From d15afd3925bfe01eddeddc523724bc29332b4547 Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Tue, 21 Jun 2022 14:48:40 +0200
Subject: [PATCH] Add some convenience to simulation creation. (#1904)
Encapsulates 80% of cases:
```cxx
rec = recipe()
ctx = make_context()
dec = partition_load_balance(rec, ctx)
sim = simulation(rec, dec, ctx)
```
is now written as
```cxx
rec = recipe()
sim = simulation(rec)
```
In python we use keyword args to allow
both to be specified separatly.
Partially fixes #1862
---
arbor/include/arbor/load_balance.hpp | 2 +-
arbor/include/arbor/simulation.hpp | 9 ++++++++-
arbor/partition_load_balance.cpp | 2 +-
arbor/simulation.cpp | 4 ++--
doc/concepts/simulation.rst | 12 ++++++++----
example/bench/bench.cpp | 2 +-
example/brunel/brunel.cpp | 5 +++--
example/drybench/drybench.cpp | 4 +---
example/dryrun/dryrun.cpp | 4 +---
example/gap_junctions/gap_junctions.cpp | 2 +-
example/generators/generators.cpp | 5 +----
example/lfp/lfp.cpp | 18 +++++++-----------
example/probe-demo/probe-demo.cpp | 3 +--
example/ring/ring.cpp | 6 +++---
example/single/single.cpp | 3 +--
python/context.cpp | 2 +-
python/example/brunel.py | 2 +-
python/example/dynamic-catalogue.py | 4 +---
python/example/gap_junctions.py | 6 ++----
python/example/network_ring.py | 5 ++---
python/example/network_ring_mpi.py | 3 +--
python/example/single_cell_cable.py | 6 +-----
python/example/single_cell_detailed_recipe.py | 14 ++++----------
.../single_cell_extracellular_potentials.py | 4 +---
python/example/single_cell_recipe.py | 7 +------
python/example/single_cell_stdp.py | 4 +---
python/example/two_cell_gap_junctions.py | 6 +-----
python/simulation.cpp | 16 +++++++++++-----
python/single_cell_model.cpp | 2 +-
python/test/fixtures.py | 2 +-
python/test/unit/test_cable_probes.py | 2 +-
python/test/unit/test_catalogues.py | 2 +-
python/test/unit/test_multiple_connections.py | 8 +++-----
python/test/unit/test_profiling.py | 2 +-
python/test/unit_distributed/test_simulator.py | 2 +-
test/unit/test_event_delivery.cpp | 11 ++++++-----
test/unit/test_fvm_lowered.cpp | 4 ++--
test/unit/test_lif_cell_group.cpp | 6 +++---
test/unit/test_probe.cpp | 10 +++++-----
test/unit/test_recipe.cpp | 16 ++++++++--------
test/unit/test_simulation.cpp | 6 +++---
test/unit/test_spikes.cpp | 2 +-
42 files changed, 105 insertions(+), 130 deletions(-)
diff --git a/arbor/include/arbor/load_balance.hpp b/arbor/include/arbor/load_balance.hpp
index b9e8e71b..1c073980 100644
--- a/arbor/include/arbor/load_balance.hpp
+++ b/arbor/include/arbor/load_balance.hpp
@@ -23,5 +23,5 @@ using partition_hint_map = std::unordered_map<cell_kind, partition_hint>;
ARB_ARBOR_API domain_decomposition partition_load_balance(
const recipe& rec,
const context& ctx,
- partition_hint_map hint_map = {});
+ const partition_hint_map& hint_map = {});
} // namespace arb
diff --git a/arbor/include/arbor/simulation.hpp b/arbor/include/arbor/simulation.hpp
index 7e116719..c2dd5311 100644
--- a/arbor/include/arbor/simulation.hpp
+++ b/arbor/include/arbor/simulation.hpp
@@ -4,11 +4,13 @@
#include <memory>
#include <unordered_map>
#include <vector>
+#include <functional>
#include <arbor/export.hpp>
#include <arbor/common_types.hpp>
#include <arbor/context.hpp>
#include <arbor/domain_decomposition.hpp>
+#include <arbor/load_balance.hpp>
#include <arbor/recipe.hpp>
#include <arbor/sampling.hpp>
#include <arbor/schedule.hpp>
@@ -25,7 +27,12 @@ class simulation_state;
class ARB_ARBOR_API simulation {
public:
- simulation(const recipe& rec, const domain_decomposition& decomp, const context& ctx);
+
+ simulation(const recipe& rec, const context& ctx, const domain_decomposition& decomp);
+
+ simulation(const recipe& rec,
+ const context& ctx=make_context(),
+ std::function<domain_decomposition(const recipe&, const context&)> balancer=[](auto& r, auto& c) { return partition_load_balance(r, c); }): simulation(rec, ctx, balancer(rec, ctx)) {}
void reset();
diff --git a/arbor/partition_load_balance.cpp b/arbor/partition_load_balance.cpp
index 19f3ac09..71467aab 100644
--- a/arbor/partition_load_balance.cpp
+++ b/arbor/partition_load_balance.cpp
@@ -23,7 +23,7 @@ namespace arb {
ARB_ARBOR_API domain_decomposition partition_load_balance(
const recipe& rec,
const context& ctx,
- partition_hint_map hint_map)
+ const partition_hint_map& hint_map)
{
using util::make_span;
diff --git a/arbor/simulation.cpp b/arbor/simulation.cpp
index 21a07d3c..f604e19b 100644
--- a/arbor/simulation.cpp
+++ b/arbor/simulation.cpp
@@ -510,8 +510,8 @@ void simulation_state::inject_events(const cse_vector& events) {
simulation::simulation(
const recipe& rec,
- const domain_decomposition& decomp,
- const context& ctx)
+ const context& ctx,
+ const domain_decomposition& decomp)
{
impl_.reset(new simulation_state(rec, decomp, *ctx));
}
diff --git a/doc/concepts/simulation.rst b/doc/concepts/simulation.rst
index 2a63cc69..6dc7c055 100644
--- a/doc/concepts/simulation.rst
+++ b/doc/concepts/simulation.rst
@@ -9,12 +9,16 @@ group are scheduled.
