Merge branch 'master' into gcc9

README.md

+# DCDB
+
+The *DataCenter* *DataBase* (DCDB) is a modular, continuous and holistic monitoring framework targeted at HPC environments. The framework consists of the three main parts:
+
+* _Storage_ _Backend_: Here all the collected data is stored. By default a Cassandra database is used but the framework is intended to support usage of other data storage solutions as well.
+* _Collect_ _Agent_: The collect agent functions as intermediary between one storage backend and one or multiple pushers.
+* _Pusher_: The main part for collecting data is the pusher framework. It allows to run arbitrary data collection plugins and pushes the data to the collect agent via MQTT messages.
+
+Other features included by DCDB:
+* libdcdb: a library to access the storage backend with external tools
+* a set of tools leveraging libdcdb (e.g. a command line tool to query the storage backend)
+* built in data analytics framework
+* pusher plugins for a variety of typical HPC data sources
+
+## Build, install and run
+
+Prerequisites:
+* cmake
+* C++11 compiler
+
+```bash
+//Create a new directory for DCDB
+$ mkdir DCDB && cd DCDB
+
+//Download the DCDB sources
+$ git clone https://gitlab.lrz.de/dcdb/dcdb.git
+
+//Start building and installation of DCDB and all of its dependencies.
+$ cd dcdb
+$ make depsinstall install
+//OR use this make command instead to also build the doxygen documentation
+$ make depsinstall install doc
+```
+
+To run DCDB locally with the included default config files:
+
+```bash
+//Change to the DCDB directory you created during installation
+$ cd DCDB
+//Set required environment variables
+$ source install/dcdb.bash
+//Start one storage backend and one collect agent locally
+$ install/etc/init.d/dcdb start
+
+//Start a dcdbpusher instance
+$ cd dcdb/dcdbpusher
+$ ./dcdbpusher config/
+```
+
+## License and Copyright
+
+Copyright (C) 2011-2019 Leibniz Supercomputing Centre
+
+DCDB (except for the libdcdb parts) is licensed under the terms
+and conditions of the GNU GENERAL PUBLIC LICENSE (Version 2 or later).
+
+Libdcdb is licensed under the terms and conditions of the GNU LESSER
+GENERAL PUBLIC LICENSE (Version 2.1 or later).
+
+See the `LICENSE` file for more information.
+
+<!---
+ TODO:
+ write pages for:
+ -how to use dcdb
+ -architecture of dcdb
+ -develop plugin for pusher/analyzer
+ -develop for framework itself
+ -dig deeper into doxygen to get a beatiful documentation. perhaps use
+  markdown files for pages (for tutorials, architecture explanation)
+-->
\ No newline at end of file

analytics/README.md

-# Table of contents
+# DCDB Data Analytics Framework
+
+### Table of contents
 1. [Introduction](#introduction)
 2. [DCDBAnalytics](#dcdbanalytics)
     1. [Global Configuration](#globalConfiguration)

analytics/analyzers/aggregator/AggregatorAnalyzer.cpp

@@ -67,7 +67,7 @@ void AggregatorAnalyzer::computeSum(int unitID) {
         // Getting the most recent values as specified in _window
         _buffer = _queryEngine.querySensor(in->getName(), _window, 0, _buffer);
         if(!_buffer || _buffer->empty()) {
-            LOG(error) << "Analyzer " << _name << " cannot read from sensor " << in->getName() << "!";
+            LOG(debug) << "Analyzer " << _name << " cannot read from sensor " << in->getName() << "!";
             return;
         }
 
@@ -88,7 +88,7 @@ void AggregatorAnalyzer::computeAvg(int unitID) {
         // Getting the most recent values as specified in _window
         _buffer = _queryEngine.querySensor(in->getName(), _window, 0, _buffer);
         if(!_buffer || _buffer->empty()) {
-            LOG(error) << "Analyzer " << _name << " cannot read from sensor " << in->getName() << "!";
+            LOG(debug) << "Analyzer " << _name << " cannot read from sensor " << in->getName() << "!";
             return;
         }
 
