[BBPBGLIB-712] Estimate memory usage for synapse and connection

_benchmarks/synstats.py

@@ -0,0 +1,64 @@
+# Small script to measure memory usage of synapse objects in NEURON.
+# Usage: nrniv (or special) -python synstats.py
+
+from neuron import h
+import os
+
+
+def get_mem_usage():
+    """
+    Return memory usage information in MB.
+    """
+    with open("/proc/self/statm") as fd:
+        _, data_size, _ = fd.read().split(maxsplit=2)
+    usage_mb = float(data_size) * os.sysconf("SC_PAGE_SIZE") / 1024 ** 2
+
+    return usage_mb
+
+
+# Dummy class to pass to synapse objects
+class SynParams:
+    def __getattr__(self, item):
+        return 1
+
+
+n_inst = 1000000
+
+h.load_file("RNGSettings.hoc")
+h.load_file("Map.hoc")
+
+map_hoc = h.Map()
+RNGset = h.RNGSettings()
+RNGset.interpret(map_hoc)
+
+pc = h.ParallelContext()
+
+sec = h.Section()
+sec.push()
+params_obj = SynParams()
+
+h.load_file("AMPANMDAHelper.hoc")
+mem = get_mem_usage()
+AMPA_helper = [h.AMPANMDAHelper(1, params_obj, 0.5, i, 0) for i in range(n_inst)]
+netcon_ampa = [pc.gid_connect(1000, helper.synapse) for helper in AMPA_helper]
+mem2 = get_mem_usage()
+print('Memory usage per object ProbAMPA: %f KB' % ((mem2 - mem) / n_inst * 1024))
+
+h.load_file("GABAABHelper.hoc")
+mem = get_mem_usage()
+GABAAB_helper = [h.GABAABHelper(1, params_obj, 0.5, i, 0) for i in range(n_inst)]
+netcon_gabaab = [pc.gid_connect(1000, helper.synapse) for helper in GABAAB_helper]
+mem2 = get_mem_usage()
+print('Memory usage per object ProbGABAAB: %f KB' % ((mem2 - mem) / n_inst * 1024))
+
+h.load_file("GluSynapseHelper.hoc")
+mem = get_mem_usage()
+GluSynapse_helper = [h.GluSynapseHelper(1, params_obj, 0.5, i, 0, map_hoc) for i in range(n_inst)]
+netcon_glu = [pc.gid_connect(1000, helper.synapse) for helper in GluSynapse_helper]
+mem2 = get_mem_usage()
+print('Memory usage per object GluSynapse: %f KB' % ((mem2 - mem) / n_inst * 1024))
+
+mem = get_mem_usage()
+Gap_helper = [h.Gap(0.5) for i in range(n_inst)]
+mem2 = get_mem_usage()
+print('Memory usage per object Gap: %f KB' % ((mem2 - mem) / n_inst * 1024))

neurodamus/node.py

@@ -33,6 +33,7 @@
 from .utils import compat
 from .utils.logging import log_stage, log_verbose, log_all
 from .utils.memory import trim_memory, pool_shrink, free_event_queues, print_mem_usage
+from .utils.memory import SynapseMemoryUsage
 from .utils.timeit import TimerManager, timeit
 # Internal Plugins
 from . import ngv as _ngv  # NOQA
@@ -629,15 +630,26 @@ def _find_config_file(self, filepath, path_conf_entries=(), alt_filename=None):
     def _collect_display_syn_counts(local_syn_counter):
         xelist = [local_syn_counter] + [None] * (MPI.size - 1)  # send to rank0
         counters = MPI.py_alltoall(xelist)
+        inh = exc = 0
+        syn_mem = SynapseMemoryUsage()
 
         if MPI.rank == 0:
-            log_stage("Synapse counts (per type)")
+            log_stage("Synapse memory estimate (per type)")
             master_counter = Counter()
             for c in counters:
                 master_counter.update(c)
 
-            for synpse_type, count in master_counter.items():
-                logging.info(f" - {synpse_type}: {count}")
+            for synapse_type, count in master_counter.items():
+                logging.debug(f" - {synapse_type}: {count}")
+                if synapse_type < 100:
+                    inh += count
+                if synapse_type >= 100:
+                    exc += count
+            logging.info(" - Estimated synapse memory usage (KB):")
+            in_mem = syn_mem.get_memory_usage(inh, "ProbGABAAB")
+            ex_mem = syn_mem.get_memory_usage(exc, "ProbAMPANMDA")
+            logging.info(f"   - Inhibitory: {in_mem}")
+            logging.info(f"   - Excitatory: {ex_mem}")
 
     # -
     @mpi_no_errors

neurodamus/utils/memory.py

@@ -99,3 +99,27 @@ def get_mem_usage():
     usage_mb = float(data_size) * os.sysconf("SC_PAGE_SIZE") / 1024 ** 2
 
     return usage_mb
+
+
+class SynapseMemoryUsage:
+    ''' A small class that works as a lookup table
+    for the memory used by each type of synapse.
+    The values are in KB. The values cannot be set by the user.
+    '''
+    def __init__(self):
+        self._synapse_memory_usage = {
+            "ProbAMPANMDA": 1.7,
+            "ProbGABAAB": 2.0,
+            "Gap": 2.0,
+            "Glue": 0.5
+        }
+
+    def __getitem__(self, item):
+        return self._synapse_memory_usage[item]
+
+    def __setitem__(self, key, value):
+        raise ValueError("Cannot set values in SynapseMemoryUsage. "
+                         "Values are hardcoded.")
+
+    def get_memory_usage(self, count, synapse_type):
+        return count * self._synapse_memory_usage[synapse_type]