Logo ROOT  
Reference Guide
 
Loading...
Searching...
No Matches
RPageStorageFile.cxx
Go to the documentation of this file.
1/// \file RPageStorageFile.cxx
2/// \ingroup NTuple ROOT7
3/// \author Jakob Blomer <jblomer@cern.ch>
4/// \date 2019-11-25
5/// \warning This is part of the ROOT 7 prototype! It will change without notice. It might trigger earthquakes. Feedback
6/// is welcome!
7
8/*************************************************************************
9 * Copyright (C) 1995-2019, Rene Brun and Fons Rademakers. *
10 * All rights reserved. *
11 * *
12 * For the licensing terms see $ROOTSYS/LICENSE. *
13 * For the list of contributors see $ROOTSYS/README/CREDITS. *
14 *************************************************************************/
15
16#include <ROOT/RCluster.hxx>
17#include <ROOT/RClusterPool.hxx>
18#include <ROOT/RField.hxx>
19#include <ROOT/RLogger.hxx>
21#include <ROOT/RNTupleModel.hxx>
23#include <ROOT/RNTupleZip.hxx>
24#include <ROOT/RPage.hxx>
26#include <ROOT/RPagePool.hxx>
28#include <ROOT/RRawFile.hxx>
29
30#include <RVersion.h>
31#include <TError.h>
32
33#include <algorithm>
34#include <cstdio>
35#include <cstdlib>
36#include <iostream>
37#include <utility>
38
39#include <atomic>
40#include <condition_variable>
41#include <functional>
42#include <mutex>
43#include <thread>
44#include <queue>
45
47 const RNTupleWriteOptions &options)
48 : RPageSink(ntupleName, options)
49 , fPageAllocator(std::make_unique<RPageAllocatorHeap>())
50{
51 R__LOG_WARNING(NTupleLog()) << "The RNTuple file format will change. " <<
52 "Do not store real data with this version of RNTuple!";
53 fCompressor = std::make_unique<RNTupleCompressor>();
54 EnableDefaultMetrics("RPageSinkFile");
55}
56
57
58ROOT::Experimental::Detail::RPageSinkFile::RPageSinkFile(std::string_view ntupleName, std::string_view path,
59 const RNTupleWriteOptions &options)
60 : RPageSinkFile(ntupleName, options)
61{
62 fWriter = std::unique_ptr<Internal::RNTupleFileWriter>(Internal::RNTupleFileWriter::Recreate(
63 ntupleName, path, options.GetCompression(), options.GetContainerFormat()));
64}
65
66
68 const RNTupleWriteOptions &options)
69 : RPageSinkFile(ntupleName, options)
70{
71 fWriter = std::unique_ptr<Internal::RNTupleFileWriter>(Internal::RNTupleFileWriter::Append(ntupleName, file));
72}
73
74
75ROOT::Experimental::Detail::RPageSinkFile::RPageSinkFile(std::string_view ntupleName, std::string_view path,
76 const RNTupleWriteOptions &options, std::unique_ptr<TFile> &file)
77 : RPageSinkFile(ntupleName, options)
78{
79 fWriter = std::unique_ptr<Internal::RNTupleFileWriter>(
81}
82
83
85{
86}
87
89 unsigned char *serializedHeader, std::uint32_t length)
90{
91 auto zipBuffer = std::make_unique<unsigned char[]>(length);
92 auto szZipHeader = fCompressor->Zip(serializedHeader, length, GetWriteOptions().GetCompression(),
94 fWriter->WriteNTupleHeader(zipBuffer.get(), szZipHeader, length);
95}
96
97
100 const RPageStorage::RSealedPage &sealedPage, std::size_t bytesPacked)
101{
102 std::uint64_t offsetData;
103 {
104 RNTupleAtomicTimer timer(fCounters->fTimeWallWrite, fCounters->fTimeCpuWrite);
105 offsetData = fWriter->WriteBlob(sealedPage.fBuffer, sealedPage.fSize, bytesPacked);
106 }
107
109 result.fPosition = offsetData;
110 result.fBytesOnStorage = sealedPage.fSize;
111 fCounters->fNPageCommitted.Inc();
112 fCounters->fSzWritePayload.Add(sealedPage.fSize);
113 fNBytesCurrentCluster += sealedPage.fSize;
114 return result;
115}
116
117
120{
121 auto element = columnHandle.fColumn->GetElement();
122 RPageStorage::RSealedPage sealedPage;
123 {
124 RNTupleAtomicTimer timer(fCounters->fTimeWallZip, fCounters->fTimeCpuZip);
125 sealedPage = SealPage(page, *element, GetWriteOptions().GetCompression());
126 }
127
128 fCounters->fSzZip.Add(page.GetNBytes());
129 return WriteSealedPage(sealedPage, element->GetPackedSize(page.GetNElements()));
130}
131
132
135 DescriptorId_t columnId, const RPageStorage::RSealedPage &sealedPage)
136{
137 const auto bitsOnStorage = RColumnElementBase::GetBitsOnStorage(
138 fDescriptorBuilder.GetDescriptor().GetColumnDescriptor(columnId).GetModel().GetType());
