From 4dc40c5869e74be68ae1df4c4f1e44dbb41bb541 Mon Sep 17 00:00:00 2001
From: Sam Yates <yates@cscs.ch>
Date: Fri, 1 Feb 2019 11:47:39 +0100
Subject: [PATCH] Feature/expunge spike emitter (#682)
Remove `sup::spike_emitter` and replace usages in `miniapp` and `brunel-miniapp`.
* Replaces instances of `spike_emitter` in `miniapp` and `brunel-miniapp` with a callback that saves spikes to a vector and which is written to a file after the simulation ends.
* Remove unused fields from `cl_options` in `brunel-miniapp`, including spike output file components.
* Hard code spike output path to `spikes.gdf` in `brunel-miniapp` and write saved spikes after simulation end.
* Correctly set 'rank' in `miniapp` (used in spike output paths).
* Read spike output options from JSON config in `miniapp` unconditionally.
* Make line comments in `miniapp` and `brunel-miniapp` main functions a bit more consistent in
formatting.
Fixes #677.
---
example/brunel/brunel_miniapp.cpp | 41 ++++++++++++++------------
example/brunel/io.cpp | 3 +-
example/brunel/io.hpp | 7 +----
example/miniapp/io.cpp | 12 ++++----
example/miniapp/miniapp.cpp | 48 ++++++++++++++++++++-----------
sup/CMakeLists.txt | 1 -
sup/include/sup/spike_emitter.hpp | 16 -----------
sup/spike_emitter.cpp | 23 ---------------
test/unit/CMakeLists.txt | 1 -
test/unit/test_spike_emitter.cpp | 30 -------------------
10 files changed, 60 insertions(+), 122 deletions(-)
delete mode 100644 sup/include/sup/spike_emitter.hpp
delete mode 100644 sup/spike_emitter.cpp
delete mode 100644 test/unit/test_spike_emitter.cpp
diff --git a/example/brunel/brunel_miniapp.cpp b/example/brunel/brunel_miniapp.cpp
index 2041b7bf..1c83d2bc 100644
--- a/example/brunel/brunel_miniapp.cpp
+++ b/example/brunel/brunel_miniapp.cpp
@@ -1,6 +1,7 @@
#include <cmath>
#include <exception>
#include <fstream>
+#include <iomanip>
#include <iostream>
#include <memory>
#include <set>
@@ -24,7 +25,6 @@
#include <sup/ioutil.hpp>
#include <sup/json_meter.hpp>
#include <sup/path.hpp>
-#include <sup/spike_emitter.hpp>
#include <sup/strsub.hpp>
#ifdef ARB_MPI_ENABLED
@@ -216,7 +216,12 @@ int main(int argc, char** argv) {
meters.start(context);
// read parameters
- io::cl_options options = io::read_options(argc, argv, root);
+ io::cl_options options = io::read_options(argc, argv);
+
+ std::fstream spike_out;
+ if (options.spike_file_output && root) {
+ spike_out = sup::open_or_throw("./spikes.gdf", std::ios_base::out, false);
+ }
meters.checkpoint("setup", context);
@@ -257,31 +262,29 @@ int main(int argc, char** argv) {
simulation sim(recipe, decomp, context);
- // Initialize the spike exporting interface
- std::fstream spike_out;
- if (options.spike_file_output) {
- using std::ios_base;
-
- sup::path p = options.output_path;
- p /= sup::strsub("%_%.%", options.file_name, rank, options.file_extension);
-
- if (options.single_file_per_rank) {
- spike_out = sup::open_or_throw(p, ios_base::out, !options.over_write);
- sim.set_local_spike_callback(sup::spike_emitter(spike_out));
- }
- else if (root) {
- spike_out = sup::open_or_throw(p, ios_base::out, !options.over_write);
- sim.set_global_spike_callback(sup::spike_emitter(spike_out));
- }
+ // Set up spike recording.
+ std::vector<arb::spike> recorded_spikes;
+ if (spike_out) {
+ sim.set_global_spike_callback([&recorded_spikes](auto& spikes) {
+ recorded_spikes.insert(recorded_spikes.end(), spikes.begin(), spikes.end());
+ });
}
meters.checkpoint("model-init", context);
- // run simulation
+ // Run simulation.
sim.run(options.tfinal, options.dt);
meters.checkpoint("model-simulate", context);
+ // Output spikes if requested.
+ if (spike_out) {
+ spike_out << std::fixed << std::setprecision(4);
+ for (auto& s: recorded_spikes) {
+ spike_out << s.source.gid << ' ' << s.time << '\n';
+ }
+ }
+
// output profile and diagnostic feedback
std::cout << profile::profiler_summary() << "\n";
std::cout << "\nThere were " << sim.num_spikes() << " spikes\n";
diff --git a/example/brunel/io.cpp b/example/brunel/io.cpp
index 540cc559..72b6ca81 100644
--- a/example/brunel/io.cpp
+++ b/example/brunel/io.cpp
@@ -79,9 +79,8 @@ namespace io {
}
// Read options from (optional) json file and command line arguments.
