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https://issues.apache.org/jira/browse/PHOENIX-2892?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15321857#comment-15321857
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James Taylor commented on PHOENIX-2892:
---------------------------------------
FYI, Phoenix has the similar behavior with other databases wrt to batch and
auto commit:
http://stackoverflow.com/questions/19536513/addbatch-used-together-with-autocommit-true
> Scan for pre-warming the block cache for 2ndary index should be removed
> -----------------------------------------------------------------------
>
> Key: PHOENIX-2892
> URL: https://issues.apache.org/jira/browse/PHOENIX-2892
> Project: Phoenix
> Issue Type: Bug
> Reporter: Enis Soztutar
> Assignee: Enis Soztutar
> Fix For: 4.8.0
>
> Attachments: phoenix-2892_v1.patch
>
>
> We have run into an issue in a mid-sized cluster with secondary indexes. The
> problem is that all handlers for doing writes were blocked waiting on a
> single scan from the secondary index to complete for > 5mins, thus causing
> all incoming RPCs to timeout and causing write un-availability and further
> problems (disabling the index, etc). We've taken jstack outputs continuously
> from the servers to understand what is going on.
> In the jstack outputs from that particular server, we can see three types of
> stacks (this is raw jstack so the thread names are not there unfortunately).
> - First, there are a lot of threads waiting for the MVCC transactions
> started previously:
> {code}
> Thread 15292: (state = BLOCKED)
> - java.lang.Object.wait(long) @bci=0 (Compiled frame; information may be
> imprecise)
> -
> org.apache.hadoop.hbase.regionserver.MultiVersionConsistencyControl.waitForPreviousTransactionsComplete(org.apache.hadoop.hbase.regionserver.MultiVersionConsistencyControl$WriteEntry)
> @bci=86, line=253 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.MultiVersionConsistencyControl.completeMemstoreInsertWithSeqNum(org.apache.hadoop.hbase.regionserver.MultiVersionConsistencyControl$WriteEntry,
> org.apache.hadoop.hbase.regionserver.SequenceId) @bci=29, line=135 (Compiled
> frame)
> -
> org.apache.hadoop.hbase.regionserver.HRegion.doMiniBatchMutation(org.apache.hadoop.hbase.regionserver.HRegion$BatchOperationInProgress)
> @bci=1906, line=3187 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.HRegion.batchMutate(org.apache.hadoop.hbase.regionserver.HRegion$BatchOperationInProgress)
> @bci=79, line=2819 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.HRegion.batchMutate(org.apache.hadoop.hbase.client.Mutation[],
> long, long) @bci=12, line=2761 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.RSRpcServices.doBatchOp(org.apache.hadoop.hbase.protobuf.generated.ClientProtos$RegionActionResult$Builder,
> org.apache.hadoop.hbase.regionserver.Region,
> org.apache.hadoop.hbase.quotas.OperationQuota, java.util.List,
> org.apache.hadoop.hbase.CellScanner) @bci=150, line=692 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.RSRpcServices.doNonAtomicRegionMutation(org.apache.hadoop.hbase.regionserver.Region,
> org.apache.hadoop.hbase.quotas.OperationQuota,
> org.apache.hadoop.hbase.protobuf.generated.ClientProtos$RegionAction,
> org.apache.hadoop.hbase.CellScanner,
> org.apache.hadoop.hbase.protobuf.generated.ClientProtos$RegionActionResult$Builder,
> java.util.List, long) @bci=547, line=654 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.RSRpcServices.multi(com.google.protobuf.RpcController,
> org.apache.hadoop.hbase.protobuf.generated.ClientProtos$MultiRequest)
> @bci=407, line=2032 (Compiled frame)
> -
> org.apache.hadoop.hbase.protobuf.generated.ClientProtos$ClientService$2.callBlockingMethod(com.google.protobuf.Descriptors$MethodDescriptor,
> com.google.protobuf.RpcController, com.google.protobuf.Message) @bci=167,
> line=32213 (Compiled frame)
> -
> org.apache.hadoop.hbase.ipc.RpcServer.call(com.google.protobuf.BlockingService,
> com.google.protobuf.Descriptors$MethodDescriptor,
> com.google.protobuf.Message, org.apache.hadoop.hbase.CellScanner, long,
> org.apache.hadoop.hbase.monitoring.MonitoredRPCHandler) @bci=59, line=2114
> (Compiled frame)
> - org.apache.hadoop.hbase.ipc.CallRunner.run() @bci=345, line=101 (Compiled
> frame)
> -
> org.apache.hadoop.hbase.ipc.RpcExecutor.consumerLoop(java.util.concurrent.BlockingQueue)
> @bci=54, line=130 (Compiled frame)
> - org.apache.hadoop.hbase.ipc.RpcExecutor$1.run() @bci=20, line=107
> (Interpreted frame)
> - java.lang.Thread.run() @bci=11, line=745 (Interpreted frame)
> {code}
> The way MVCC works is that it assumes that transactions are short living, and
> it guarantees that transactions are committed in strict serial order.