139 const auto bytesPacked = (bitsOnStorage * sealedPage.fNElements + 7) / 8;
140
141 return WriteSealedPage(sealedPage, bytesPacked);
142}
143
144
145std::uint64_t
147{
148 auto result = fNBytesCurrentCluster;
149 fNBytesCurrentCluster = 0;
150 return result;
151}
152
155 std::uint32_t length)
156{
157 auto bufPageListZip = std::make_unique<unsigned char[]>(length);
158 auto szPageListZip = fCompressor->Zip(serializedPageList, length, GetWriteOptions().GetCompression(),
159 RNTupleCompressor::MakeMemCopyWriter(bufPageListZip.get()));
160
162 result.fBytesOnStorage = szPageListZip;
163 result.fPosition = fWriter->WriteBlob(bufPageListZip.get(), szPageListZip, length);
164 return result;
165}
166
167void ROOT::Experimental::Detail::RPageSinkFile::CommitDatasetImpl(unsigned char *serializedFooter, std::uint32_t length)
168{
169 auto bufFooterZip = std::make_unique<unsigned char[]>(length);
170 auto szFooterZip = fCompressor->Zip(serializedFooter, length, GetWriteOptions().GetCompression(),
171 RNTupleCompressor::MakeMemCopyWriter(bufFooterZip.get()));
172 fWriter->WriteNTupleFooter(bufFooterZip.get(), szFooterZip, length);
173 fWriter->Commit();
174}
175
178{
179 if (nElements == 0)
180 throw RException(R__FAIL("invalid call: request empty page"));
181 auto elementSize = columnHandle.fColumn->GetElement()->GetSize();
182 return fPageAllocator->NewPage(columnHandle.fId, elementSize, nElements);
183}
184
186{
187 fPageAllocator->DeletePage(page);
188}
189
190
191////////////////////////////////////////////////////////////////////////////////
192
193
195 ColumnId_t columnId, void *mem, std::size_t elementSize, std::size_t nElements)
196{
197 RPage newPage(columnId, mem, elementSize, nElements);
198 newPage.GrowUnchecked(nElements);
199 return newPage;
200}
201
203{
204 if (page.IsNull())
205 return;
206 delete[] reinterpret_cast<unsigned char *>(page.GetBuffer());
207}
208
209
210////////////////////////////////////////////////////////////////////////////////
211
212
214 const RNTupleReadOptions &options)
215 : RPageSource(ntupleName, options)
216 , fPageAllocator(std::make_unique<RPageAllocatorFile>())
217 , fPagePool(std::make_shared<RPagePool>())
218 , fClusterPool(std::make_unique<RClusterPool>(*this, options.GetClusterBunchSize()))
219{
220 fDecompressor = std::make_unique<RNTupleDecompressor>();
221 EnableDefaultMetrics("RPageSourceFile");
222}
223
224
225ROOT::Experimental::Detail::RPageSourceFile::RPageSourceFile(std::string_view ntupleName, std::string_view path,
226 const RNTupleReadOptions &options)
227 : RPageSourceFile(ntupleName, options)
228{
232}
233
235{
236 fDescriptorBuilder.SetOnDiskHeaderSize(anchor.fNBytesHeader);
237 auto buffer = std::make_unique<unsigned char[]>(anchor.fLenHeader);
238 auto zipBuffer = std::make_unique<unsigned char[]>(anchor.fNBytesHeader);
239 fReader.ReadBuffer(zipBuffer.get(), anchor.fNBytesHeader, anchor.fSeekHeader);
240 fDecompressor->Unzip(zipBuffer.get(), anchor.fNBytesHeader, anchor.fLenHeader, buffer.get());
241 Internal::RNTupleSerializer::DeserializeHeaderV1(buffer.get(), anchor.fLenHeader, fDescriptorBuilder);
242
243 fDescriptorBuilder.AddToOnDiskFooterSize(anchor.fNBytesFooter);
244 buffer = std::make_unique<unsigned char[]>(anchor.fLenFooter);
245 zipBuffer = std::make_unique<unsigned char[]>(anchor.fNBytesFooter);
246 fReader.ReadBuffer(zipBuffer.get(), anchor.fNBytesFooter, anchor.fSeekFooter);
247 fDecompressor->Unzip(zipBuffer.get(), anchor.fNBytesFooter, anchor.fLenFooter, buffer.get());
248 Internal::RNTupleSerializer::DeserializeFooterV1(buffer.get(), anchor.fLenFooter, fDescriptorBuilder);
249}
250
251std::unique_ptr<ROOT::Experimental::Detail::RPageSourceFile>
253 std::string_view path, const RNTupleReadOptions &options)
254{
255 auto pageSource = std::make_unique<RPageSourceFile>("", path, options);
256 pageSource->InitDescriptor(anchor);
257 pageSource->fNTupleName = pageSource->fDescriptorBuilder.GetDescriptor().GetName();
258 return pageSource;
259}
260
262
263
265{
266 // If we constructed the page source with (ntuple name, path), we need to find the anchor first.
