Do not checkpoint adaptivity and fix output of memory usage (#166)

* Do not checkpoint adaptivity and fix output of memory usage

* Remove checkpointing completely

* Add CHANGELOG entry

Author: IshaanDesai

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ## latest
 
+- Remove checkpointing of adaptivity and fix output of memory usage https://github.com/precice/micro-manager/pull/166
 - Performance improvements: restricting data types, in-place modifications https://github.com/precice/micro-manager/pull/162
 - Handle adaptivity case when deactivation and activation happens in the same time window https://github.com/precice/micro-manager/pull/165
 - Add command line input argument to set log file https://github.com/precice/micro-manager/pull/163

micro_manager/adaptivity/global_adaptivity.py

@@ -234,27 +234,6 @@ def log_metrics(self, n: int) -> None:
                 )
             )
 
-    def write_checkpoint(self) -> None:
-        """
-        Write checkpoint.
-        """
-        self._similarity_dists_cp = np.copy(self._similarity_dists)
-        self._is_sim_active_cp = np.copy(self._is_sim_active)
-        self._sim_is_associated_to_cp = np.copy(self._sim_is_associated_to)
-
-    def read_checkpoint(self) -> None:
-        """
-        Read checkpoint.
-        """
-        self._similarity_dists = np.copy(self._similarity_dists_cp)
-        del self._similarity_dists_cp
-
-        self._is_sim_active = np.copy(self._is_sim_active_cp)
-        del self._is_sim_active_cp
-
-        self._sim_is_associated_to = np.copy(self._sim_is_associated_to_cp)
-        del self._sim_is_associated_to_cp
-
     def _communicate_micro_output(
         self,
         micro_output: list,

micro_manager/adaptivity/local_adaptivity.py

@@ -179,22 +179,6 @@ def log_metrics(self, n: int) -> None:
                 )
             )
 
-    def write_checkpoint(self) -> None:
-        """
-        Write checkpoint.
-        """
-        self._similarity_dists_cp = np.copy(self._similarity_dists)
-        self._is_sim_active_cp = np.copy(self._is_sim_active)
-        self._sim_is_associated_to_cp = np.copy(self._sim_is_associated_to)
-
-    def read_checkpoint(self) -> None:
-        """
-        Read checkpoint.
-        """
-        self._similarity_dists = np.copy(self._similarity_dists_cp)
-        self._is_sim_active = np.copy(self._is_sim_active_cp)
-        self._sim_is_associated_to = np.copy(self._sim_is_associated_to_cp)
-
     def _update_inactive_sims(self, micro_sims: list) -> None:
         """
         Update set of inactive micro simulations. Each inactive micro simulation is compared to all active ones

micro_manager/micro_manager.py

@@ -212,10 +212,6 @@ def solve(self) -> None:
                         self._data_for_adaptivity,
                     )
 
-                    # Only checkpoint the adaptivity configuration if adaptivity is computed
-                    # once in every time window
-                    self._adaptivity_controller.write_checkpoint()
-
                     active_sim_ids = self._adaptivity_controller.get_active_sim_ids()
 
                     for active_id in active_sim_ids:
@@ -272,11 +268,6 @@ def solve(self) -> None:
                 t = t_checkpoint
                 first_iteration = False
 
-                # If adaptivity is computed only once per time window, the states of sims need to be reset too
-                if self._is_adaptivity_on:
-                    if not self._adaptivity_in_every_implicit_step:
-                        self._adaptivity_controller.read_checkpoint()
-
             if (
                 self._participant.is_time_window_complete()
             ):  # Time window has converged, now micro output can be generated
@@ -294,14 +285,15 @@ def solve(self) -> None:
 
                 self._logger.log_info_rank_zero("Time window {} converged.".format(n))
 
-        mem_usage_output_file = (
-            self._output_dir + "mem_usage_" + str(self._rank) + ".csv"
-        )
-        with open(mem_usage_output_file, mode="w", newline="") as file:
-            writer = csv.writer(file)
-            writer.writerow(["Time window", "RSS (MB)"])
-            for i, rss_mb in enumerate(mem_usage):
-                writer.writerow([i, rss_mb])
+        if self._output_memory_usage:
+            mem_usage_output_file = (
+                self._output_dir + "mem_usage_" + str(self._rank) + ".csv"
+            )
+            with open(mem_usage_output_file, mode="w", newline="") as file:
+                writer = csv.writer(file)
+                writer.writerow(["Time window", "RSS (MB)"])
+                for i, rss_mb in enumerate(mem_usage):
+                    writer.writerow([i, rss_mb])
 
         self._participant.finalize()