diff --git a/miniapp/miniapp.cpp b/miniapp/miniapp.cpp
index 9e96afa63a6a98cec68575d98c4e5683093e76de..9f98b08fd5e740291d34142997b487db095a6bad 100644
--- a/miniapp/miniapp.cpp
+++ b/miniapp/miniapp.cpp
@@ -10,14 +10,14 @@
#include <common_types.hpp>
#include <cell.hpp>
#include <cell_group.hpp>
+#include <communication/communicator.hpp>
+#include <communication/global_policy.hpp>
#include <fvm_cell.hpp>
+#include <io/exporter_spike_file.hpp>
#include <mechanism_catalogue.hpp>
#include <model.hpp>
-#include <threading/threading.hpp>
#include <profiling/profiler.hpp>
-#include <communication/communicator.hpp>
-#include <communication/global_policy.hpp>
-#include <io/exporter_spike_file.hpp>
+#include <threading/threading.hpp>
#include <util/ioutil.hpp>
#include <util/optional.hpp>
@@ -28,7 +28,6 @@
using namespace nest::mc;
using global_policy = communication::global_policy;
-
using lowered_cell = fvm::fvm_cell<double, cell_local_size_type>;
using model_type = model<lowered_cell>;
using time_type = model_type::time_type;
@@ -219,5 +218,3 @@ void write_trace_json(const sample_trace_type& trace, const std::string& prefix)
std::ofstream file(path);
file << std::setw(1) << jrep << std::endl;
}
-
-
diff --git a/src/io/exporter_spike_file.hpp b/src/io/exporter_spike_file.hpp
index 032d847fedbf49c8a9299f030a21c3d81d3b5ae7..e74169d19f17090c3ca16781a5f380fc0d29cc89 100644
--- a/src/io/exporter_spike_file.hpp
+++ b/src/io/exporter_spike_file.hpp
@@ -1,7 +1,5 @@
#pragma once
-#include <cstring>
-#include <cstdio>
#include <fstream>
#include <iomanip>
#include <memory>
@@ -9,6 +7,9 @@
#include <stdexcept>
#include <vector>
+#include <cstring>
+#include <cstdio>
+
#include <common_types.hpp>
#include <io/exporter.hpp>
#include <spike.hpp>
@@ -19,8 +20,8 @@ namespace mc {
namespace io {
template <typename Time, typename CommunicationPolicy>
-class exporter_spike_file : public exporter<Time, CommunicationPolicy>
-{
+class exporter_spike_file : public exporter<Time, CommunicationPolicy> {
+
public:
using time_type = Time;
using spike_type = spike<cell_member_type, time_type>;
@@ -31,7 +32,8 @@ public:
// output_path relative or absolute path
// file_name will be appended with "_x" with x the rank number
// file_extention a seperator will be added automatically
- exporter_spike_file(const std::string& file_name, const std::string& path,
+ exporter_spike_file(
+ const std::string& file_name, const std::string& path,
const std::string& file_extention, bool over_write=true)
{
auto file_path =
@@ -39,8 +41,7 @@ public:
communication_policy_.id());
//test if the file exist and depending on over_write throw or delete
- if (!over_write && file_exists(file_path))
- {
+ if (!over_write && file_exists(file_path)) {
throw std::runtime_error("Tried opening file for writing but it exists and over_write is false: " +
file_path);
}
@@ -51,8 +52,8 @@ public:
// Performs the a export of the spikes to file
// one id and spike time with 4 decimals after the comma on a
// line space separated
- void output(const std::vector<spike_type>& spikes) override
- {
+ void output(const std::vector<spike_type>& spikes) override {
+
for (auto spike : spikes) {
char linebuf[45];
auto n = std::snprintf(linebuf, sizeof(linebuf), "%u %.4f\n",
@@ -61,15 +62,15 @@ public:
}
}
- bool good() const override
- {
+ bool good() const override {
+
return file_handle_.good();
}
// Creates an indexed filename
- static std::string create_output_file_path(const std::string& file_name,
- const std::string& path, const std::string& file_extention,
- unsigned index)
+ static std::string create_output_file_path(
+ const std::string& file_name, const std::string& path,
+ const std::string& file_extention, unsigned index)
{
// Nest does not produce the indexing for nrank == 0
// I have the feeling this disrupts consistent output. Id rather
@@ -80,9 +81,8 @@ public:
}
private:
+ bool file_exists(const std::string& file_path) {
- bool file_exists(const std::string& file_path)
- {
std::ifstream fid(file_path);
return fid.good();
}
@@ -91,7 +91,6 @@ private:
std::ofstream file_handle_;
communication_policy_type communication_policy_;
-
};
} //communication
diff --git a/src/model.hpp b/src/model.hpp
index e78cb44e902cff63e333705f9d4ddb5f08b405a7..823fcd45662cfc414b7a04964bc7fb91b9b78281 100644