@@ -113,7 +113,7 @@ void AggregatorAnalyzer::computeMax(int unitID) {
         // Getting the most recent values as specified in _window
         _buffer = _queryEngine.querySensor(in->getName(), _window, 0, _buffer);
         if(!_buffer || _buffer->empty()) {
-            LOG(error) << "Analyzer " << _name << " cannot read from sensor " << in->getName() << "!";
+            LOG(debug) << "Analyzer " << _name << " cannot read from sensor " << in->getName() << "!";
             return;
         }
 
@@ -136,7 +136,7 @@ void AggregatorAnalyzer::computeMin(int unitID) {
         // Getting the most recent values as specified in _window
         _buffer = _queryEngine.querySensor(in->getName(), _window, 0, _buffer);
         if(!_buffer || _buffer->empty()) {
-            LOG(error) << "Analyzer " << _name << " cannot read from sensor " << in->getName() << "!";
+            LOG(debug) << "Analyzer " << _name << " cannot read from sensor " << in->getName() << "!";
             return;
         }
 

common/include/dcdbdaemon.h

@@ -34,7 +34,7 @@
 static int dcdbdaemon()
 {
 #ifdef __linux__
-  return daemon(0, 0);
+  return daemon(1, 0);
 #else
   switch(fork()) {
   case -1:

common/src/RESTHttpsServer.cpp

@@ -170,7 +170,7 @@ serverError:
     //this is not strictly necessary.
     //Fails if client already disconnected from socket.
     socket.shutdown(tcp::socket::shutdown_both, ec);
-    if(ec) { ServerLOG(warning) << "socket shutdown: " << ec.message(); }
+    if(ec) { ServerLOG(debug) << "socket shutdown: " << ec.message(); }
 
     socket.close(ec);
     if(ec) { ServerLOG(error) << "socket close: " << ec.message(); }

config.mk

@@ -6,5 +6,5 @@ DEFAULT_VERSION = 0.3
 GIT_VERSION = $(shell git describe --tags 2>/dev/null|sed 's/-\([0-9]*\)/.\1/')
 VERSION := $(if $(GIT_VERSION),$(GIT_VERSION),$(DEFAULT_VERSION))
 
-CXXFLAGS = -std=c++11 -O2 -g -Wall -fmessage-length=0 -DBOOST_DATE_TIME_POSIX_TIME_STD_CONFIG -DBOOST_LOG_DYN_LINK -DVERSION=\"$(VERSION)\" 
+CXXFLAGS = -std=c++11 -O2 -g -Wall -fmessage-length=0 -DBOOST_DATE_TIME_POSIX_TIME_STD_CONFIG -DBOOST_LOG_DYN_LINK -DVERSION=\"$(VERSION)\" -Wno-unused-function -Wno-unused-variable
 OS = $(shell uname -s)

dcdbpusher/Caliper/dcdbpusher/CMakeLists.txt

+set(CALIPER_DCDBPUSHER_SOURCES
+  DcdbPusher.cpp)
+
+add_service_sources(${CALIPER_DCDBPUSHER_SOURCES})
+add_caliper_service("dcdbpusher")

