Ah thanks! I knew you'd fixed some of these, now i know my patch of NUTCH-2466 silently removes your commit!
My bad, thanks! Markus -----Original message----- > From:Sebastian Nagel <[email protected]> > Sent: Wednesday 17th January 2018 13:32 > To: [email protected] > Subject: Re: SitemapProcessor destroyed our CrawlDB > > Hi Markus, > > the problem should be fixed with NUTCH-2442. It wasn't the case with the > first version of the > sitemap processor. It's mandatory to check also the return value of > job.waitForCompletion(true), > only checking for exceptions isn't enough! > > Sebastian > > On 01/17/2018 11:51 AM, Markus Jelsma wrote: > > Hello, > > > > We noticed some abnormalities in our crawl cycle caused by a sudden > > reduction of our CrawlDB's size. The SitemapProcessor ran, failed (timed > > out, see below) and left us with a decimated CrawlDB. > > > > This is odd because of: > > > > } catch (Exception e) { > > if (fs.exists(tempCrawlDb)) > > fs.delete(tempCrawlDb, true); > > > > LockUtil.removeLockFile(fs, lock); > > throw e; > > } > > > > Any ideas? > > > > Thanks, > > Markus > > > > Full thread dump OpenJDK 64-Bit Server VM (25.151-b12 mixed mode): > > > > "Thread-52" #74 prio=5 os_prio=0 tid=0x00007fe2adc85000 nid=0x6cf8 runnable > > [0x00007fe28a86d000] > > java.lang.Thread.State: RUNNABLE > > at java.util.regex.Pattern$BmpCharProperty.match(Pattern.java:3797) > > at java.util.regex.Pattern$Start.match(Pattern.java:3461) > > at java.util.regex.Matcher.search(Matcher.java:1248) > > at java.util.regex.Matcher.find(Matcher.java:637) > > at java.util.regex.Matcher.replaceAll(Matcher.java:951) > > at > > org.apache.nutch.net.urlnormalizer.regex.RegexURLNormalizer.regexNormalize(RegexURLNormalizer.java:193) > > > > at > > org.apache.nutch.net.urlnormalizer.regex.RegexURLNormalizer.normalize(RegexURLNormalizer.java:200) > > > > at org.apache.nutch.net.URLNormalizers.normalize(URLNormalizers.java:319) > > at > > org.apache.nutch.util.SitemapProcessor$SitemapMapper.filterNormalize(SitemapProcessor.java:176) > > > > at > > org.apache.nutch.util.SitemapProcessor$SitemapMapper.generateSitemapUrlDatum(SitemapProcessor.java:225) > > > > at > > org.apache.nutch.util.SitemapProcessor$SitemapMapper.generateSitemapUrlDatum(SitemapProcessor.java:264) > > > > at > > org.apache.nutch.util.SitemapProcessor$SitemapMapper.map(SitemapProcessor.java:154) > > > > at > > org.apache.nutch.util.SitemapProcessor$SitemapMapper.map(SitemapProcessor.java:95) > > > > at org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:146) > > at > > org.apache.hadoop.mapreduce.lib.map.MultithreadedMapper$MapRunner.run(MultithreadedMapper.java:273) > > > > "SpillThread" #34 daemon prio=5 os_prio=0 tid=0x00007fe2ada12000 nid=0x6c2f > > waiting on condition [0x00007fe28d2ad000] > > java.lang.Thread.State: WAITING (parking) > > at sun.misc.Unsafe.park(Native Method) > > - parking to wait for <0x00000000ede6dc80> (a > > java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject) > > at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175) > > at > > java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039) > > > > at > > org.apache.hadoop.mapred.MapTask$MapOutputBuffer$SpillThread.run(MapTask.java:1530) > > > > "org.apache.hadoop.hdfs.PeerCache@1fc0053e" #33 daemon prio=5 os_prio=0 > > tid=0x00007fe2ad7fe000 nid=0x6be7 waiting on condition [0x00007fe28d3ae000] > > java.lang.Thread.State: TIMED_WAITING (sleeping) > > at java.lang.Thread.sleep(Native Method) > > at org.apache.hadoop.hdfs.PeerCache.run(PeerCache.java:253) > > at org.apache.hadoop.hdfs.PeerCache.access$000(PeerCache.java:46) > > at org.apache.hadoop.hdfs.PeerCache$1.run(PeerCache.java:124) > > at