AODJAlienReaderHelpers.cxx

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// Copyright 2019-2020 CERN and copyright holders of ALICE O2.
// See https://alice-o2.web.cern.ch/copyright for details of the copyright holders.
// All rights not expressly granted are reserved.
//
// This software is distributed under the terms of the GNU General Public
// License v3 (GPL Version 3), copied verbatim in the file "COPYING".
//
// In applying this license CERN does not waive the privileges and immunities
// granted to it by virtue of its status as an Intergovernmental Organization
// or submit itself to any jurisdiction.
 
#include "AODJAlienReaderHelpers.h"
#include <memory>
#include "Framework/TableTreeHelpers.h"
#include "Framework/AnalysisHelpers.h"
#include "Framework/DataProcessingStats.h"
#include "Framework/RootArrowFilesystem.h"
#include "Framework/AlgorithmSpec.h"
#include "Framework/ConfigParamRegistry.h"
#include "Framework/ControlService.h"
#include "Framework/CallbackService.h"
#include "Framework/EndOfStreamContext.h"
#include "Framework/DeviceSpec.h"
#include "Framework/RawDeviceService.h"
#include "Framework/DataSpecUtils.h"
#include "Framework/ConfigContext.h"
#include "DataInputDirector.h"
#include "Framework/SourceInfoHeader.h"
#include "Framework/ChannelInfo.h"
#include "Framework/Logger.h"
 
#if __has_include(<TJAlienFile.h>)
#include <TJAlienFile.h>
#endif
#include <TGrid.h>
#include <TFile.h>
#include <TTreeCache.h>
#include <TSystem.h>
 
#include <arrow/ipc/reader.h>
#include <arrow/ipc/writer.h>
#include <arrow/io/interfaces.h>
#include <arrow/table.h>
#include <arrow/util/key_value_metadata.h>
#include <arrow/dataset/dataset.h>
#include <arrow/dataset/file_base.h>
 
using namespace o2;
using namespace o2::aod;
 
struct RuntimeWatchdog {
  int numberTimeFrames;
  uint64_t startTime;
  uint64_t lastTime;
  double runTime;
  uint64_t runTimeLimit;
 
  RuntimeWatchdog(Long64_t limit)
  {
    numberTimeFrames = -1;
    startTime = uv_hrtime();
    lastTime = startTime;
    runTime = 0.;
    runTimeLimit = limit;
  }
  RuntimeWatchdog(Long64_t limit) {…}
 
  bool update()
  {
    numberTimeFrames++;
    if (runTimeLimit <= 0) {
      return true;
    }
 
    auto nowTime = uv_hrtime();
 
    // time spent to process the time frame
    double time_spent = numberTimeFrames < 1 ? (double)(nowTime - lastTime) / 1.E9 : 0.;
    runTime += time_spent;
    lastTime = nowTime;
 
    return ((double)(lastTime - startTime) / 1.E9 + runTime / (numberTimeFrames + 1)) < runTimeLimit;
  }
  bool update() {…}
 
  void printOut()
  {
    LOGP(info, "RuntimeWatchdog");
    LOGP(info, "  run time limit: {}", runTimeLimit);
    LOGP(info, "  number of time frames: {}", numberTimeFrames);
    LOGP(info, "  estimated run time per time frame: {}", (numberTimeFrames >= 0) ? runTime / (numberTimeFrames + 1) : 0.);
    LOGP(info, "  estimated total run time: {}", (double)(lastTime - startTime) / 1.E9 + ((numberTimeFrames >= 0) ? runTime / (numberTimeFrames + 1) : 0.));
  }
  void printOut() {…}
};
struct RuntimeWatchdog {…};
 
using o2::monitoring::Metric;
using o2::monitoring::Monitoring;
using o2::monitoring::tags::Key;
using o2::monitoring::tags::Value;
 