267 // Otherwise, the page source was created by OpenFromAnchor() and the header and footer are already processed.
268 if (fDescriptorBuilder.GetDescriptor().GetOnDiskHeaderSize() == 0) {
269 auto anchor = fReader.GetNTuple(fNTupleName).Unwrap();
270 InitDescriptor(anchor);
271 }
272
273 auto ntplDesc = fDescriptorBuilder.MoveDescriptor();
274
275 for (const auto &cgDesc : ntplDesc.GetClusterGroupIterable()) {
276 auto buffer = std::make_unique<unsigned char[]>(cgDesc.GetPageListLength());
277 auto zipBuffer = std::make_unique<unsigned char[]>(cgDesc.GetPageListLocator().fBytesOnStorage);
278 fReader.ReadBuffer(zipBuffer.get(), cgDesc.GetPageListLocator().fBytesOnStorage,
279 cgDesc.GetPageListLocator().GetPosition<std::uint64_t>());
280 fDecompressor->Unzip(zipBuffer.get(), cgDesc.GetPageListLocator().fBytesOnStorage, cgDesc.GetPageListLength(),
281 buffer.get());
282
283 auto clusters = RClusterGroupDescriptorBuilder::GetClusterSummaries(ntplDesc, cgDesc.GetId());
284 Internal::RNTupleSerializer::DeserializePageListV1(buffer.get(), cgDesc.GetPageListLength(), clusters);
285 for (std::size_t i = 0; i < clusters.size(); ++i) {
286 ntplDesc.AddClusterDetails(clusters[i].MoveDescriptor().Unwrap());
287 }
288 }
289
290 return ntplDesc;
291}
292
293
295 DescriptorId_t columnId, const RClusterIndex &clusterIndex, RSealedPage &sealedPage)
296{
297 const auto clusterId = clusterIndex.GetClusterId();
298
300 {
301 auto descriptorGuard = GetSharedDescriptorGuard();
302 const auto &clusterDescriptor = descriptorGuard->GetClusterDescriptor(clusterId);
303 pageInfo = clusterDescriptor.GetPageRange(columnId).Find(clusterIndex.GetIndex());
304 }
305
306 const auto bytesOnStorage = pageInfo.fLocator.fBytesOnStorage;
307 sealedPage.fSize = bytesOnStorage;
308 sealedPage.fNElements = pageInfo.fNElements;
309 if (sealedPage.fBuffer)
310 fReader.ReadBuffer(const_cast<void *>(sealedPage.fBuffer), bytesOnStorage,
311 pageInfo.fLocator.GetPosition<std::uint64_t>());
312}
313
316 const RClusterInfo &clusterInfo,
317 ClusterSize_t::ValueType idxInCluster)
318{
319 const auto columnId = columnHandle.fId;
320 const auto clusterId = clusterInfo.fClusterId;
321 const auto pageInfo = clusterInfo.fPageInfo;
322
323 const auto element = columnHandle.fColumn->GetElement();
324 const auto elementSize = element->GetSize();
325 const auto bytesOnStorage = pageInfo.fLocator.fBytesOnStorage;
326
327 const void *sealedPageBuffer = nullptr; // points either to directReadBuffer or to a read-only page in the cluster
328 std::unique_ptr<unsigned char []> directReadBuffer; // only used if cluster pool is turned off
329
330 if (fOptions.GetClusterCache() == RNTupleReadOptions::EClusterCache::kOff) {
331 directReadBuffer = std::make_unique<unsigned char[]>(bytesOnStorage);
332 fReader.ReadBuffer(directReadBuffer.get(), bytesOnStorage, pageInfo.fLocator.GetPosition<std::uint64_t>());
333 fCounters->fNPageLoaded.Inc();
334 fCounters->fNRead.Inc();
335 fCounters->fSzReadPayload.Add(bytesOnStorage);
336 sealedPageBuffer = directReadBuffer.get();
337 } else {
338 if (!fCurrentCluster || (fCurrentCluster->GetId() != clusterId) || !fCurrentCluster->ContainsColumn(columnId))
339 fCurrentCluster = fClusterPool->GetCluster(clusterId, fActiveColumns);
340 R__ASSERT(fCurrentCluster->ContainsColumn(columnId));
341
342 auto cachedPage = fPagePool->GetPage(columnId, RClusterIndex(clusterId, idxInCluster));
343 if (!cachedPage.IsNull())
344 return cachedPage;
345
346 ROnDiskPage::Key key(columnId, pageInfo.fPageNo);
347 auto onDiskPage = fCurrentCluster->GetOnDiskPage(key);
348 R__ASSERT(onDiskPage && (bytesOnStorage == onDiskPage->GetSize()));
349 sealedPageBuffer = onDiskPage->GetAddress();
350 }
351
352 std::unique_ptr<unsigned char []> pageBuffer;
353 {
354 RNTupleAtomicTimer timer(fCounters->fTimeWallUnzip, fCounters->fTimeCpuUnzip);
355 pageBuffer = UnsealPage({sealedPageBuffer, bytesOnStorage, pageInfo.fNElements}, *element);
356 fCounters->fSzUnzip.Add(elementSize * pageInfo.fNElements);
357 }
358
359 auto newPage = fPageAllocator->NewPage(columnId, pageBuffer.release(), elementSize, pageInfo.fNElements);
