diff --git a/CMakeLists.txt b/CMakeLists.txt
index 98b536095bcf261e5596edc26d0f639e02e15037..0f353a3a9533aa8eac20067f01f6665f45dbb853 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -105,6 +105,7 @@ project( ${MODULE_NAME} CXX )
# Add cpprestsdk
find_package(cpprestsdk REQUIRED)
+find_package(libpqxx REQUIRED)
# Get the Python executable (for help generation).
execute_process(
@@ -283,7 +284,7 @@ if ( BUILD_SHARED_LIBS )
install( TARGETS ${MODULE_NAME}_module
DESTINATION ${CMAKE_INSTALL_LIBDIR}
)
- target_link_libraries(${MODULE_NAME}_module PRIVATE cpprestsdk::cpprest)
+ target_link_libraries(${MODULE_NAME}_module PRIVATE cpprestsdk::cpprest pqxx)
endif ()
# Build dynamic/static library for standard linking from NEST.
diff --git a/Dockerfile b/Dockerfile
index 2581d9c4f0567b4eced2f10b5748ddabccf0e6b3..b5121457b25a5000a5dfbb1c2c87c3ae3e485130 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -8,6 +8,7 @@ RUN apt-get update && apt-get install -y \
libwebsocketpp-dev openssl libssl-dev ninja-build \
openmpi-bin libopenmpi-dev
RUN pip3 install Cython
+
RUN git clone --single-branch --branch nest-3 https://github.com/nest/nest-simulator.git nest && \
cd nest && \
git checkout 5c0f41230dda9e4b99b8df89729ea43b340246ad && \
@@ -20,6 +21,7 @@ RUN cmake \
-DCMAKE_BUILD_TYPE=Release \
/nest
RUN ninja && ninja install
+
RUN git clone --single-branch --branch v2.10.14 --recurse-submodules https://github.com/microsoft/cpprestsdk.git /cpprestsdk
WORKDIR /cpprestsdk-build
RUN cmake \
@@ -28,6 +30,17 @@ RUN cmake \
-DBUILD_TESTS=OFF \
/cpprestsdk
RUN ninja && ninja install
+
+RUN apt-get update && apt-get install -y libpq-dev postgresql-server-dev-all
+RUN git clone --single-branch --branch 6.4.6 https://github.com/jtv/libpqxx.git /libpqxx
+WORKDIR /libpqxx-build
+RUN cmake \
+ -G Ninja \
+ -DCMAKE_BUILD_TYPE=Release \
+ -DBUILD_TESTS=OFF \
+ /libpqxx
+RUN ninja && ninja install
+
COPY . /insite
WORKDIR /insite-build
RUN cmake \
diff --git a/recording_backend_insite.cpp b/recording_backend_insite.cpp
index 5a8b6791505b82eccac53c696b9afad7bfdcd13a..1fe1114c726116f369a51d97c401abd7c088ce87 100644
--- a/recording_backend_insite.cpp
+++ b/recording_backend_insite.cpp
@@ -20,26 +20,18 @@ namespace insite {
RecordingBackendInsite::RecordingBackendInsite()
: data_storage_("tgest"),
http_server_("http://0.0.0.0:" + get_port_string(), &data_storage_),
- info_node_("http://info-node:8080"),
- address_("insite-nest-module:" + get_port_string()) {
- web::uri_builder builder("/node");
- builder.append_query("node_type", "nest_simulation", true);
- builder.append_query("address", address_, true);
-
- try {
- info_node_.request(web::http::methods::PUT, builder.to_string())
- .then([](const web::http::http_response& response) {
- if (response.status_code() != web::http::status_codes::OK) {
- throw std::runtime_error(response.to_string());
- }
- })
- .wait();
- } catch (const std::exception& exception) {
- std::cerr << "Failed to register to info node: \n"
- << exception.what() << "\n"
- << std::endl;
- throw;
- }
+ database_connection_("postgresql://postgres@database") {
+ pqxx::work txn(database_connection_);
+ simulation_node_id_ = txn.exec1(
+ "INSERT INTO nest_simulation_node (address) "
+ "VALUES ('http://insite-nest-module:" +
+ get_port_string() +
+ "') "
+ "RETURNING id;")[0]
+ .as<int>();
+ std::cout << "Simulation node registered to database. Node ID: "
+ << simulation_node_id_ << std::endl;
+ txn.commit();
}
RecordingBackendInsite::~RecordingBackendInsite() throw() {}
@@ -55,7 +47,7 @@ void RecordingBackendInsite::finalize() {
void RecordingBackendInsite::enroll(const nest::RecordingDevice& device,
const DictionaryDatum& params) {
std::cout << "RecordingBackendInsite::enroll(" << device.get_label() << ")\n";
-
+
if (device.get_type() == nest::RecordingDevice::MULTIMETER) {
auto id = device.get_node_id();
multimeter_infos_.emplace(std::make_pair(id, MultimeterInfo{id, true}));