From recipe to simulation
-------------------------
-To build a simulation the following are needed:
+To build a simulation the following is needed:
* A :ref:`recipe <modelrecipe>` that describes the cells and connections in the model.
-* A :ref:`domain decomposition <modeldomdec>` that describes the distribution of the
- model over the local and distributed :ref:`hardware resources <modelhardware>`.
-* An :ref:`execution context <modelcontext>` used to execute the simulation.
+* A :ref:`domain decomposition <modeldomdec>` that describes the distribution of
+ the model over the local and distributed :ref:`hardware resources
+ <modelhardware>`. If not given, a default algorithm will be used which assigns
+ cells to groups one to one; each group is assigned to a thread from the context.
+* An :ref:`execution context <modelcontext>` used to execute the simulation. If
+ not given, the default context will be used, which allocates one thread, one
+ process (MPI task), and no GPU.
Simulation execution and interaction
------------------------------------
diff --git a/example/bench/bench.cpp b/example/bench/bench.cpp
index 0d6fb976..1057ff74 100644
--- a/example/bench/bench.cpp
+++ b/example/bench/bench.cpp
@@ -165,7 +165,7 @@ int main(int argc, char** argv) {
meters.checkpoint("domain-decomp", context);
// Construct the model.
- arb::simulation sim(recipe, decomp, context);
+ arb::simulation sim(recipe, context, decomp);
meters.checkpoint("model-build", context);
// Run the simulation for 100 ms, with time steps of 0.01 ms.
diff --git a/example/brunel/brunel.cpp b/example/brunel/brunel.cpp
index 4343e593..351e656f 100644
--- a/example/brunel/brunel.cpp
+++ b/example/brunel/brunel.cpp
@@ -246,9 +246,10 @@ int main(int argc, char** argv) {
partition_hint_map hints;
hints[cell_kind::lif].cpu_group_size = group_size;
- auto decomp = partition_load_balance(recipe, context, hints);
- simulation sim(recipe, decomp, context);
+ simulation sim(recipe,
+ context,
+ [&hints](auto& r, auto& c) { return partition_load_balance(r, c, hints); });
// Set up spike recording.
std::vector<arb::spike> recorded_spikes;
diff --git a/example/drybench/drybench.cpp b/example/drybench/drybench.cpp
index ac891cdd..c5300d1a 100644
--- a/example/drybench/drybench.cpp
+++ b/example/drybench/drybench.cpp
@@ -156,10 +156,8 @@ int main(int argc, char** argv) {
auto tile = std::make_unique<tile_desc>(params);
arb::symmetric_recipe recipe(std::move(tile));
- auto decomp = arb::partition_load_balance(recipe, ctx);
-
// Construct the model.
- arb::simulation sim(recipe, decomp, ctx);
+ arb::simulation sim(recipe, ctx);
meters.checkpoint("model-init", ctx);
diff --git a/example/dryrun/dryrun.cpp b/example/dryrun/dryrun.cpp
index 8a057d09..6f38d968 100644
--- a/example/dryrun/dryrun.cpp
+++ b/example/dryrun/dryrun.cpp
@@ -174,10 +174,8 @@ int main(int argc, char** argv) {
params.num_ranks, params.cell, params.min_delay);
arb::symmetric_recipe recipe(std::move(tile));
- auto decomp = arb::partition_load_balance(recipe, ctx);
-
// Construct the model.
- arb::simulation sim(recipe, decomp, ctx);
+ arb::simulation sim(recipe, ctx);
// The id of the only probe on the cell: the cell_member type points to (cell 0, probe 0)
auto probe_id = cell_member_type{0, 0};
diff --git a/example/gap_junctions/gap_junctions.cpp b/example/gap_junctions/gap_junctions.cpp
index f61b835e..10b124d1 100644
--- a/example/gap_junctions/gap_junctions.cpp
+++ b/example/gap_junctions/gap_junctions.cpp
@@ -172,7 +172,7 @@ int main(int argc, char** argv) {
auto decomp = arb::partition_load_balance(recipe, context);
// Construct the model.
- arb::simulation sim(recipe, decomp, context);
+ arb::simulation sim(recipe, context, decomp);
// Set up the probe that will measure voltage in the cell.
diff --git a/example/generators/generators.cpp b/example/generators/generators.cpp
index 94bc75be..9e72aff2 100644
--- a/example/generators/generators.cpp
+++ b/example/generators/generators.cpp
@@ -132,11 +132,8 @@ int main() {
// Create an instance of our recipe.
generator_recipe recipe;
- // Make the domain decomposition for the model
- auto decomp = arb::partition_load_balance(recipe, context);
-
// Construct the model.