360 newPage.SetWindow(clusterInfo.fColumnOffset + pageInfo.fFirstInPage,
361 RPage::RClusterInfo(clusterId, clusterInfo.fColumnOffset));
362 fPagePool->RegisterPage(newPage,
363 RPageDeleter([](const RPage &page, void * /*userData*/)
364 {
366 }, nullptr));
367 fCounters->fNPagePopulated.Inc();
368 return newPage;
369}
370
371
373 ColumnHandle_t columnHandle, NTupleSize_t globalIndex)
374{
375 const auto columnId = columnHandle.fId;
376 auto cachedPage = fPagePool->GetPage(columnId, globalIndex);
377 if (!cachedPage.IsNull())
378 return cachedPage;
379
380 std::uint64_t idxInCluster;
381 RClusterInfo clusterInfo;
382 {
383 auto descriptorGuard = GetSharedDescriptorGuard();
384 clusterInfo.fClusterId = descriptorGuard->FindClusterId(columnId, globalIndex);
386
387 const auto &clusterDescriptor = descriptorGuard->GetClusterDescriptor(clusterInfo.fClusterId);
388 clusterInfo.fColumnOffset = clusterDescriptor.GetColumnRange(columnId).fFirstElementIndex;
389 R__ASSERT(clusterInfo.fColumnOffset <= globalIndex);
390 idxInCluster = globalIndex - clusterInfo.fColumnOffset;
391 clusterInfo.fPageInfo = clusterDescriptor.GetPageRange(columnId).Find(idxInCluster);
392 }
393
394 return PopulatePageFromCluster(columnHandle, clusterInfo, idxInCluster);
395}
396
397
399 ColumnHandle_t columnHandle, const RClusterIndex &clusterIndex)
400{
401 const auto clusterId = clusterIndex.GetClusterId();
402 const auto idxInCluster = clusterIndex.GetIndex();
403 const auto columnId = columnHandle.fId;
404 auto cachedPage = fPagePool->GetPage(columnId, clusterIndex);
405 if (!cachedPage.IsNull())
406 return cachedPage;
407
408 R__ASSERT(clusterId != kInvalidDescriptorId);
409 RClusterInfo clusterInfo;
410 {
411 auto descriptorGuard = GetSharedDescriptorGuard();
412 const auto &clusterDescriptor = descriptorGuard->GetClusterDescriptor(clusterId);
413 clusterInfo.fClusterId = clusterId;
414 clusterInfo.fColumnOffset = clusterDescriptor.GetColumnRange(columnId).fFirstElementIndex;
415 clusterInfo.fPageInfo = clusterDescriptor.GetPageRange(columnId).Find(idxInCluster);
416 }
417
418 return PopulatePageFromCluster(columnHandle, clusterInfo, idxInCluster);
419}
420
422{
423 fPagePool->ReturnPage(page);
424}
425
426std::unique_ptr<ROOT::Experimental::Detail::RPageSource> ROOT::Experimental::Detail::RPageSourceFile::Clone() const
427{
428 auto clone = new RPageSourceFile(fNTupleName, fOptions);
429 clone->fFile = fFile->Clone();
430 clone->fReader = Internal::RMiniFileReader(clone->fFile.get());
431 return std::unique_ptr<RPageSourceFile>(clone);
432}
433
434std::unique_ptr<ROOT::Experimental::Detail::RCluster>
436 const RCluster::RKey &clusterKey,
437 std::vector<ROOT::Internal::RRawFile::RIOVec> &readRequests)
438{
439 struct ROnDiskPageLocator {
442 std::uint64_t fOffset = 0;
443 std::uint64_t fSize = 0;
444 std::size_t fBufPos = 0;
445 };
446
447 std::vector<ROnDiskPageLocator> onDiskPages;
448 auto activeSize = 0;
449 {
450 auto descriptorGuard = GetSharedDescriptorGuard();
451 const auto &clusterDesc = descriptorGuard->GetClusterDescriptor(clusterKey.fClusterId);
452
453 // Collect the page necessary page meta-data and sum up the total size of the compressed and packed pages
454 for (auto columnId : clusterKey.fColumnSet) {
455 const auto &pageRange = clusterDesc.GetPageRange(columnId);
456 NTupleSize_t pageNo = 0;
457 for (const auto &pageInfo : pageRange.fPageInfos) {
458 const auto &pageLocator = pageInfo.fLocator;
459 activeSize += pageLocator.fBytesOnStorage;
460 onDiskPages.push_back(
461 {columnId, pageNo, pageLocator.GetPosition<std::uint64_t>(), pageLocator.fBytesOnStorage, 0});
462 ++pageNo;
463 }
464 }
465 }
466
467 // Linearize the page requests by file offset
468 std::sort(onDiskPages.begin(), onDiskPages.end(),
469 [](const ROnDiskPageLocator &a, const ROnDiskPageLocator &b) {return a.fOffset < b.fOffset;});
470
471 // In order to coalesce close-by pages, we collect the sizes of the gaps between pages on disk. We then order
472 // the gaps by size, sum them up and find a cutoff for the largest gap that we tolerate when coalescing pages.
