From 025bed06b6297a1dd7de32f6a19a3e1d11c52927 Mon Sep 17 00:00:00 2001
From: Ben Cumming <bcumming@cscs.ch>
Date: Thu, 29 Aug 2019 11:41:00 +0200
Subject: [PATCH] Consistent source naming and layout for examples (#848)
Refactor the example code so that all examples have a single C++ source file, and the source file, source path and executable all have the same name.
Fixes #847.
---
example/bench/CMakeLists.txt | 2 +-
example/bench/bench.cpp | 171 ++++++++++-
example/bench/parameters.cpp | 81 ------
example/bench/parameters.hpp | 43 ---
example/bench/readme.md | 2 +-
example/bench/recipe.cpp | 72 -----
example/bench/recipe.hpp | 22 --
example/brunel/CMakeLists.txt | 8 +-
.../brunel/{brunel_miniapp.cpp => brunel.cpp} | 265 ++++++++++++++++--
example/brunel/io.cpp | 207 --------------
example/brunel/io.hpp | 56 ----
example/brunel/readme.md | 2 +-
example/dryrun/dryrun.cpp | 71 ++++-
example/dryrun/parameters.hpp | 81 ------
example/gap_junctions/CMakeLists.txt | 2 +-
example/gap_junctions/gap_junctions.cpp | 58 +++-
example/gap_junctions/parameters.hpp | 65 -----
example/generators/CMakeLists.txt | 6 +-
.../{event_gen.cpp => generators.cpp} | 0
example/ring/parameters.hpp | 81 ------
example/ring/ring.cpp | 76 ++++-
21 files changed, 622 insertions(+), 749 deletions(-)
delete mode 100644 example/bench/parameters.cpp
delete mode 100644 example/bench/parameters.hpp
delete mode 100644 example/bench/recipe.cpp
delete mode 100644 example/bench/recipe.hpp
rename example/brunel/{brunel_miniapp.cpp => brunel.cpp} (53%)
delete mode 100644 example/brunel/io.cpp
delete mode 100644 example/brunel/io.hpp
delete mode 100644 example/dryrun/parameters.hpp
delete mode 100644 example/gap_junctions/parameters.hpp
rename example/generators/{event_gen.cpp => generators.cpp} (100%)
delete mode 100644 example/ring/parameters.hpp
diff --git a/example/bench/CMakeLists.txt b/example/bench/CMakeLists.txt
index aa23ea36..3db3345f 100644
--- a/example/bench/CMakeLists.txt
+++ b/example/bench/CMakeLists.txt
@@ -1,4 +1,4 @@
-add_executable(bench EXCLUDE_FROM_ALL bench.cpp recipe.cpp parameters.cpp)
+add_executable(bench EXCLUDE_FROM_ALL bench.cpp)
add_dependencies(examples bench)
target_link_libraries(bench PRIVATE arbor arborenv arbor-sup ext-tclap ext-json)
diff --git a/example/bench/bench.cpp b/example/bench/bench.cpp
index af985c66..bd530d1f 100644
--- a/example/bench/bench.cpp
+++ b/example/bench/bench.cpp
@@ -9,6 +9,7 @@
#include <nlohmann/json.hpp>
#include <arbor/profile/meter_manager.hpp>
+#include <arbor/benchmark_cell.hpp>
#include <arbor/context.hpp>
#include <arbor/domain_decomposition.hpp>
#include <arbor/load_balance.hpp>
@@ -23,14 +24,123 @@
#include <sup/ioutil.hpp>
#include <sup/json_meter.hpp>
+#include <sup/json_params.hpp>
#ifdef ARB_MPI_ENABLED
#include <mpi.h>
#include <arborenv/with_mpi.hpp>
#endif
-#include "parameters.hpp"
-#include "recipe.hpp"
+struct bench_params {
+ struct cell_params {
+ double spike_freq_hz = 10; // Frequency in hz that cell will generate (poisson) spikes.
+ double realtime_ratio = 0.1; // Integration speed relative to real time, e.g. 10 implies
+ // that a cell is integrated 10 times slower than real time.
+ };
+ struct network_params {
+ unsigned fan_in = 5000; // Number of incoming connections on each cell.
+ double min_delay = 10; // Used as the delay on all connections.
+ };
+ std::string name = "default"; // Name of the model.
+ unsigned num_cells = 1000; // Number of cells in model.
+ arb::time_type duration = 100; // Simulation duration in ms.
+
+ cell_params cell; // Cell parameters for all cells in model.
+ network_params network; // Description of the network.
+
+ // Expected simulation performance properties based on model parameters.
+
+ // Time to finish simulation if only cell overheads are counted.
+ double expected_advance_time() const {
+ return cell.realtime_ratio * duration*1e-3 * num_cells;
+ }
+ // Total expected number of spikes generated by simulation.
+ unsigned expected_spikes() const {
+ return num_cells * duration*1e-3 * cell.spike_freq_hz;
+ }
+ // Expected number of spikes generated per min_delay/2 interval.
+ unsigned expected_spikes_per_interval() const {
+ return num_cells * network.min_delay*1e-3/2 * cell.spike_freq_hz;
+ }
+ // Expected number of post-synaptic events delivered over simulation.
+ unsigned expected_events() const {
+ return expected_spikes() * network.fan_in;
+ }
+ // Expected number of post-synaptic events delivered per min_delay/2 interval.
+ unsigned expected_events_per_interval() const {
+ return expected_spikes_per_interval() * network.fan_in;
+ }
+};
+
+bench_params read_options(int argc, char** argv);
+std::ostream& operator<<(std::ostream& o, const bench_params& p);
+
+class bench_recipe: public arb::recipe {
+ bench_params params_;
+
+public:
+ bench_recipe(bench_params p): params_(std::move(p)) {}
+
+ arb::cell_size_type num_cells() const override {
+ return params_.num_cells;
+ }
+
+ arb::util::unique_any get_cell_description(arb::cell_gid_type gid) const override {
+ std::mt19937_64 rng(gid);
+ arb::benchmark_cell cell;
+ cell.realtime_ratio = params_.cell.realtime_ratio;
+
+ // The time_sequence of the cell produces the series of time points at
+ // which it will spike. We use a poisson_schedule with a random sequence
+ // seeded with the gid. In this way, a cell's random stream depends only
+ // on its gid, and will hence give reproducable results when run with
+ // different MPI ranks and threads.
+ cell.time_sequence = arb::poisson_schedule(1e-3*params_.cell.spike_freq_hz, rng);
+ return std::move(cell);
+ }
+
+ arb::cell_kind get_cell_kind(arb::cell_gid_type gid) const override {
+ return arb::cell_kind::benchmark;
+ }
+
+ arb::cell_size_type num_targets(arb::cell_gid_type gid) const override {
+ // Only one target, to which all incoming connections connect.
+ // This could be parameterized, in which case the connections
+ // generated in connections_on should end on random cell-local targets.
+ return 1;
+ }
+
+ arb::cell_size_type num_sources(arb::cell_gid_type gid) const override {
+ return 1;
+ }
+
+ std::vector<arb::cell_connection> connections_on(arb::cell_gid_type gid) const override {
+ const auto n = params_.network.fan_in;
+ std::vector<arb::cell_connection> cons;
+ cons.reserve(n);
+ using rng_type = std::mt19937_64;
+ rng_type rng(gid);
+
+ // Generate n incoming connections on this cell with random sources, where
+ // the source can't equal gid (i.e. no self-connections).
+ // We want a random distribution that will uniformly draw values from the
+ // union of the two ranges: [0, gid-1] AND [gid+1, num_cells-1].
+ // To do this, we draw random values in the range [0, num_cells-2], then
+ // add 1 to values ≥ gid.