- cl_options read_options(int argc, char** argv, bool allow_write) {
+ cl_options read_options(int argc, char** argv) {
cl_options options;
- std::string save_file = "";
// Parse command line arguments.
try {
diff --git a/example/brunel/io.hpp b/example/brunel/io.hpp
index 370e02ac..28c76bdb 100644
--- a/example/brunel/io.hpp
+++ b/example/brunel/io.hpp
@@ -30,11 +30,6 @@ namespace io {
// Parameters for spike output.
bool spike_file_output = false;
- bool single_file_per_rank = false;
- bool over_write = true;
- std::string output_path = "./";
- std::string file_name = "spikes";
- std::string file_extension = "gdf";
// Turn on/off profiling output for all ranks.
bool profile_only_zero = false;
@@ -57,5 +52,5 @@ namespace io {
std::ostream& operator<<(std::ostream& o, const cl_options& opt);
- cl_options read_options(int argc, char** argv, bool allow_write = true);
+ cl_options read_options(int argc, char** argv);
} // namespace io
diff --git a/example/miniapp/io.cpp b/example/miniapp/io.cpp
index ac171ca5..4d8b1970 100644
--- a/example/miniapp/io.cpp
+++ b/example/miniapp/io.cpp
@@ -229,13 +229,11 @@ cl_options read_options(int argc, char** argv, bool allow_write) {
// Parameters for spike output
update_option(options.spike_file_output, fopts, "spike_file_output");
- if (options.spike_file_output) {
- update_option(options.single_file_per_rank, fopts, "single_file_per_rank");
- update_option(options.over_write, fopts, "over_write");
- update_option(options.output_path, fopts, "output_path");
- update_option(options.file_name, fopts, "file_name");
- update_option(options.file_extension, fopts, "file_extension");
- }
+ update_option(options.single_file_per_rank, fopts, "single_file_per_rank");
+ update_option(options.over_write, fopts, "over_write");
+ update_option(options.output_path, fopts, "output_path");
+ update_option(options.file_name, fopts, "file_name");
+ update_option(options.file_extension, fopts, "file_extension");
update_option(options.dry_run_ranks, fopts, "dry_run_ranks");
}
diff --git a/example/miniapp/miniapp.cpp b/example/miniapp/miniapp.cpp
index 5fe1cc5f..f4d74440 100644
--- a/example/miniapp/miniapp.cpp
+++ b/example/miniapp/miniapp.cpp
@@ -1,5 +1,6 @@
#include <cmath>
#include <exception>
+#include <iomanip>
#include <iostream>
#include <fstream>
#include <memory>
@@ -23,7 +24,6 @@
#include <sup/ioutil.hpp>
#include <sup/json_meter.hpp>
#include <sup/path.hpp>
-#include <sup/spike_emitter.hpp>
#include <sup/strsub.hpp>
#ifdef ARB_MPI_ENABLED
@@ -62,7 +62,8 @@ int main(int argc, char** argv) {
arbenv::with_mpi guard(argc, argv, false);
resources.gpu_id = arbenv::find_private_gpu(MPI_COMM_WORLD);
auto context = arb::make_context(resources, MPI_COMM_WORLD);
- root = arb::rank(context) == 0;
+ rank = arb::rank(context);
+ root = rank == 0;
#else
resources.gpu_id = arbenv::default_gpu();
auto context = arb::make_context(resources);
@@ -85,6 +86,14 @@ int main(int argc, char** argv) {
// threading back end, and 1 gpu if available.
banner(context);
+ // Set up spike output if requested.
+ std::fstream spike_out;
+ if (options.spike_file_output && (root || options.single_file_per_rank)) {
+ sup::path p = options.output_path;
+ p /= sup::strsub("%_%.%", options.file_name, rank, options.file_extension);
+ spike_out = sup::open_or_throw(p, std::ios_base::out, !options.over_write);
+ }
+
meters.checkpoint("setup", context);
// determine what to attach probes to
@@ -130,37 +139,42 @@ int main(int argc, char** argv) {
sim.set_binning_policy(binning_policy, options.bin_dt);
- // Initialize the spike exporting interface
- std::fstream spike_out;
- if (options.spike_file_output) {
- using std::ios_base;
-
- sup::path p = options.output_path;
- p /= sup::strsub("%_%.%", options.file_name, rank, options.file_extension);
+ // Set up spike recording.