--- a/src/model.hpp
+++ b/src/model.hpp
@@ -1,18 +1,19 @@
#pragma once
-#include <cstdlib>
+#include <memory>
#include <vector>
+#include <cstdlib>
+
#include <common_types.hpp>
#include <cell.hpp>
#include <cell_group.hpp>
-#include <fvm_cell.hpp>
-#include <memory>
-#include <recipe.hpp>
-#include <thread_private_spike_store.hpp>
#include <communication/communicator.hpp>
#include <communication/global_policy.hpp>
+#include <fvm_cell.hpp>
#include <profiling/profiler.hpp>
+#include <recipe.hpp>
+#include <thread_private_spike_store.hpp>
#include "trace_sampler.hpp"
@@ -138,8 +139,8 @@ public:
PE("stepping", "exchange");
auto local_spikes = previous_spikes().gather();
local_export_callback_(local_spikes);
- future_events() = communicator_.exchange(local_spikes,
- global_export_callback_);
+ future_events() = communicator_.exchange(
+ local_spikes, global_export_callback_);
PL(2);
};
@@ -180,15 +181,15 @@ public:
// register a callback that will perform a export of the global
// spike vector
- void set_global_spike_callback(spike_export_function export_callback)
- {
+ void set_global_spike_callback(spike_export_function export_callback) {
+
global_export_callback_ = export_callback;
}
// register a callback that will perform a export of the rank local
// spike vector
- void set_local_spike_callback(spike_export_function export_callback)
- {
+ void set_local_spike_callback(spike_export_function export_callback) {
+
local_export_callback_ = export_callback;
}
@@ -200,7 +201,6 @@ private:
communicator_type communicator_;
std::vector<probe_record> probes_;
-
using event_queue_type = typename communicator_type::event_queue;
util::double_buffer< std::vector<event_queue_type> > event_queues_;
@@ -209,6 +209,7 @@ private:
spike_export_function global_export_callback_;
spike_export_function local_export_callback_;
+
// Convenience functions that map the spike buffers and event queues onto
// the appropriate integration interval.
//
diff --git a/tests/performance/io/disk_io.cpp b/tests/performance/io/disk_io.cpp
index 2ca05c8b8caa9357927839fae41b7102847c3dd6..526263bf395a81eb36ed050b96cfe1923e04cd25 100644
--- a/tests/performance/io/disk_io.cpp
+++ b/tests/performance/io/disk_io.cpp
@@ -1,18 +1,15 @@
-#include <cstdlib>
-#include <ctime>
+#include <stdio.h>
+
#include <fstream>
#include <iostream>
#include <numeric>
-#include <stdio.h>
-#include <cstring>
#include <cell.hpp>
#include <cell_group.hpp>
#include <common_types.hpp>
-#include <fvm_cell.hpp>
-
#include <communication/communicator.hpp>
#include <communication/global_policy.hpp>
+#include <fvm_cell.hpp>
#include <io/exporter_spike_file.hpp>
#include <profiling/profiler.hpp>
@@ -22,35 +19,37 @@ using global_policy = communication::global_policy;
using lowered_cell = fvm::fvm_cell<double, cell_local_size_type>;
using cell_group_type = cell_group<lowered_cell>;
using time_type = typename cell_group_type::time_type;
-using spike_type = io::exporter_spike_file<time_type,
- global_policy>::spike_type;
+using spike_type = io::exporter_spike_file<time_type, global_policy>::spike_type;
using timer = util::timer_type;
-int main(int argc, char** argv)
-{
+int main(int argc, char** argv) {
+
//Setup the possible mpi environment
communication::global_policy_guard global_guard(argc, argv);
// very simple command line parsing
if (argc < 3) {
std::cout << "disk_io <int nrspikes> <int nr_repeats> [simple_output (false|true)]\n"
- << " Simple performance test runner for the exporter manager\n"
- << " It exports nrspikes nr_repeats using the export_manager and will produce\n"
- << " the total, mean and std of the time needed to perform the output to disk\n"
- << " <file_per_rank> true will produce a single file per mpi rank\n"
- << " <simple_output> true will produce a simplyfied comma seperated output for automatic parsing\n"
- << " The application can be started with mpi support and will produce output on a single rank\n"
- << " if nrspikes is not a multiple of the nr of mpi rank, floor is take\n" ;
+ << " Simple performance test runner for the exporter manager\n"
+ << " It exports nrspikes nr_repeats using the export_manager and will produce\n"
+ << " the total, mean and std of the time needed to perform the output to disk\n\n"