+
+ std::uniform_int_distribution<arb::cell_gid_type> dist(0, params_.num_cells-2);
+ for (unsigned i=0; i<n; ++i) {
+ // Draw random source and adjust to avoid self-connections if neccesary.
+ arb::cell_gid_type src = dist(rng);
+ if (src>=gid) ++src;
+ // Note: target is {gid, 0}, i.e. the first (and only) target on the cell.
+ arb::cell_connection con({src, 0}, {gid, 0}, 1.f, params_.network.min_delay);
+ cons.push_back(con);
+ }
+
+ return cons;
+ }
+};
namespace profile = arb::profile;
@@ -105,3 +215,60 @@ int main(int argc, char** argv) {
std::cerr << "exception caught running benchmark miniapp:\n" << e.what() << std::endl;
}
}
+
+std::ostream& operator<<(std::ostream& o, const bench_params& p) {
+ o << "benchmark parameters:\n"
+ << " name: " << p.name << "\n"
+ << " num cells: " << p.num_cells << "\n"
+ << " duration: " << p.duration << " ms\n"
+ << " fan in: " << p.network.fan_in << " connections/cell\n"
+ << " min delay: " << p.network.min_delay << " ms\n"
+ << " spike freq: " << p.cell.spike_freq_hz << " Hz\n"
+ << " cell overhead: " << p.cell.realtime_ratio << " ms to advance 1 ms\n";
+ o << "expected:\n"
+ << " cell advance: " << p.expected_advance_time() << " s\n"
+ << " spikes: " << p.expected_spikes() << "\n"
+ << " events: " << p.expected_events() << "\n"
+ << " spikes: " << p.expected_spikes_per_interval() << " per interval\n"
+ << " events: " << p.expected_events_per_interval()/p.num_cells << " per cell per interval";
+ return o;
+}
+
+bench_params read_options(int argc, char** argv) {
+ using sup::param_from_json;
+
+ bench_params params;
+ if (argc<2) {
+ std::cout << "Using default parameters.\n";
+ return params;
+ }
+ if (argc>2) {
+ throw std::runtime_error("More than command line one option not permitted.");
+ }
+
+ std::string fname = argv[1];
+ std::cout << "Loading parameters from file: " << fname << "\n";
+ std::ifstream f(fname);
+
+ if (!f.good()) {
+ throw std::runtime_error("Unable to open input parameter file: "+fname);
+ }
+
+ nlohmann::json json;
+ json << f;
+
+ param_from_json(params.name, "name", json);
+ param_from_json(params.num_cells, "num-cells", json);
+ param_from_json(params.duration, "duration", json);
+ param_from_json(params.network.min_delay, "min-delay", json);
+ param_from_json(params.network.fan_in, "fan-in", json);
+ param_from_json(params.cell.realtime_ratio, "realtime-ratio", json);
+ param_from_json(params.cell.spike_freq_hz, "spike-frequency", json);
+
+ for (auto it=json.begin(); it!=json.end(); ++it) {
+ std::cout << " Warning: unused input parameter: \"" << it.key() << "\"\n";
+ }
+ std::cout << "\n";
+
+ return params;
+}
diff --git a/example/bench/parameters.cpp b/example/bench/parameters.cpp
deleted file mode 100644
index d2a42621..00000000
--- a/example/bench/parameters.cpp
+++ /dev/null
@@ -1,81 +0,0 @@
-#include <exception>
-#include <fstream>
-#include <iostream>
-#include <string>
-
-#include <sup/json_params.hpp>
-
-#include "parameters.hpp"
-
-double bench_params::expected_advance_time() const {
- return cell.realtime_ratio * duration*1e-3 * num_cells;
-}
-unsigned bench_params::expected_spikes() const {
- return num_cells * duration*1e-3 * cell.spike_freq_hz;
-}
-unsigned bench_params::expected_spikes_per_interval() const {
- return num_cells * network.min_delay*1e-3/2 * cell.spike_freq_hz;
-}
-unsigned bench_params::expected_events() const {
- return expected_spikes() * network.fan_in;
-}
-unsigned bench_params::expected_events_per_interval() const {
- return expected_spikes_per_interval() * network.fan_in;
-}
-
-std::ostream& operator<<(std::ostream& o, const bench_params& p) {
- o << "benchmark parameters:\n"
- << " name: " << p.name << "\n"
- << " num cells: " << p.num_cells << "\n"
- << " duration: " << p.duration << " ms\n"
- << " fan in: " << p.network.fan_in << " connections/cell\n"
- << " min delay: " << p.network.min_delay << " ms\n"
- << " spike freq: " << p.cell.spike_freq_hz << " Hz\n"
- << " cell overhead: " << p.cell.realtime_ratio << " ms to advance 1 ms\n";
- o << "expected:\n"
- << " cell advance: " << p.expected_advance_time() << " s\n"
- << " spikes: " << p.expected_spikes() << "\n"
- << " events: " << p.expected_events() << "\n"
- << " spikes: " << p.expected_spikes_per_interval() << " per interval\n"
- << " events: " << p.expected_events_per_interval()/p.num_cells << " per cell per interval";
- return o;
-}
-
-bench_params read_options(int argc, char** argv) {
- using sup::param_from_json;
-
- bench_params params;
- if (argc<2) {
- std::cout << "Using default parameters.\n";
- return params;
- }
- if (argc>2) {
- throw std::runtime_error("More than command line one option not permitted.");
- }
-
- std::string fname = argv[1];
- std::cout << "Loading parameters from file: " << fname << "\n";
- std::ifstream f(fname);
-
- if (!f.good()) {
- throw std::runtime_error("Unable to open input parameter file: "+fname);
- }
-
- nlohmann::json json;
- json << f;
-
- param_from_json(params.name, "name", json);
- param_from_json(params.num_cells, "num-cells", json);
- param_from_json(params.duration, "duration", json);
- param_from_json(params.network.min_delay, "min-delay", json);
- param_from_json(params.network.fan_in, "fan-in", json);
- param_from_json(params.cell.realtime_ratio, "realtime-ratio", json);
- param_from_json(params.cell.spike_freq_hz, "spike-frequency", json);
-
- for (auto it=json.begin(); it!=json.end(); ++it) {
- std::cout << " Warning: unused input parameter: \"" << it.key() << "\"\n";
- }
- std::cout << "\n";
-
- return params;
-}
diff --git a/example/bench/parameters.hpp b/example/bench/parameters.hpp
deleted file mode 100644
index 9f6fdc9f..00000000
--- a/example/bench/parameters.hpp
+++ /dev/null
@@ -1,43 +0,0 @@
-#pragma once
-
-#include <ostream>
-#include <string>
-
-#include <arbor/common_types.hpp>
-
-using arb::time_type;
-
-struct bench_params {
- struct cell_params {
- double spike_freq_hz = 10; // Frequency in hz that cell will generate (poisson) spikes.
- double realtime_ratio = 0.1; // Integration speed relative to real time, e.g. 10 implies
- // that a cell is integrated 10 times slower than real time.
- };
- struct network_params {
- unsigned fan_in = 5000; // Number of incoming connections on each cell.
- double min_delay = 10; // Used as the delay on all connections.
- };
- std::string name = "default"; // Name of the model.
- unsigned num_cells = 1000; // Number of cells in model.
- time_type duration = 100; // Simulation duration in ms.
-
- cell_params cell; // Cell parameters for all cells in model.
- network_params network; // Description of the network.
-
- // Expected simulation performance properties based on model parameters.
-
- // Time to finish simulation if only cell overheads are counted.
- double expected_advance_time() const;
- // Total expected number of spikes generated by simulation.
- unsigned expected_spikes() const;
- // Expected number of spikes generated per min_delay/2 interval.
