Appending real time stats (#692)

* Appending real time stats

* Validating checkpoint and online analysis intervals

* online analysis interval multiple of checkpoint interval in tests

---------

Co-authored-by: Mike Henry <[email protected]>

openmmtools/multistate/multistatereporter.py

@@ -137,8 +137,9 @@ def __init__(self, storage, open_mode=None,
         self._analysis_particle_indices = tuple(analysis_particle_indices)
         if open_mode is not None:
             self.open(open_mode)
-        # Flag to check whether to overwrite real time statistics file
-        self._overwrite_statistics = True
+        # TODO: Maybe we want to expose this flag to control ovrwriting/appending
+        # Flag to check whether to overwrite real time statistics file -- Defaults to append
+        self._overwrite_statistics = False
 
     @property
     def filepath(self):
@@ -266,6 +267,7 @@ def open(self, mode='r', convention='ReplicaExchange', netcdf_format='NETCDF4'):
         self.close()
 
         # Create directory if we want to write.
+        # TODO: We probably want to check here specifically for w when we want to write
         if mode != 'r':
             for storage_path in self._storage_paths:
                 # normpath() transform '' to '.' for makedirs().

openmmtools/multistate/multistatesampler.py

@@ -590,6 +590,12 @@ def create(self, thermodynamic_states: list, sampler_states, storage,
             raise RuntimeError('Storage file {} already exists; cowardly '
                                'refusing to overwrite.'.format(self._reporter.filepath))
 
+        # Make sure online analysis interval is a multiples of the reporter's checkpoint interval
+        # this avoids having redundant iteration information in the real time yaml files
+        if self.online_analysis_interval % self._reporter.checkpoint_interval != 0:
+            raise ValueError(f"Online analysis interval: {self.online_analysis_interval}, must be a "
+                             f"multiple of the checkpoint interval: {self._reporter.checkpoint_interval}")
+
         # Make sure sampler_states is an iterable of SamplerStates.
         if isinstance(sampler_states, states.SamplerState):
             sampler_states = [sampler_states]

openmmtools/tests/test_mcmc.py

@@ -364,7 +364,7 @@ def test_mcmc_move_context_cache_shallow_copy():
     )
     # Create temporary reporter storage file
     with tempfile.NamedTemporaryFile() as storage:
-        reporter = multistate.MultiStateReporter(storage.name, checkpoint_interval=999999)
+        reporter = multistate.MultiStateReporter(storage.name, checkpoint_interval=200)
     simulation.create(
         thermodynamic_states=thermodynamic_states,
         sampler_states=SamplerState(

openmmtools/tests/test_sampling.py

@@ -141,7 +141,8 @@ def teardown_class(cls):
     def run(self, include_unsampled_states=False):
         # Create and configure simulation object
         move = mmtools.mcmc.MCDisplacementMove(displacement_sigma=1.0*unit.angstroms)
-        simulation = self.SAMPLER(mcmc_moves=move, number_of_iterations=self.N_ITERATIONS)
+        simulation = self.SAMPLER(mcmc_moves=move, number_of_iterations=self.N_ITERATIONS,
+                                  online_analysis_interval=self.N_ITERATIONS)
 
         # Define file for temporary storage.
         with temporary_directory() as tmp_dir:
@@ -587,6 +588,7 @@ class TestBaseMultistateSampler(object):
 
     N_SAMPLERS = 3
     N_STATES = 5
+    # TODO: Once we migrate to pytest SAMPLER and REPORTER should be fixtures!
     SAMPLER = MultiStateSampler
     REPORTER = MultiStateReporter
 
@@ -999,7 +1001,7 @@ def actual_stored_properties_check(self, additional_properties=None):
         thermodynamic_states, sampler_states, unsampled_states = copy.deepcopy(self.alanine_test)
 
         with self.temporary_storage_path() as storage_path:
-            sampler = self.SAMPLER(number_of_iterations=5)
+            sampler = self.SAMPLER(number_of_iterations=5, online_analysis_interval=1)
             reporter = self.REPORTER(storage_path, checkpoint_interval=1)
             self.call_sampler_create(sampler, reporter,
                                      thermodynamic_states, sampler_states,
@@ -1451,7 +1453,8 @@ def test_online_analysis_works(self):
             sampler = self.SAMPLER(mcmc_moves=move, number_of_iterations=n_iterations,
                                    online_analysis_interval=online_interval,
                                    online_analysis_minimum_iterations=3)
-            self.call_sampler_create(sampler, storage_path,
+            reporter = self.REPORTER(storage_path, checkpoint_interval=online_interval)
+            self.call_sampler_create(sampler, reporter,
                                      thermodynamic_states, sampler_states,
                                      unsampled_states)
             # Run
@@ -1510,7 +1513,8 @@ def test_online_analysis_stops(self):
                                    online_analysis_interval=online_interval,
                                    online_analysis_minimum_iterations=0,
                                    online_analysis_target_error=np.inf)  # use infinite error to stop right away
-            self.call_sampler_create(sampler, storage_path,
+            reporter = self.REPORTER(storage_path, checkpoint_interval=online_interval)
+            self.call_sampler_create(sampler, reporter,
                                      thermodynamic_states, sampler_states,
                                      unsampled_states)
             # Run
@@ -1570,7 +1574,8 @@ def test_real_time_analysis_yaml(self):
             move = mmtools.mcmc.IntegratorMove(openmm.VerletIntegrator(1.0 * unit.femtosecond), n_steps=1)
             sampler = self.SAMPLER(mcmc_moves=move, number_of_iterations=n_iterations,
                                    online_analysis_interval=online_interval)
-            self.call_sampler_create(sampler, storage_path,
+            reporter = self.REPORTER(storage_path, checkpoint_interval=online_interval)
+            self.call_sampler_create(sampler, reporter,
                                      thermodynamic_states, sampler_states,
                                      unsampled_states)
             # Run