- arb::simulation sim(recipe, decomp, context);
+ arb::simulation sim(recipe, context);
// Set up the probe that will measure voltage in the cell.
diff --git a/example/lfp/lfp.cpp b/example/lfp/lfp.cpp
index 9669c26e..cb4f7ec2 100644
--- a/example/lfp/lfp.cpp
+++ b/example/lfp/lfp.cpp
@@ -3,7 +3,6 @@
#include <vector>
#include <iostream>
-#include <arbor/load_balance.hpp>
#include <arbor/cable_cell.hpp>
#include <arbor/morph/morphology.hpp>
#include <arbor/morph/place_pwlin.hpp>
@@ -79,8 +78,7 @@ private:
// Apical dendrite, length 490 μm, radius 1 μm, with SWC tag 4.
tree.append(soma_apex, {0, 0, 10, 1}, {0, 0, 500, 1}, 4);
- decor dec;
-
+ auto dec = arb::decor();
// Use NEURON defaults for reversal potentials, ion concentrations etc., but override ra, cm.
dec.set_default(axial_resistivity{100}); // [Ω·cm]
dec.set_default(membrane_capacitance{0.01}); // [F/m²]
@@ -183,24 +181,22 @@ struct {
// Run simulation.
int main(int argc, char** argv) {
- auto context = arb::make_context();
-
- // Weight 0.005 μS, onset at t = 0 ms, mean frequency 0.1 kHz.
- auto events = arb::poisson_generator({"syn"}, .005, 0., 0.1, std::minstd_rand{});
- lfp_demo_recipe R(events);
-
+ // Configuration
const double t_stop = 100; // [ms]
const double sample_dt = 0.1; // [ms]
const double dt = 0.1; // [ms]
- arb::simulation sim(R, arb::partition_load_balance(R, context), context);
+ // Weight 0.005 μS, onset at t = 0 ms, mean frequency 0.1 kHz.
+ auto events = arb::poisson_generator({"syn"}, .005, 0., 0.1, std::minstd_rand{});
+ lfp_demo_recipe recipe(events);
+ arb::simulation sim(recipe);
std::vector<position> electrodes = {
{30, 0, 0},
{30, 0, 100}
};
- arb::morphology cell_morphology = any_cast<arb::cable_cell>(R.get_cell_description(0)).morphology();
+ arb::morphology cell_morphology = any_cast<arb::cable_cell>(recipe.get_cell_description(0)).morphology();
arb::place_pwlin placed_cell(cell_morphology);
auto probe0_metadata = sim.get_probe_metadata(cell_member_type{0, 0});
diff --git a/example/probe-demo/probe-demo.cpp b/example/probe-demo/probe-demo.cpp
index 9e9f7854..0d27c111 100644
--- a/example/probe-demo/probe-demo.cpp
+++ b/example/probe-demo/probe-demo.cpp
@@ -145,8 +145,7 @@ int main(int argc, char** argv) {
cable_recipe R(opt.probe_addr, opt.n_cv);
- auto context = arb::make_context();
- arb::simulation sim(R, arb::partition_load_balance(R, context), context);
+ arb::simulation sim(R);
sim.add_sampler(arb::all_probes,
arb::regular_schedule(opt.sample_dt),
diff --git a/example/ring/ring.cpp b/example/ring/ring.cpp
index 45a3b55b..fa47d3f2 100644
--- a/example/ring/ring.cpp
+++ b/example/ring/ring.cpp
@@ -13,6 +13,7 @@
#include <arborio/label_parse.hpp>
+#include <arbor/load_balance.hpp>
#include <arbor/assert_macro.hpp>
#include <arbor/common_types.hpp>
#include <arbor/cable_cell.hpp>
@@ -160,10 +161,9 @@ int main(int argc, char** argv) {
// Create an instance of our recipe.
ring_recipe recipe(params.num_cells, params.cell, params.min_delay);
- auto decomp = arb::partition_load_balance(recipe, context);
-
// Construct the model.
- arb::simulation sim(recipe, decomp, context);
+ auto decomposition = arb::partition_load_balance(recipe, context);
+ arb::simulation sim(recipe, context, decomposition);
// Set up the probe that will measure voltage in the cell.
diff --git a/example/single/single.cpp b/example/single/single.cpp
index 2721d2fd..4befabcd 100644
--- a/example/single/single.cpp
+++ b/example/single/single.cpp
@@ -89,8 +89,7 @@ int main(int argc, char** argv) {
options opt = parse_options(argc, argv);
single_recipe R(opt.swc_file.empty()? default_morphology(): read_swc(opt.swc_file), opt.policy);
- auto context = arb::make_context();
- arb::simulation sim(R, arb::partition_load_balance(R, context), context);
+ arb::simulation sim(R);
// Attach a sampler to the probe described in the recipe, sampling every 0.1 ms.
diff --git a/python/context.cpp b/python/context.cpp
index 80fcbc61..1da55c86 100644
--- a/python/context.cpp
+++ b/python/context.cpp
@@ -123,7 +123,7 @@ void register_contexts(pybind11::module& m) {
.def("__repr__", util::to_string<proc_allocation_shim>);
// context
- pybind11::class_<context_shim> context(m, "context", "An opaque handle for the hardware resources used in a simulation.");
+ pybind11::class_<context_shim, std::shared_ptr<context_shim>> context(m, "context", "An opaque handle for the hardware resources used in a simulation.");
context
.def(pybind11::init(
[](unsigned threads, pybind11::object gpu, pybind11::object mpi){
diff --git a/python/example/brunel.py b/python/example/brunel.py
index 6a01f411..5455ca69 100755
--- a/python/example/brunel.py
+++ b/python/example/brunel.py
@@ -257,7 +257,7 @@ if __name__ == "__main__":
meters.checkpoint("load-balance", context)
- sim = arbor.simulation(recipe, decomp, context)
+ sim = arbor.simulation(recipe, context, decomp)
sim.record(arbor.spike_recording.all)
meters.checkpoint("simulation-init", context)
diff --git a/python/example/dynamic-catalogue.py b/python/example/dynamic-catalogue.py
index 6fc5e8fc..67fc7725 100644
--- a/python/example/dynamic-catalogue.py
+++ b/python/example/dynamic-catalogue.py
@@ -42,7 +42,5 @@ where <arbor> is the location of the arbor source tree."""