- unsigned expected_spikes_per_interval() const;
- // Expected number of post-synaptic events delivered over simulation.
- unsigned expected_events() const;
- // Expected number of post-synaptic events delivered per min_delay/2 interval.
- unsigned expected_events_per_interval() const;
-};
-
-bench_params read_options(int argc, char** argv);
-
-std::ostream& operator<<(std::ostream& o, const bench_params& p);
diff --git a/example/bench/readme.md b/example/bench/readme.md
index c6dbc2f9..b862132e 100644
--- a/example/bench/readme.md
+++ b/example/bench/readme.md
@@ -21,7 +21,7 @@ pattern are varied, without having to tweak parameters on a model that uses
The model can be configured using a json configuration file:
```
-./bench.exe params.json
+./bench params.json
```
An example parameter file is:
diff --git a/example/bench/recipe.cpp b/example/bench/recipe.cpp
deleted file mode 100644
index aa9c94b8..00000000
--- a/example/bench/recipe.cpp
+++ /dev/null
@@ -1,72 +0,0 @@
-#include <random>
-
-#include <arbor/benchmark_cell.hpp>
-#include <arbor/common_types.hpp>
-#include <arbor/schedule.hpp>
-
-#include "recipe.hpp"
-
-using arb::cell_gid_type;
-using arb::cell_size_type;
-using arb::cell_kind;
-
-cell_size_type bench_recipe::num_cells() const {
- return params_.num_cells;
-}
-
-arb::util::unique_any bench_recipe::get_cell_description(cell_gid_type gid) const {
- std::mt19937_64 rng(gid);
- arb::benchmark_cell cell;
- cell.realtime_ratio = params_.cell.realtime_ratio;
-
- // The time_sequence of the cell produces the series of time points at
- // which it will spike. We use a poisson_schedule with a random sequence
- // seeded with the gid. In this way, a cell's random stream depends only
- // on its gid, and will hence give reproducable results when run with
- // different MPI ranks and threads.
- cell.time_sequence = arb::poisson_schedule(1e-3*params_.cell.spike_freq_hz, rng);
- return std::move(cell);
-}
-
-cell_kind bench_recipe::get_cell_kind(cell_gid_type gid) const {
- return cell_kind::benchmark;
-}
-
-std::vector<arb::cell_connection> bench_recipe::connections_on(cell_gid_type gid) const {
- const auto n = params_.network.fan_in;
- std::vector<arb::cell_connection> cons;
- cons.reserve(n);
- using rng_type = std::mt19937_64;
- rng_type rng(gid);
-
- // Generate n incoming connections on this cell with random sources, where
- // the source can't equal gid (i.e. no self-connections).
- // We want a random distribution that will uniformly draw values from the
- // union of the two ranges: [0, gid-1] AND [gid+1, num_cells-1].
- // To do this, we draw random values in the range [0, num_cells-2], then
- // add 1 to values ≥ gid.
-
- std::uniform_int_distribution<cell_gid_type> dist(0, params_.num_cells-2);
- for (unsigned i=0; i<n; ++i) {
- // Draw random source and adjust to avoid self-connections if neccesary.
- cell_gid_type src = dist(rng);
- if (src>=gid) ++src;
- // Note: target is {gid, 0}, i.e. the first (and only) target on the cell.
- arb::cell_connection con({src, 0}, {gid, 0}, 1.f, params_.network.min_delay);
- cons.push_back(con);
- }
-
- return cons;
-}
-
-cell_size_type bench_recipe::num_targets(cell_gid_type gid) const {
- // Only one target, to which all incoming connections connect.
- // This could be parameterized, in which case the connections
- // generated in connections_on should end on random cell-local targets.
- return 1;
-}
-
-// one spike source per cell
-cell_size_type bench_recipe::num_sources(cell_gid_type gid) const {
- return 1;
-}
diff --git a/example/bench/recipe.hpp b/example/bench/recipe.hpp
deleted file mode 100644
index e95f6077..00000000
--- a/example/bench/recipe.hpp
+++ /dev/null
@@ -1,22 +0,0 @@
-#pragma once
-
-#include <arbor/common_types.hpp>
-#include <arbor/recipe.hpp>
-#include <arbor/util/unique_any.hpp>
-
-#include "parameters.hpp"
-
-class bench_recipe: public arb::recipe {
-private:
- bench_params params_;
-
-public:
- bench_recipe(bench_params p): params_(std::move(p)) {}
- arb::cell_size_type num_cells() const override;
- arb::util::unique_any get_cell_description(arb::cell_gid_type gid) const override;
- arb::cell_kind get_cell_kind(arb::cell_gid_type gid) const override;
- arb::cell_size_type num_targets(arb::cell_gid_type gid) const override;
- arb::cell_size_type num_sources(arb::cell_gid_type gid) const override;
- std::vector<arb::cell_connection> connections_on(arb::cell_gid_type) const override;
-};
-
diff --git a/example/brunel/CMakeLists.txt b/example/brunel/CMakeLists.txt
index 99b26743..79b68394 100644
--- a/example/brunel/CMakeLists.txt
+++ b/example/brunel/CMakeLists.txt
@@ -1,6 +1,4 @@
-add_executable(brunel-miniapp EXCLUDE_FROM_ALL
- brunel_miniapp.cpp
- io.cpp)
-add_dependencies(examples brunel-miniapp)
+add_executable(brunel EXCLUDE_FROM_ALL brunel.cpp)
+add_dependencies(examples brunel)
-target_link_libraries(brunel-miniapp PRIVATE arbor arborenv arbor-sup ext-tclap)
+target_link_libraries(brunel PRIVATE arbor arborenv arbor-sup ext-tclap)
diff --git a/example/brunel/brunel_miniapp.cpp b/example/brunel/brunel.cpp
similarity index 53%
rename from example/brunel/brunel_miniapp.cpp
rename to example/brunel/brunel.cpp
index 131f2730..22a49674 100644
--- a/example/brunel/brunel_miniapp.cpp
+++ b/example/brunel/brunel.cpp
@@ -7,6 +7,8 @@
#include <set>
#include <vector>
+#include <tclap/CmdLine.h>
+
#include <arbor/context.hpp>
#include <arbor/common_types.hpp>
#include <arbor/domain_decomposition.hpp>
@@ -17,6 +19,7 @@
#include <arbor/profile/profiler.hpp>
#include <arbor/recipe.hpp>
#include <arbor/simulation.hpp>
+#include <arbor/util/optional.hpp>
#include <arbor/version.hpp>
#include <arborenv/concurrency.hpp>
@@ -32,26 +35,46 @@
#include <arborenv/with_mpi.hpp>
#endif
-#include "io.hpp"
-
using namespace arb;
+// Holds the options for a simulation run.
+// Default constructor gives default options.
+struct cl_options {
+ // Cell parameters:
+ uint32_t nexc = 400;
+ uint32_t ninh = 100;
+ uint32_t next = 40;
+ double syn_per_cell_prop = 0.05;
+ float weight = 1.2;
+ float delay = 0.1;
+ float rel_inh_strength = 1;
+ double poiss_lambda = 1;
+
+ // Simulation running parameters:
+ double tfinal = 100.;
+ double dt = 1;
+ uint32_t group_size = 10;
+ uint32_t seed = 42;
+
+ // Parameters for spike output.
+ bool spike_file_output = false;
+
+ // Turn on/off profiling output for all ranks.
+ bool profile_only_zero = false;
+
+ // Be more verbose with informational messages.
+ bool verbose = false;
+};
+
+std::ostream& operator<<(std::ostream& o, const cl_options& opt);
+
+cl_options read_options(int argc, char** argv);
+
void banner(const context& ctx);
// Samples m unique values in interval [start, end) - gid.
// We exclude gid because we don't want self-loops.
