Change CLI option name to --coreneuron-direct-mode

neurodamus/commands.py

@@ -58,7 +58,8 @@ def neurodamus(args=None):
         --model-stats           Show model stats in CoreNEURON simulations [default: False]
         --dry-run               Dry-run simulation to estimate memory usage [default: False]
         --num-target-ranks=<number>  Number of ranks to target for dry-run load balancing
-        --skip-write-model      Run CoreNeuron in direct mode, without writing model data to disk
+        --coreneuron-direct-mode     Run CoreNeuron in direct memory mode transfered from Neuron,
+                                     without writing model data to disk.
     """
     options = docopt_sanitize(docopt(neurodamus.__doc__, args))
     config_file = options.pop("ConfigFile")

neurodamus/core/configuration.py

@@ -75,11 +75,8 @@ class CliOptions(ConfigT):
     model_stats = False
     simulator = None
     dry_run = False
-<<<<<<< HEAD
     num_target_ranks = None
-=======
-    skip_write_model = False
->>>>>>> a8a10a6... Cli option
+    coreneuron_direct_mode = False
 
     # Restricted Functionality support, mostly for testing
 
@@ -240,11 +237,8 @@ class _SimConfig(object):
     spike_location = "soma"
     spike_threshold = -30
     dry_run = False
-<<<<<<< HEAD
     num_target_ranks = None
-=======
-    skip_write_model = False
->>>>>>> a8a10a6... Cli option
+    coreneuron_direct_mode = False
 
     _validators = []
     _requisitors = []
@@ -280,11 +274,8 @@ def init(cls, config_file, cli_options):
         cls.modifications = compat.Map(cls._config_parser.parsedModifications or {})
         cls.cli_options = CliOptions(**(cli_options or {}))
         cls.dry_run = cls.cli_options.dry_run
-<<<<<<< HEAD
         cls.num_target_ranks = cls.cli_options.num_target_ranks
-=======
-        cls.skip_write_model = cls.cli_options.skip_write_model
->>>>>>> a8a10a6... Cli option
+        cls.coreneuron_direct_mode = cls.cli_options.coreneuron_direct_mode
         # change simulator by request before validator and init hoc config
         if cls.cli_options.simulator:
             cls._parsed_run["Simulator"] = cls.cli_options.simulator
@@ -1020,15 +1011,13 @@ def _spikes_sort_order(config: _SimConfig, run_conf):
 
 
 @SimConfig.validator
-def _skip_write_coreneuron_model(config: _SimConfig, run_conf):
-    if config.skip_write_model:
+def _coreneuron_direct_mode(config: _SimConfig, run_conf):
+    if config.coreneuron_direct_mode:
         if config.use_coreneuron:
             logging.info("Run CORENEURON without writing model data to disk")
-            # config.use_neuron = True
-            # config.use_coreneuron = False
         else:
-            logging.warning("--skip-write-model not valid for NEURON, continue as usual")
-            config.skip_write_model = False
+            logging.warning("--coreneuron-direct-mode not valid for NEURON, continue with NEURON")
+            config.coreneuron_direct_mode = False
 
 
 def get_debug_cell_gid(cli_options):

neurodamus/core/coreneuron_configuration.py

@@ -3,7 +3,6 @@
 from pathlib import Path
 from ._utils import run_only_rank0
 from . import NeurodamusCore as Nd
-from ..utils.logging import log_verbose
 
 
 class CompartmentMapping:
@@ -207,25 +206,21 @@ def write_spike_filename(self, filename):
             fp.write(filename)
             fp.write("\n")
 
-    def psolve_core(self, save_path=None, restore_path=None, skip_write_model=False):
+    def psolve_core(self, save_path=None, restore_path=None, coreneuron_direct_mode=False):
         from neuron import coreneuron
         from . import NeurodamusCore as Nd
 