java.lang.Thread.run(Thread.java:748) > > > > "communication thread" #28 daemon prio=5 os_prio=0 tid=0x00007fe2ad975800 > > nid=0x6b9e in Object.wait() [0x00007fe28d8b1000] > > java.lang.Thread.State: TIMED_WAITING (on object monitor) > > at java.lang.Object.wait(Native Method) > > at org.apache.hadoop.mapred.Task$TaskReporter.run(Task.java:799) > > - locked <0x00000000ede69ae8> (a java.lang.Object) > > at java.lang.Thread.run(Thread.java:748) > > > > "client DomainSocketWatcher" #27 daemon prio=5 os_prio=0 > > tid=0x00007fe2ad952000 nid=0x6b95 runnable [0x00007fe28d9b2000] > > java.lang.Thread.State: RUNNABLE > > at org.apache.hadoop.net.unix.DomainSocketWatcher.doPoll0(Native Method) > > at > > org.apache.hadoop.net.unix.DomainSocketWatcher.access$900(DomainSocketWatcher.java:52) > > > > at > > org.apache.hadoop.net.unix.DomainSocketWatcher$2.run(DomainSocketWatcher.java:503) > > > > at java.lang.Thread.run(Thread.java:748) > > > > "Thread for syncLogs" #26 daemon prio=5 os_prio=0 tid=0x00007fe2ad820000 > > nid=0x6b81 waiting on condition [0x00007fe28deb3000] > > java.lang.Thread.State: TIMED_WAITING (parking) > > at sun.misc.Unsafe.park(Native Method) > > - parking to wait for <0x00000000e7118190> (a > > java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject) > > at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215) > > at > > java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078) > > > > at > > java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1093) > > > > at > > java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:809) > > > > at > > java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1074) > > > > at > > java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134) > > > > at > > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) > > > > at java.lang.Thread.run(Thread.java:748) > > > > "org.apache.hadoop.fs.FileSystem$Statistics$StatisticsDataReferenceCleaner" > > #24 daemon prio=5 os_prio=0 tid=0x00007fe2ad746800 nid=0x6b79 in > > Object.wait() [0x00007fe28e1cc000] > > java.lang.Thread.State: WAITING (on object monitor) > > at java.lang.Object.wait(Native Method) > > - waiting on <0x00000000e7171060> (a java.lang.ref.ReferenceQueue$Lock) > > at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143) > > - locked <0x00000000e7171060> (a java.lang.ref.ReferenceQueue$Lock) > > at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164) > > at > > org.apache.hadoop.fs.FileSystem$Statistics$StatisticsDataReferenceCleaner.run(FileSystem.java:3212) > > > > at java.lang.Thread.run(Thread.java:748) > > > > "IPC Parameter Sending Thread #0" #23 daemon prio=5 os_prio=0 > > tid=0x00007fe2ad637000 nid=0x6b6d waiting on condition [0x00007fe28e4cd000] > > java.lang.Thread.State: TIMED_WAITING (parking) > > at sun.misc.Unsafe.park(Native Method) > > - parking to wait for <0x00000000e7117338> (a > > java.util.concurrent.SynchronousQueue$TransferStack) > > at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215) > > at > > java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:460) > > > > at > > java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:362) > > > > at java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:941) > > at > > java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1073) > > > > at > > java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134) > > > > at > > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) > > > > at java.lang.Thread.run(Thread.java:748) > > > > "IPC Client (1373419525) connection to /89.188.14.3:36783 from > > job_1516025831039_0247" #22 daemon prio=5 os_prio=0 tid=0x00007fe2ad632000 > > nid=0x6b6c in Object.wait() [0x00007fe28e5ce000] > > java.lang.Thread.State: TIMED_WAITING (on object monitor) > > at java.lang.Object.wait(Native Method) > > at org.apache.hadoop.ipc.Client$Connection.waitForWork(Client.java:1008) > > - locked <0x00000000e7119130> (a org.apache.hadoop.ipc.Client$Connection) > > at org.apache.hadoop.ipc.Client$Connection.run(Client.java:1052) > > > > "Timer for 'MapTask' metrics system" #21 daemon prio=5 os_prio=0 > > tid=0x00007fe2ad525800 nid=0x6b5f in Object.wait() [0x00007fe28f551000] > > java.lang.Thread.State: TIMED_WAITING (on object monitor) > > at java.lang.Object.wait(Native Method) > > at java.util.TimerThread.mainLoop(Timer.java:552) > > - locked <0x00000000e713ca30> (a java.util.TaskQueue) > > at java.util.TimerThread.run(Timer.java:505) > > > > "Service Thread" #17 daemon prio=9 os_prio=0 tid=0x00007fe2ac0f8800 > > nid=0x6b36 runnable [0x0000000000000000] > > java.lang.Thread.State: RUNNABLE > > > > "C1 CompilerThread11" #16 daemon prio=9 os_prio=0 tid=0x00007fe2ac0eb800 > > nid=0x6b34 waiting on condition [0x0000000000000000] > > java.lang.Thread.State: RUNNABLE > > > > "C1 CompilerThread10" #15 daemon prio=9 os_prio=0 tid=0x00007fe2ac0e9800 > > nid=0x6b33 waiting on condition [0x0000000000000000] > > java.lang.Thread.State: RUNNABLE > > > > "C1 CompilerThread9" #14 daemon prio=9 os_prio=0 tid=0x00007fe2ac0e7000 > > nid=0x6b32 waiting on condition [0x0000000000000000] > > java.lang.Thread.State: RUNNABLE > > > > "C1 CompilerThread8" #13 daemon prio=9 os_prio=0 tid=0x00007fe2ac0e5000 > > nid=0x6b31 waiting on condition [0x0000000000000000] > > java.lang.Thread.State: RUNNABLE > > > > "C2 CompilerThread7" #12 daemon prio=9 os_prio=0 tid=0x00007fe2ac0e3000 > > nid=0x6b30 waiting on condition [0x0000000000000000] > > java.lang.Thread.State: RUNNABLE > > > > "C2 CompilerThread6" #11 daemon prio=9 os_prio=0 tid=0x00007fe2ac0e1000 > > nid=0x6b2f waiting on condition [0x0000000000000000] > > java.lang.Thread.State: RUNNABLE > > > > "C2 CompilerThread5" #10 daemon prio=9 os_prio=0 tid=0x00007fe2ac0de800 > > nid=0x6b2d waiting on condition [0x0000000000000000] > > java.lang.Thread.State: RUNNABLE > > > > "C2 CompilerThread4" #9 daemon prio=9 os_prio=0 tid=0x00007fe2ac0d4800 > > nid=0x6b2b waiting on condition [0x0000000000000000] > > java.lang.Thread.State: RUNNABLE > > > > "C2 CompilerThread3" #8 daemon prio=9 os_prio=0 tid=0x00007fe2ac0d2800 > > nid=0x6b2a waiting on condition [0x0000000000000000] > > java.lang.Thread.State: RUNNABLE > > > > "C2 CompilerThread2" #7 daemon prio=9 os_prio=0 tid=0x00007fe2ac0ce000 > > nid=0x6b29 waiting on condition [0x0000000000000000] > > java.lang.Thread.State: RUNNABLE > > > > "C2 CompilerThread1" #6 daemon prio=9 os_prio=0 tid=0x00007fe2ac0cc000 > > nid=0x6b28 waiting on condition [0x0000000000000000] > > java.lang.Thread.State: RUNNABLE > > > > "C2 CompilerThread0" #5 daemon prio=9 os_prio=0 tid=0x00007fe2ac0c9000 > > nid=0x6b26 waiting on condition [0x0000000000000000] > > java.lang.Thread.State: RUNNABLE > > > > "Signal Dispatcher" #4 daemon prio=9 os_prio=0 tid=0x00007fe2ac0c7000 > > nid=0x6b24 waiting on condition [0x0000000000000000] > > java.lang.Thread.State: RUNNABLE > > > > "Finalizer" #3 daemon prio=8 os_prio=0 tid=0x00007fe2ac0a0000 nid=0x6ab7 in > > Object.wait() [0x00007fe29592c000] > > java.lang.Thread.State: WAITING (on object monitor) > > at java.lang.Object.wait(Native Method) > > at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143) > > - locked <0x00000000e72f0140> (a java.lang.ref.ReferenceQueue$Lock) > > at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164) > > at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:209) > > > > "Reference Handler" #2 daemon prio=10 os_prio=0 tid=0x00007fe2ac09b800 > > nid=0x6ab6 in