-std::vector<cell_gid_type> sample_subset(cell_gid_type gid, cell_gid_type start, cell_gid_type end, unsigned m) {
- std::set<cell_gid_type> s;
- std::mt19937 gen(gid + 42);
- std::uniform_int_distribution<cell_gid_type> dis(start, end - 1);
- while (s.size() < m) {
- auto val = dis(gen);
- if (val != gid) {
- s.insert(val);
- }
- }
- return {s.begin(), s.end()};
-}
+std::vector<cell_gid_type> sample_subset(cell_gid_type gid, cell_gid_type start, cell_gid_type end, unsigned m);
/*
A Brunel network consists of nexc excitatory LIF neurons and ninh inhibitory LIF neurons.
@@ -214,7 +237,7 @@ int main(int argc, char** argv) {
meters.start(context);
// read parameters
- io::cl_options options = io::read_options(argc, argv);
+ cl_options options = read_options(argc, argv);
std::fstream spike_out;
if (options.spike_file_output && root) {
@@ -296,16 +319,12 @@ int main(int argc, char** argv) {
fid << std::setw(1) << sup::to_json(report) << "\n";
}
}
- catch (io::usage_error& e) {
- // only print usage/startup errors on master
+ catch (std::exception& e) {
+ // only print errors on master
std::cerr << sup::mask_stream(root);
std::cerr << e.what() << "\n";
return 1;
}
- catch (std::exception& e) {
- std::cerr << e.what() << "\n";
- return 2;
- }
return 0;
}
@@ -318,3 +337,207 @@ void banner(const context& ctx) {
std::cout << " - gpus : " << (arb::has_gpu(ctx)? "yes": "no") << "\n";
std::cout << "==========================================\n";
}
+
+std::vector<cell_gid_type> sample_subset(cell_gid_type gid, cell_gid_type start, cell_gid_type end, unsigned m) {
+ std::set<cell_gid_type> s;
+ std::mt19937 gen(gid + 42);
+ std::uniform_int_distribution<cell_gid_type> dis(start, end - 1);
+ while (s.size() < m) {
+ auto val = dis(gen);
+ if (val != gid) {
+ s.insert(val);
+ }
+ }
+ return {s.begin(), s.end()};
+}
+
+// Let TCLAP understand value arguments that are of an optional type.
+namespace TCLAP {
+ template <typename V>
+ struct ArgTraits<arb::util::optional<V>> {
+ using ValueCategory = ValueLike;
+ };
+} // namespace TCLAP
+
+namespace arb {
+ namespace util {
+ // Using static here because we do not want external linkage for this operator.
+ template <typename V>
+ static std::istream& operator>>(std::istream& I, optional<V>& v) {
+ V u;
+ if (I >> u) {
+ v = u;
+ }
+ return I;
+ }
+ }
+}
+
+// Override annoying parameters listed back-to-front behaviour.
+//
+// TCLAP argument creation _prepends_ its arguments to the internal
+// list (_argList), where standard options --help etc. are already
+// pre-inserted.
+//
+// reorder_arguments() reverses the arguments to restore ordering,
+// and moves the standard options to the end.
+class CustomCmdLine: public TCLAP::CmdLine {
+public:
+ CustomCmdLine(const std::string &message, const std::string &version = "none"):
+ TCLAP::CmdLine(message, ' ', version, true)
+ {}
+
+ void reorder_arguments() {
+ _argList.reverse();
+ for (auto opt: {"help", "version", "ignore_rest"}) {
+ auto i = std::find_if(
+ _argList.begin(), _argList.end(),
+ [&opt](TCLAP::Arg* a) { return a->getName()==opt; });
+
+ if (i!=_argList.end()) {
+ auto a = *i;
+ _argList.erase(i);
+ _argList.push_back(a);
+ }
+ }
+ }
+};
+
+// Update an option value from command line argument if set.
+template <
+ typename T,
+ typename Arg,
+ typename = std::enable_if_t<std::is_base_of<TCLAP::Arg, Arg>::value>
+>
+static void update_option(T& opt, Arg& arg) {
+ if (arg.isSet()) {
+ opt = arg.getValue();
+ }
+}
+
+// Read options from (optional) json file and command line arguments.
+cl_options read_options(int argc, char** argv) {
+ cl_options options;
+
+ // Parse command line arguments.
+ try {
+ cl_options defopts;
+
+ CustomCmdLine cmd("nest brunel miniapp harness", "0.1");
+
+ TCLAP::ValueArg<uint32_t> nexc_arg
+ ("n", "n-excitatory", "total number of cells in the excitatory population",
+ false, defopts.nexc, "integer", cmd);
+
+ TCLAP::ValueArg<uint32_t> ninh_arg
+ ("m", "n-inhibitory", "total number of cells in the inhibitory population",
+ false, defopts.ninh, "integer", cmd);
+
+ TCLAP::ValueArg<uint32_t> next_arg
+ ("e", "n-external", "total number of incoming Poisson (external) connections per cell.",
+ false, defopts.ninh, "integer", cmd);
+
+ TCLAP::ValueArg<double> syn_prop_arg
+ ("p", "in-degree-prop", "the proportion of connections both the excitatory and inhibitory populations that each neuron receives",
+ false, defopts.syn_per_cell_prop, "double", cmd);
+
+ TCLAP::ValueArg<float> weight_arg
+ ("w", "weight", "the weight of all excitatory connections",
+ false, defopts.weight, "float", cmd);
+
+ TCLAP::ValueArg<float> delay_arg
+ ("d", "delay", "the delay of all connections",
+ false, defopts.delay, "float", cmd);
+
+ TCLAP::ValueArg<float> rel_inh_strength_arg
+ ("g", "rel-inh-w", "relative strength of inhibitory synapses with respect to the excitatory ones",
+ false, defopts.rel_inh_strength, "float", cmd);
+
+ TCLAP::ValueArg<double> poiss_lambda_arg
+ ("l", "lambda", "Expected number of spikes from a single poisson cell per ms",
+ false, defopts.poiss_lambda, "double", cmd);
+
+ TCLAP::ValueArg<double> tfinal_arg
+ ("t", "tfinal", "length of the simulation period [ms]",
+ false, defopts.tfinal, "time", cmd);
+
+ TCLAP::ValueArg<double> dt_arg
+ ("s", "delta-t", "simulation time step [ms] (this parameter is ignored)",
+ false, defopts.dt, "time", cmd);
+
+ TCLAP::ValueArg<uint32_t> group_size_arg
+ ("G", "group-size", "number of cells per cell group",
+ false, defopts.group_size, "integer", cmd);
+
+ TCLAP::ValueArg<uint32_t> seed_arg
+ ("S", "seed", "seed for poisson spike generators",
+ false, defopts.seed, "integer", cmd);
+
+ TCLAP::SwitchArg spike_output_arg
+ ("f","spike-file-output","save spikes to file", cmd, false);
+
+ TCLAP::SwitchArg profile_only_zero_arg
+ ("z", "profile-only-zero", "Only output profile information for rank 0",
+ cmd, false);
+
+ TCLAP::SwitchArg verbose_arg
+ ("v", "verbose", "Present more verbose information to stdout", cmd, false);
+
+ cmd.reorder_arguments();
+ cmd.parse(argc, argv);
+
+ // Handle verbosity separately from other options: it is not considered part
+ // of the saved option state.