+ std::vector<arb::spike> recorded_spikes;
+ if (spike_out) {
+ auto spike_callback = [&recorded_spikes](auto& spikes) {
+ recorded_spikes.insert(recorded_spikes.end(), spikes.begin(), spikes.end());
+ };
if (options.single_file_per_rank) {
- spike_out = sup::open_or_throw(p, ios_base::out, !options.over_write);
- sim.set_local_spike_callback(sup::spike_emitter(spike_out));
+ sim.set_local_spike_callback(spike_callback);
}
- else if (rank==0) {
- spike_out = sup::open_or_throw(p, ios_base::out, !options.over_write);
- sim.set_global_spike_callback(sup::spike_emitter(spike_out));
+ else {
+ sim.set_global_spike_callback(spike_callback);
}
}
meters.checkpoint("model-init", context);
- // run model
+ // Run model.
sim.run(options.tfinal, options.dt);
meters.checkpoint("model-simulate", context);
- // output profile and diagnostic feedback
+ // Output profile and diagnostic feedback.
auto profile = profile::profiler_summary();
std::cout << profile << "\n";
std::cout << "\nthere were " << sim.num_spikes() << " spikes\n";
- // save traces
+ // Save spikes.
+ if (spike_out) {
+ spike_out << std::fixed << std::setprecision(4);
+ for (auto& s: recorded_spikes) {
+ spike_out << s.source.gid << ' ' << s.time << '\n';
+ }
+ }
+
+ // Save traces.
auto write_trace = options.trace_format=="json"? write_trace_json: write_trace_csv;
for (const auto& trace: sample_traces) {
write_trace(trace, options.trace_prefix);
diff --git a/sup/CMakeLists.txt b/sup/CMakeLists.txt
index 9e014f07..227a760b 100644
--- a/sup/CMakeLists.txt
+++ b/sup/CMakeLists.txt
@@ -3,7 +3,6 @@ set(sup-sources
ioutil.cpp
json_meter.cpp
path.cpp
- spike_emitter.cpp
)
add_library(arbor-sup ${sup-sources})
diff --git a/sup/include/sup/spike_emitter.hpp b/sup/include/sup/spike_emitter.hpp
deleted file mode 100644
index 0656f00b..00000000
--- a/sup/include/sup/spike_emitter.hpp
+++ /dev/null
@@ -1,16 +0,0 @@
-#include <functional>
-#include <iosfwd>
-#include <vector>
-
-#include <arbor/spike.hpp>
-
-namespace sup {
-
-struct spike_emitter {
- std::reference_wrapper<std::ostream> out;
-
- spike_emitter(std::ostream& out);
- void operator()(const std::vector<arb::spike>&);
-};
-
-} // namespace sup
diff --git a/sup/spike_emitter.cpp b/sup/spike_emitter.cpp
deleted file mode 100644
index ec451be1..00000000
--- a/sup/spike_emitter.cpp
+++ /dev/null
@@ -1,23 +0,0 @@
-#include <functional>
-#include <iostream>
-
-#include <arbor/spike.hpp>
-#include <sup/spike_emitter.hpp>
-
-namespace sup {
-
-spike_emitter::spike_emitter(std::ostream& out): out(out) {}
-
-void spike_emitter::operator()(const std::vector<arb::spike>& spikes) {
- char line[45];
- for (auto& s: spikes) {
- int n = std::snprintf(line, sizeof(line), "%u %.4f", s.source.gid, s.time);
- if (n<0) {
- throw std::system_error(errno, std::generic_category());
- }
-
- out.get().write(line, n).put('\n');
- }
-};
-
-} // namespace sup
diff --git a/test/unit/CMakeLists.txt b/test/unit/CMakeLists.txt
index b89cece7..439a1034 100644
--- a/test/unit/CMakeLists.txt
+++ b/test/unit/CMakeLists.txt
@@ -99,7 +99,6 @@ set(unit_sources
test_span.cpp
test_spikes.cpp
test_spike_store.cpp
- test_spike_emitter.cpp
test_stats.cpp
test_strprintf.cpp
test_swcio.cpp
diff --git a/test/unit/test_spike_emitter.cpp b/test/unit/test_spike_emitter.cpp
deleted file mode 100644
index a6681277..00000000
--- a/test/unit/test_spike_emitter.cpp
+++ /dev/null
@@ -1,30 +0,0 @@
-#include "../gtest.h"
-
-#include <sstream>
-#include <string>
-#include <vector>
-
-#include <arbor/spike.hpp>
-#include <sup/spike_emitter.hpp>
-
-TEST(spike_emitter, formatting) {
- std::stringstream out;
- auto callback = sup::spike_emitter(out);
-
- std::vector<arb::spike> spikes = {
- { { 0, 0 }, 0.0 },
- { { 0, 0 }, 0.1 },
- { { 1, 0 }, 1.0 },
- { { 1, 0 }, 1.1 }
- };
-
- callback(spikes);
-
- std::string expected =
- "0 0.0000\n"
- "0 0.1000\n"
- "1 1.0000\n"
- "1 1.1000\n";
-
- EXPECT_EQ(expected, out.str());
-}
--
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