@@ -75,13 +67,33 @@ void RecordingBackendInsite::set_value_names(
if (device.get_type() == nest::RecordingDevice::MULTIMETER) {
auto& multimeter = multimeter_infos_.at(device.get_node_id());
-
- for (auto& name : double_value_names)
- multimeter.double_attributes.push_back(name.toString());
- for (auto& name : long_value_names)
- multimeter.long_attributes.push_back(name.toString());
- multimeter.needs_update = true;
+ std::stringstream multimeter_query;
+ multimeter_query << "INSERT INTO nest_multimeter (id, attributes) "
+ << "VALUES (" << device.get_node_id() << ",\'{";
+
+ bool first = true;
+ for (auto& name : double_value_names) {
+ const auto& name_string = name.toString();
+ multimeter.double_attributes.push_back(name_string);
+
+ multimeter_query << (first ? "" : ",") << '\"' << name_string << "\"";
+ first = false;
+ }
+ for (auto& name : long_value_names) {
+ const auto& name_string = name.toString();
+ multimeter.long_attributes.push_back(name_string);
+
+ multimeter_query << (first ? "" : ",") << '\"' << name_string << "\"";
+ first = false;
+ }
+ multimeter_query << "}\') ON CONFLICT DO NOTHING;";
+
+ multimeter.needs_update = true;
+
+ pqxx::work txn(database_connection_);
+ txn.exec0(multimeter_query.str());
+ txn.commit();
}
}
@@ -102,63 +114,58 @@ void RecordingBackendInsite::post_run_hook() {
void RecordingBackendInsite::post_step_hook() {
// Send simulation time
{
- web::uri_builder builder("/current_time");
- builder.append_query("time", latest_simulation_time_, false);
- builder.append_query("node_address", address_, true);
-
- info_node_.request(web::http::methods::PUT, builder.to_string())
- .then([](const web::http::http_response& response) {
- if (response.status_code() != web::http::status_codes::OK) {
- std::cerr << "Failed to send time to info node: \n"
- << response.to_string() << "\n"
- << std::endl;
- throw std::runtime_error(response.to_string());
- }
- }).wait(); // TODO: this wait definitely needs to go!
+ pqxx::work txn(database_connection_);
+ txn.exec0(
+ "UPDATE nest_simulation_node "
+ "SET current_simulation_time = " +
+ std::to_string(latest_simulation_time_) +
+ ""
+ "WHERE id = " +
+ std::to_string(simulation_node_id_));
+ txn.commit();
}
if (new_neuron_infos_.size() > 0) {
- // Send new gids
- web::uri_builder builder("/gids");
+ std::stringstream neuron_query;
+ neuron_query << "INSERT INTO nest_neuron (id, simulation_node_id, "
+ "population_id, position) "
+ << "VALUES ";
for (auto& neuron_info : new_neuron_infos_) {
- builder.append_query("gids", neuron_info.gid, false);
- }
- builder.append_query("address", address_, true);
-
- info_node_.request(web::http::methods::PUT, builder.to_string())
- .then([](const web::http::http_response& response) {
- if (response.status_code() != web::http::status_codes::OK) {
- std::cerr << "Failed to send gids to info node: \n"
- << response.to_string() << "\n"
- << std::endl;
- throw std::runtime_error(response.to_string());
+ const bool first = neuron_info.gid == new_neuron_infos_[0].gid;
+ if (!first) {
+ neuron_query << ",";
+ }
+
+ uint64_t population_id = 0;
+ for (const nest::NodeIDTriple& node_id_triple :
+ *neuron_info.gid_collection.get()) {
+ population_id ^= node_id_triple.node_id * 938831;
+ }
+
+ neuron_query << "(" << neuron_info.gid << "," << simulation_node_id_
+ << "," << population_id % 0x800000;
+
+ const auto position_size = neuron_info.position.size();
+ if (position_size > 0) {
+ assert(position_size <= 3);
+ neuron_query << ",\'{";
+ for (size_t i = 0; i < position_size; ++i) {
+ if (i > 0) {
+ neuron_query << ",";
}
- }).wait();
-
- // Send new properties
- builder = web::uri_builder("/neuron_properties");
- web::json::value request_body =
- web::json::value::array(new_neuron_infos_.size());
- for (std::size_t i = 0; i < new_neuron_infos_.size(); ++i) {
- auto& neuron_info = new_neuron_infos_[i];
- request_body[i]["gid"] = neuron_info.gid;
- request_body[i]["properties"] = web::json::value();
- if (!neuron_info.position.empty())