+ options.verbose = verbose_arg.getValue();
+ update_option(options.nexc, nexc_arg);
+ update_option(options.ninh, ninh_arg);
+ update_option(options.next, next_arg);
+ update_option(options.syn_per_cell_prop, syn_prop_arg);
+ update_option(options.weight, weight_arg);
+ update_option(options.delay, delay_arg);
+ update_option(options.rel_inh_strength, rel_inh_strength_arg);
+ update_option(options.poiss_lambda, poiss_lambda_arg);
+ update_option(options.tfinal, tfinal_arg);
+ update_option(options.dt, dt_arg);
+ update_option(options.group_size, group_size_arg);
+ update_option(options.seed, seed_arg);
+ update_option(options.spike_file_output, spike_output_arg);
+ update_option(options.profile_only_zero, profile_only_zero_arg);
+
+ if (options.group_size < 1) {
+ throw std::runtime_error("minimum of one cell per group");
+ }
+
+ if (options.rel_inh_strength <= 0 || options.rel_inh_strength > 1) {
+ throw std::runtime_error("relative strength of inhibitory connections must be in the interval (0, 1].");
+ }
+ }
+ catch (TCLAP::ArgException& e) {
+ throw std::runtime_error("error parsing command line argument "+e.argId()+": "+e.error());
+ }
+
+ // If verbose output requested, emit option summary.
+ if (options.verbose) {
+ std::cout << options << "\n";
+ }
+
+ return options;
+}
+
+std::ostream& operator<<(std::ostream& o, const cl_options& options) {
+ o << "simulation options:\n";
+ o << " excitatory cells : " << options.nexc << "\n";
+ o << " inhibitory cells : " << options.ninh << "\n";
+ o << " Poisson connections per cell : " << options.next << "\n";
+ o << " proportion of synapses/cell from each population : " << options.syn_per_cell_prop << "\n";
+ o << " weight of excitatory synapses : " << options.weight << "\n";
+ o << " relative strength of inhibitory synapses : " << options.rel_inh_strength << "\n";
+ o << " delay of all synapses : " << options.delay << "\n";
+ o << " expected number of spikes from a single poisson cell per ms: " << options.poiss_lambda << "\n";
+ o << "\n";
+ o << " simulation time : " << options.tfinal << "\n";
+ o << " dt : " << options.dt << "\n";
+ o << " group size : " << options.group_size << "\n";
+ o << " seed : " << options.seed << "\n";
+ return o;
+}
diff --git a/example/brunel/io.cpp b/example/brunel/io.cpp
deleted file mode 100644
index 72b6ca81..00000000
--- a/example/brunel/io.cpp
+++ /dev/null
@@ -1,207 +0,0 @@
-#include <algorithm>
-#include <exception>
-#include <fstream>
-#include <iostream>
-#include <memory>
-#include <sstream>
-#include <string>
-#include <type_traits>
-
-#include <tclap/CmdLine.h>
-
-#include <arbor/util/optional.hpp>
-
-#include "io.hpp"
-
-// Let TCLAP understand value arguments that are of an optional type.
-namespace TCLAP {
- template <typename V>
- struct ArgTraits<arb::util::optional<V>> {
- using ValueCategory = ValueLike;
- };
-} // namespace TCLAP
-
-namespace arb {
- namespace util {
- // Using static here because we do not want external linkage for this operator.
- template <typename V>
- static std::istream& operator>>(std::istream& I, optional<V>& v) {
- V u;
- if (I >> u) {
- v = u;
- }
- return I;
- }
- }
-}
-
-namespace io {
- // Override annoying parameters listed back-to-front behaviour.
- //
- // TCLAP argument creation _prepends_ its arguments to the internal
- // list (_argList), where standard options --help etc. are already
- // pre-inserted.
- //
- // reorder_arguments() reverses the arguments to restore ordering,
- // and moves the standard options to the end.
- class CustomCmdLine: public TCLAP::CmdLine {
- public:
- CustomCmdLine(const std::string &message, const std::string &version = "none"):
- TCLAP::CmdLine(message, ' ', version, true)
- {}
-
- void reorder_arguments() {
- _argList.reverse();
- for (auto opt: {"help", "version", "ignore_rest"}) {
- auto i = std::find_if(
- _argList.begin(), _argList.end(),
- [&opt](TCLAP::Arg* a) { return a->getName()==opt; });
-
- if (i!=_argList.end()) {
- auto a = *i;
- _argList.erase(i);
- _argList.push_back(a);
- }
- }
- }
- };
-
- // Update an option value from command line argument if set.
- template <
- typename T,
- typename Arg,
- typename = std::enable_if_t<std::is_base_of<TCLAP::Arg, Arg>::value>
- >
- static void update_option(T& opt, Arg& arg) {
- if (arg.isSet()) {
- opt = arg.getValue();
- }
- }
-
- // Read options from (optional) json file and command line arguments.
- cl_options read_options(int argc, char** argv) {
- cl_options options;
-
- // Parse command line arguments.
- try {
- cl_options defopts;
-
- CustomCmdLine cmd("nest brunel miniapp harness", "0.1");
-
- TCLAP::ValueArg<uint32_t> nexc_arg
- ("n", "n-excitatory", "total number of cells in the excitatory population",
- false, defopts.nexc, "integer", cmd);
-
- TCLAP::ValueArg<uint32_t> ninh_arg
- ("m", "n-inhibitory", "total number of cells in the inhibitory population",
- false, defopts.ninh, "integer", cmd);
-
- TCLAP::ValueArg<uint32_t> next_arg
- ("e", "n-external", "total number of incoming Poisson (external) connections per cell.",
- false, defopts.ninh, "integer", cmd);
-
- TCLAP::ValueArg<double> syn_prop_arg
- ("p", "in-degree-prop", "the proportion of connections both the excitatory and inhibitory populations that each neuron receives",
- false, defopts.syn_per_cell_prop, "double", cmd);
-
- TCLAP::ValueArg<float> weight_arg
- ("w", "weight", "the weight of all excitatory connections",
- false, defopts.weight, "float", cmd);
-
- TCLAP::ValueArg<float> delay_arg
- ("d", "delay", "the delay of all connections",
- false, defopts.delay, "float", cmd);
-
- TCLAP::ValueArg<float> rel_inh_strength_arg
- ("g", "rel-inh-w", "relative strength of inhibitory synapses with respect to the excitatory ones",
- false, defopts.rel_inh_strength, "float", cmd);
-
- TCLAP::ValueArg<double> poiss_lambda_arg
- ("l", "lambda", "Expected number of spikes from a single poisson cell per ms",
- false, defopts.poiss_lambda, "double", cmd);
-
- TCLAP::ValueArg<double> tfinal_arg
- ("t", "tfinal", "length of the simulation period [ms]",
- false, defopts.tfinal, "time", cmd);
-
- TCLAP::ValueArg<double> dt_arg
- ("s", "delta-t", "simulation time step [ms] (this parameter is ignored)",
- false, defopts.dt, "time", cmd);
-
- TCLAP::ValueArg<uint32_t> group_size_arg
- ("G", "group-size", "number of cells per cell group",
- false, defopts.group_size, "integer", cmd);
-
- TCLAP::ValueArg<uint32_t> seed_arg
- ("S", "seed", "seed for poisson spike generators",
- false, defopts.seed, "integer", cmd);
-
- TCLAP::SwitchArg spike_output_arg
- ("f","spike-file-output","save spikes to file", cmd, false);
-
- TCLAP::SwitchArg profile_only_zero_arg
- ("z", "profile-only-zero", "Only output profile information for rank 0",
- cmd, false);
-
- TCLAP::SwitchArg verbose_arg
- ("v", "verbose", "Present more verbose information to stdout", cmd, false);
-
- cmd.reorder_arguments();
- cmd.parse(argc, argv);
-
- // Handle verbosity separately from other options: it is not considered part
- // of the saved option state.