473 // The size of the cutoff is given by the fraction of extra bytes we are willing to read in order to reduce
474 // the number of read requests. We thus schedule the lowest number of requests given a tolerable fraction
475 // of extra bytes.
476 // TODO(jblomer): Eventually we may want to select the parameter at runtime according to link latency and speed,
477 // memory consumption, device block size.
478 float maxOverhead = 0.25 * float(activeSize);
479 std::vector<std::size_t> gaps;
480 for (unsigned i = 1; i < onDiskPages.size(); ++i) {
481 gaps.emplace_back(onDiskPages[i].fOffset - (onDiskPages[i-1].fSize + onDiskPages[i-1].fOffset));
482 }
483 std::sort(gaps.begin(), gaps.end());
484 std::size_t gapCut = 0;
485 std::size_t currentGap = 0;
486 float szExtra = 0.0;
487 for (auto g : gaps) {
488 if (g != currentGap) {
489 gapCut = currentGap;
490 currentGap = g;
491 }
492 szExtra += g;
493 if (szExtra > maxOverhead)
494 break;
495 }
496
497 // In a first step, we coalesce the read requests and calculate the cluster buffer size.
498 // In a second step, we'll fix-up the memory destinations for the read calls given the
499 // address of the allocated buffer. We must not touch, however, the read requests from previous
500 // calls to PrepareSingleCluster()
501 const auto currentReadRequestIdx = readRequests.size();
502
504 std::size_t szPayload = 0;
505 std::size_t szOverhead = 0;
506 for (auto &s : onDiskPages) {
507 R__ASSERT(s.fSize > 0);
508 auto readUpTo = req.fOffset + req.fSize;
509 R__ASSERT(s.fOffset >= readUpTo);
510 auto overhead = s.fOffset - readUpTo;
511 szPayload += s.fSize;
512 if (overhead <= gapCut) {
513 szOverhead += overhead;
514 s.fBufPos = reinterpret_cast<intptr_t>(req.fBuffer) + req.fSize + overhead;
515 req.fSize += overhead + s.fSize;
516 continue;
517 }
518
519 // close the current request and open new one
520 if (req.fSize > 0)
521 readRequests.emplace_back(req);
522
523 req.fBuffer = reinterpret_cast<unsigned char *>(req.fBuffer) + req.fSize;
524 s.fBufPos = reinterpret_cast<intptr_t>(req.fBuffer);
525
526 req.fOffset = s.fOffset;
527 req.fSize = s.fSize;
528 }
529 readRequests.emplace_back(req);
530 fCounters->fSzReadPayload.Add(szPayload);
531 fCounters->fSzReadOverhead.Add(szOverhead);
532
533 // Register the on disk pages in a page map
534 auto buffer = new unsigned char[reinterpret_cast<intptr_t>(req.fBuffer) + req.fSize];
535 auto pageMap = std::make_unique<ROnDiskPageMapHeap>(std::unique_ptr<unsigned char []>(buffer));
536 for (const auto &s : onDiskPages) {
537 ROnDiskPage::Key key(s.fColumnId, s.fPageNo);
538 pageMap->Register(key, ROnDiskPage(buffer + s.fBufPos, s.fSize));
539 }
540 fCounters->fNPageLoaded.Add(onDiskPages.size());
541 for (auto i = currentReadRequestIdx; i < readRequests.size(); ++i) {
542 readRequests[i].fBuffer = buffer + reinterpret_cast<intptr_t>(readRequests[i].fBuffer);
543 }
544
545 auto cluster = std::make_unique<RCluster>(clusterKey.fClusterId);
546 cluster->Adopt(std::move(pageMap));
547 for (auto colId : clusterKey.fColumnSet)
548 cluster->SetColumnAvailable(colId);
549 return cluster;
550}
551
552std::vector<std::unique_ptr<ROOT::Experimental::Detail::RCluster>>
554{
555 fCounters->fNClusterLoaded.Add(clusterKeys.size());
556
557 std::vector<std::unique_ptr<ROOT::Experimental::Detail::RCluster>> clusters;
558 std::vector<ROOT::Internal::RRawFile::RIOVec> readRequests;
559
560 for (auto key: clusterKeys) {
561 clusters.emplace_back(PrepareSingleCluster(key, readRequests));
562 }
563
564 auto nReqs = readRequests.size();
565 {
566 RNTupleAtomicTimer timer(fCounters->fTimeWallRead, fCounters->fTimeCpuRead);
567 fFile->ReadV(&readRequests[0], nReqs);
