diff --git a/miniapp/io.cpp b/miniapp/io.cpp
index 66a8bdecb1b35d1b400b6aec8708b4f649a77be8..d7f328e76e587c3ca506a9928738d0369d4c9e0a 100644
--- a/miniapp/io.cpp
+++ b/miniapp/io.cpp
@@ -113,9 +113,18 @@ static void update_option(util::optional<T>& opt, const nlohmann::json& j, const
cl_options read_options(int argc, char** argv) {
// Default options:
- const cl_options defopts{1000, 500, "expsyn", 100, 100., 0.025, false,
-
- false, 1.0, "trace_", util::nothing,
+ const cl_options defopts{
+ 1000, // number of cells
+ 500, // synapses_per_cell
+ "expsyn", // synapse type
+ 100, // compartments_per_segment
+ 100., // tfinal
+ 0.025, // dt
+ false, // all_to_all
+ false, // probe_soma_only
+ 1.0, // probe_ratio
+ "trace_", // trace_prefix
+ util::nothing, // trace_max_gid
// spike_output_parameters:
false, // no spike output
diff --git a/miniapp/miniapp.cpp b/miniapp/miniapp.cpp
index 195bfa55813bc47893e0f022cd0a42cabbe57b4c..f77d96be4c0e0e317d679aca057d7f79e71c0c26 100644
--- a/miniapp/miniapp.cpp
+++ b/miniapp/miniapp.cpp
@@ -17,7 +17,7 @@
#include <profiling/profiler.hpp>
#include <communication/communicator.hpp>
#include <communication/global_policy.hpp>
-#include <communication/exporter_spike_file.hpp>
+#include <io/exporter_spike_file.hpp>
#include <util/ioutil.hpp>
#include <util/optional.hpp>
diff --git a/src/communication/exporter_interface.hpp b/src/communication/exporter_interface.hpp
deleted file mode 100644
index 58178a9f5234cc62a5c2f33ca0cdd72129b88093..0000000000000000000000000000000000000000
--- a/src/communication/exporter_interface.hpp
+++ /dev/null
@@ -1,37 +0,0 @@
-#pragma once
-
-#include <random>
-#include <string>
-
-#include <common_types.hpp>
-#include <spike.hpp>
-
-namespace nest {
-namespace mc {
-namespace communication {
-
-// interface for exporters.
-// Exposes one virtual functions:
-// do_export(vector<type>) receiving a vector of parameters to export
-
-template <typename Time, typename CommunicationPolicy>
-class exporter_interface {
-
-public:
- using time_type = Time;
- using spike_type = spike<cell_member_type, time_type>;
-
- // Performs the export of the data
- virtual void do_export(const std::vector<spike_type>&) = 0;
-
- // Returns the status of the exporter
- virtual bool good() const = 0;
-
- // Static version of the do_export function for NOP callbacks
- static void do_nothing(const std::vector<spike_type>&)
- {}
-};
-
-} //communication
-} // namespace mc
-} // namespace nest
diff --git a/src/communication/exporter_spike_file.hpp b/src/communication/exporter_spike_file.hpp
deleted file mode 100644
index cad61fbb7774594d234fd3761c740738f12c7bc6..0000000000000000000000000000000000000000
--- a/src/communication/exporter_spike_file.hpp
+++ /dev/null
@@ -1,101 +0,0 @@
-#pragma once
-
-#include <cstring>
-#include <cstdio>
-#include <fstream>
-#include <iomanip>
-#include <memory>
-#include <random>
-#include <stdexcept>
-#include <vector>
-
-#include <common_types.hpp>
-#include <communication/exporter_interface.hpp>
-#include <spike.hpp>
-#include <util.hpp>
-
-namespace nest {
-namespace mc {
-namespace communication {
-
-template <typename Time, typename CommunicationPolicy>
-class exporter_spike_file : public exporter_interface<Time, CommunicationPolicy>
-{
-public:
- using time_type = Time;
- using spike_type = spike<cell_member_type, time_type>;
- using communication_policy_type = CommunicationPolicy;
-
- // Constructor
- // over_write if true will overwrite the specified output file (default = true)
- // 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,
- const std::string& file_extention, bool over_write=true)
- {
- auto file_path =
- create_output_file_path(file_name, path, file_extention,
- communication_policy_.id());
-
- //test if the file exist and depending on over_write throw or delete
- if (!over_write && file_exists(file_path))
- {
- std::string error_string("Tried opening file for writing but it exists and over_write is false: "
- + file_path);
- throw std::runtime_error(error_string);
- }
-