> Transactions in this case are write requests coming in and being executed
> from handlers. Each handler will start a transaction, get a mvcc write index
> (which is the mvcc trx number) and does the WAL append + memstore append.
> Then it marks the mvcc trx to be complete, and before returning to the user,
> we have to guarantee that the transaction is visible. So we wait for the mvcc
> read point to be advanced beyond our own write trx number. This is done at
> the above stack trace (waitForPreviousTransactionsComplete). A lot of threads
> with this stack means that one or more handlers have started a mvcc
> transaction, but did not finish the work and thus did not complete their
> transactions. MVCC read point can only advance serially, otherwise ongoing
> transactions will be visible, thus we just wait for the previously started
> transactions to complete.
> - second set of threads are waiting with this stack trace:
> {code}
> Thread 15274: (state = BLOCKED)
> - sun.misc.Unsafe.park(boolean, long) @bci=0 (Compiled frame; information
> may be imprecise)
> - java.util.concurrent.locks.LockSupport.parkNanos(java.lang.Object, long)
> @bci=20, line=226 (Interpreted frame)
> -
> java.util.concurrent.locks.AbstractQueuedSynchronizer.doAcquireSharedNanos(int,
> long) @bci=122, line=1033 (Interpreted frame)
> -
> java.util.concurrent.locks.AbstractQueuedSynchronizer.tryAcquireSharedNanos(int,
> long) @bci=25, line=1326 (Interpreted frame)
> - java.util.concurrent.CountDownLatch.await(long,
> java.util.concurrent.TimeUnit) @bci=10, line=282 (Interpreted frame)
> - org.apache.hadoop.hbase.regionserver.HRegion.getRowLockInternal(byte[],
> boolean) @bci=94, line=5044 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.HRegion.doMiniBatchMutation(org.apache.hadoop.hbase.regionserver.HRegion$BatchOperationInProgress)
> @bci=386, line=2962 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.HRegion.batchMutate(org.apache.hadoop.hbase.regionserver.HRegion$BatchOperationInProgress)
> @bci=79, line=2819 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.HRegion.batchMutate(org.apache.hadoop.hbase.client.Mutation[],
> long, long) @bci=12, line=2761 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.RSRpcServices.doBatchOp(org.apache.hadoop.hbase.protobuf.generated.ClientProtos$RegionActionResult$Builder,
> org.apache.hadoop.hbase.regionserver.Region,
> org.apache.hadoop.hbase.quotas.OperationQuota, java.util.List,
> org.apache.hadoop.hbase.CellScanner) @bci=150, line=692 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.RSRpcServices.doNonAtomicRegionMutation(org.apache.hadoop.hbase.regionserver.Region,
> org.apache.hadoop.hbase.quotas.OperationQuota,
> org.apache.hadoop.hbase.protobuf.generated.ClientProtos$RegionAction,
> org.apache.hadoop.hbase.CellScanner,
> org.apache.hadoop.hbase.protobuf.generated.ClientProtos$RegionActionResult$Builder,
> java.util.List, long) @bci=547, line=654 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.RSRpcServices.multi(com.google.protobuf.RpcController,
> org.apache.hadoop.hbase.protobuf.generated.ClientProtos$MultiRequest)
> @bci=407, line=2032 (Compiled frame)
> -
> org.apache.hadoop.hbase.protobuf.generated.ClientProtos$ClientService$2.callBlockingMethod(com.google.protobuf.Descriptors$MethodDescriptor,
> com.google.protobuf.RpcController, com.google.protobuf.Message) @bci=167,
> line=32213 (Compiled frame)
> -
> org.apache.hadoop.hbase.ipc.RpcServer.call(com.google.protobuf.BlockingService,
> com.google.protobuf.Descriptors$MethodDescriptor,
> com.google.protobuf.Message, org.apache.hadoop.hbase.CellScanner, long,
> org.apache.hadoop.hbase.monitoring.MonitoredRPCHandler) @bci=59, line=2114
> (Compiled frame)
> - org.apache.hadoop.hbase.ipc.CallRunner.run() @bci=345, line=101 (Compiled
> frame)
> -
> org.apache.hadoop.hbase.ipc.RpcExecutor.consumerLoop(java.util.concurrent.BlockingQueue)
> @bci=54, line=130 (Compiled frame)
> - org.apache.hadoop.hbase.ipc.RpcExecutor$1.run() @bci=20, line=107
> (Interpreted frame)
> - java.lang.Thread.run() @bci=11, line=745 (Interpreted frame)
> {code}
> These are the threads that want to write something, but they have to wait for
> the row lock(s) that are held from the other threads. It is very likely that
> the threads in the previous set are holding the actual row locks that these
> set of threads wants to acquire. This is normal behavior, nothing concerning.