Object.wait() [0x00007fe295a2d000] > > java.lang.Thread.State: WAITING (on object monitor) > > at java.lang.Object.wait(Native Method) > > at java.lang.Object.wait(Object.java:502) > > at java.lang.ref.Reference.tryHandlePending(Reference.java:191) > > - locked <0x00000000e72f0180> (a java.lang.ref.Reference$Lock) > > at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:153) > > > > "main" #1 prio=5 os_prio=0 tid=0x00007fe2ac014000 nid=0x6a69 in > > Object.wait() [0x00007fe2b5747000] > > java.lang.Thread.State: WAITING (on object monitor) > > at java.lang.Object.wait(Native Method) > > - waiting on <0x00000000edb32e88> (a > > org.apache.hadoop.mapreduce.lib.map.MultithreadedMapper$MapRunner) > > at java.lang.Thread.join(Thread.java:1252) > > - locked <0x00000000edb32e88> (a > > org.apache.hadoop.mapreduce.lib.map.MultithreadedMapper$MapRunner) > > at java.lang.Thread.join(Thread.java:1326) > > at > > org.apache.hadoop.mapreduce.lib.map.MultithreadedMapper.run(MultithreadedMapper.java:146) > > > > at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:787) > > at org.apache.hadoop.mapred.MapTask.run(MapTask.java:341) > > at org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:175) > > at java.security.AccessController.doPrivileged(Native Method) > > at javax.security.auth.Subject.doAs(Subject.java:422) > > at > > org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1836) > > > > at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:169) > > > > "VM Thread" os_prio=0 tid=0x00007fe2ac093800 nid=0x6aad runnable > > > > "GC task thread#0 (ParallelGC)" os_prio=0 tid=0x00007fe2ac029000 nid=0x6a77 > > runnable > > > > "GC task thread#1 (ParallelGC)" os_prio=0 tid=0x00007fe2ac02b000 nid=0x6a79 > > runnable > > > > "GC task thread#2 (ParallelGC)" os_prio=0 tid=0x00007fe2ac02c800 nid=0x6a7b > > runnable > > > > "GC task thread#3 (ParallelGC)" os_prio=0 tid=0x00007fe2ac02e800 nid=0x6a7d > > runnable > > > > "GC task thread#4 (ParallelGC)" os_prio=0 tid=0x00007fe2ac030000 nid=0x6a80 > > runnable > > > > "GC task thread#5 (ParallelGC)" os_prio=0 tid=0x00007fe2ac032000 nid=0x6a95 > > runnable > > > > "GC task thread#6 (ParallelGC)" os_prio=0 tid=0x00007fe2ac033800 nid=0x6a96 > > runnable > > > > "GC task thread#7 (ParallelGC)" os_prio=0 tid=0x00007fe2ac035800 nid=0x6a97 > > runnable > > > > "GC task thread#8 (ParallelGC)" os_prio=0 tid=0x00007fe2ac037000 nid=0x6a98 > > runnable > > > > "GC task thread#9 (ParallelGC)" os_prio=0 tid=0x00007fe2ac039000 nid=0x6a99 > > runnable > > > > "GC task thread#10 (ParallelGC)" os_prio=0 tid=0x00007fe2ac03a800 > > nid=0x6a9a runnable > > > > "GC task thread#11 (ParallelGC)" os_prio=0 tid=0x00007fe2ac03c800 > > nid=0x6a9b runnable > > > > "GC task thread#12 (ParallelGC)" os_prio=0 tid=0x00007fe2ac03e000 > > nid=0x6a9c runnable > > > > "VM Periodic Task Thread" os_prio=0 tid=0x00007fe2ac0fb000 nid=0x6b38 > > waiting on condition > > > > JNI global references: 275 > > > > Heap > > PSYoungGen total 116224K, used 105934K [0x00000000f7b00000, > > 0x0000000100000000, 0x0000000100000000) > > eden space 100864K, 89% used > > [0x00000000f7b00000,0x00000000fd3a6228,0x00000000fdd80000) > > from space 15360K, 98% used > > [0x00000000fdd80000,0x00000000fec4d7a0,0x00000000fec80000) > > to space 19456K, 0% used > > [0x00000000fed00000,0x00000000fed00000,0x0000000100000000) > > ParOldGen total 273408K, used 189187K [0x00000000e7000000, > > 0x00000000f7b00000, 0x00000000f7b00000) > > object space 273408K, 69% used > > [0x00000000e7000000,0x00000000f28c0c88,0x00000000f7b00000) > > Metaspace used 33001K, capacity 33602K, committed 34048K, reserved > > 1079296K > > class space used 3581K, capacity 3675K, committed 3840K, reserved > > 1048576K > > > >