namespace o2::framework::readers
{
auto setEOSCallback(InitContext& ic)
{
  ic.services().get<CallbackService>().set<CallbackService::Id::EndOfStream>(
    [](EndOfStreamContext& eosc) {
      auto& control = eosc.services().get<ControlService>();
      control.endOfStream();
      control.readyToQuit(QuitRequest::Me);
    });
}
auto setEOSCallback(InitContext& ic) {…}
 
template <typename O>
static inline auto extractTypedOriginal(ProcessingContext& pc)
{
  return O{pc.inputs().get<TableConsumer>(aod::MetadataTrait<O>::metadata::tableLabel())->asArrowTable()};
}
 
template <typename... Os>
static inline auto extractOriginalsTuple(framework::pack<Os...>, ProcessingContext& pc)
{
  return std::make_tuple(extractTypedOriginal<Os>(pc)...);
}
 
AlgorithmSpec AODJAlienReaderHelpers::rootFileReaderCallback(ConfigContext const& ctx)
{
  // aod-parent-base-path-replacement is now a workflow option, so it needs to be
  // retrieved from the ConfigContext. This is because we do not allow workflow options
  // to change over start-stop-start because they can affect the topology generation.
  std::string parentFileReplacement;
  if (ctx.options().isSet("aod-parent-base-path-replacement")) {
    parentFileReplacement = ctx.options().get<std::string>("aod-parent-base-path-replacement");
  }
  int parentAccessLevel = 0;
  if (ctx.options().isSet("aod-parent-access-level")) {
    parentAccessLevel = ctx.options().get<int>("aod-parent-access-level");
  }
  auto callback = AlgorithmSpec{adaptStateful([parentFileReplacement, parentAccessLevel](ConfigParamRegistry const& options,
                                                                                         DeviceSpec const& spec,
                                                                                         Monitoring& monitoring,
                                                                                         DataProcessingStats& stats) {
    // FIXME: not actually needed, since data processing stats can specify that we should
    // send the initial value.
    stats.updateStats({static_cast<short>(ProcessingStatsId::ARROW_BYTES_CREATED), DataProcessingStats::Op::Set, 0});
    stats.updateStats({static_cast<short>(ProcessingStatsId::ARROW_MESSAGES_CREATED), DataProcessingStats::Op::Set, 0});
    stats.updateStats({static_cast<short>(ProcessingStatsId::ARROW_BYTES_DESTROYED), DataProcessingStats::Op::Set, 0});
    stats.updateStats({static_cast<short>(ProcessingStatsId::ARROW_MESSAGES_DESTROYED), DataProcessingStats::Op::Set, 0});
    stats.updateStats({static_cast<short>(ProcessingStatsId::ARROW_BYTES_EXPIRED), DataProcessingStats::Op::Set, 0});
 
    if (!options.isSet("aod-file-private")) {
      LOGP(fatal, "No input file defined!");
      throw std::runtime_error("Processing is stopped!");
    }
 
    auto filename = options.get<std::string>("aod-file-private");
 
    auto maxRate = options.get<float>("aod-max-io-rate");
 
    // create a DataInputDirector
    auto didir = std::make_shared<DataInputDirector>(filename, &monitoring, parentAccessLevel, parentFileReplacement);
    if (options.isSet("aod-reader-json")) {
      auto jsonFile = options.get<std::string>("aod-reader-json");
      if (!didir->readJson(jsonFile)) {
        LOGP(error, "Check the JSON document! Can not be properly parsed!");
      }
    }
 
    // get the run time watchdog
    auto* watchdog = new RuntimeWatchdog(options.get<int64_t>("time-limit"));
 
