[Wikidata-bugs] [Maniphest] [Commented On] T164773: Error replicating wikidata blazegraph setup

2018-03-22 Thread Smalyshev 
Smalyshev added a comment.
Is this still an issue?TASK DETAILhttps://phabricator.wikimedia.org/T164773EMAIL PREFERENCEShttps://phabricator.wikimedia.org/settings/panel/emailpreferences/To: SmalyshevCc: Hjfocs, Gehel, Smalyshev, Aklapper, Yurik, Lahi, Gq86, Darkminds3113, Lucas_Werkmeister_WMDE, GoranSMilovanovic, QZanden, EBjune, merbst, LawExplorer, Avner, Jonas, FloNight, Xmlizer, jkroll, Wikidata-bugs, Jdouglas, aude, Tobias1984, Manybubbles, Mbch331___
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[Wikidata-bugs] [Maniphest] [Commented On] T164773: Error replicating wikidata blazegraph setup

2017-09-23 Thread Yurik 
Yurik added a comment.
@Smalyshev, I force-killed it, and it dumped this (I couldn't copy all of it - just some parts):

at com.bigdata.rdf.sail.webapp.RESTServlet.doGet(RESTServlet.java:240)
  at com.bigdata.rdf.sail.webapp.MultiTenancyServlet.doGet(MultiTenancyServlet.java:271)
  at javax.servlet.http.HttpServlet.service(HttpServlet.java:687)
  at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
  at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:769)
  at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1667)
  at org.wikidata.query.rdf.blazegraph.throttling.ThrottlingFilter.doFilter(ThrottlingFilter.java:244)
  at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1650)
  at ch.qos.logback.classic.helpers.MDCInsertingServletFilter.doFilter(MDCInsertingServletFilter.java:51)
  at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1650)
  at org.wikidata.query.rdf.blazegraph.filters.ClientIPFilter.doFilter(ClientIPFilter.java:42)
  at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1650)
  at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:583)
  at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
  at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:577)
  at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:223)
  at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1125)
  at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:515)
  at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:185)
  at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1059)
  at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
  at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:215)
  at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:110)
  at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97)
  at org.eclipse.jetty.server.Server.handle(Server.java:497)
  at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:311)
  at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:248)
  at org.eclipse.jetty.io.AbstractConnection$2.run(AbstractConnection.java:540)
  at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:610)
  at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:539)
  at java.lang.Thread.run(Thread.java:748)

"qtp931919113-27686" #27686 prio=5 os_prio=0 tid=0x7fbb5c00c000 nid=0x2c11 waiting on condition [0x7fba671f3000]
java.lang.Thread.State: WAITING (parking)
  at sun.misc.Unsafe.park(Native Method)
  - parking to wait for  <0x0007febc0168> (a java.util.concurrent.FutureTask)
  at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
  at java.util.concurrent.FutureTask.awaitDone(FutureTask.java:429)
  at java.util.concurrent.FutureTask.get(FutureTask.java:191)
  at com.bigdata.rdf.sail.webapp.BigdataServlet.submitApiTask(BigdataServlet.java:286)
  at com.bigdata.rdf.sail.webapp.QueryServlet.doSparqlQuery(QueryServlet.java:653)
  at com.bigdata.rdf.sail.webapp.QueryServlet.doGet(QueryServlet.java:288)
  at com.bigdata.rdf.sail.webapp.RESTServlet.doGet(RESTServlet.java:240)
  at com.bigdata.rdf.sail.webapp.MultiTenancyServlet.doGet(MultiTenancyServlet.java:271)
  at javax.servlet.http.HttpServlet.service(HttpServlet.java:687)
  at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
  at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:769)
  at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1667)
  at org.wikidata.query.rdf.blazegraph.throttling.ThrottlingFilter.doFilter(ThrottlingFilter.java:244)
  at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1650)
  at ch.qos.logback.classic.helpers.MDCInsertingServletFilter.doFilter(MDCInsertingServletFilter.java:51)
  at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1650)
  at org.wikidata.query.rdf.blazegraph.filters.ClientIPFilter.doFilter(ClientIPFilter.java:42)
  at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1650)
  at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:583)
  at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
  at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:577)
  at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:223)
  at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1125)
  at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:515)
  at

[Wikidata-bugs] [Maniphest] [Commented On] T164773: Error replicating wikidata blazegraph setup