- file_handle_.open(file_path);
- }
-
- // 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 do_export(const std::vector<spike_type>& spikes) override
- {
- for (auto spike : spikes) {
- char linebuf[45];
- auto n = std::snprintf(linebuf, sizeof(linebuf), "%u %.4f\n",
- spike.source.gid, spike.time);
- file_handle_.write(linebuf, n);
- }
- }
-
- 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)
- {
- std::string file_path = path + file_name + "_" +
- std::to_string(index) + "." + file_extention;
- // Nest does not produce the indexing for nrank == 0
- // I have the feeling this disrupts consistent output. Id rather
- // always put the zero in. it allows a simpler regex when opening
- // files
- return file_path;
- }
-
-private:
-
- bool file_exists(const std::string& file_path)
- {
- std::ifstream fid(file_path);
- return fid.good();
- }
-
- // Handle to opened file handle
- std::ofstream file_handle_;
-
- communication_policy_type communication_policy_;
-
-};
-
-} //communication
-} // namespace mc
-} // namespace nest
diff --git a/src/model.hpp b/src/model.hpp
index 1e98bddf74ff7fe2c55264a05f222082cc8f4edc..9c183d6aa10629ef0a463f35dd689c63b386ab2a 100644
--- a/src/model.hpp
+++ b/src/model.hpp
@@ -23,7 +23,7 @@ template <typename Cell>
class model {
public:
using cell_group_type = cell_group<Cell>;
- using time_type = typename cell_group_type::time_type;
+ using time_type = typename cell_group_type::time_type;
using value_type = typename cell_group_type::value_type;
using communicator_type = communication::communicator<time_type, communication::global_policy>;
using sampler_function = typename cell_group_type::sampler_function;
@@ -179,7 +179,7 @@ public:
std::size_t num_groups() const { return cell_groups_.size(); }
// register a callback that will perform a export of the global
- // spike vector
+ // spike vector
void set_global_spike_callback(std::function<void(
const std::vector<spike_type>&)> global_export_callback)
{
@@ -203,7 +203,7 @@ private:
std::vector<cell_group_type> cell_groups_;
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_;
diff --git a/tests/performance/io/disk_io.cpp b/tests/performance/io/disk_io.cpp
index 6800176ef27def4cff03810d4be60e34c2c825ec..8cec648594eb58533b4c059a336b621128c974ae 100644
--- a/tests/performance/io/disk_io.cpp
+++ b/tests/performance/io/disk_io.cpp
@@ -13,7 +13,7 @@
#include <communication/communicator.hpp>
#include <communication/global_policy.hpp>
-#include <communication/exporter_spike_file.hpp>
+#include <io/exporter_spike_file.hpp>
#include <profiling/profiler.hpp>
using namespace nest::mc;
@@ -54,7 +54,7 @@ int main(int argc, char** argv)
if (nr_repeats == 0) {
std::cout << "disk_io <nrspikes>\n";
- std::cout << " nr_repeats should be a valid integer higher then zero\n";
+ std::cout << " nr_repeats should be a valid integer higher then zero\n";
return 1;
}
@@ -67,7 +67,7 @@ int main(int argc, char** argv)
}
}
- // Create the sut
+ // Create the sut
communication::exporter_spike_file<time_type, global_policy> exporter(
"spikes", "./", "gdf", true);
@@ -82,7 +82,7 @@ int main(int argc, char** argv)
// *********************************************************************
// To have a somewhat realworld data set we calculate from the nr of spikes
- // (assuming 20 hz average) the number of nr of 'simulated' neurons,
+ // (assuming 20 hz average) the number of nr of 'simulated' neurons,
// and create idxs using this value. The number of chars in the number
// influences the size of the output and thus the speed
// Also taken that we have only a single second of simulated time
@@ -112,7 +112,7 @@ int main(int argc, char** argv)
for (auto idx = 0; idx < nr_repeats; ++idx) {
timings.push_back(timings_arr[idx]);
}
-
+
// Calculate some statistics
auto sum = std::accumulate(timings.begin(), timings.end(), 0.0);
@@ -135,7 +135,7 @@ int main(int argc, char** argv)
// and output
if (simple_stats) {
- std::cout << time_total<< ","
+ std::cout << time_total<< ","
<< mean << ","
<< stdev << ","
<< min << ","