    // selected the TFN input and
    // create list of requested tables
    bool reportTFN = false;
    bool reportTFFileName = false;
    header::DataHeader TFNumberHeader;
    header::DataHeader TFFileNameHeader;
    std::vector<OutputRoute> requestedTables;
    std::vector<OutputRoute> routes(spec.outputs);
    for (auto route : routes) {
      if (DataSpecUtils::partialMatch(route.matcher, header::DataOrigin("TFN"))) {
        auto concrete = DataSpecUtils::asConcreteDataMatcher(route.matcher);
        TFNumberHeader = header::DataHeader(concrete.description, concrete.origin, concrete.subSpec);
        reportTFN = true;
      } else if (DataSpecUtils::partialMatch(route.matcher, header::DataOrigin("TFF"))) {
        auto concrete = DataSpecUtils::asConcreteDataMatcher(route.matcher);
        TFFileNameHeader = header::DataHeader(concrete.description, concrete.origin, concrete.subSpec);
        reportTFFileName = true;
      } else {
        requestedTables.emplace_back(route);
      }
    }
 
    auto fileCounter = std::make_shared<int>(0);
    auto numTF = std::make_shared<int>(-1);
    return adaptStateless([TFNumberHeader,
                           TFFileNameHeader,
                           requestedTables,
                           fileCounter,
                           numTF,
                           watchdog,
                           maxRate,
                           didir, reportTFN, reportTFFileName](Monitoring& monitoring, DataAllocator& outputs, ControlService& control, DeviceSpec const& device) {
      // Each parallel reader device.inputTimesliceId reads the files fileCounter*device.maxInputTimeslices+device.inputTimesliceId
      // the TF to read is numTF
      assert(device.inputTimesliceId < device.maxInputTimeslices);
      int fcnt = (*fileCounter * device.maxInputTimeslices) + device.inputTimesliceId;
      int ntf = *numTF + 1;
      static int currentFileCounter = -1;
      static int filesProcessed = 0;
      if (currentFileCounter != *fileCounter) {
        currentFileCounter = *fileCounter;
        monitoring.send(Metric{(uint64_t)++filesProcessed, "files-opened"}.addTag(Key::Subsystem, monitoring::tags::Value::DPL));
      }
 
      // loop over requested tables
      bool first = true;
      static size_t totalSizeUncompressed = 0;
      static size_t totalSizeCompressed = 0;
      static uint64_t totalDFSent = 0;
 
      // check if RuntimeLimit is reached
      if (!watchdog->update()) {
        LOGP(info, "Run time exceeds run time limit of {} seconds. Exiting gracefully...", watchdog->runTimeLimit);
        LOGP(info, "Stopping reader {} after time frame {}.", device.inputTimesliceId, watchdog->numberTimeFrames - 1);
        didir->closeInputFiles();
        monitoring.flushBuffer();
        control.endOfStream();
        control.readyToQuit(QuitRequest::Me);
        return;
      }
 
      int64_t startTime = uv_hrtime();
      int64_t startSize = totalSizeCompressed;
      for (auto& route : requestedTables) {
        if ((device.inputTimesliceId % route.maxTimeslices) != route.timeslice) {
          continue;
        }
 
        // create header
        auto concrete = DataSpecUtils::asConcreteDataMatcher(route.matcher);
        auto dh = header::DataHeader(concrete.description, concrete.origin, concrete.subSpec);
 
        if (!didir->readTree(outputs, dh, fcnt, ntf, totalSizeCompressed, totalSizeUncompressed)) {
          if (first) {
            // check if there is a next file to read
            fcnt += device.maxInputTimeslices;
            if (didir->atEnd(fcnt)) {
              LOGP(info, "No input files left to read for reader {}!", device.inputTimesliceId);
              didir->closeInputFiles();
              monitoring.flushBuffer();
              control.endOfStream();
              control.readyToQuit(QuitRequest::Me);
              return;
            }
            // get first folder of next file
            ntf = 0;
            if (!didir->readTree(outputs, dh, fcnt, ntf, totalSizeCompressed, totalSizeUncompressed)) {
              LOGP(fatal, "Can not retrieve tree for table {}: fileCounter {}, timeFrame {}", concrete.origin.as<std::string>(), fcnt, ntf);
              throw std::runtime_error("Processing is stopped!");
            }
          } else {
            LOGP(fatal, "Can not retrieve tree for table {}: fileCounter {}, timeFrame {}", concrete.origin.as<std::string>(), fcnt, ntf);
            throw std::runtime_error("Processing is stopped!");
          }
        }
 