> However, if the handler cannot acquire the row lock in 60 seconds, then the
> handler will throw an exception, and RPC will be retried.
> - Finally the only thread in the third set is doing a scan for the index
> update:
> {code}
> Thread 15276: (state = IN_JAVA)
> -
> org.apache.hadoop.hbase.regionserver.DefaultMemStore$MemStoreScanner.peek()
> @bci=0, line=847 (Compiled frame; information may be imprecise)
> -
> org.apache.hadoop.hbase.regionserver.KeyValueHeap$KVScannerComparator.compare(org.apache.hadoop.hbase.regionserver.KeyValueScanner,
> org.apache.hadoop.hbase.regionserver.KeyValueScanner) @bci=2, line=181
> (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.KeyValueHeap$KVScannerComparator.compare(java.lang.Object,
> java.lang.Object) @bci=9, line=171 (Compiled frame)
> - java.util.PriorityQueue.siftUpUsingComparator(int, java.lang.Object)
> @bci=25, line=649 (Compiled frame)
> - java.util.PriorityQueue.siftUp(int, java.lang.Object) @bci=10, line=627
> (Compiled frame)
> - java.util.PriorityQueue.offer(java.lang.Object) @bci=67, line=329
> (Compiled frame)
> - java.util.PriorityQueue.add(java.lang.Object) @bci=2, line=306 (Compiled
> frame)
> - org.apache.hadoop.hbase.regionserver.KeyValueHeap.generalizedSeek(boolean,
> org.apache.hadoop.hbase.Cell, boolean, boolean) @bci=36, line=289 (Compiled
> frame)
> -
> org.apache.hadoop.hbase.regionserver.KeyValueHeap.reseek(org.apache.hadoop.hbase.Cell)
> @bci=5, line=256 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.StoreScanner.reseek(org.apache.hadoop.hbase.Cell)
> @bci=53, line=817 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.StoreScanner.seekAsDirection(org.apache.hadoop.hbase.Cell)
> @bci=2, line=803 (Compiled frame)
> - org.apache.hadoop.hbase.regionserver.StoreScanner.next(java.util.List,
> org.apache.hadoop.hbase.regionserver.ScannerContext) @bci=876, line=636
> (Compiled frame)
> - org.apache.hadoop.hbase.regionserver.KeyValueHeap.next(java.util.List,
> org.apache.hadoop.hbase.regionserver.ScannerContext) @bci=29, line=147
> (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.HRegion$RegionScannerImpl.populateResult(java.util.List,
> org.apache.hadoop.hbase.regionserver.KeyValueHeap,
> org.apache.hadoop.hbase.regionserver.ScannerContext, byte[], int, short)
> @bci=22, line=5483 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.HRegion$RegionScannerImpl.nextInternal(java.util.List,
> org.apache.hadoop.hbase.regionserver.ScannerContext) @bci=385, line=5634
> (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.HRegion$RegionScannerImpl.nextRaw(java.util.List,
> org.apache.hadoop.hbase.regionserver.ScannerContext) @bci=29, line=5421
> (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.HRegion$RegionScannerImpl.nextRaw(java.util.List)
> @bci=6, line=5407 (Compiled frame)
> -
> org.apache.phoenix.index.PhoenixIndexBuilder.batchStarted(org.apache.hadoop.hbase.regionserver.MiniBatchOperationInProgress)
> @bci=279, line=88 (Compiled frame)
> -
> org.apache.phoenix.hbase.index.builder.IndexBuildManager.getIndexUpdate(org.apache.hadoop.hbase.regionserver.MiniBatchOperationInProgress,
> java.util.Collection) @bci=5, line=121 (Compiled frame)
> -
> org.apache.phoenix.hbase.index.Indexer.preBatchMutateWithExceptions(org.apache.hadoop.hbase.coprocessor.ObserverContext,
> org.apache.hadoop.hbase.regionserver.MiniBatchOperationInProgress) @bci=300,
> line=278 (Compiled frame)
> -
> org.apache.phoenix.hbase.index.Indexer.preBatchMutate(org.apache.hadoop.hbase.coprocessor.ObserverContext,
> org.apache.hadoop.hbase.regionserver.MiniBatchOperationInProgress) @bci=17,
