bug fix: large config

notebooks/25_sensitivity_peak_2.ipynb

@@ -26,7 +26,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -43,7 +43,6 @@
     "from synbio_morpher.utils.misc.units import per_mol_to_per_molecule\n",
     "from synbio_morpher.utils.common.setup import prepare_config, construct_circuit_from_cfg\n",
     "from synbio_morpher.utils.data.data_format_tools.common import load_json_as_dict\n",
-    "from synbio_morpher.utils.circuit.agnostic_circuits.circuit_manager import CircuitModeller\n",
     "from synbio_morpher.srv.io.manage.script_manager import script_preamble\n",
     "from synbio_morpher.utils.circuit.agnostic_circuits.circuit_manager import CircuitModeller\n",
     "from synbio_morpher.utils.misc.type_handling import flatten_listlike\n",

run_main.py

@@ -11,7 +11,7 @@
 # from synbio_morpher.scripts.ensemble_generate_circuits.run_ensemble_generate_circuits import main
 # from synbio_morpher.scripts.gather_interaction_stats.run_gather_interaction_stats import main
 # from synbio_morpher.scripts.mutation_effect_on_interactions_signal.run_mutation_effect_on_interactions_signal import main
-# from synbio_morpher.scripts.summarise_simulation.run_summarise_simulation import main
+from synbio_morpher.scripts.summarise_simulation.run_summarise_simulation import main
 # from synbio_morpher.scripts.analyse_mutated_templates.run_analyse_mutated_templates import main
 # from synbio_morpher.scripts.vis_0_histplots.run_vis_0_histplots import main
 # from synbio_morpher.scripts.vis_0_histplots_nosig.run_vis_0_histplots_nosig import main
@@ -22,7 +22,7 @@
 # from synbio_morpher.scripts.vis_3_mutation_types_positions_2.run_vis_3_mutation_types_positions_2 import main
 # from synbio_morpher.scripts.vis_4_histplots_thresholded.run_vis_4_histplots_thresholded import main
 # from synbio_morpher.scripts.vis_5_means_analytics.run_vis_5_means_analytics import main
-from synbio_morpher.scripts.ensemble_mutation_effect_analysis.run_ensemble_mutation_effect_analysis import main
+# from synbio_morpher.scripts.ensemble_mutation_effect_analysis.run_ensemble_mutation_effect_analysis import main
 # from synbio_morpher.scripts.ensemble_visualisation.run_ensemble_visualisation import main
 # from synbio_morpher.scripts.parameter_based_simulation.run_parameter_based_simulation import main
 # from synbio_morpher.scripts.stitch_parameter_grid.run_stitch_parameter_grid import main

synbio_morpher/scripts/ensemble_mutation_effect_analysis/configs/test_large_scale.json

@@ -62,7 +62,7 @@
                 "min_num_interacting": 0,
                 "min_num_self_interacting": 0,
                 "max_self_interacting": null,
-                "max_total": 10000,
+                "max_total": 20000,
                 "not_in_dirs": []
             },
             "mutations_args": {
@@ -92,7 +92,7 @@
                 "solver": "diffrax",
                 "use_batch_mutations": true,
                 "interaction_factor": 1,
-                "batch_size": 1000,
+                "batch_size": 3000,
                 "max_circuits": 60000,
                 "device": "gpu",
                 "threshold_steady_states": 0.05, 

synbio_morpher/scripts/ensemble_mutation_effect_analysis/configs/test_small.json

@@ -16,7 +16,7 @@
             },
             "molecular_params": "./synbio_morpher/utils/common/configs/RNA_circuit/molecular_params.json",
             "circuit_generation": {
-                "repetitions": 300,
+                "repetitions": 500,
                 "species_count": 3,
                 "sequence_length": 20,
                 "generator_protocol": "random",
@@ -94,7 +94,7 @@
                 "interaction_factor": 1,
                 "batch_size": 800,
                 "max_circuits": 60000,
-                "device": "cpu",
+                "device": "gpu",
                 "threshold_steady_states": 0.05, 
                 "use_initial_to_add_signal": false,
                 "use_rate_scaling": true,

synbio_morpher/scripts/summarise_simulation/configs/base_config.json

@@ -4,7 +4,7 @@
     },
     "source_dirs": {
         "is_source_dir_incomplete": false,
-        "source_dir": ["./data/ensemble_mutation_effect_analysis/2023_07_17_105328/mutation_effect_on_interactions_signal"],
+        "source_dir": ["./data/ensemble_mutation_effect_analysis/2024_11_20_224946/mutation_effect_on_interactions_signal"],
         "purpose_to_get_source_dir_from": null,
         "source_dir_actually_used_POSTERITY": null
     },

synbio_morpher/utils/circuit/agnostic_circuits/circuit_manager.py

@@ -74,8 +74,13 @@ def __init__(self, result_writer=None, config: dict = {}) -> None:
         self.debug_mode = config.get('experiment', {}).get('debug_mode', False)
         self.sim_func = None
 
-        jax.config.update('jax_platform_name', config.get(
-            'simulation', {}).get('device', 'cpu'))
+        try:
+            jax.config.update('jax_platform_name', config.get(
+                'simulation', {}).get('device', 'gpu'))
+        except:
+            jax.config.update('jax_platform_name', 'cpu')
+            logging.warning(
+                'Could not set device to GPU, defaulting to CPU.')
 
         if self.debug_mode:
             jax.config.update("jax_disable_jit", True)
@@ -145,6 +150,7 @@ def write_interactions(self, circuit):
         return circuit
 
     def compute_interactions_batch(self, circuits: List[Circuit], batch=True):
+        """ This will not work with GPU """
         # Make sure multi-threading is on
         if self.simulator_args['name'] == 'IntaRNA':
             if self.simulator_args['simulator_kwargs']['threads'] > 1: