diff --git a/miniapp/io.cpp b/miniapp/io.cpp
index 8c72f46375456e9994022f434d6f43b11ccbd9dc..0c9acd016c50ff5cacfe2180533eef9ba3150592 100644
--- a/miniapp/io.cpp
+++ b/miniapp/io.cpp
@@ -43,8 +43,9 @@ namespace io {
cl_options read_options(int argc, char** argv) {
// set default options
- // TODO: the declaration of this defopts is realistic if we have allot
- // more options. We should use a name scheme.
+ // TODO: the declaration of this defopts is not realistic if we have allot
+ // more options. We should use a named scheme or import the defopts from
+ // a valid json file
const cl_options defopts{"", 1000, 500, "expsyn", 100, 100., 0.025, false,
false, 1.0, "trace_", util::nothing,
diff --git a/miniapp/miniapp.cpp b/miniapp/miniapp.cpp
index 9433ffadf1de34e23a1adc52e72b5437f2a21beb..f0c608309c67d258fecce2f84e44c061bb2a474a 100644
--- a/miniapp/miniapp.cpp
+++ b/miniapp/miniapp.cpp
@@ -62,7 +62,7 @@ int main(int argc, char** argv) {
auto cell_range = distribute_cells(recipe->num_cells());
// build model from recipe
-
+ // TODO: I would rather just forward the options object.
model_type::file_output_parameters model_params(
options.spike_file_output,
options.single_file_per_rank,
diff --git a/src/communication/communicator.hpp b/src/communication/communicator.hpp
index 0289fc3192e268bd5e647d659747635509914ef8..37b6d44cc4222d7314c1bc0d2ae0915be8f64f55 100644
--- a/src/communication/communicator.hpp
+++ b/src/communication/communicator.hpp
@@ -94,15 +94,15 @@ public:
std::vector<event_queue> exchange(const std::vector<spike_type>& local_spikes,
std::function<void (const std::vector<spike_type>&)> do_export_rank,
std::function<void(const std::vector<spike_type>&)> do_export_single)
- {
- // global all-to-all to gather a local copy of the global spike list on each node.
-
-
+ {
+ // Export of (rank) local spikes
do_export_rank(local_spikes);
+ // global all-to-all to gather a local copy of the global spike list on each node.
auto global_spikes = communication_policy_.gather_spikes( local_spikes );
num_spikes_ += global_spikes.size();
+ // Export of global spikes
do_export_single(global_spikes);
// check each global spike in turn to see it generates local events.
diff --git a/src/communication/export_manager.hpp b/src/communication/export_manager.hpp
index 52e73071ba4ad9734a99023778add93773f2472b..492be63bca57f0cb0af218f386d9ea47a8b08652 100644
--- a/src/communication/export_manager.hpp
+++ b/src/communication/export_manager.hpp
@@ -31,43 +31,54 @@ public:
{
return;
}
- if (single_file_per_rank) { // single file per rank
+ // single file per rank
+ if (single_file_per_rank) {
rank_exporters_.push_back(
nest::mc::util::make_unique<
nest::mc::communication::exporter_spike_file<Time, CommunicationPolicy> >(
file_name, output_path, file_extention, over_write));
}
-
- if (!single_file_per_rank) { // single file per simulation
+ // single file per simulation
+ if (!single_file_per_rank) {
single_exporters_.push_back(
nest::mc::util::make_unique<
- nest::mc::communication::exporter_spike_single_file<Time, CommunicationPolicy> >(
+ nest::mc::communication::exporter_spike_file<Time, CommunicationPolicy> >(
file_name, output_path, file_extention, over_write));
}
}
- void do_export_rank(const std::vector<spike_type>& spikes)
+ void do_export_local(const std::vector<spike_type>& spikes)
{
- // TODO: do the buffering of the spikes here and not in the
- // exporters itself!!!
+ local_spikes_.insert(std::end(local_spikes_),
+ std::begin(spikes), std::end(spikes));
+
for (auto &exporter : rank_exporters_)
{
- exporter->add_and_export(spikes);
+ exporter->do_export(spikes);
}
+
+ local_spikes_.clear();
}
- void do_export_single(const std::vector<spike_type>& spikes)
+ void do_export_global(const std::vector<spike_type>& spikes)
{
+ // We only output on a single rank
if (!communication_policy_.id() == 0) {
return;
}
+ global_spikes_.insert(std::end(global_spikes_),
+ std::begin(spikes), std::end(spikes));
+
+
for (auto &exporter : single_exporters_)
{
- exporter->add_and_export(spikes);
+ exporter->do_export(spikes);
}
+
+ global_spikes_.clear();
}
private:
@@ -76,12 +87,15 @@ private:
std::vector<std::unique_ptr<exporter_interface<Time, CommunicationPolicy> > > single_exporters_;
-
CommunicationPolicy communication_policy_;
+
+ // local storage for sending spikes
+ std::vector<spike_type> local_spikes_;
+ std::vector<spike_type> global_spikes_;
};
} //communication
} // namespace mc
-} // namespace nest
\ No newline at end of file
+} // namespace nest
diff --git a/src/communication/exporter_interface.hpp b/src/communication/exporter_interface.hpp
index 3fb101a7dc4eeef06acc2f8f6de5a99f8fc8b638..8093ec3fb60b2fd406cf3d061864fa6b30ac57f0 100644
--- a/src/communication/exporter_interface.hpp
+++ b/src/communication/exporter_interface.hpp
@@ -18,15 +18,7 @@ public:
using spike_type = spike<cell_member_type, time_type>;
// Performs the export of the data, thread safe buffered
- virtual void do_export() = 0;
-
- // Add data to the internal storage to be exported
- // Does not do the actual export
- virtual void add_data(std::vector<spike_type>) = 0;
-
-
- virtual void add_and_export(const std::vector<spike_type>&) = 0;
-
+ virtual void do_export(const std::vector<spike_type>&) = 0;
// Internal state is ok
// Export might encounter problems in a separate thread.
diff --git a/src/communication/exporter_spike_file.hpp b/src/communication/exporter_spike_file.hpp
index 033fa97d3ff5749b4107c444bde9f5e357bca476..41e83f16aac61c142955c14e2817bf77f4bf7981 100644
--- a/src/communication/exporter_spike_file.hpp
+++ b/src/communication/exporter_spike_file.hpp
@@ -31,7 +31,8 @@ public:
//
exporter_spike_file(std::string file_name, std::string path,
- std::string file_extention, bool over_write=true)
+ std::string file_extention, bool over_write=true,
+ bool single_file_per_rank=true)
:
ok_(false)
{
@@ -52,33 +53,18 @@ public:
}
buffer = new char[length];
- /*
- // Manually setting buffer did not help (version 1)
- //http://stackoverflow.com/questions/12997131/stdfstream-buffering-vs-manual-buffering-why-10x-gain-with-manual-buffering
-
-
- file_handle_ = nest::mc::util::make_unique<std::ofstream>();
- file_handle_->rdbuf()->pubsetbuf(buffer, length);
- file_handle_ ->open(file_path, std::fstream::app);
- */
-
file_handle_ = nest::mc::util::make_unique<std::ofstream>(file_path,
std::fstream::app);
if (file_handle_->good()) {
ok_ = true;
}
-
- // Force output of the spike times with precision
- // TODO: We need to make this selectable
- file_handle_->precision(4);
- file_handle_->setf(std::ios::fixed, std::ios::floatfield);
}
// Performs the export of the data,
// Does not throw
- void do_export() override
+ void do_export(const std::vector<spike_type>& spikes) override
{
unsigned current_loc_in_buffer = 0;
unsigned nr_chars_written = 0;
@@ -88,7 +74,7 @@ public:
const char * space = " ";
const char * endline = "\n";
- for (auto spike : spikes_)
+ for (auto spike : spikes)
{
// First the id as output
nr_chars_written = std::snprintf(single_value_buffer, 20, "%u",
@@ -119,6 +105,7 @@ public:
current_loc_in_buffer = 0;
}
}
+
// also write to buffer at end of the spikes processing
if (current_loc_in_buffer != 0)
{
@@ -126,6 +113,7 @@ public:
current_loc_in_buffer = 0; // not needed
}
+
file_handle_->flush();
@@ -133,23 +121,6 @@ public:
ok_ = false;
}
- spikes_.clear();
- }
-
- // Add data to the internal storage to be exported
- // Does not do the actual export
- void add_data(std::vector<spike_type>spikes) override
- {
- spikes_.insert(std::end(spikes_),
- std::begin(spikes), std::end(spikes));
- }
-
- // Add and export data to file in a single function
- void add_and_export(const std::vector<spike_type>& spikes) override //std::vector<spike_type>spikes
- {
-
- add_data(spikes);
- do_export();
}
// Internal state is ok
@@ -179,13 +150,10 @@ private:
// Handle to our owned opened file handle
std::unique_ptr<std::ofstream> file_handle_;
- // local storage for sending spikes
- std::vector<spike_type> spikes_;
-
communication_policy_type communication_policy_;
+ // Buffer (and size) for raw output of spikes
char *buffer;
-
const unsigned int length = 4096;
};
diff --git a/src/communication/exporter_spike_single_file.hpp b/src/communication/exporter_spike_single_file.hpp
deleted file mode 100644
index 249e7583b28b6043e20b719ba8d1d9facfb8c339..0000000000000000000000000000000000000000
--- a/src/communication/exporter_spike_single_file.hpp
+++ /dev/null
@@ -1,137 +0,0 @@
-#pragma once
-
-#include <cstdio>
-#include <fstream>
-#include <iomanip>
-#include <memory>
-#include <random>
-#include <stdexcept>
-#include <vector>
-
-#include <common_types.hpp>
-#include <util.hpp>
-#include <spike.hpp>
-
-
-#include "exporter_interface.hpp"
-
-namespace nest {
-namespace mc {
-namespace communication {
-
-template <typename Time, typename CommunicationPolicy> // TODO: Templating on data type, for now only spike_type
-class exporter_spike_single_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;
-
- //
- exporter_spike_single_file(std::string file_name, std::string path,
- std::string file_extention, bool over_write=true)
- :
- ok_(false)
- {
- if (!communication_policy_.id() == 0) {
- ok_ = true;
- return;
- }
-
- std::string 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
- std::ifstream f(file_path);
- if (f.good()) {
- if (!over_write) {
- std::string error_string("Tried opening file for writing but it exists and over_write is false:\n" +
- file_path);
-
- throw std::runtime_error(error_string);
- }
-
- std::remove(file_path.c_str());
- }
-
- file_handle_ = nest::mc::util::make_unique<std::ofstream>(file_path,
- std::fstream::app);
-
- if (file_handle_->good()) {
- ok_ = true;
- }
-
- // Force output of the spike times with precision
- // TODO: We need to make this selectable
- file_handle_->precision(4);
- file_handle_->setf(std::ios::fixed, std::ios::floatfield);
- }
-
-
- // Performs the export of the data,
- // Does not throw
- void do_export() override
- {
- for (auto spike : spikes_) {
- *file_handle_ << spike.source.gid << " " << spike.time << std::endl;
- }
- if (!file_handle_->good()){
- ok_ = false;
- }
-
- spikes_.clear();
- }
-
- // Add data to the internal storage to be exported
- // Does not do the actual export
- void add_data(std::vector<spike_type>spikes) override
- {
-
- spikes_.insert(std::end(spikes_),
- std::begin(spikes), std::end(spikes));
- }
-
- // Add and export data to file in a single function
- void add_and_export(const std::vector<spike_type>& spikes) override
- {
- add_data(spikes);
- do_export();
- }
-
- // Internal state is ok
- // We are working with fstreams possibly on a seperate thread
- // We need a way to assertain the status of the stream
- bool ok() const override
- {
-
- return ok_ && file_handle_->good();
- }
-
- // Creates an indexed filename
- static std::string create_output_file_path(std::string file_name, std::string path,
- std::string file_extention, unsigned index)
- {
- std::string file_path = path + file_name + "_" + std::to_string(index) +
- "." + file_extention;
- // TODO: Nest does not produce the indexing for nrank == 0
- // I have the feeling this disrupts consistent output. Id rather
- // always put the zero in.
- return file_path;
- }
-
-private:
- // Are we in a valid state?
- bool ok_;
-
- // Handle to our owned opened file handle
- std::unique_ptr<std::ofstream> file_handle_;
-
- // local storage for sending spikes
- std::vector<spike_type> spikes_;
-
- communication_policy_type communication_policy_;
-};
-
-} //communication
-} // namespace mc
-} // namespace nest
diff --git a/src/model.hpp b/src/model.hpp
index 816b32611ae3565df7fafe360929b813e92b054c..5cf4a71fde0dab9d2f45cef0dcc657f3002d09d7 100644
--- a/src/model.hpp
+++ b/src/model.hpp
@@ -172,8 +172,8 @@ public:
PE("stepping", "exchange");
auto local_spikes = previous_spikes().gather();
future_events() = communicator_.exchange(local_spikes,
- [&](const std::vector<spike_type>& spikes) { exporter_->do_export_rank(spikes); },
- [&] (const std::vector<spike_type>& spikes){ exporter_->do_export_single(spikes); });
+ [&](const std::vector<spike_type>& spikes) { exporter_->do_export_local(spikes); },
+ [&] (const std::vector<spike_type>& spikes){ exporter_->do_export_global(spikes); });
PL(2);
};
diff --git a/tests/global_communication/CMakeLists.txt b/tests/global_communication/CMakeLists.txt
index dff31ad71c6ac5c30a840073fb012405f652a584..82bb6583ea1310db1657e2a5110143fc484abd86 100644
--- a/tests/global_communication/CMakeLists.txt
+++ b/tests/global_communication/CMakeLists.txt
@@ -3,7 +3,6 @@ set(HEADERS
)
set(COMMUNICATION_SOURCES
test_exporter_spike_file.cpp
- test_exporter_spike_single_file.cpp
# unit test driver
test.cpp
)
diff --git a/tests/global_communication/test_exporter_spike_file.cpp b/tests/global_communication/test_exporter_spike_file.cpp
index 12f3300131166e97c498bb8f0a8e6384fc68a933..6201c73103dda2bcce10e68c638798ac78bab384 100644
--- a/tests/global_communication/test_exporter_spike_file.cpp
+++ b/tests/global_communication/test_exporter_spike_file.cpp
@@ -97,11 +97,9 @@ TEST_F(exporter_spike_file_fixture, do_export)
spikes.push_back({ { 1, 0 }, 1.0 });
spikes.push_back({ { 1, 0 }, 1.1 });
- // add to the exporter
- exporter.add_data(spikes);
// now do the export
- exporter.do_export();
+ exporter.do_export(spikes);
// Test if we have spikes in the file
std::ifstream f(get_standard_file_name());
diff --git a/tests/global_communication/test_exporter_spike_single_file.cpp b/tests/global_communication/test_exporter_spike_single_file.cpp
deleted file mode 100644
index 8f78aa7c45882c6da26c715286523b37b3d4f5c3..0000000000000000000000000000000000000000
--- a/tests/global_communication/test_exporter_spike_single_file.cpp
+++ /dev/null
@@ -1,118 +0,0 @@
-#include "gtest.h"
-
-#include <cstdio>
-#include <fstream>
-#include <iostream>
-#include <string>
-#include <vector>
-
-#include <communication/communicator.hpp>
-#include <communication/global_policy.hpp>
-#include <communication/exporter_spike_single_file.hpp>
-
-class exporter_spike_single_file_fixture : public ::testing::Test {
-
-protected:
- using time_type = float;
- using communicator_type = nest::mc::communication::global_policy;
-
- using spike_type = nest::mc::communication::exporter_spike_single_file<time_type,
- communicator_type>::spike_type;
-
- using exporter_type = nest::mc::communication::exporter_spike_single_file<time_type, communicator_type>;
- std::string file_name;
- std::string path;
- std::string extention;
- unsigned index;
-
- exporter_spike_single_file_fixture()
- :
- file_name("spikes_exporter_spike_single_file_fixture"),
- path("./"),
- extention("gdf"),
- index(0)
- {}
-
- std::string get_standard_file_name()
- {
- return exporter_type::create_output_file_path(
- file_name, path, extention, index);
- }
-
- void SetUp() {
- // code here will execute just before the test ensues
- }
-
- void TearDown() {
- // delete the start create file
- std::remove(get_standard_file_name().c_str());
- }
-
- ~exporter_spike_single_file_fixture() {
-
- }
-};
-
-TEST_F(exporter_spike_single_file_fixture, constructor)
-{
- exporter_type exporter(file_name,
- path, extention);
-
- // after construction the state of the exporter should be valid
- EXPECT_TRUE(exporter.ok());
-
-
- //test if the file exist and depending on over_write throw or delete
- std::ifstream f(get_standard_file_name());
- EXPECT_TRUE(f.good());
-}
-
-TEST_F(exporter_spike_single_file_fixture, create_output_file_path)
-{
- // Create some random paths, no need for fancy tests here
- std::string produced_filename =
- exporter_type::create_output_file_path(
- "spikes", "./", "gdf", 0);
- EXPECT_STREQ(produced_filename.c_str(), "./spikes_0.gdf");
-
- produced_filename =
- exporter_type::create_output_file_path(
- "a_name", "../../", "txt", 5);
- EXPECT_STREQ(produced_filename.c_str(), "../../a_name_5.txt");
-}
-
-TEST_F(exporter_spike_single_file_fixture, do_export)
-{
-
-
- exporter_type exporter(file_name,
- path, extention);
-
- // Create some spikes
- std::vector<spike_type> spikes;
- spikes.push_back({ { 0, 0 }, 0.0});
- spikes.push_back({ { 0, 0 }, 0.1 });
- spikes.push_back({ { 1, 0 }, 1.0 });
- spikes.push_back({ { 1, 0 }, 1.1 });
-
- // add to the exporter
- exporter.add_data(spikes);
-
- // now do the export
- exporter.do_export();
-
- // Test if we have spikes in the file
- std::ifstream f(get_standard_file_name());
- EXPECT_TRUE(f.good());
-
- std::string line;
-
- EXPECT_TRUE(std::getline(f, line));
- EXPECT_STREQ(line.c_str(), "0 0.0000");
- EXPECT_TRUE(std::getline(f, line));
- EXPECT_STREQ(line.c_str(), "0 0.1000");
- EXPECT_TRUE(std::getline(f, line));
- EXPECT_STREQ(line.c_str(), "1 1.0000");
- EXPECT_TRUE(std::getline(f, line));
- EXPECT_STREQ(line.c_str(), "1 1.1000");
-}
diff --git a/tests/performance/io/disk_io.cpp b/tests/performance/io/disk_io.cpp
index 98868f2bf1ee6e8d4dcd56ae31b0758751bf4ca7..e0a2c7d7e6a5889d4028819ee853198ac319741f 100644
--- a/tests/performance/io/disk_io.cpp
+++ b/tests/performance/io/disk_io.cpp
@@ -113,7 +113,7 @@ int main(int argc, char** argv) {
{
int time_start = clock();
- manager.do_export_rank(spikes);
+ manager.do_export_local(spikes);
int time_stop = clock();