         Nd.cvode.cache_efficient(1)
         coreneuron.enable = True
-        if not skip_write_model:
-            coreneuron.file_mode = True
-            coreneuron.sim_config = f"{self.output_root}/{self.sim_config_file}"
-            if save_path:
-                coreneuron.save_path = save_path
-            if restore_path:
-                coreneuron.restore_path = restore_path
-            # Model is already written to disk by calling pc.nrncore_write()
-            coreneuron.skip_write_model_to_disk = True
-            coreneuron.model_path = f"{self.datadir}"
-        else:
-            log_verbose("Run CORENEURON direct mode")
-            coreneuron.sim_config = f"{self.output_root}/{self.sim_config_file}"
+        coreneuron.file_mode = not coreneuron_direct_mode
+        coreneuron.sim_config = f"{self.output_root}/{self.sim_config_file}"
+        if save_path:
+            coreneuron.save_path = save_path
+        if restore_path:
+            coreneuron.restore_path = restore_path
+        # Model is already written to disk by calling pc.nrncore_write()
+        coreneuron.skip_write_model_to_disk = True
+        coreneuron.model_path = f"{self.datadir}"
         Nd.pc.psolve(Nd.tstop)
 
 

neurodamus/node.py

@@ -282,7 +282,7 @@ def __init__(self, config_file, options=None):
             self._run_conf = SimConfig.run_conf
             self._target_manager = TargetManager(self._run_conf)
             self._target_spec = TargetSpec(self._run_conf.get("CircuitTarget"))
-            if SimConfig.use_neuron or SimConfig.skip_write_model:
+            if SimConfig.use_neuron or SimConfig.coreneuron_direct_mode:
                 self._sonatareport_helper = Nd.SonataReportHelper(Nd.dt, True)
             self._base_circuit: CircuitConfig = SimConfig.base_circuit
             self._extra_circuits = SimConfig.extra_circuits
@@ -772,7 +772,7 @@ def _enable_replay(self, source, target, stim_conf, tshift=.0, delay=.0,
 
                 logging.info("=> Population pathway %s -> %s. Source offset: %d",
                              src_pop_str, dst_pop_str, src_pop_offset)
-                if SimConfig.use_coreneuron and not SimConfig.skip_write_model:
+                if SimConfig.use_coreneuron and not SimConfig.coreneuron_direct_mode:
                     self._coreneuron_replay_append(spike_manager, src_pop_offset)
                 else:
                     conn_manager.replay(spike_manager, source, target, delay)
@@ -1092,7 +1092,7 @@ def sim_init(self, corenrn_gen=None, **sim_opts):
         if corenrn_gen:
             self._sim_corenrn_write_config()
 
-        if SimConfig.use_neuron or SimConfig.skip_write_model:
+        if SimConfig.use_neuron or SimConfig.coreneuron_direct_mode:
             self._sim_init_neuron()
 
         if ospath.isfile("debug_gids.txt"):
@@ -1276,11 +1276,11 @@ def _sim_corenrn_write_config(self, corenrn_restore=False):
 
         if not corenrn_restore:
             CompartmentMapping(self._circuits.global_manager).register_mapping()
-            if not SimConfig.skip_write_model:
+            if not SimConfig.coreneuron_direct_mode:
                 with self._coreneuron_ensure_all_ranks_have_gids(CoreConfig.datadir):
                     self._pc.nrnbbcore_write(CoreConfig.datadir)
                     MPI.barrier()  # wait for all ranks to finish corenrn data generation
-            
+
         CoreConfig.write_sim_config(
             Nd.tstop,
             Nd.dt,
@@ -1311,10 +1311,10 @@ def run_all(self):
             self.sonata_spikes()
         if SimConfig.use_coreneuron:
             print_mem_usage()
-            if not SimConfig.skip_write_model:
+            if not SimConfig.coreneuron_direct_mode:
                 self.clear_model(avoid_clearing_queues=False)
             self._run_coreneuron()
-            if SimConfig.skip_write_model:
+            if SimConfig.coreneuron_direct_mode:
                 self.sonata_spikes()
         return timings
 
@@ -1332,7 +1332,7 @@ def _run_coreneuron(self):
         CoreConfig.psolve_core(
             getattr(SimConfig, "save", None),
             getattr(SimConfig, "restore", None),
-            SimConfig.skip_write_model
+            SimConfig.coreneuron_direct_mode
         )
 
     #

tests/integration-e2e/test_coreneuron_directmode.py

@@ -10,7 +10,7 @@ def test_coreneuron_no_write_model(USECASE3):
     nd = Neurodamus(
         str(USECASE3 / "simulation_sonata_coreneuron.json"),
         keep_build=True,
-        skip_write_model=True
+        coreneuron_direct_mode=True
     )
     nd.run()
     coreneuron_data = SimConfig.coreneuron_datadir