568 }
569 fCounters->fNReadV.Inc();
570 fCounters->fNRead.Add(nReqs);
571
572 return clusters;
573}
574
575
577{
578 RNTupleAtomicTimer timer(fCounters->fTimeWallUnzip, fCounters->fTimeCpuUnzip);
579 fTaskScheduler->Reset();
580
581 const auto clusterId = cluster->GetId();
582 auto descriptorGuard = GetSharedDescriptorGuard();
583 const auto &clusterDescriptor = descriptorGuard->GetClusterDescriptor(clusterId);
584
585 std::vector<std::unique_ptr<RColumnElementBase>> allElements;
586
587 const auto &columnsInCluster = cluster->GetAvailColumns();
588 for (const auto columnId : columnsInCluster) {
589 const auto &columnDesc = descriptorGuard->GetColumnDescriptor(columnId);
590
591 allElements.emplace_back(RColumnElementBase::Generate(columnDesc.GetModel().GetType()));
592
593 const auto &pageRange = clusterDescriptor.GetPageRange(columnId);
594 std::uint64_t pageNo = 0;
595 std::uint64_t firstInPage = 0;
596 for (const auto &pi : pageRange.fPageInfos) {
597 ROnDiskPage::Key key(columnId, pageNo);
598 auto onDiskPage = cluster->GetOnDiskPage(key);
599 R__ASSERT(onDiskPage && (onDiskPage->GetSize() == pi.fLocator.fBytesOnStorage));
600
601 auto taskFunc =
602 [this, columnId, clusterId, firstInPage, onDiskPage,
603 element = allElements.back().get(),
604 nElements = pi.fNElements,
605 indexOffset = clusterDescriptor.GetColumnRange(columnId).fFirstElementIndex
606 ] () {
607 auto pageBuffer = UnsealPage({onDiskPage->GetAddress(), onDiskPage->GetSize(), nElements}, *element);
608 fCounters->fSzUnzip.Add(element->GetSize() * nElements);
609
610 auto newPage = fPageAllocator->NewPage(columnId, pageBuffer.release(), element->GetSize(), nElements);
611 newPage.SetWindow(indexOffset + firstInPage, RPage::RClusterInfo(clusterId, indexOffset));
612 fPagePool->PreloadPage(newPage,
613 RPageDeleter([](const RPage &page, void * /*userData*/)
614 {
616 }, nullptr));
617 };
618
619 fTaskScheduler->AddTask(taskFunc);
620
621 firstInPage += pi.fNElements;
622 pageNo++;
623 } // for all pages in column
624 } // for all columns in cluster
625
626 fCounters->fNPagePopulated.Add(cluster->GetNOnDiskPages());
627
628 fTaskScheduler->Wait();
629}
size_t fSize
#define R__FAIL(msg)
Short-hand to return an RResult<T> in an error state; the RError is implicitly converted into RResult...
Definition RError.hxx:303
#define R__LOG_WARNING(...)
Definition RLogger.hxx:363
#define b(i)
Definition RSha256.hxx:100
#define g(i)
Definition RSha256.hxx:105
#define a(i)
Definition RSha256.hxx:99
#define R__ASSERT(e)
Definition TError.h:117
Option_t Option_t TPoint TPoint const char GetTextMagnitude GetFillStyle GetLineColor GetLineWidth GetMarkerStyle GetTextAlign GetTextColor GetTextSize void char Point_t Rectangle_t WindowAttributes_t Float_t Float_t Float_t Int_t Int_t UInt_t UInt_t Rectangle_t result
Option_t Option_t TPoint TPoint const char GetTextMagnitude GetFillStyle GetLineColor GetLineWidth GetMarkerStyle GetTextAlign GetTextColor GetTextSize void char Point_t Rectangle_t WindowAttributes_t Float_t Float_t Float_t Int_t Int_t UInt_t UInt_t Rectangle_t Int_t Int_t Window_t TString Int_t GCValues_t GetPrimarySelectionOwner GetDisplay GetScreen GetColormap GetNativeEvent const char const char dpyName wid window const char font_name cursor keysym reg const char only_if_exist regb h Point_t winding char text const char depth char const char Int_t count const char ColorStruct_t color const char Pixmap_t Pixmap_t PictureAttributes_t attr const char char ret_data h unsigned char height h length
Managed a set of clusters containing compressed and packed pages.
An in-memory subset of the packed and compressed pages of a cluster.