- options.verbose = verbose_arg.getValue();
- update_option(options.nexc, nexc_arg);
- update_option(options.ninh, ninh_arg);
- update_option(options.next, next_arg);
- update_option(options.syn_per_cell_prop, syn_prop_arg);
- update_option(options.weight, weight_arg);
- update_option(options.delay, delay_arg);
- update_option(options.rel_inh_strength, rel_inh_strength_arg);
- update_option(options.poiss_lambda, poiss_lambda_arg);
- update_option(options.tfinal, tfinal_arg);
- update_option(options.dt, dt_arg);
- update_option(options.group_size, group_size_arg);
- update_option(options.seed, seed_arg);
- update_option(options.spike_file_output, spike_output_arg);
- update_option(options.profile_only_zero, profile_only_zero_arg);
-
- if (options.group_size < 1) {
- throw usage_error("minimum of one cell per group");
- }
-
- if (options.rel_inh_strength <= 0 || options.rel_inh_strength > 1) {
- throw usage_error("relative strength of inhibitory connections must be in the interval (0, 1].");
- }
- }
- catch (TCLAP::ArgException& e) {
- throw usage_error("error parsing command line argument "+e.argId()+": "+e.error());
- }
-
- // If verbose output requested, emit option summary.
- if (options.verbose) {
- std::cout << options << "\n";
- }
-
- return options;
- }
-
- std::ostream& operator<<(std::ostream& o, const cl_options& options) {
- o << "simulation options:\n";
- o << " excitatory cells : " << options.nexc << "\n";
- o << " inhibitory cells : " << options.ninh << "\n";
- o << " Poisson connections per cell : " << options.next << "\n";
- o << " proportion of synapses/cell from each population : " << options.syn_per_cell_prop << "\n";
- o << " weight of excitatory synapses : " << options.weight << "\n";
- o << " relative strength of inhibitory synapses : " << options.rel_inh_strength << "\n";
- o << " delay of all synapses : " << options.delay << "\n";
- o << " expected number of spikes from a single poisson cell per ms: " << options.poiss_lambda << "\n";
- o << "\n";
- o << " simulation time : " << options.tfinal << "\n";
- o << " dt : " << options.dt << "\n";
- o << " group size : " << options.group_size << "\n";
- o << " seed : " << options.seed << "\n";
- return o;
- }
-} // namespace io
diff --git a/example/brunel/io.hpp b/example/brunel/io.hpp
deleted file mode 100644
index 28c76bdb..00000000
--- a/example/brunel/io.hpp
+++ /dev/null
@@ -1,56 +0,0 @@
-#pragma once
-
-#include <stdexcept>
-#include <string>
-#include <utility>
-#include <vector>
-
-#include <arbor/common_types.hpp>
-#include <arbor/util/optional.hpp>
-
-namespace io {
- // Holds the options for a simulation run.
- // Default constructor gives default options.
- struct cl_options {
- // Cell parameters:
- uint32_t nexc = 400;
- uint32_t ninh = 100;
- uint32_t next = 40;
- double syn_per_cell_prop = 0.05;
- float weight = 1.2;
- float delay = 0.1;
- float rel_inh_strength = 1;
- double poiss_lambda = 1;
-
- // Simulation running parameters:
- double tfinal = 100.;
- double dt = 1;
- uint32_t group_size = 10;
- uint32_t seed = 42;
-
- // Parameters for spike output.
- bool spike_file_output = false;
-
- // Turn on/off profiling output for all ranks.
- bool profile_only_zero = false;
-
- // Be more verbose with informational messages.
- bool verbose = false;
- };
-
- class usage_error: public std::runtime_error {
- public:
- template <typename S>
- usage_error(S&& whatmsg): std::runtime_error(std::forward<S>(whatmsg)) {}
- };
-
- class model_description_error: public std::runtime_error {
- public:
- template <typename S>
- model_description_error(S&& whatmsg): std::runtime_error(std::forward<S>(whatmsg)) {}
- };
-
- std::ostream& operator<<(std::ostream& o, const cl_options& opt);
-
- cl_options read_options(int argc, char** argv);
-} // namespace io
diff --git a/example/brunel/readme.md b/example/brunel/readme.md
index 46b7fc52..8168b6fe 100644
--- a/example/brunel/readme.md
+++ b/example/brunel/readme.md
@@ -31,5 +31,5 @@ The parameters that can be passed as command-line arguments are the following:
For example, we could run the miniapp as follows:
```
-./example/brunel_miniapp.exe -n 400 -m 100 -e 20 -p 0.1 -w 1.2 -d 1 -g 0.5 -l 5 -t 100 -s 1 -G 50 -S 123 -f
+./brunel -n 400 -m 100 -e 20 -p 0.1 -w 1.2 -d 1 -g 0.5 -l 5 -t 100 -s 1 -G 50 -S 123 -f
```
diff --git a/example/dryrun/dryrun.cpp b/example/dryrun/dryrun.cpp
index b9e5619e..42b4ca7e 100644
--- a/example/dryrun/dryrun.cpp
+++ b/example/dryrun/dryrun.cpp
@@ -24,14 +24,38 @@
#include <sup/ioutil.hpp>
#include <sup/json_meter.hpp>
-
-#include "parameters.hpp"
+#include <sup/json_params.hpp>
#ifdef ARB_MPI_ENABLED
#include <mpi.h>
#include <arborenv/with_mpi.hpp>
#endif
+// Parameters used to generate the random cell morphologies.
+struct cell_parameters {
+ // Maximum number of levels in the cell (not including the soma)
+ unsigned max_depth = 5;
+
+ // The following parameters are described as ranges.
+ // The first value is at the soma, and the last value is used on the last level.
+ // Values at levels in between are found by linear interpolation.
+ std::array<double,2> branch_probs = {1.0, 0.5}; // Probability of a branch occuring.
+ std::array<unsigned,2> compartments = {20, 2}; // Compartment count on a branch.
+ std::array<double,2> lengths = {200, 20}; // Length of branch in μm.
+};
+
+struct run_params {
+ std::string name = "default";
+ bool dry_run = false;
+ unsigned num_cells_per_rank = 10;
+ unsigned num_ranks = 1;
+ double min_delay = 10;
+ double duration = 100;
+ cell_parameters cell;
+};
+
+run_params read_options(int argc, char** argv);
+
using arb::cell_gid_type;
using arb::cell_lid_type;
using arb::cell_size_type;
@@ -360,3 +384,46 @@ arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& param
return cell;
}
+run_params read_options(int argc, char** argv) {
+ using sup::param_from_json;
+
+ run_params params;
+ if (argc<2) {
+ std::cout << "Using default parameters.\n";
+ return params;
+ }
+ if (argc>2) {
+ throw std::runtime_error("More than command line one option not permitted.");
+ }
+
+ std::string fname = argv[1];
+ std::cout << "Loading parameters from file: " << fname << "\n";
+ std::ifstream f(fname);
+
+ if (!f.good()) {
+ throw std::runtime_error("Unable to open input parameter file: "+fname);
+ }
+
+ nlohmann::json json;
+ json << f;
+
+ param_from_json(params.name, "name", json);
+ param_from_json(params.dry_run, "dry-run", json);
+ param_from_json(params.num_cells_per_rank, "num-cells-per-rank", json);
+ param_from_json(params.num_ranks, "num-ranks", json);
+ param_from_json(params.duration, "duration", json);
+ param_from_json(params.min_delay, "min-delay", json);
+ param_from_json(params.cell.max_depth, "depth", json);
+ param_from_json(params.cell.branch_probs, "branch-probs", json);
+ param_from_json(params.cell.compartments, "compartments", json);
+ param_from_json(params.cell.lengths, "lengths", json);
+
+ if (!json.empty()) {
+ for (auto it=json.begin(); it!=json.end(); ++it) {
+ std::cout << " Warning: unused input parameter: \"" << it.key() << "\"\n";
+ }
+ std::cout << "\n";
+ }
+
+ return params;
+}
diff --git a/example/dryrun/parameters.hpp b/example/dryrun/parameters.hpp
deleted file mode 100644
index e355fcf8..00000000
--- a/example/dryrun/parameters.hpp
+++ /dev/null
@@ -1,81 +0,0 @@
-#include <iostream>
-
-#include <array>
-#include <cmath>
-#include <fstream>
-#include <random>
-
-#include <arbor/cable_cell.hpp>
-
-#include <sup/json_params.hpp>
-
-// Parameters used to generate the random cell morphologies.