dcdbpusher/Caliper/dcdbpusher/DcdbPusher.cpp

+// This program is to be used with Caliper.
+// Caliper belongs to Lawrence Livermore National Security, LLC.
+// LLNL-CODE-678900
+// All rights reserved.
+//
+// For details, see https://github.com/scalability-llnl/Caliper.
+
+//================================================================================
+// Name        : DcdbPusher.cpp
+// Author      : Micha Mueller
+// Copyright   : Leibniz Supercomputing Centre
+// Description : Caliper service to forward snapshot data to dcdb pusher.
+//================================================================================
+
+//================================================================================
+// This file is part of DCDB (DataCenter DataBase)
+// Copyright (C) 2019-2019 Leibniz Supercomputing Centre
+//
+// This program is free software; you can redistribute it and/or
+// modify it under the terms of the GNU General Public License
+// as published by the Free Software Foundation; either version 2
+// of the License, or (at your option) any later version.
+//
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with this program; if not, write to the Free Software
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+//================================================================================
+
+/**
+ * @file DcdbPusher.cpp
+ *
+ * @brief Caliper service to forward snapshot data to dcdb pusher.
+ *
+ * @details Service for the runtime processing level. Relies on the sampler,
+ *          symbollookup and timestamp service. To avoid a detour to the flush
+ *          level the symbollookup service is invoked manually when processing a
+ *          snapshot. This way all required information is available without
+ *          having to explicitly trigger a flush and the relevant data can be
+ *          instantly forwarded. Unneeded atttributes are stripped off and
+ *          discarded.
+ *
+ */
+
+#include "caliper/CaliperService.h"
+
+#include "caliper/Caliper.h"
+#include "caliper/SnapshotRecord.h"
+
+#include "caliper/common/Log.h"
+#include "caliper/common/RuntimeConfig.h"
+
+using namespace cali;
+
+namespace {
+
+class DcdbPusher {
+
+private:
+
+    static const ConfigSet::Entry s_configdata[];
+
+    //TODO reduce snapshot frequency during runtime
+    unsigned snapshot_threshold = 10;
+
+    unsigned threshold_exceeded  = 0;
+    unsigned snapshots_processed = 0;
+    unsigned snapshots_failed    = 0;
+
+    bool initialized = false;
+
+    Attribute sampler    { Attribute::invalid };
+    Attribute symbol_fun { Attribute::invalid };
+    Attribute timestamp  { Attribute::invalid };
+
+    void post_init_cb(Caliper* c, Channel* chn) {
+        // manually issue a pre-flush event to set up the SymbolLookup service
+        chn->events().pre_flush_evt(c, chn, nullptr);
+
+        // Check if required services sampler, symbollookup and timestamp are
+        // active by searching for identifying attributes.
+
+        //TODO support data collection if event triggered snapshots are used
+        sampler    = c->get_attribute("cali.sampler.pc");
+        symbol_fun = c->get_attribute("source.function#cali.sampler.pc");
+        timestamp  = c->get_attribute("time.timestamp");
+
+        if (sampler    == Attribute::invalid ||
+            symbol_fun == Attribute::invalid ||
+            timestamp  == Attribute::invalid) {
+
+            Log(1).stream() << chn->name() << ": DcdbPusher: not all required services "
+                    "sampler, symbollookup and timestamp are running." << std::endl;
+            return;
+        }
+
+        initialized = true;
+    }
+
+    void process_snapshot_cb(Caliper* c, Channel* chn, const SnapshotRecord*, const SnapshotRecord* sbuf) {
+        ++snapshots_processed;
+        //TODO check if signal safety is required
+        //if (c->is_signal()) {
+        //    ++snapshots_failed;
+        //    return;
+        //}
+
+        if (!initialized) {
+            ++snapshots_failed;
+            return;
+        }
+
+        SnapshotRecord::Sizes sizes = sbuf->size();
+
+        if ((sizes.n_nodes + sizes.n_immediate) == 0) {
+            ++snapshots_failed;
+            return;
+        }
+
+        std::vector<Entry> rec = sbuf->to_entrylist();
+
+        // manually issue a postprocess-snapshot event to enrich snapshot with
+        // symbollookup data
+        chn->events().postprocess_snapshot(c, chn, rec);
+
+        Log(1).stream() << chn->name() << ": DcdbPusher: printing snapshot" << std::endl;
+
+        for (const Entry& e : rec) {
+
+            //print attribute values for timestamp and looked up function symbol name
+            cali_id_t entryId = c->get_attribute(e.attribute()).id();
+            if (entryId == symbol_fun.id() || entryId == timestamp.id()) {
+
+                Log(1).stream() << chn->name() << ": DcdbPusher: "
+                                << c->get_attribute(e.attribute()).name()
+                                << " = " << e.value().to_string()
+                                << std::endl;
+            }
+        }
+        Log(1).stream() << chn->name() << std::endl;
+    }
+
+    void finish_cb(Caliper* c, Channel* chn) {
+        if (threshold_exceeded > 0) {
+            Log(1).stream() << chn->name() << ": DcdbPusher: threshold was exceeded "
+                                           << threshold_exceeded << " times." << std::endl;
+        }
+
+        Log(1).stream() << chn->name() << ": DcdbPusher: "
+                        << snapshots_processed << " snapshots processed of which "
+                        << snapshots_failed    << " failed." << std::endl;
+    }
+
+    DcdbPusher(Caliper* c, Channel* chn) {
+        ConfigSet config = chn->config().init("dcdbpusher", s_configdata);
+
+        snapshot_threshold = config.get("snapshot_threshold").to_uint();
+    }
+
+public:
+
+    ~DcdbPusher() {
+
+    }
+
+    static void dcdbpusher_register(Caliper* c, Channel* chn) {
+        DcdbPusher* instance = new DcdbPusher(c, chn);
+
+        chn->events().post_init_evt.connect(
+            [instance](Caliper* c, Channel* chn){
+                instance->post_init_cb(c, chn);
+            });
+        chn->events().process_snapshot.connect(
+            [instance](Caliper* c, Channel* chn, const SnapshotRecord* trigger, const SnapshotRecord* snapshot){
+                instance->process_snapshot_cb(c, chn, trigger, snapshot);
+            });
+        chn->events().finish_evt.connect(
+            [instance](Caliper* c, Channel* chn){
+                instance->finish_cb(c, chn);
+                delete instance;
+            });
+
+        Log(1).stream() << chn->name() << ": Registered dcdbpusher service" << std::endl;
+    }
+}; // class DcdbPusher
+
+const ConfigSet::Entry DcdbPusher::s_configdata[] = {
+    { "snapshot_threshold", CALI_TYPE_UINT, "10",
+      "Maximum number of snapshots per second we are allowed to process",
+      "Maximum number of snapshots per second we are allowed to process.\n"
+      "If the threshold is exceeded snapshots get discarded until the\n"
+      "limit is met again." },
+
+    ConfigSet::Terminator
+};
+
+} // namespace
+
+namespace cali {
+    CaliperService dcdbpusher_service { "dcdbpusher", ::DcdbPusher::dcdbpusher_register };
+}
+

