Add CLI option for registering section-segment mapping info (#27)

* add CLI option for registering report mapping and writing out sim.conf and report.conf
* add reference data for soma report

args.py

@@ -88,3 +88,9 @@
 
 parser.add_argument("-multisplit", action='store_true', default=False,
                    help="intra-rank thread balance. All pieces of cell on same rank.")
+
+parser.add_argument("-registermapping",
+                    dest='register_mapping',
+                    action='store_true',
+                    help="write section-segment mapping to gid_3.dat file, used for BBP reporting",
+                    default=False)

commonutils.py

@@ -1,6 +1,8 @@
 import errno
 import os
 from neuron import h
+from pathlib import Path
+from typing import List
 
 def mkdir_p(path):
     try:
@@ -107,14 +109,6 @@ def setup_nrnbbcore_register_mapping(rings):
     #for recording
     recordlist = []
 
-    #vector for soma sections and segment
-    somasec = h.Vector()
-    somaseg = h.Vector()
-
-    #vector for dendrite sections and segment
-    densec = h.Vector()
-    denseg = h.Vector()
-
     pc = h.ParallelContext()
 
     #all rings in the simulation
@@ -123,11 +117,13 @@ def setup_nrnbbcore_register_mapping(rings):
         #every gid in the ring
         for gid in ring.gids:
 
-            #clear previous vector if any
-            somasec.size(0)
-            somaseg.size(0)
-            densec.size(0)
-            denseg.size(0)
+            #vector for soma sections and segment
+            somasec = h.Vector()
+            somaseg = h.Vector()
+
+            #vector for dendrite sections and segment
+            densec = h.Vector()
+            denseg = h.Vector()
 
             #if gid exist on rank
             if (pc.gid_exists(gid)):
@@ -170,3 +166,52 @@ def setup_nrnbbcore_register_mapping(rings):
                 pc.nrnbbcore_register_mapping(gid, "dend", densec, denseg)
 
     return recordlist
+
+def write_report_config(output_file, report_name, target_name, report_type, report_variable,
+                        unit, report_format, target_type, dt, start_time, end_time, gids,
+                        buffer_size=8):
+    import struct
+    num_gids = len(gids)
+    report_conf = Path(output_file)
+    report_conf.parent.mkdir(parents=True, exist_ok=True)
+    with report_conf.open("wb") as fp:
+        # Write the formatted string to the file
+        fp.write(b"1\n")
+        fp.write(("%s %s %s %s %s %s %d %lf %lf %lf %d %d\n" % (
+            report_name,
+            target_name,
+            report_type,
+            report_variable,
+            unit,
+            report_format,
+            target_type,
+            dt,
+            start_time,
+            end_time,
+            num_gids,
+            buffer_size
+        )).encode())
+        # Write the array of integers to the file in binary format
+        fp.write(struct.pack(f'{num_gids}i', *gids))
+        fp.write(b'\n')
+
+def write_spike_config(output_file: str, spike_filename: str,
+                       population_names: List[str], population_offsets: List[int]):
+    report_conf = Path(output_file)
+    num_population = len(population_names)
+    with report_conf.open("a") as fp:
+        fp.write(f"{num_population}\n")
+        for pop_name, offset in zip(population_names, population_offsets):
+            fp.write(f"{pop_name} {offset}\n")
+        fp.write(f"{spike_filename}\n")
+
+def write_sim_config(output_file, coredata_dir, report_conf, tstop):
+    sim_conf = Path(output_file)
+    sim_conf.parent.mkdir(parents=True, exist_ok=True)
+    os.makedirs(coredata_dir, exist_ok=True)
+    with sim_conf.open("w") as fp:
+        fp.write("outpath=./\n")
+        fp.write(f"datpath=./{coredata_dir}\n")
+        fp.write(f"tstop={tstop}\n")
+        fp.write(f"report-conf='{report_conf}'\n")
+        fp.write("mpi=true\n")

reference_data/README.md

@@ -2,6 +2,8 @@
 
 This repository also contains reference output from running the `ringtest.py`
 script. This can be compared against NEURON and CoreNEURON results in
-integration tests. At present there is just one reference file generated using
-NEURON (`special -python ringtest.py -tstop 100`) with the contemporary
+integration tests.
+
+* spk1.100ms.std.ref : generated using NEURON (`special -python ringtest.py -tstop 100`) with the contemporary
 `master` commit b55c6e1630665a792ced67c6446ed4fb852c7f79.
+* soma.h5 : generated using CORENEURON (`LIBSONATA_ZERO_BASED_GIDS=1 special -mpi -python ringtest.py -tstop 100 -coreneuron -registermapping`)

ringtest.py

@@ -160,6 +160,17 @@ def prun(tstop):
             print("Error: multi-split is not supported with CoreNEURON\n")
             quit()
 
+        if args.register_mapping:
+            setup_nrnbbcore_register_mapping(rings)
+            report_conf_file = "report.conf"
+            sim_conf_file = "sim.conf"
+            if settings.rank == 0:
+                write_report_config(report_conf_file, "soma.h5", "Mosaic", "compartment", "v",
+                                    "mV", "SONATA", 2, 1, 0, tstop, list(range(ncell)))
+                write_spike_config(report_conf_file, "spikes.h5", ["default"], [0])
+                write_sim_config(sim_conf_file, "corenrn_data", report_conf_file, tstop)
+            coreneuron.sim_config=sim_conf_file
+
     ## Record spikes ##
 
     spike_record()