-struct cell_parameters {
- cell_parameters() = default;
-
- // Maximum number of levels in the cell (not including the soma)
- unsigned max_depth = 5;
-
- // The following parameters are described as ranges.
- // The first value is at the soma, and the last value is used on the last level.
- // Values at levels in between are found by linear interpolation.
- std::array<double,2> branch_probs = {1.0, 0.5}; // Probability of a branch occuring.
- std::array<unsigned,2> compartments = {20, 2}; // Compartment count on a branch.
- std::array<double,2> lengths = {200, 20}; // Length of branch in μm.
-};
-
-struct run_params {
- run_params() = default;
-
- std::string name = "default";
- bool dry_run = false;
- unsigned num_cells_per_rank = 10;
- unsigned num_ranks = 1;
- double min_delay = 10;
- double duration = 100;
- cell_parameters cell;
-};
-
-run_params read_options(int argc, char** argv) {
- using sup::param_from_json;
-
- run_params params;
- if (argc<2) {
- std::cout << "Using default parameters.\n";
- return params;
- }
- if (argc>2) {
- throw std::runtime_error("More than command line one option not permitted.");
- }
-
- std::string fname = argv[1];
- std::cout << "Loading parameters from file: " << fname << "\n";
- std::ifstream f(fname);
-
- if (!f.good()) {
- throw std::runtime_error("Unable to open input parameter file: "+fname);
- }
-
- nlohmann::json json;
- json << f;
-
- param_from_json(params.name, "name", json);
- param_from_json(params.dry_run, "dry-run", json);
- param_from_json(params.num_cells_per_rank, "num-cells-per-rank", json);
- param_from_json(params.num_ranks, "num-ranks", json);
- param_from_json(params.duration, "duration", json);
- param_from_json(params.min_delay, "min-delay", json);
- param_from_json(params.cell.max_depth, "depth", json);
- param_from_json(params.cell.branch_probs, "branch-probs", json);
- param_from_json(params.cell.compartments, "compartments", json);
- param_from_json(params.cell.lengths, "lengths", json);
-
- if (!json.empty()) {
- for (auto it=json.begin(); it!=json.end(); ++it) {
- std::cout << " Warning: unused input parameter: \"" << it.key() << "\"\n";
- }
- std::cout << "\n";
- }
-
- return params;
-}
diff --git a/example/gap_junctions/CMakeLists.txt b/example/gap_junctions/CMakeLists.txt
index 60a68d61..abd78ebe 100644
--- a/example/gap_junctions/CMakeLists.txt
+++ b/example/gap_junctions/CMakeLists.txt
@@ -1,4 +1,4 @@
-add_executable(gap_junctions EXCLUDE_FROM_ALL gap_junctions.cpp parameters.hpp)
+add_executable(gap_junctions EXCLUDE_FROM_ALL gap_junctions.cpp)
add_dependencies(examples gap_junctions)
target_link_libraries(gap_junctions PRIVATE arbor arborenv arbor-sup ext-json)
diff --git a/example/gap_junctions/gap_junctions.cpp b/example/gap_junctions/gap_junctions.cpp
index 4a633a77..f3e1e26e 100644
--- a/example/gap_junctions/gap_junctions.cpp
+++ b/example/gap_junctions/gap_junctions.cpp
@@ -10,6 +10,7 @@
#include <nlohmann/json.hpp>
#include <arbor/assert_macro.hpp>
+#include <arbor/cable_cell.hpp>
#include <arbor/common_types.hpp>
#include <arbor/context.hpp>
#include <arbor/load_balance.hpp>
@@ -26,14 +27,26 @@
#include <sup/ioutil.hpp>
#include <sup/json_meter.hpp>
-
-#include "parameters.hpp"
+#include <sup/json_params.hpp>
#ifdef ARB_MPI_ENABLED
#include <mpi.h>
#include <arborenv/with_mpi.hpp>
#endif
+struct gap_params {
+ std::string name = "default";
+ unsigned n_cables = 3;
+ unsigned n_cells_per_cable = 5;
+ double stim_duration = 30;
+ double event_min_delay = 10;
+ double event_weight = 0.05;
+ double sim_duration = 100;
+ bool print_all = true;
+};
+
+gap_params read_options(int argc, char** argv);
+
using arb::cell_gid_type;
using arb::cell_lid_type;
using arb::cell_size_type;
@@ -371,3 +384,44 @@ arb::cable_cell gj_cell(cell_gid_type gid, unsigned ncell, double stim_duration)
return cell;
}
+gap_params read_options(int argc, char** argv) {
+ using sup::param_from_json;
+
+ gap_params params;
+ if (argc<2) {
+ std::cout << "Using default parameters.\n";
+ return params;
+ }
+ if (argc>2) {
+ throw std::runtime_error("More than command line one option not permitted.");
+ }
+
+ std::string fname = argv[1];
+ std::cout << "Loading parameters from file: " << fname << "\n";
+ std::ifstream f(fname);
+
+ if (!f.good()) {
+ throw std::runtime_error("Unable to open input parameter file: "+fname);
+ }
+
+ nlohmann::json json;
+ json << f;
+
+ param_from_json(params.name, "name", json);
+ param_from_json(params.n_cables, "n-cables", json);
+ param_from_json(params.n_cells_per_cable, "n-cells-per-cable", json);
+ param_from_json(params.stim_duration, "stim-duration", json);
+ param_from_json(params.event_min_delay, "event-min-delay", json);
+ param_from_json(params.event_weight, "event-weight", json);
+ param_from_json(params.sim_duration, "sim-duration", json);
+ param_from_json(params.print_all, "print-all", json);
+
+ if (!json.empty()) {
+ for (auto it=json.begin(); it!=json.end(); ++it) {
+ std::cout << " Warning: unused input parameter: \"" << it.key() << "\"\n";
+ }
+ std::cout << "\n";
+ }
+
+ return params;
+}
diff --git a/example/gap_junctions/parameters.hpp b/example/gap_junctions/parameters.hpp
deleted file mode 100644
index f68ddfd2..00000000
--- a/example/gap_junctions/parameters.hpp
+++ /dev/null
@@ -1,65 +0,0 @@
-#include <iostream>
-
-#include <array>
-#include <cmath>
-#include <fstream>
-#include <random>
-
-#include <arbor/cable_cell.hpp>
-
-#include <sup/json_params.hpp>
-
-struct gap_params {
- gap_params() = default;
-
- std::string name = "default";
- unsigned n_cables = 3;
- unsigned n_cells_per_cable = 5;
- double stim_duration = 30;
- double event_min_delay = 10;
- double event_weight = 0.05;
- double sim_duration = 100;
- bool print_all = true;
-};
-
-gap_params read_options(int argc, char** argv) {
- using sup::param_from_json;
-
- gap_params params;
- if (argc<2) {
- std::cout << "Using default parameters.\n";
- return params;
- }
- if (argc>2) {
- throw std::runtime_error("More than command line one option not permitted.");
- }
-
- std::string fname = argv[1];
- std::cout << "Loading parameters from file: " << fname << "\n";
- std::ifstream f(fname);
-
- if (!f.good()) {
- throw std::runtime_error("Unable to open input parameter file: "+fname);
- }
-
- nlohmann::json json;
- json << f;
-
- param_from_json(params.name, "name", json);
- param_from_json(params.n_cables, "n-cables", json);
- param_from_json(params.n_cells_per_cable, "n-cells-per-cable", json);
- param_from_json(params.stim_duration, "stim-duration", json);
- param_from_json(params.event_min_delay, "event-min-delay", json);
- param_from_json(params.event_weight, "event-weight", json);
- param_from_json(params.sim_duration, "sim-duration", json);
- param_from_json(params.print_all, "print-all", json);
-
- if (!json.empty()) {
- for (auto it=json.begin(); it!=json.end(); ++it) {
- std::cout << " Warning: unused input parameter: \"" << it.key() << "\"\n";
- }
- std::cout << "\n";
- }
-
- return params;
-}
diff --git a/example/generators/CMakeLists.txt b/example/generators/CMakeLists.txt
index 5b917bad..7bfaca9f 100644
--- a/example/generators/CMakeLists.txt
+++ b/example/generators/CMakeLists.txt
@@ -1,4 +1,4 @@
-add_executable(event-gen EXCLUDE_FROM_ALL event_gen.cpp)
-add_dependencies(examples event-gen)
+add_executable(generators EXCLUDE_FROM_ALL generators.cpp)
+add_dependencies(examples generators)
-target_link_libraries(event-gen PRIVATE arbor arbor-sup ext-json)
+target_link_libraries(generators PRIVATE arbor arbor-sup ext-json)
diff --git a/example/generators/event_gen.cpp b/example/generators/generators.cpp
similarity index 100%
rename from example/generators/event_gen.cpp
rename to example/generators/generators.cpp
diff --git a/example/ring/parameters.hpp b/example/ring/parameters.hpp
deleted file mode 100644
index 6343cb3c..00000000
--- a/example/ring/parameters.hpp
+++ /dev/null
@@ -1,81 +0,0 @@
-#include <iostream>
-
-#include <array>
-#include <cmath>
-#include <fstream>
-#include <random>
-
-#include <arbor/cable_cell.hpp>
-
-#include <sup/json_params.hpp>
-
-// Parameters used to generate the random cell morphologies.