        if (first) {
          if (reportTFN) {
            // TF number
            auto timeFrameNumber = didir->getTimeFrameNumber(dh, fcnt, ntf);
            auto o = Output(TFNumberHeader);
            outputs.make<uint64_t>(o) = timeFrameNumber;
          }
 
          if (reportTFFileName) {
            // Origin file name for derived output map
            auto o2 = Output(TFFileNameHeader);
            auto fileAndFolder = didir->getFileFolder(dh, fcnt, ntf);
            auto rootFS = std::dynamic_pointer_cast<TFileFileSystem>(fileAndFolder.filesystem());
            auto* f = dynamic_cast<TFile*>(rootFS->GetFile());
            std::string currentFilename(f->GetFile()->GetName());
            if (strcmp(f->GetEndpointUrl()->GetProtocol(), "file") == 0 && f->GetEndpointUrl()->GetFile()[0] != '/') {
              // This is not an absolute local path. Make it absolute.
              static std::string pwd = gSystem->pwd() + std::string("/");
              currentFilename = pwd + std::string(f->GetName());
            }
            outputs.make<std::string>(o2) = currentFilename;
          }
        }
        first = false;
      }
      int64_t stopSize = totalSizeCompressed;
      int64_t bytesDelta = stopSize - startSize;
      int64_t stopTime = uv_hrtime();
      float currentDelta = float(stopTime - startTime) / 1000000000; // in s
      if (ceil(maxRate) > 0.) {
        float extraTime = (bytesDelta / 1000000 - currentDelta * maxRate) / maxRate;
        // We only sleep if we read faster than the max-read-rate.
        if (extraTime > 0.) {
          LOGP(info, "Read {} MB in {} s. Sleeping for {} seconds to stay within {} MB/s limit.", bytesDelta / 1000000, currentDelta, extraTime, maxRate);
          uv_sleep(extraTime * 1000); // in milliseconds
        }
      }
      totalDFSent++;
      monitoring.send(Metric{(uint64_t)totalDFSent, "df-sent"}.addTag(Key::Subsystem, monitoring::tags::Value::DPL));
      monitoring.send(Metric{(uint64_t)totalSizeUncompressed / 1000, "aod-bytes-read-uncompressed"}.addTag(Key::Subsystem, monitoring::tags::Value::DPL));
      monitoring.send(Metric{(uint64_t)totalSizeCompressed / 1000, "aod-bytes-read-compressed"}.addTag(Key::Subsystem, monitoring::tags::Value::DPL));
 
      // save file number and time frame
      *fileCounter = (fcnt - device.inputTimesliceId) / device.maxInputTimeslices;
      *numTF = ntf;
 
      // Check if the next timeframe is available or
      // if there are more files to be processed. If not, simply exit.
      fcnt = (*fileCounter * device.maxInputTimeslices) + device.inputTimesliceId;
      ntf = *numTF + 1;
      auto& firstRoute = requestedTables.front();
      auto concrete = DataSpecUtils::asConcreteDataMatcher(firstRoute.matcher);
      auto dh = header::DataHeader(concrete.description, concrete.origin, concrete.subSpec);
      auto fileAndFolder = didir->getFileFolder(dh, fcnt, ntf);
 
      // In case the filesource is empty, move to the next one.
      if (fileAndFolder.path().empty()) {
        fcnt += 1;
        ntf = 0;
        if (didir->atEnd(fcnt)) {
          LOGP(info, "No input files left to read for reader {}!", device.inputTimesliceId);
          didir->closeInputFiles();
          monitoring.flushBuffer();
          control.endOfStream();
          control.readyToQuit(QuitRequest::Me);
          return;
        }
      }
    });
  })};
 
  return callback;
}
AlgorithmSpec AODJAlienReaderHelpers::rootFileReaderCallback(ConfigContext const& ctx) {…}
 
} // namespace o2::framework::readers
namespace o2::framework::readers {…}