Definition RCluster.hxx:154
const ColumnSet_t & GetAvailColumns() const
Definition RCluster.hxx:198
const ROnDiskPage * GetOnDiskPage(const ROnDiskPage::Key &key) const
Definition RCluster.cxx:37
static std::unique_ptr< RColumnElementBase > Generate(EColumnType type)
RColumnElementBase * GetElement() const
Definition RColumn.hxx:308
static Writer_t MakeMemCopyWriter(unsigned char *dest)
Record wall time and CPU time between construction and destruction.
A page as being stored on disk, that is packed and compressed.
Definition RCluster.hxx:43
static RPage NewPage(ColumnId_t columnId, void *mem, std::size_t elementSize, std::size_t nElements)
Uses standard C++ memory allocation for the column data pages.
A closure that can free the memory associated with a mapped page.
A thread-safe cache of column pages.
Definition RPagePool.hxx:47
Storage provider that write ntuple pages into a file.
RNTupleLocator CommitSealedPageImpl(DescriptorId_t columnId, const RPageStorage::RSealedPage &sealedPage) final
RPage ReservePage(ColumnHandle_t columnHandle, std::size_t nElements) final
Get a new, empty page for the given column that can be filled with up to nElements.
RNTupleLocator CommitPageImpl(ColumnHandle_t columnHandle, const RPage &page) final
std::uint64_t CommitClusterImpl(NTupleSize_t nEntries) final
Returns the number of bytes written to storage (excluding metadata)
void CreateImpl(const RNTupleModel &model, unsigned char *serializedHeader, std::uint32_t length) final
RPageSinkFile(std::string_view ntupleName, const RNTupleWriteOptions &options)
void ReleasePage(RPage &page) final
Every page store needs to be able to free pages it handed out.
void CommitDatasetImpl(unsigned char *serializedFooter, std::uint32_t length) final
std::unique_ptr< Internal::RNTupleFileWriter > fWriter
RNTupleLocator WriteSealedPage(const RPageStorage::RSealedPage &sealedPage, std::size_t bytesPacked)
RNTupleLocator CommitClusterGroupImpl(unsigned char *serializedPageList, std::uint32_t length) final
Returns the locator of the page list envelope of the given buffer that contains the serialized page l...
Abstract interface to write data into an ntuple.
void EnableDefaultMetrics(const std::string &prefix)
Enables the default set of metrics provided by RPageSink.
std::unique_ptr< RNTupleCompressor > fCompressor
Helper to zip pages and header/footer; includes a 16MB (kMAXZIPBUF) zip buffer.
Storage provider that reads ntuple pages from a file.
void LoadSealedPage(DescriptorId_t columnId, const RClusterIndex &clusterIndex, RSealedPage &sealedPage) final
Read the packed and compressed bytes of a page into the memory buffer provided by selaedPage.
std::vector< std::unique_ptr< RCluster > > LoadClusters(std::span< RCluster::RKey > clusterKeys) final
Populates all the pages of the given cluster ids and columns; it is possible that some columns do not...
void InitDescriptor(const Internal::RFileNTupleAnchor &anchor)
Deserialized header and footer into a minimal descriptor held by fDescriptorBuilder.
Internal::RMiniFileReader fReader
Takes the fFile to read ntuple blobs from it.
void ReleasePage(RPage &page) final
Every page store needs to be able to free pages it handed out.
static std::unique_ptr< RPageSourceFile > CreateFromAnchor(const Internal::RFileNTupleAnchor &anchor, std::string_view path, const RNTupleReadOptions &options)
Used from the RNTuple class to build a datasource if the anchor is already available.
std::unique_ptr< RCluster > PrepareSingleCluster(const RCluster::RKey &clusterKey, std::vector< ROOT::Internal::RRawFile::RIOVec > &readRequests)
Helper function for LoadClusters: it prepares the memory buffer (page map) and the read requests for ...
std::unique_ptr< RPageSource > Clone() const final
The cloned page source creates a new raw file and reader and opens its own file descriptor to the dat...
void UnzipClusterImpl(RCluster *cluster) final
RPageSourceFile(std::string_view ntupleName, const RNTupleReadOptions &options)
std::unique_ptr< ROOT::Internal::RRawFile > fFile
An RRawFile is used to request the necessary byte ranges from a local or a remote file.
RPage PopulatePage(ColumnHandle_t columnHandle, NTupleSize_t globalIndex) final
Allocates and fills a page that contains the index-th element.
RPage PopulatePageFromCluster(ColumnHandle_t columnHandle, const RClusterInfo &clusterInfo, ClusterSize_t::ValueType idxInCluster)
Abstract interface to read data from an ntuple.
void EnableDefaultMetrics(const std::string &prefix)
Enables the default set of metrics provided by RPageSource.
std::unique_ptr< RNTupleDecompressor > fDecompressor
Helper to unzip pages and header/footer; comprises a 16MB (kMAXZIPBUF) unzip buffer.