-struct cell_parameters {
- cell_parameters() = default;
-
- // Maximum number of levels in the cell (not including the soma)
- unsigned max_depth = 5;
-
- // The following parameters are described as ranges.
- // The first value is at the soma, and the last value is used on the last level.
- // Values at levels in between are found by linear interpolation.
- std::array<double,2> branch_probs = {1.0, 0.5}; // Probability of a branch occuring.
- std::array<unsigned,2> compartments = {20, 2}; // Compartment count on a branch.
- std::array<double,2> lengths = {200, 20}; // Length of branch in μm.
-
- // The number of synapses per cell.
- unsigned synapses = 1;
-};
-
-struct ring_params {
- ring_params() = default;
-
- std::string name = "default";
- unsigned num_cells = 10;
- double min_delay = 10;
- double duration = 100;
- cell_parameters cell;
-};
-
-ring_params read_options(int argc, char** argv) {
- using sup::param_from_json;
-
- ring_params params;
- if (argc<2) {
- std::cout << "Using default parameters.\n";
- return params;
- }
- if (argc>2) {
- throw std::runtime_error("More than command line one option not permitted.");
- }
-
- std::string fname = argv[1];
- std::cout << "Loading parameters from file: " << fname << "\n";
- std::ifstream f(fname);
-
- if (!f.good()) {
- throw std::runtime_error("Unable to open input parameter file: "+fname);
- }
-
- nlohmann::json json;
- json << f;
-
- param_from_json(params.name, "name", json);
- param_from_json(params.num_cells, "num-cells", json);
- param_from_json(params.duration, "duration", json);
- param_from_json(params.min_delay, "min-delay", json);
- param_from_json(params.cell.max_depth, "depth", json);
- param_from_json(params.cell.branch_probs, "branch-probs", json);
- param_from_json(params.cell.compartments, "compartments", json);
- param_from_json(params.cell.lengths, "lengths", json);
- param_from_json(params.cell.synapses, "synapses", json);
-
- if (!json.empty()) {
- for (auto it=json.begin(); it!=json.end(); ++it) {
- std::cout << " Warning: unused input parameter: \"" << it.key() << "\"\n";
- }
- std::cout << "\n";
- }
-
- return params;
-}
diff --git a/example/ring/ring.cpp b/example/ring/ring.cpp
index 55c4cea2..6f426032 100644
--- a/example/ring/ring.cpp
+++ b/example/ring/ring.cpp
@@ -11,6 +11,7 @@
#include <arbor/assert_macro.hpp>
#include <arbor/common_types.hpp>
+#include <arbor/cable_cell.hpp>
#include <arbor/context.hpp>
#include <arbor/load_balance.hpp>
#include <arbor/cable_cell.hpp>
@@ -26,14 +27,42 @@
#include <sup/ioutil.hpp>
#include <sup/json_meter.hpp>
-
-#include "parameters.hpp"
+#include <sup/json_params.hpp>
#ifdef ARB_MPI_ENABLED
#include <mpi.h>
#include <arborenv/with_mpi.hpp>
#endif
+// Parameters used to generate the random cell morphologies.
+struct cell_parameters {
+ cell_parameters() = default;
+
+ // Maximum number of levels in the cell (not including the soma)
+ unsigned max_depth = 5;
+
+ // The following parameters are described as ranges.
+ // The first value is at the soma, and the last value is used on the last level.
+ // Values at levels in between are found by linear interpolation.
+ std::array<double,2> branch_probs = {1.0, 0.5}; // Probability of a branch occuring.
+ std::array<unsigned,2> compartments = {20, 2}; // Compartment count on a branch.
+ std::array<double,2> lengths = {200, 20}; // Length of branch in μm.
+
+ // The number of synapses per cell.
+ unsigned synapses = 1;
+};
+
+struct ring_params {
+ ring_params() = default;
+
+ std::string name = "default";
+ unsigned num_cells = 10;
+ double min_delay = 10;
+ double duration = 100;
+ cell_parameters cell;
+};
+
+ring_params read_options(int argc, char** argv);
using arb::cell_gid_type;
using arb::cell_lid_type;
using arb::cell_size_type;
@@ -364,3 +393,46 @@ arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& param
return cell;
}
+ring_params read_options(int argc, char** argv) {
+ using sup::param_from_json;
+
+ ring_params params;
+ if (argc<2) {
+ std::cout << "Using default parameters.\n";
+ return params;
+ }
+ if (argc>2) {
+ throw std::runtime_error("More than command line one option not permitted.");
+ }
+
+ std::string fname = argv[1];
+ std::cout << "Loading parameters from file: " << fname << "\n";
+ std::ifstream f(fname);
+
+ if (!f.good()) {
+ throw std::runtime_error("Unable to open input parameter file: "+fname);
+ }
+
+ nlohmann::json json;
+ json << f;
+
+ param_from_json(params.name, "name", json);
+ param_from_json(params.num_cells, "num-cells", json);
+ param_from_json(params.duration, "duration", json);
+ param_from_json(params.min_delay, "min-delay", json);
+ param_from_json(params.cell.max_depth, "depth", json);
+ param_from_json(params.cell.branch_probs, "branch-probs", json);
+ param_from_json(params.cell.compartments, "compartments", json);
+ param_from_json(params.cell.lengths, "lengths", json);
+ param_from_json(params.cell.synapses, "synapses", json);
+
+ if (!json.empty()) {
+ for (auto it=json.begin(); it!=json.end(); ++it) {
+ std::cout << " Warning: unused input parameter: \"" << it.key() << "\"\n";
+ }
+ std::cout << "\n";
+ }
+
+ return params;
+}
+
--
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