exit(1)
rcp = recipe()
-ctx = arb.context()
-dom = arb.partition_load_balance(rcp, ctx)
-sim = arb.simulation(rcp, dom, ctx)
+sim = arb.simulation(rcp)
sim.run(tfinal=30)
diff --git a/python/example/gap_junctions.py b/python/example/gap_junctions.py
index 2b6b3221..8d5ce084 100644
--- a/python/example/gap_junctions.py
+++ b/python/example/gap_junctions.py
@@ -133,10 +133,8 @@ ncells = nchains * ncells_per_chain
# Instantiate recipe
recipe = chain_recipe(ncells_per_chain, nchains)
-# Create a default execution context, domain decomposition and simulation
-context = arbor.context()
-decomp = arbor.partition_load_balance(recipe, context)
-sim = arbor.simulation(recipe, decomp, context)
+# Create a default simulation
+sim = arbor.simulation(recipe)
# Set spike generators to record
sim.record(arbor.spike_recording.all)
diff --git a/python/example/network_ring.py b/python/example/network_ring.py
index 9eec3cbd..9cb97a3a 100755
--- a/python/example/network_ring.py
+++ b/python/example/network_ring.py
@@ -123,9 +123,8 @@ ncells = 4
recipe = ring_recipe(ncells)
# (12) Create an execution context using all locally available threads, domain decomposition and simulation
-context = arbor.context("avail_threads")
-decomp = arbor.partition_load_balance(recipe, context)
-sim = arbor.simulation(recipe, decomp, context)
+ctx = arbor.context("avail_threads")
+sim = arbor.simulation(recipe, context=ctx)
# (13) Set spike generators to record
sim.record(arbor.spike_recording.all)
diff --git a/python/example/network_ring_mpi.py b/python/example/network_ring_mpi.py
index 84aa7daa..7ccd2d53 100644
--- a/python/example/network_ring_mpi.py
+++ b/python/example/network_ring_mpi.py
@@ -132,8 +132,7 @@ context = arbor.context(mpi=comm)
print(context)
# (13) Create a default domain decomposition and simulation
-decomp = arbor.partition_load_balance(recipe, context)
-sim = arbor.simulation(recipe, decomp, context)
+sim = arbor.simulation(recipe, context)
# (14) Set spike generators to record
sim.record(arbor.spike_recording.all)
diff --git a/python/example/single_cell_cable.py b/python/example/single_cell_cable.py
index c7116fc9..b375ec37 100755
--- a/python/example/single_cell_cable.py
+++ b/python/example/single_cell_cable.py
@@ -208,12 +208,8 @@ if __name__ == "__main__":
]
recipe = Cable(probes, **vars(args))
- # create a default execution context and a default domain decomposition
- context = arbor.context()
- domains = arbor.partition_load_balance(recipe, context)
-
# configure the simulation and handles for the probes
- sim = arbor.simulation(recipe, domains, context)
+ sim = arbor.simulation(recipe)
dt = 0.001
handles = [
sim.sample((0, i), arbor.regular_schedule(dt)) for i in range(len(probes))
diff --git a/python/example/single_cell_detailed_recipe.py b/python/example/single_cell_detailed_recipe.py
index 25da4580..dd658f66 100644
--- a/python/example/single_cell_detailed_recipe.py
+++ b/python/example/single_cell_detailed_recipe.py
@@ -145,14 +145,8 @@ class single_recipe(arbor.recipe):
# Pass the probe in a list because that it what single_recipe expects.
recipe = single_recipe(cell, [probe])
-# (4) Create an execution context
-context = arbor.context()
-
-# (5) Create a domain decomposition
-domains = arbor.partition_load_balance(recipe, context)
-
-# (6) Create a simulation
-sim = arbor.simulation(recipe, domains, context)
+# (7) Create a simulation
+sim = arbor.simulation(recipe)
# Instruct the simulation to record the spikes and sample the probe
sim.record(arbor.spike_recording.all)
@@ -160,10 +154,10 @@ sim.record(arbor.spike_recording.all)
probe_id = arbor.cell_member(0, 0)
handle = sim.sample(probe_id, arbor.regular_schedule(0.02))
-# (7) Run the simulation
+# (8) Run the simulation
sim.run(tfinal=100, dt=0.025)
-# (8) Print or display the results
+# (9) Print or display the results
spikes = sim.spikes()
print(len(spikes), "spikes recorded:")
for s in spikes:
diff --git a/python/example/single_cell_extracellular_potentials.py b/python/example/single_cell_extracellular_potentials.py
index a5c13334..413ebb90 100644
--- a/python/example/single_cell_extracellular_potentials.py
+++ b/python/example/single_cell_extracellular_potentials.py
@@ -124,9 +124,7 @@ p, cell = make_cable_cell(morphology, clamp_location)
recipe = Recipe(cell)
# instantiate simulation
-context = arbor.context()
-domains = arbor.partition_load_balance(recipe, context)
-sim = arbor.simulation(recipe, domains, context)
+sim = arbor.simulation(recipe)
# set up sampling on probes with sampling every 1 ms
schedule = arbor.regular_schedule(1.0)
diff --git a/python/example/single_cell_recipe.py b/python/example/single_cell_recipe.py
index eae1e436..facd5c8d 100644
--- a/python/example/single_cell_recipe.py
+++ b/python/example/single_cell_recipe.py
@@ -60,15 +60,10 @@ class single_recipe(arbor.recipe):
recipe = single_recipe(cell, [arbor.cable_probe_membrane_voltage('"midpoint"')])
-# (6) Create a default execution context and a default domain decomposition.