> line=207 (Interpreted frame)
> -
> org.apache.hadoop.hbase.regionserver.RegionCoprocessorHost$35.call(org.apache.hadoop.hbase.coprocessor.RegionObserver,
> org.apache.hadoop.hbase.coprocessor.ObserverContext) @bci=6, line=991
> (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.RegionCoprocessorHost$RegionOperation.call(org.apache.hadoop.hbase.Coprocessor,
> org.apache.hadoop.hbase.coprocessor.ObserverContext) @bci=6, line=1673
> (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.RegionCoprocessorHost.execOperation(boolean,
>
> org.apache.hadoop.hbase.regionserver.RegionCoprocessorHost$CoprocessorOperation)
> @bci=88, line=1748 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.RegionCoprocessorHost.execOperation(org.apache.hadoop.hbase.regionserver.RegionCoprocessorHost$CoprocessorOperation)
> @bci=3, line=1705 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.RegionCoprocessorHost.preBatchMutate(org.apache.hadoop.hbase.regionserver.MiniBatchOperationInProgress)
> @bci=26, line=987 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.HRegion.doMiniBatchMutation(org.apache.hadoop.hbase.regionserver.HRegion$BatchOperationInProgress)
> @bci=996, line=3044 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.HRegion.batchMutate(org.apache.hadoop.hbase.regionserver.HRegion$BatchOperationInProgress)
> @bci=79, line=2819 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.HRegion.batchMutate(org.apache.hadoop.hbase.client.Mutation[],
> long, long) @bci=12, line=2761 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.RSRpcServices.doBatchOp(org.apache.hadoop.hbase.protobuf.generated.ClientProtos$RegionActionResult$Builder,
> org.apache.hadoop.hbase.regionserver.Region,
> org.apache.hadoop.hbase.quotas.OperationQuota, java.util.List,
> org.apache.hadoop.hbase.CellScanner) @bci=150, line=692 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.RSRpcServices.doNonAtomicRegionMutation(org.apache.hadoop.hbase.regionserver.Region,
> org.apache.hadoop.hbase.quotas.OperationQuota,
> org.apache.hadoop.hbase.protobuf.generated.ClientProtos$RegionAction,
> org.apache.hadoop.hbase.CellScanner,
> org.apache.hadoop.hbase.protobuf.generated.ClientProtos$RegionActionResult$Builder,
> java.util.List, long) @bci=547, line=654 (Compiled frame)
> -
> org.apache.hadoop.hbase.regionserver.RSRpcServices.multi(com.google.protobuf.RpcController,
> org.apache.hadoop.hbase.protobuf.generated.ClientProtos$MultiRequest)
> @bci=407, line=2032 (Compiled frame)
> -
> org.apache.hadoop.hbase.protobuf.generated.ClientProtos$ClientService$2.callBlockingMethod(com.google.protobuf.Descriptors$MethodDescriptor,
> com.google.protobuf.RpcController, com.google.protobuf.Message) @bci=167,
> line=32213 (Compiled frame)
> -
> org.apache.hadoop.hbase.ipc.RpcServer.call(com.google.protobuf.BlockingService,
> com.google.protobuf.Descriptors$MethodDescriptor,
> com.google.protobuf.Message, org.apache.hadoop.hbase.CellScanner, long,
> org.apache.hadoop.hbase.monitoring.MonitoredRPCHandler) @bci=59, line=2114
> (Compiled frame)
> - org.apache.hadoop.hbase.ipc.CallRunner.run() @bci=345, line=101 (Compiled
> frame)
> -
> org.apache.hadoop.hbase.ipc.RpcExecutor.consumerLoop(java.util.concurrent.BlockingQueue)
> @bci=54, line=130 (Compiled frame)
> - org.apache.hadoop.hbase.ipc.RpcExecutor$1.run() @bci=20, line=107
> (Interpreted frame)
> - java.lang.Thread.run() @bci=11, line=745 (Interpreted frame)
> {code}
> This thread is doing a "scan" to be able to compute the index updates (note
> HRegion.doMiniBatchMutation -> IndexBuildManager.getIndexUpdate -> Region
> Scan).