+
+ << " <file_per_rank> true will produce a single file per mpi rank\n"
+ << " <simple_output> true will produce a simplyfied comma seperated output for automatic parsing\n\n"
+
+ << " The application can be started with mpi support and will produce output on a single rank\n"
+ << " if nrspikes is not a multiple of the nr of mpi rank, floor is take\n" ;
return 1;
}
- int nr_spikes = atoi(argv[1]);
+ auto nr_spikes = atoi(argv[1]);
if (nr_spikes == 0) {
std::cout << "disk_io <nrspikes>\n";
std::cout << " nrspikes should be a valid integer higher then zero\n";
+
return 1;
}
- int nr_repeats = atoi(argv[2]);
+ auto nr_repeats = atoi(argv[2]);
if (nr_repeats == 0) {
std::cout << "disk_io <nrspikes>\n";
@@ -58,8 +57,8 @@ int main(int argc, char** argv)
return 1;
}
- bool simple_stats = false;
- if (argc == 5) {
+ auto simple_stats = false;
+ if (argc == 4) {
std::string simple(argv[3]);
if (simple == std::string("true"))
{
@@ -68,14 +67,15 @@ int main(int argc, char** argv)
}
// Create the sut
- io::exporter_spike_file<time_type, global_policy> exporter(
+ io::exporter_spike_file<time_type, global_policy> exporter(
"spikes", "./", "gdf", true);
// We need the nr of ranks to calculate the nr of spikes to produce per
// rank
global_policy communication_policy;
- unsigned nr_ranks = communication_policy.size();
- unsigned spikes_per_rank = nr_spikes / nr_ranks;
+
+ auto nr_ranks = unsigned( communication_policy.size() );
+ auto spikes_per_rank = nr_spikes / nr_ranks;
// Create a set of spikes
std::vector<spike_type> spikes;
@@ -87,10 +87,13 @@ int main(int argc, char** argv)
// influences the size of the output and thus the speed
// Also taken that we have only a single second of simulated time
// all spike times should be between 0.0 and 1.0:
- unsigned simulated_neurons = spikes_per_rank / 20;
- for (unsigned idx = 0; idx < spikes_per_rank; ++idx) {
- spikes.push_back({ { idx % simulated_neurons, 0 }, // correct idx
- 0.0f + 1 / (0.05f + idx % 20) }); // semi random float
+ auto simulated_neurons = spikes_per_rank / 20;
+ for (auto idx = unsigned{ 0 }; idx < spikes_per_rank; ++idx) {
+
+ spikes.push_back({
+ {idx % simulated_neurons, 0 }, // correct idx
+ 0.0f + 1 / (0.05f + idx % 20)
+ }); // semi random float
}
double timings_arr[nr_repeats];
@@ -99,9 +102,9 @@ int main(int argc, char** argv)
// now output to disk nr_repeats times, while keeping track of the times
for (auto idx = 0; idx < nr_repeats; ++idx) {
auto time_start = timer::tic();
-
exporter.output(spikes);
auto run_time = timer::toc(time_start);
+
time_total += run_time;
timings_arr[idx] = run_time;
}
@@ -119,10 +122,14 @@ int main(int argc, char** argv)
auto mean = sum / timings.size();
std::vector<double> diff(timings.size());
- std::transform(timings.begin(), timings.end(), diff.begin(),
- std::bind2nd(std::minus<double>(), mean));
- auto sq_sum = std::inner_product(diff.begin(), diff.end(), diff.begin(),
- 0.0);
+ std::transform(
+ timings.begin(), timings.end(), diff.begin(),
+ std::bind2nd(std::minus<double>(), mean)
+ );
+ auto sq_sum = std::inner_product(
+ diff.begin(), diff.end(), diff.begin(),
+ 0.0
+ );
auto stdev = std::sqrt(sq_sum / timings.size());
auto min = *std::min_element(timings.begin(), timings.end());
diff --git a/tests/performance/io/disk_io.py b/tests/performance/io/disk_io.py
index e0ab58ef71e0b4cf662671f0b360c2245ec1bf95..ea42304b23e2da851058b8b6d7625f8185ec0db3 100644
--- a/tests/performance/io/disk_io.py
+++ b/tests/performance/io/disk_io.py
@@ -2,10 +2,17 @@ import matplotlib.pyplot as plt
import subprocess
import os
+
+
current_script_dir = os.path.dirname(os.path.abspath(__file__))
spikes_to_save = 1000000
+print ( "Simple performance runner for spike output to file. \n" +
+ str(spikes_to_save) + " spikes will be written to a file and the duration of this \n" +
+ "operation measured for different number of ranks\n" )
+
+
range_nr_rank = [1, 2, 4, 8, 16, 24, 32, 48, 64]
mean = []
std = []
@@ -15,7 +22,7 @@ for n_rank in range_nr_rank:
# open the disk_io executable
p1 = subprocess.Popen(["mpirun", "-n",str(n_rank),
os.path.join(current_script_dir, "disk_io.exe"),
- str(spikes_to_save), str(10), "true" ,"true"],
+ str(spikes_to_save), str(10), "true"],
stdout=subprocess.PIPE)
#and grab the raw stats