-
-context = arbor.context()
-domains = arbor.partition_load_balance(recipe, context)
-
# (7) Create and run simulation and set up 10 kHz (every 0.1 ms) sampling on the probe.
# The probe is located on cell 0, and is the 0th probe on that cell, thus has probe_id (0, 0).
-sim = arbor.simulation(recipe, domains, context)
+sim = arbor.simulation(recipe)
sim.record(arbor.spike_recording.all)
handle = sim.sample((0, 0), arbor.regular_schedule(0.1))
sim.run(tfinal=30)
diff --git a/python/example/single_cell_stdp.py b/python/example/single_cell_stdp.py
index 2f0d75bc..8c2d443c 100755
--- a/python/example/single_cell_stdp.py
+++ b/python/example/single_cell_stdp.py
@@ -78,9 +78,7 @@ class single_recipe(arbor.recipe):
def run(dT, n_pairs=1, do_plots=False):
recipe = single_recipe(dT, n_pairs)
- context = arbor.context()
- domains = arbor.partition_load_balance(recipe, context)
- sim = arbor.simulation(recipe, domains, context)
+ sim = arbor.simulation(recipe)
sim.record(arbor.spike_recording.all)
diff --git a/python/example/two_cell_gap_junctions.py b/python/example/two_cell_gap_junctions.py
index add860b9..c303802c 100755
--- a/python/example/two_cell_gap_junctions.py
+++ b/python/example/two_cell_gap_junctions.py
@@ -153,12 +153,8 @@ if __name__ == "__main__":
probes = [arbor.cable_probe_membrane_voltage('"gj_site"')]
recipe = TwoCellsWithGapJunction(probes, **vars(args))
- # create a default execution context and a default domain decomposition
- context = arbor.context()
- domains = arbor.partition_load_balance(recipe, context)
-
# configure the simulation and handles for the probes
- sim = arbor.simulation(recipe, domains, context)
+ sim = arbor.simulation(recipe)
dt = 0.01
handles = []
diff --git a/python/simulation.cpp b/python/simulation.cpp
index b506ff17..90689f84 100644
--- a/python/simulation.cpp
+++ b/python/simulation.cpp
@@ -55,11 +55,11 @@ class simulation_shim {
std::unordered_map<arb::sampler_association_handle, sampler_callback> sampler_map_;
public:
- simulation_shim(std::shared_ptr<py_recipe>& rec, const arb::domain_decomposition& decomp, const context_shim& ctx, pyarb_global_ptr global_ptr):
+ simulation_shim(std::shared_ptr<py_recipe>& rec, const context_shim& ctx, const arb::domain_decomposition& decomp, pyarb_global_ptr global_ptr):
global_ptr_(global_ptr)
{
try {
- sim_.reset(new arb::simulation(py_recipe_shim(rec), decomp, ctx.context));
+ sim_.reset(new arb::simulation(py_recipe_shim(rec), ctx.context, decomp));
}
catch (...) {
py_reset_and_throw();
@@ -195,9 +195,13 @@ void register_simulation(pybind11::module& m, pyarb_global_ptr global_ptr) {
// A custom constructor that wraps a python recipe with arb::py_recipe_shim
// before forwarding it to the arb::recipe constructor.
.def(pybind11::init(
- [global_ptr](std::shared_ptr<py_recipe>& rec, const arb::domain_decomposition& decomp, const context_shim& ctx) {
+ [global_ptr](std::shared_ptr<py_recipe>& rec,
+ const std::shared_ptr<context_shim>& ctx_,
+ const std::optional<arb::domain_decomposition>& decomp) {
try {
- return new simulation_shim(rec, decomp, ctx, global_ptr);
+ auto ctx = ctx_ ? ctx_ : std::make_shared<context_shim>(arb::make_context());
+ auto dec = decomp.value_or(arb::partition_load_balance(py_recipe_shim(rec), ctx->context));
+ return new simulation_shim(rec, *ctx, dec, global_ptr);
}
catch (...) {
py_reset_and_throw();
@@ -208,7 +212,9 @@ void register_simulation(pybind11::module& m, pyarb_global_ptr global_ptr) {
pybind11::call_guard<pybind11::gil_scoped_release>(),
"Initialize the model described by a recipe, with cells and network distributed\n"
"according to the domain decomposition and computational resources described by a context.",
- "recipe"_a, "domain_decomposition"_a, "context"_a)
+ "recipe"_a,
+ pybind11::arg_v("context", pybind11::none(), "Execution context"),
+ pybind11::arg_v("domains", pybind11::none(), "Domain decomposition"))
.def("reset", &simulation_shim::reset,
pybind11::call_guard<pybind11::gil_scoped_release>(),
"Reset the state of the simulation to its initial state.")
diff --git a/python/single_cell_model.cpp b/python/single_cell_model.cpp
index 5165aa02..cc8c0cb6 100644
--- a/python/single_cell_model.cpp
+++ b/python/single_cell_model.cpp
@@ -171,7 +171,7 @@ public:
auto domdec = arb::partition_load_balance(rec, ctx_);
- sim_ = std::make_unique<arb::simulation>(rec, domdec, ctx_);
+ sim_ = std::make_unique<arb::simulation>(rec, ctx_, domdec);
// Create one trace for each probe.