> Normally, this scan should finish in a short interval, but for whatever
> reason it takes more than 5 minutes. We know that it takes more than 5
> minutes, because in the jstacks from epoch 1462985796 to epoch 1462985958, we
> see the exact same thread (Thread 15276) continuing the scan.
> So, we do a skip scan which takes >5 minutes while holding some row locks,
> and holding the MVCC write transaction open. All the other handlers that
> start write transactions after this also holds some other row locks and waits
> for the handler doing the scan to finish. The other handlers are just waiting
> for some of the same row locks. So in effect everybody is waiting on one
> handler thread to finish the scan.
> So, why we are doing a scan in the index builder code, and why it is taking
> more than 5 minutes?
> Apparently, we are doing a skip scan in PhoenixIndexBuilder:
> {code}
> public void batchStarted(MiniBatchOperationInProgress<Mutation>
> miniBatchOp, IndexMetaData context) throws IOException {
> // The entire purpose of this method impl is to get the existing rows
> for the
> // table rows being indexed into the block cache, as the index
> maintenance code
> // does a point scan per row.
> List<IndexMaintainer> indexMaintainers =
> ((PhoenixIndexMetaData)context).getIndexMaintainers();
> List<KeyRange> keys =
> Lists.newArrayListWithExpectedSize(miniBatchOp.size());
> Map<ImmutableBytesWritable, IndexMaintainer> maintainers =
> new HashMap<ImmutableBytesWritable, IndexMaintainer>();
> ImmutableBytesWritable indexTableName = new ImmutableBytesWritable();
> for (int i = 0; i < miniBatchOp.size(); i++) {
> Mutation m = miniBatchOp.getOperation(i);
> keys.add(PVarbinary.INSTANCE.getKeyRange(m.getRow()));
>
> for(IndexMaintainer indexMaintainer: indexMaintainers) {
> if (indexMaintainer.isImmutableRows()) continue;
> indexTableName.set(indexMaintainer.getIndexTableName());
> if (maintainers.get(indexTableName) != null) continue;
> maintainers.put(indexTableName, indexMaintainer);
> }
> }
> if (maintainers.isEmpty()) return;
> Scan scan = IndexManagementUtil.newLocalStateScan(new
> ArrayList<IndexMaintainer>(maintainers.values()));
> ScanRanges scanRanges = ScanRanges.createPointLookup(keys);
> scanRanges.initializeScan(scan);
> scan.setFilter(new
> SkipScanFilter(scanRanges.getSkipScanFilter(),true));
> Region region = env.getRegion();
> RegionScanner scanner = region.getScanner(scan);
> // Run through the scanner using internal nextRaw method
> region.startRegionOperation();
> try {
> synchronized (scanner) {
> boolean hasMore;
> do {
> List<Cell> results = Lists.newArrayList();
> // Results are potentially returned even when the return
> value of s.next is
> // false since this is an indication of whether or not
> there are more values
> // after the ones returned
> hasMore = scanner.nextRaw(results);
> } while (hasMore);
> }
> }
> {code}
> I think that for some cases, this skip scan turns into an expensive and long
> scan (instead of point lookup scan). However, there is no easy way to debug
> the actual rows and the schema from that.
> The comments say that it is done to bring the results to the block cache for
> the following gets to come. However, there should not be a need for that at
> all since the reads themselves will bring those results to the block cache.
> The only explanation maybe to use prefetching from the skip scan, but it is
> still not correct to do double-work.
> The other thing is that we execute the getIndexUpdate()'s in parallel later,
> but we are still processing the skip scan serially.
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