- request_body[i]["properties"]["position"] =
- web::json::value::array(std::vector<web::json::value>(
- neuron_info.position.begin(), neuron_info.position.end()));
+ neuron_query << neuron_info.position[i];
+ }
+ neuron_query << "}\'";
+ } else {
+ neuron_query << ",NULL";
+ }
+ neuron_query << ")";
}
+ neuron_query << ";";
- info_node_
- .request(web::http::methods::PUT, builder.to_string(), request_body)
- .then([](const web::http::http_response& response) {
- if (response.status_code() != web::http::status_codes::OK) {
- std::cerr << "Failed to send neuron properties to info node: \n"
- << response.to_string() << "\n"
- << std::endl;
- throw std::runtime_error(response.to_string());
- }
- }).wait();
+ pqxx::work txn(database_connection_);
+ txn.exec0(neuron_query.str());
+ txn.commit();
neuron_infos_.insert(neuron_infos_.end(), new_neuron_infos_.begin(),
new_neuron_infos_.end());
@@ -169,64 +176,28 @@ void RecordingBackendInsite::post_step_hook() {
// Send multimeter info
for (auto& kvp : multimeter_infos_) {
auto& multimeter = kvp.second;
- if (!multimeter.needs_update)
- continue;
+ if (!multimeter.needs_update) continue;
multimeter.needs_update = false;
-
- web::uri_builder builder("/multimeter_info");
- builder.append_query("id", multimeter.device_id, true);
- for (auto attribute : multimeter.double_attributes)
- builder.append_query("attributes", attribute, true);
- for (auto attribute : multimeter.long_attributes)
- builder.append_query("attributes", attribute, true);
- for (auto gid : multimeter.gids)
- builder.append_query("gids", gid, false);
-
- try {
- info_node_.request(web::http::methods::PUT, builder.to_string())
- .then([](const web::http::http_response& response) {
- if (response.status_code() != web::http::status_codes::OK) {
- throw std::runtime_error(response.to_string());
- }
- })
- .wait();
- } catch (const std::exception& exception) {
- std::cerr << "Failed to put multimeter info: \n"
- << exception.what() << "\n"
- << std::endl;
- throw;
- }
- }
- // Send new collections
- for (const auto& node_collection : node_collections_to_register_) {
- web::uri_builder builder("/populations");
- for (auto node_id_triple : *node_collection) {
- builder.append_query("gids", node_id_triple.node_id, false);
- }
- // Initialize to "invalid" state
- registered_node_collections_[node_collection] = -1;
- info_node_.request(web::http::methods::PUT, builder.to_string())
- .then([this,
- node_collection](const web::http::http_response& response) {
- if (response.status_code() != web::http::status_codes::OK) {
- std::cerr << "Failed to send population to info node: \n"
- << response.to_string() << "\n"
- << std::endl;
- throw std::runtime_error(response.to_string());
- } else {
- response.extract_json().then(
- [this, node_collection](const web::json::value& population_id) {
- std::cout << "Got id for node collection " << node_collection
- << ": " << population_id << std::endl;
- registered_node_collections_[node_collection] =
- population_id.as_number().to_int64();
- });
- }
- })
- .wait(); // Wait because it may cause a race condition
+ if (multimeter.gids.size() > 0) {
+ std::stringstream neuron_multimeter_query;
+ neuron_multimeter_query
+ << "INSERT INTO nest_neuron_multimeter (neuron_id, multimeter_id) "
+ << "VALUES ";
+
+ for (const auto& neuron_id : multimeter.gids) {
+ const bool first = neuron_id == multimeter.gids[0];
+ neuron_multimeter_query << (first ? "" : ",") << "(" << neuron_id << ","
+ << multimeter.device_id << ")";
+ }
+
+ neuron_multimeter_query << " ON CONFLICT DO NOTHING;";
+
+ pqxx::work txn(database_connection_);
+ txn.exec0(neuron_multimeter_query.str());
+ txn.commit();
+ }
}
- node_collections_to_register_.clear();
}
void RecordingBackendInsite::write(const nest::RecordingDevice& device,
@@ -245,19 +216,19 @@ void RecordingBackendInsite::write(const nest::RecordingDevice& device,
// If the measurement is from a GID we previously do not know, add.