traces_.reserve(probes_.size());
diff --git a/python/test/fixtures.py b/python/test/fixtures.py
index 9f44c516..7885b12a 100644
--- a/python/test/fixtures.py
+++ b/python/test/fixtures.py
@@ -246,4 +246,4 @@ def sum_weight_hh_spike_2():
@art_spiker_recipe
def art_spiking_sim(context, art_spiker_recipe):
dd = arbor.partition_load_balance(art_spiker_recipe, context)
- return arbor.simulation(art_spiker_recipe, dd, context)
+ return arbor.simulation(art_spiker_recipe, context, dd)
diff --git a/python/test/unit/test_cable_probes.py b/python/test/unit/test_cable_probes.py
index 59e8e610..d2a66057 100644
--- a/python/test/unit/test_cable_probes.py
+++ b/python/test/unit/test_cable_probes.py
@@ -91,7 +91,7 @@ class TestCableProbes(unittest.TestCase):
recipe = cc_recipe()
context = A.context()
dd = A.partition_load_balance(recipe, context)
- sim = A.simulation(recipe, dd, context)
+ sim = A.simulation(recipe, context, dd)
all_cv_cables = [A.cable(0, 0, 1)]
diff --git a/python/test/unit/test_catalogues.py b/python/test/unit/test_catalogues.py
index e4bd1e63..6ef96f91 100644
--- a/python/test/unit/test_catalogues.py
+++ b/python/test/unit/test_catalogues.py
@@ -60,7 +60,7 @@ class TestCatalogues(unittest.TestCase):
rcp = recipe()
ctx = arb.context()
dom = arb.partition_load_balance(rcp, ctx)
- sim = arb.simulation(rcp, dom, ctx)
+ sim = arb.simulation(rcp, ctx, dom)
sim.run(tfinal=30)
def test_empty(self):
diff --git a/python/test/unit/test_multiple_connections.py b/python/test/unit/test_multiple_connections.py
index 89cc32d7..37b0f16e 100644
--- a/python/test/unit/test_multiple_connections.py
+++ b/python/test/unit/test_multiple_connections.py
@@ -134,8 +134,7 @@ class TestMultipleConnections(unittest.TestCase):
self.assertAlmostEqual(connections_from_recipe[3].delay, 1.4)
# construct domain_decomposition and simulation object
- dd = arb.partition_load_balance(art_spiker_recipe, context)
- sim = arb.simulation(art_spiker_recipe, dd, context)
+ sim = arb.simulation(art_spiker_recipe, context)
sim.record(arb.spike_recording.all)
# create schedule and handle to record the membrane potential of neuron 3
@@ -365,9 +364,8 @@ class TestMultipleConnections(unittest.TestCase):
self.assertAlmostEqual(connections_from_recipe[1].weight, weight2)
self.assertAlmostEqual(connections_from_recipe[1].delay, 1.4)
- # construct domain_decomposition and simulation object
- dd = arb.partition_load_balance(art_spiker_recipe, context)
- sim = arb.simulation(art_spiker_recipe, dd, context)
+ # construct simulation object
+ sim = arb.simulation(art_spiker_recipe, context)
sim.record(arb.spike_recording.all)
# create schedule and handle to record the membrane potential of neuron 3
diff --git a/python/test/unit/test_profiling.py b/python/test/unit/test_profiling.py
index 92a17e23..0c0d484d 100644
--- a/python/test/unit/test_profiling.py
+++ b/python/test/unit/test_profiling.py
@@ -93,7 +93,7 @@ class TestProfiling(unittest.TestCase):
arb.profiler_initialize(context)
recipe = a_recipe()
dd = arb.partition_load_balance(recipe, context)
- arb.simulation(recipe, dd, context).run(1)
+ arb.simulation(recipe, context, dd).run(1)
summary = arb.profiler_summary()
self.assertEqual(str, type(summary), "profiler summary must be str")
self.assertTrue(summary, "empty summary")
diff --git a/python/test/unit_distributed/test_simulator.py b/python/test/unit_distributed/test_simulator.py
index 8ac2a983..ea657a95 100644
--- a/python/test/unit_distributed/test_simulator.py
+++ b/python/test/unit_distributed/test_simulator.py
@@ -69,7 +69,7 @@ class TestSimulator(unittest.TestCase):
self.assertEqual(1, len(local_groups))
self.assertEqual([self.rank], local_groups[0].gids)
- return A.simulation(recipe, dd, context)
+ return A.simulation(recipe, context, dd)
def test_local_spikes(self):
sim = self.init_sim()
diff --git a/test/unit/test_event_delivery.cpp b/test/unit/test_event_delivery.cpp
index 1294240c..82a029f8 100644
--- a/test/unit/test_event_delivery.cpp
+++ b/test/unit/test_event_delivery.cpp
@@ -49,17 +49,18 @@ using gid_vector = std::vector<cell_gid_type>;
using group_gids_type = std::vector<gid_vector>;
std::vector<cell_gid_type> run_test_sim(const recipe& R, const group_gids_type& group_gids) {
- arb::context ctx = make_context(proc_allocation{});
- unsigned n = R.num_cells();
+ unsigned n = R.num_cells();
std::vector<group_description> groups;
for (const auto& gidvec: group_gids) {
groups.emplace_back(cell_kind::cable, gidvec, backend_kind::multicore);
}
- auto D = domain_decomposition(R, ctx, groups);
- std::vector<spike> spikes;
