro-manager-configuration.html).

docs/running.md

@@ -17,6 +17,12 @@ The Micro Manager can also be run in parallel
 mpiexec -n micro-manager-precice micro-manager-config.json
 ```
 
+A log file can optionally be passed as a command line argument
+
+```bash
+micro-manager-precice micro-manager-precice.json micro-manager.log
+```
+
 ### What happens when a micro simulation crashes?
 
 If a micro simulation crashes and the Micro Manager is configured to [interpolate a crashed micro simulation](tooling-micro-manager-configuration.html#interpolate-a-crashed-micro-simulation), the Micro Manager attempts to continue running. The error message from the micro simulation, along with the macro location are logged in the Micro Manager log file. The Micro Manager continues the simulation run even if a micro simulation crashes. Results of the crashed micro simulation are generated by interpolating results of a certain number of similar running simulations. The [inverse distance weighed](https://en.wikipedia.org/wiki/Inverse_distance_weighting) method is used. If more than 20% of global micro simulations crash or if locally no neighbors are available for interpolation, the Micro Manager terminates.

micro_manager/__init__.py

@@ -21,17 +21,24 @@ def main():
     parser.add_argument(
         "--snapshot", action="store_true", help="compute offline snapshot database"
     )
+    parser.add_argument(
+        "log_file",
+        type=str,
+        nargs="?",
+        default="",
+        help="Path to the log file. If not provided, logs are printed to stdout.",
+    )
 
     args = parser.parse_args()
     config_file_path = args.config_file
     if not os.path.isabs(config_file_path):
         config_file_path = os.getcwd() + "/" + config_file_path
 
     if not args.snapshot:
-        manager = MicroManagerCoupling(config_file_path)
+        manager = MicroManagerCoupling(config_file_path, log_file=args.log_file)
     else:
         if is_snapshot_possible:
-            manager = MicroManagerSnapshot(config_file_path)
+            manager = MicroManagerSnapshot(config_file_path, log_file=args.log_file)
         else:
             raise ImportError(
                 "The Micro Manager snapshot computation requires the h5py package."

micro_manager/micro_manager.py

@@ -45,7 +45,7 @@
 
 
 class MicroManagerCoupling(MicroManager):
-    def __init__(self, config_file: str) -> None:
+    def __init__(self, config_file: str, log_file: str = "") -> None:
         """
         Constructor.
 
@@ -56,7 +56,7 @@ def __init__(self, config_file: str) -> None:
         """
         super().__init__(config_file)
 
-        self._logger = Logger(__name__, None, self._rank)
+        self._logger = Logger(__name__, log_file, self._rank)
 
         self._config.set_logger(self._logger)
         self._config.read_json_micro_manager()

micro_manager/snapshot/snapshot.py

@@ -26,7 +26,7 @@
 
 
 class MicroManagerSnapshot(MicroManager):
-    def __init__(self, config_file: str) -> None:
+    def __init__(self, config_file: str, log_file: str = "") -> None:
         """
         Constructor.
 
@@ -37,9 +37,7 @@ def __init__(self, config_file: str) -> None:
         """
         super().__init__(config_file)
 
-        self._logger = Logger(
-            "MicroManagerSnapshot", "micro-manager-snapshot.log", self._rank
-        )
+        self._logger = Logger(__name__, log_file, self._rank)
 
         self._config.set_logger(self._logger)
         self._config.read_json_snapshot()

micro_manager/tools/logging_wrapper.py

@@ -12,7 +12,12 @@ class Logger:
     """
 
     def __init__(
-        self, name, log_file=None, rank=0, level=logging.INFO, csv_logger=False
+        self,
+        name: str,
+        log_file: str = "",
+        rank: int = 0,
+        level=logging.INFO,
+        csv_logger: bool = False,
     ):
         """
         Set up a logger.
@@ -33,7 +38,7 @@ def __init__(
 
         self._rank = rank
 
-        if log_file is None:
+        if not log_file:
             handler = logging.StreamHandler(sys.stdout)
         else:
             handler = logging.FileHandler(log_file)