if (!binary_search(gids.begin(), gids.end(), sender_gid)) {
- gids.insert(std::lower_bound(gids.begin(), gids.end(), sender_gid),
- sender_gid);
+ gids.insert(std::lower_bound(gids.begin(), gids.end(), sender_gid),
+ sender_gid);
multimeter.needs_update = true;
}
for (std::size_t i = 0; i < double_values.size(); ++i)
- data_storage_.AddMultimeterMeasurement(device_id,
- multimeter.double_attributes[i], time_stamp, sender_gid,
- double_values[i]);
+ data_storage_.AddMultimeterMeasurement(
+ device_id, multimeter.double_attributes[i], time_stamp, sender_gid,
+ double_values[i]);
for (std::size_t i = 0; i < long_values.size(); ++i)
- data_storage_.AddMultimeterMeasurement(device_id,
- multimeter.long_attributes[i], time_stamp, sender_gid,
- double(long_values[i]));
+ data_storage_.AddMultimeterMeasurement(
+ device_id, multimeter.long_attributes[i], time_stamp, sender_gid,
+ double(long_values[i]));
}
latest_simulation_time_ = std::max(latest_simulation_time_, time_stamp);
@@ -278,20 +249,6 @@ void RecordingBackendInsite::write(const nest::RecordingDevice& device,
std::lower_bound(new_neuron_infos_.begin(), new_neuron_infos_.end(),
neuron_info),
neuron_info);
-
- // Check if the node collection (population) is already sent to the
- // info-node
- const auto sender_node_collection = event.get_sender().get_nc();
- if (registered_node_collections_.count(sender_node_collection) == 0 &&
- !binary_search(node_collections_to_register_.begin(),
- node_collections_to_register_.end(),
- sender_node_collection)) {
- node_collections_to_register_.insert(
- std::lower_bound(node_collections_to_register_.begin(),
- node_collections_to_register_.end(),
- sender_node_collection),
- sender_node_collection);
- }
}
}
diff --git a/recording_backend_insite.h b/recording_backend_insite.h
index aeaefd31ebbfedc7bf755af8a99aac2841251ab9..aa8ec277c0b42494f00ca8a632c7cf690c100d52 100644
--- a/recording_backend_insite.h
+++ b/recording_backend_insite.h
@@ -3,6 +3,7 @@
#include <unordered_map>
#include <cpprest/http_client.h>
+#include <pqxx/pqxx>
#include "data_storage.hpp"
#include "http_server.hpp"
@@ -62,12 +63,10 @@ class RecordingBackendInsite : public nest::RecordingBackend {
DataStorage data_storage_;
HttpServer http_server_;
- web::http::client::http_client info_node_;
- std::string address_;
+ pqxx::connection database_connection_;
+ int simulation_node_id_;
std::vector<NeuronInfo> neuron_infos_;
std::vector<NeuronInfo> new_neuron_infos_;
- std::unordered_map<nest::NodeCollectionPTR, int64_t> registered_node_collections_;
- std::vector<nest::NodeCollectionPTR> node_collections_to_register_;
std::unordered_map<nest::index, MultimeterInfo> multimeter_infos_;
double latest_simulation_time_ = 0;
};