Release RAM and use threads instead of proc (#13)

Author: alejoe91

Dockerfile

@@ -31,9 +31,9 @@ RUN git clone https://github.com/SpikeInterface/spikeinterface.git && \
 # Install spikeinterface-gui from source
 RUN git clone https://github.com/alejoe91/spikeinterface-gui.git && \
     cd spikeinterface-gui && \
-    git checkout c165cfe91ea8dcfdc69836184db9827304d357f9 && \
+    git checkout b8d461ce5e5178880a32fd25cb5c87b94dab86e1 && \
     pip install . && cd ..
 
 
 EXPOSE 8000
-ENTRYPOINT ["sh", "-c", "panel serve src/aind_ephys_portal/ephys_gui_app.py src/aind_ephys_portal/ephys_portal_app.py src/aind_ephys_portal/ephys_launcher_app.py src/aind_ephys_portal/ephys_monitor_app.py --setup src/aind_ephys_portal/setup.py --static-dirs images=src/aind_ephys_portal/images --address 0.0.0.0 --port 8000 --allow-websocket-origin ${ALLOW_WEBSOCKET_ORIGIN} --index ephys_portal_app.py --check-unused-sessions 2000 --unused-session-lifetime 5000 --num-procs 4"]
+ENTRYPOINT ["sh", "-c", "panel serve src/aind_ephys_portal/ephys_gui_app.py src/aind_ephys_portal/ephys_portal_app.py src/aind_ephys_portal/ephys_launcher_app.py src/aind_ephys_portal/ephys_monitor_app.py --setup src/aind_ephys_portal/setup.py --static-dirs images=src/aind_ephys_portal/images --address 0.0.0.0 --port 8000 --allow-websocket-origin ${ALLOW_WEBSOCKET_ORIGIN} --index ephys_portal_app.py --check-unused-sessions 2000 --unused-session-lifetime 5000 --num-threads 8"]

launch.sh

@@ -12,4 +12,4 @@ panel serve \
     --static-dirs images=src/aind_ephys_portal/images \
     --check-unused-sessions 2000 \
     --unused-session-lifetime 5000 \
-    --num-procs 4
+    --num-threads 8

src/aind_ephys_portal/ephys_gui_app.py

@@ -35,3 +35,7 @@ class Settings(param.Parameterized):
 ephys_gui = EphysGuiView(analyzer_path=settings.analyzer_path, recording_path=settings.recording_path, fast_mode=settings.fast_mode)
 
 ephys_gui.panel().servable(title="AIND Ephys GUI")
+
+# Don't keep a module-level reference to the heavy GUI object.
+# The servable layout is now owned by Panel/Bokeh's document.
+del ephys_gui

src/aind_ephys_portal/panel/ephys_gui.py

@@ -1,7 +1,9 @@
+import ctypes
 import psutil
 import param
 import time
 import gc
+from copy import deepcopy
 
 import panel as pn
 
@@ -59,6 +61,13 @@
     zone8=["correlogram", "metrics", "mainsettings"],
 )
 
+def _malloc_trim():
+    """Force glibc to return freed memory to the OS (Linux only)."""
+    try:
+        ctypes.CDLL("libc.so.6").malloc_trim(0)
+    except Exception:
+        pass
+
 
 class EphysGuiView(param.Parameterized):
 
@@ -73,6 +82,7 @@ def __init__(self, analyzer_path, recording_path, fast_mode=False, **params):
         self.fast_mode = fast_mode
         self.analyzer = None
         self._cleanup_registered = False
+        self._init_cb = None
 
         self.spinner = pn.indicators.LoadingSpinner(value=True, sizing_mode="stretch_width")
         self.log_output = pn.widgets.TextAreaInput(value="", sizing_mode="stretch_both")
@@ -102,9 +112,15 @@ def _register_cleanup(self):
             return
         doc = pn.state.curdoc
         if doc is not None and hasattr(doc, "on_session_destroyed"):
+            # Use a weak-like reference pattern: store the id and look up via the doc
+            # to avoid the closure preventing GC of self
+            view_ref = [self]  # mutable container we can clear
 
-            def _on_destroy(session_context, view=self):
-                view.cleanup()
+            def _on_destroy(session_context):
+                view = view_ref[0]
+                if view is not None:
+                    view.cleanup()
+                    view_ref[0] = None  # break the reference
 
             doc.on_session_destroyed(_on_destroy)
             self._cleanup_registered = True
@@ -188,7 +204,7 @@ def _set_processed_recording(self):
     def _create_main_window(self):
         if self.analyzer is not None:
             # prepare the curation data using decoder labels
-            curation_dict = default_curation_dict
+            curation_dict = deepcopy(default_curation_dict)
             curation_dict["unit_ids"] = self.analyzer.unit_ids
             if "decoder_label" in self.analyzer.sorting.get_property_keys():
                 decoder_labels = self.analyzer.get_sorting_property("decoder_label")
@@ -235,19 +251,17 @@ def cleanup(self):
 
         # 1) Release GUI controller references
         if self.win is not None:
+            self.win.controller.analyzer = None
+            del self.win.controller.analyzer
+            self.win.controller = None
+            del self.win.controller
+            self.win = None
             del self.win
 
-        # 2) Close zarr store explicitly
+        # 2) Delete the analyzer reference to release memory-mapped files and other resources
         if self.analyzer is not None:
-            # Try to close the underlying zarr store
-            zarr_root = getattr(self.analyzer, "sorting_analyzer", None) or self.analyzer
-            store = getattr(zarr_root, "_root", None)
-            if store is not None:
-                inner_store = getattr(store, "store", None)
-                if inner_store is not None and hasattr(inner_store, "close"):
-                    inner_store.close()
-                    print("Zarr store closed.")
             self.analyzer = None
+            del self.analyzer
             print("Analyzer resources released.")
 
         # 3) Clear layout references
@@ -263,6 +277,9 @@ def cleanup(self):
         gc.collect()
         gc.collect()
 
+        # 5) Force glibc to return freed memory to OS
+        _malloc_trim()
+
 
         final_mem = psutil.virtual_memory()
         current_ram_usage = final_mem.used / (1024**3)