dcdbpusher/Caliper/patch

+--- a/src/services/CMakeLists.txt	2019-06-07 10:33:20.036516054 +0200
++++ b/src/services/CMakeLists.txt	2019-06-06 17:57:54.096623744 +0200
+@@ -55,6 +55,7 @@
+   add_subdirectory(cupti)
+   add_subdirectory(cuptitrace)
+ endif()
++add_subdirectory(dcdbpusher)
+ add_subdirectory(debug)
+ add_subdirectory(env)
+ add_subdirectory(event)

dcdbpusher/PluginManager.cpp

@@ -37,7 +37,9 @@ PluginManager::PluginManager(const pluginSettings_t& pluginSettings) :
     _cfgFilePath("./") {}
 
 PluginManager::~PluginManager() {
-    unloadPlugin();
+    for(const auto& p : _plugins)
+        p.destroy(p.configurator);
+    _plugins.clear();
 }
 
 bool PluginManager::loadPlugin(const string& name,

dcdbpusher/README.md

-# Table of contents
+# DCDB Pusher
+
+### Table of contents
 1. [Introduction](#introduction)
 2. [dcdbpusher](#dcdbpusher)
     1. [Global Configuration](#globalConfiguration)
@@ -28,7 +30,7 @@ Harvesting of the data is task of the dcdbpusher.
 # dcdbpusher <a name="dcdbpusher"></a>
 
 This is a general MQTT pusher which sends values of various sensors to the DCDB-database.
-It ships with plugins for BACnet, IPMI, PDU(proprietary Power Delivery Unit, but could be used as XML plugin) ,percounter, SNMP and sysFS.
+It ships with plugins for BACnet, IPMI, PDU(proprietary Power Delivery Unit, but could be used as XML plugin), perfcounter, SNMP and sysFS.
 