- simulation sim(R, D, ctx);
+ auto C = make_context();
+ auto D = domain_decomposition(R, C, groups);
+ simulation sim(R, C, D);
+
+ std::vector<spike> spikes;
sim.set_global_spike_callback(
[&spikes](const std::vector<spike>& ss) {
spikes.insert(spikes.end(), ss.begin(), ss.end());
diff --git a/test/unit/test_fvm_lowered.cpp b/test/unit/test_fvm_lowered.cpp
index d9d1aa76..55f10243 100644
--- a/test/unit/test_fvm_lowered.cpp
+++ b/test/unit/test_fvm_lowered.cpp
@@ -485,7 +485,7 @@ TEST(fvm_lowered, derived_mechs) {
float times[] = {10.f, 20.f};
auto decomp = partition_load_balance(rec, context);
- simulation sim(rec, decomp, context);
+ simulation sim(rec, context, decomp);
sim.add_sampler(all_probes, explicit_schedule(times), sampler);
sim.run(30.0, 1.f/1024);
@@ -516,7 +516,7 @@ TEST(fvm_lowered, null_region) {
rec.catalogue().derive("custom_kin1", "test_kin1", {{"tau", 20.0}});
auto decomp = partition_load_balance(rec, context);
- simulation sim(rec, decomp, context);
+ simulation sim(rec, context, decomp);
EXPECT_NO_THROW(sim.run(30.0, 1.f/1024));
}
diff --git a/test/unit/test_lif_cell_group.cpp b/test/unit/test_lif_cell_group.cpp
index 9ca765c4..0ea015a3 100644
--- a/test/unit/test_lif_cell_group.cpp
+++ b/test/unit/test_lif_cell_group.cpp
@@ -133,7 +133,7 @@ TEST(lif_cell_group, throw) {
probe_recipe rec;
auto context = make_context();
auto decomp = partition_load_balance(rec, context);
- EXPECT_THROW(simulation(rec, decomp, context), bad_cell_probe);
+ EXPECT_THROW(simulation(rec, context, decomp), bad_cell_probe);
}
TEST(lif_cell_group, recipe)
@@ -153,7 +153,7 @@ TEST(lif_cell_group, spikes) {
auto context = make_context();
auto decomp = partition_load_balance(recipe, context);
- simulation sim(recipe, decomp, context);
+ simulation sim(recipe, context, decomp);
cse_vector events;
@@ -193,7 +193,7 @@ TEST(lif_cell_group, ring)
auto decomp = partition_load_balance(recipe, context);
// Creates a simulation with a ring recipe of lif neurons
- simulation sim(recipe, decomp, context);
+ simulation sim(recipe, context, decomp);
std::vector<spike> spike_buffer;
diff --git a/test/unit/test_probe.cpp b/test/unit/test_probe.cpp
index bc9f41c3..ca541823 100644
--- a/test/unit/test_probe.cpp
+++ b/test/unit/test_probe.cpp
@@ -826,7 +826,7 @@ void run_axial_and_ion_current_sampled_probe_test(const context& ctx) {
partition_hint_map phints = {
{cell_kind::cable, {partition_hint::max_size, partition_hint::max_size, true}}
};
- simulation sim(rec, partition_load_balance(rec, ctx, phints), ctx);
+ simulation sim(rec, ctx, partition_load_balance(rec, ctx, phints));
// Take a sample at 20 tau, and run sim for just a bit longer.
@@ -913,7 +913,7 @@ auto run_simple_samplers(
partition_hint_map phints = {
{cell_kind::cable, {partition_hint::max_size, partition_hint::max_size, true}}
};
- simulation sim(rec, partition_load_balance(rec, ctx, phints), ctx);
+ simulation sim(rec, ctx, partition_load_balance(rec, ctx, phints));
std::vector<trace_vector<SampleData, SampleMeta>> traces(n_probe);
for (unsigned i = 0; i<n_probe; ++i) {
@@ -1278,13 +1278,13 @@ void run_exact_sampling_probe_test(const context& ctx) {
};
domain_decomposition one_cell_group = partition_load_balance(rec, ctx, phints);
- simulation lax_sim(rec, one_cell_group, ctx);
+ simulation lax_sim(rec, ctx, one_cell_group);
for (unsigned i = 0; i<n_cell; ++i) {
lax_sim.add_sampler(one_probe({i, 0}), sample_sched, make_simple_sampler(lax_traces.at(i)), sampling_policy::lax);
}
lax_sim.run(t_end, max_dt);
- simulation exact_sim(rec, one_cell_group, ctx);
+ simulation exact_sim(rec, ctx, one_cell_group);
for (unsigned i = 0; i<n_cell; ++i) {
exact_sim.add_sampler(one_probe({i, 0}), sample_sched, make_simple_sampler(exact_traces.at(i)), sampling_policy::exact);
}
@@ -1366,7 +1366,7 @@ TEST(probe, get_probe_metadata) {
partition_hint_map phints = {
{cell_kind::cable, {partition_hint::max_size, partition_hint::max_size, true}}
};
- simulation sim(rec, partition_load_balance(rec, ctx, phints), ctx);
+ simulation sim(rec, ctx, partition_load_balance(rec, ctx, phints));
std::vector<probe_metadata> mm = sim.get_probe_metadata({0, 0});
ASSERT_EQ(3u, mm.size());
diff --git a/test/unit/test_recipe.cpp b/test/unit/test_recipe.cpp
index f630f851..f1ffe120 100644
--- a/test/unit/test_recipe.cpp
+++ b/test/unit/test_recipe.cpp
@@ -112,7 +112,7 @@ TEST(recipe, gap_junctions)
auto recipe_0 = custom_recipe({cell_0, cell_1}, {{}, {}}, {gjs_0, gjs_1}, {{}, {}});
auto decomp_0 = partition_load_balance(recipe_0, context);