Stores information about the cluster in which this page resides.
Definition RPage.hxx:46
A page is a slice of a column that is mapped into memory.
Definition RPage.hxx:41
ClusterSize_t::ValueType GetNElements() const
Definition RPage.hxx:83
ClusterSize_t::ValueType GetNBytes() const
The space taken by column elements in the buffer.
Definition RPage.hxx:81
void * GrowUnchecked(ClusterSize_t::ValueType nElements)
Called during writing: returns a pointer after the last element and increases the element counter in ...
Definition RPage.hxx:109
Read RNTuple data blocks from a TFile container, provided by a RRawFile.
static RNTupleFileWriter * Append(std::string_view ntupleName, TFile &file)
Add a new RNTuple identified by ntupleName to the existing TFile.
static RNTupleFileWriter * Recreate(std::string_view ntupleName, std::string_view path, int defaultCompression, ENTupleContainerFormat containerFormat)
Create or truncate the local file given by path with the new empty RNTuple identified by ntupleName.
static RResult< void > DeserializePageListV1(const void *buffer, std::uint32_t bufSize, std::vector< RClusterDescriptorBuilder > &clusters)
static RResult< void > DeserializeFooterV1(const void *buffer, std::uint32_t bufSize, RNTupleDescriptorBuilder &descBuilder)
static RResult< void > DeserializeHeaderV1(const void *buffer, std::uint32_t bufSize, RNTupleDescriptorBuilder &descBuilder)
static std::vector< RClusterDescriptorBuilder > GetClusterSummaries(const RNTupleDescriptor &ntplDesc, DescriptorId_t clusterGroupId)
Used to prepare the cluster descriptor builders when loading the page locations for a certain cluster...
Addresses a column element or field item relative to a particular cluster, instead of a global NTuple...
DescriptorId_t GetClusterId() const
ClusterSize_t::ValueType GetIndex() const
Base class for all ROOT issued exceptions.
Definition RError.hxx:78
The on-storage meta-data of an ntuple.
The RNTupleModel encapulates the schema of an ntuple.
Common user-tunable settings for reading ntuples.
Common user-tunable settings for storing ntuples.
ENTupleContainerFormat GetContainerFormat() const
static std::unique_ptr< RRawFile > Create(std::string_view url, ROptions options=ROptions())
Factory method that returns a suitable concrete implementation according to the transport in the url.
Definition RRawFile.cxx:73
A ROOT file is a suite of consecutive data records (TKey instances) with a well defined format.
Definition TFile.h:51
RLogChannel & NTupleLog()
Log channel for RNTuple diagnostics.
std::uint64_t NTupleSize_t
Integer type long enough to hold the maximum number of entries in a column.
std::uint64_t DescriptorId_t
Distriniguishes elements of the same type within a descriptor, e.g. different fields.
std::int64_t ColumnId_t
Uniquely identifies a physical column within the scope of the current process, used to tag pages.
constexpr DescriptorId_t kInvalidDescriptorId
Definition file.py:1
The identifiers that specifies the content of a (partial) cluster.
Definition RCluster.hxx:158
On-disk pages within a page source are identified by the column and page number.
Definition RCluster.hxx:53
Summarizes cluster-level information that are necessary to populate a certain page.
RClusterDescriptor::RPageRange::RPageInfoExtended fPageInfo
Location of the page on disk.
std::uint64_t fColumnOffset
The first element number of the page's column in the given cluster.
A sealed page contains the bytes of a page as written to storage (packed & compressed).
Entry point for an RNTuple in a ROOT file.
Definition RMiniFile.hxx:65
std::uint32_t fNBytesFooter
The size of the compressed ntuple footer.
Definition RMiniFile.hxx:82
std::uint64_t fSeekFooter
The file offset of the footer excluding the TKey part.
Definition RMiniFile.hxx:80
std::uint32_t fNBytesHeader
The size of the compressed ntuple header.
Definition RMiniFile.hxx:76
std::uint32_t fLenFooter
The size of the uncompressed ntuple footer.
Definition RMiniFile.hxx:84
std::uint64_t fSeekHeader
The file offset of the header excluding the TKey part.
Definition RMiniFile.hxx:74
std::uint32_t fLenHeader
The size of the uncompressed ntuple header.
Definition RMiniFile.hxx:78
We do not need to store the element size / uncompressed page size because we know to which column the...
RNTupleLocator fLocator
The meaning of fLocator depends on the storage backend.
ClusterSize_t fNElements
The sum of the elements of all the pages must match the corresponding fNElements field in fColumnRang...
Generic information about the physical location of data.
Used for vector reads from multiple offsets into multiple buffers.
Definition RRawFile.hxx:71
std::size_t fSize
The number of desired bytes.
Definition RRawFile.hxx:77
void * fBuffer
The destination for reading.
Definition RRawFile.hxx:73
std::uint64_t fOffset
The file offset.
Definition RRawFile.hxx:75