 Build it by simply running
 ```bash

dcdbpusher/dcdbpusher.cpp

@@ -441,7 +441,7 @@ int main(int argc, char** argv) {
 	mqttThread.join();
 	LOG(info) << "MQTTPusher stopped";
 
-	LOG(info) << "Tear down objects...";
+	LOG(info) << "Tearing down objects...";
 	_sensorMap.clear();
 	delete _httpsServer;
 	delete _mqttPusher;

dcdbpusher/sensors/procfs/ProcfsParser.cpp

@@ -54,7 +54,7 @@ ProcfsParser::ProcfsParser(std::string path) {
  * Class destructor.
  *
  */
-ProcfsParser::~ProcfsParser() { close(); }
+ProcfsParser::~ProcfsParser() { ProcfsParser::close(); }
 
 /**
  * Initializes the parser.
@@ -512,6 +512,11 @@ bool ProcstatParser::_readMetrics() {
 // **************************************************************
 // Definitions for the SARParser class
 
+/**
+ * Class destructor.
+ *
+ */
+SARParser::~SARParser() { SARParser::close(); }
 
 /**
  * Closes the parser.

dcdbpusher/sensors/procfs/ProcfsParser.h

@@ -201,6 +201,7 @@ class SARParser : public ProcstatParser {
 public:
     SARParser(const std::string path = "") : ProcstatParser(path) {}
     void close() override;
+    virtual ~SARParser();
 
 protected:
     bool _readMetrics() override;

dcdbpusher/sensors/tester/TesterSensorGroup.cpp

@@ -66,6 +66,11 @@ void TesterSensorGroup::start() {
 }
 
 void TesterSensorGroup::stop() {
+	if(_keepRunning == 0) {
+		LOG(info) << "Sensorgroup " << _groupName << " already stopped.";
+		return;
+	}
+	
 	_keepRunning = 0;
 	//wait before closing _file
 	wait();

doc/Doxyfile

@@ -771,7 +771,7 @@ WARN_LOGFILE           = dox_stderr.txt
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ./../analytics ./../collectagent ./../common ./../dcdbpusher ./../lib ./../tools
+INPUT                  = ./../analytics ./../collectagent ./../common ./../dcdbpusher ./../lib ./../tools ./../README.md
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -796,7 +796,7 @@ INPUT_ENCODING         = UTF-8
 # *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f, *.for, *.tcl,
 # *.vhd, *.vhdl, *.ucf, *.qsf, *.as and *.js.
 
-FILE_PATTERNS          = *.cpp *.h
+FILE_PATTERNS          = *.cpp *.h *.md
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
 # be searched for input files as well.
@@ -811,7 +811,7 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                =
+EXCLUDE                = 
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
@@ -920,7 +920,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE =
+USE_MDFILE_AS_MAINPAGE = ./../README.md
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing

lib/src/sensordatastore.cpp

@@ -24,31 +24,6 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //================================================================================
 
-/**
- * @mainpage
- * DataCenter DataBase (DCDB) is a modular, continuous and holistic monitoring
- * framework for the HPC field. The framework consists of three main parts:
- * pusher, collect agent and storage backend. Further on, DCDB ships with a
- * small set of utility tools and allows access to the data store through
- * libdcdb.
- *
- * See further:
- * - @ref libdcdb "libdcdb" or
- * - @subpage libdcdb "libdcdb"
- * - @link pusher Pusher@endlink
- */
-
-//
-// TODO:
-// write pages for:
-// -how to use dcdb
-// -architecture of dcdb
-// -develop plugin for pusher/analyzer
-// -develop for framework itself
-// -dig deeper into doxygen to get a beatiful documentation. perhaps use
-//  markdown files for pages (for tutorials, architecture explanation)
-//
-
 /**
  * @page libdcdb libdcdb
  * The libdcdb library is a dynamic runtime library providing