- EXPECT_NO_THROW(simulation(recipe_0, decomp_0, context));
+ EXPECT_NO_THROW(simulation(recipe_0, context, decomp_0));
}
{
std::vector<arb::gap_junction_connection> gjs_0 = {{{1, "gapjunction1", policy::assert_univalent}, {"gapjunction0", policy::assert_univalent}, 0.1},
@@ -126,7 +126,7 @@ TEST(recipe, gap_junctions)
auto recipe_1 = custom_recipe({cell_0, cell_1}, {{}, {}}, {gjs_0, gjs_1}, {{}, {}});
auto decomp_1 = partition_load_balance(recipe_1, context);
- EXPECT_THROW(simulation(recipe_1, decomp_1, context), arb::bad_connection_label);
+ EXPECT_THROW(simulation(recipe_1, context, decomp_1), arb::bad_connection_label);
}
}
@@ -150,7 +150,7 @@ TEST(recipe, connections)
auto recipe_0 = custom_recipe({cell_0, cell_1}, {conns_0, conns_1}, {{}, {}}, {{}, {}});
auto decomp_0 = partition_load_balance(recipe_0, context);
- EXPECT_NO_THROW(simulation(recipe_0, decomp_0, context));
+ EXPECT_NO_THROW(simulation(recipe_0, context, decomp_0));
}
{
conns_0 = {{{1, "detector0"}, {"synapse0"}, 0.1, 0.1},
@@ -164,7 +164,7 @@ TEST(recipe, connections)
auto recipe_1 = custom_recipe({cell_0, cell_1}, {conns_0, conns_1}, {{}, {}}, {{}, {}});
auto decomp_1 = partition_load_balance(recipe_1, context);
- EXPECT_THROW(simulation(recipe_1, decomp_1, context), arb::bad_connection_source_gid);
+ EXPECT_THROW(simulation(recipe_1, context, decomp_1), arb::bad_connection_source_gid);
}
{
conns_0 = {{{1, "detector0"}, {"synapse0"}, 0.1, 0.1},
@@ -178,7 +178,7 @@ TEST(recipe, connections)
auto recipe_2 = custom_recipe({cell_0, cell_1}, {conns_0, conns_1}, {{}, {}}, {{}, {}});
auto decomp_2 = partition_load_balance(recipe_2, context);
- EXPECT_THROW(simulation(recipe_2, decomp_2, context), arb::bad_connection_label);
+ EXPECT_THROW(simulation(recipe_2, context, decomp_2), arb::bad_connection_label);
}
{
conns_0 = {{{1, "detector0"}, {"synapse0"}, 0.1, 0.1},
@@ -192,7 +192,7 @@ TEST(recipe, connections)
auto recipe_4 = custom_recipe({cell_0, cell_1}, {conns_0, conns_1}, {{}, {}}, {{}, {}});
auto decomp_4 = partition_load_balance(recipe_4, context);
- EXPECT_THROW(simulation(recipe_4, decomp_4, context), arb::bad_connection_label);
+ EXPECT_THROW(simulation(recipe_4, context, decomp_4), arb::bad_connection_label);
}
}
@@ -210,7 +210,7 @@ TEST(recipe, event_generators) {
auto recipe_0 = custom_recipe({cell_0, cell_1}, {{}, {}}, {{}, {}}, {gens_0, gens_1});
auto decomp_0 = partition_load_balance(recipe_0, context);
- EXPECT_NO_THROW(simulation(recipe_0, decomp_0, context));
+ EXPECT_NO_THROW(simulation(recipe_0, context, decomp_0));
}
{
gens_0 = {arb::explicit_generator({{{"synapse0"}, 1.0, 0.1}, {{"synapse3"}, 2.0, 0.1}})};
@@ -219,6 +219,6 @@ TEST(recipe, event_generators) {
auto recipe_0 = custom_recipe({cell_0, cell_1}, {{}, {}}, {{}, {}}, {gens_0, gens_1});
auto decomp_0 = partition_load_balance(recipe_0, context);
- EXPECT_THROW(simulation(recipe_0, decomp_0, context), arb::bad_connection_label);
+ EXPECT_THROW(simulation(recipe_0, context, decomp_0), arb::bad_connection_label);
}
}
diff --git a/test/unit/test_simulation.cpp b/test/unit/test_simulation.cpp
index 3110d438..b79ac19a 100644
--- a/test/unit/test_simulation.cpp
+++ b/test/unit/test_simulation.cpp
@@ -51,7 +51,7 @@ TEST(simulation, null) {
auto r = null_recipe{};
auto c = arb::make_context();
auto d = arb::partition_load_balance(r, c);
- auto s = arb::simulation(r, d, c);
+ auto s = arb::simulation(r, c, d);
s.run(0.05, 0.01);
}
@@ -74,7 +74,7 @@ TEST(simulation, spike_global_callback) {
play_spikes rec(spike_times);
auto ctx = n_thread_context(4);
auto decomp = partition_load_balance(rec, ctx);
- simulation sim(rec, decomp, ctx);
+ simulation sim(rec, ctx, decomp);
std::vector<spike> collected;
sim.set_global_spike_callback([&](const std::vector<spike>& spikes) {
@@ -155,7 +155,7 @@ TEST(simulation, restart) {
auto ctx = n_thread_context(4);
auto decomp = partition_load_balance(rec, ctx);
- simulation sim(rec, decomp, ctx);
+ simulation sim(rec, ctx, decomp);
std::vector<spike> collected;
sim.set_global_spike_callback([&](const std::vector<spike>& spikes) {
diff --git a/test/unit/test_spikes.cpp b/test/unit/test_spikes.cpp
index 12a53234..d3279169 100644
--- a/test/unit/test_spikes.cpp
+++ b/test/unit/test_spikes.cpp
@@ -234,7 +234,7 @@ TEST(SPIKES_TEST_CLASS, threshold_watcher_interpolation) {
cable1d_recipe rec({cell});
auto decomp = arb::partition_load_balance(rec, context);
- arb::simulation sim(rec, decomp, context);
+ arb::simulation sim(rec, context, decomp);
sim.set_global_spike_callback(
[&spikes](const std::vector<arb::spike>& recorded_spikes) {
--
GitLab