2017-09-17 Thread Smalyshev 
Smalyshev added a comment.
Not sure whether it has some relation, hard to diagnose from this. Did you see the GC logs? What the status page for Blazegraph showed?TASK DETAILhttps://phabricator.wikimedia.org/T164773EMAIL PREFERENCEShttps://phabricator.wikimedia.org/settings/panel/emailpreferences/To: SmalyshevCc: Gehel, Smalyshev, Aklapper, Yurik, Lucas_Werkmeister_WMDE, GoranSMilovanovic, QZanden, EBjune, merbst, Avner, debt, Jonas, FloNight, Xmlizer, Izno, jkroll, Wikidata-bugs, Jdouglas, aude, Tobias1984, Manybubbles, Mbch331___
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[Wikidata-bugs] [Maniphest] [Commented On] T164773: Error replicating wikidata blazegraph setup

2017-09-17 Thread Yurik 
Yurik added a comment.
@Smalyshev & @Gehel  I'm not sure if this is the same error or different.  Today, the service froze in a peculiar way:  all queries would time out (both from clients and update ones), and Blazegraph wouldn't quit with Ctrl+C.  HTOP shows a single blazegraph process using 100% of a single CPU, but about once in a few minutes, almost all CPUs would jump to a 100% for about 5-10 seconds, and then go back to 0 except for a single process.  The last errors in the log, might be unrelated:

at com.bigdata.rwstore.sector.AllocationContext.allocate(AllocationContext.java:159) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.rwstore.sector.AllocationContext.alloc(AllocationContext.java:359) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.rwstore.PSOutputStream.save(PSOutputStream.java:335) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.rwstore.PSOutputStream.getAddr(PSOutputStream.java:416) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.bop.solutions.SolutionSetStream.put(SolutionSetStream.java:297) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.bop.engine.LocalNativeChunkMessage.(LocalNativeChunkMessage.java:213) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.bop.engine.LocalNativeChunkMessage.(LocalNativeChunkMessage.java:147) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.bop.engine.StandaloneChunkHandler.handleChunk(StandaloneChunkHandler.java:90) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.bop.engine.ChunkedRunningQuery$HandleChunkBuffer.outputChunk(ChunkedRunningQuery.java:1699) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.bop.engine.ChunkedRunningQuery$HandleChunkBuffer.addReorderAllowed(ChunkedRunningQuery.java:1628) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.bop.engine.ChunkedRunningQuery$HandleChunkBuffer.add(ChunkedRunningQuery.java:1569) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.bop.engine.ChunkedRunningQuery$HandleChunkBuffer.add(ChunkedRunningQuery.java:1453) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.relation.accesspath.UnsyncLocalOutputBuffer.handleChunk(UnsyncLocalOutputBuffer.java:59) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.relation.accesspath.UnsyncLocalOutputBuffer.handleChunk(UnsyncLocalOutputBuffer.java:14) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.relation.accesspath.AbstractUnsynchronizedArrayBuffer.overflow(AbstractUnsynchronizedArrayBuffer.java:287) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.relation.accesspath.AbstractUnsynchronizedArrayBuffer.add2(AbstractUnsynchronizedArrayBuffer.java:215) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.relation.accesspath.AbstractUnsynchronizedArrayBuffer.add(AbstractUnsynchronizedArrayBuffer.java:173) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.bop.join.PipelineJoin$JoinTask$AccessPathTask.handleJoin2(PipelineJoin.java:1868) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
... 17 common frames omitted

07:53:53.567 [com.bigdata.journal.Journal.executorService23435] ERROR com.bigdata.util.concurrent.Haltable IP: UA: - com.bigdata.bop.join.PipelineJoin$JoinTask{ joinOp=com.bigdata.bop.join.PipelineJoin[2]()[ BOp.bopId=2, JoinAnnotations.constraints=null, AST2BOpBase.simpleJoin=true, BOp.evaluationContext=ANY, AccessPathJoinAnnotations.predicate=com.bigdata.rdf.spo.SPOPredicate[1](osmId=null, Vocab(56)[https://wiki.openstreetmap.org/wiki/Key:place], place=null)[ IPredicate.relationName=[wdq.spo], IPredicate.timestamp=1505627633562, BOp.bopId=1, AST2BOpBase.estimatedCardinality=4549666, AST2BOpBase.originalIndex=POS, IPredicate.flags=[KEYS,VALS,READONLY,PARALLEL]]]} : isFirstCause=true : com.bigdata.rwstore.sector.MemoryManagerClosedException
com.bigdata.rwstore.sector.MemoryManagerClosedException: null
at com.bigdata.rwstore.sector.MemoryManager.assertOpen(MemoryManager.java:110) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.rwstore.sector.MemoryManager.allocate(MemoryManager.java:671) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.rwstore.sector.AllocationContext.allocate(AllocationContext.java:195) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.rwstore.sector.AllocationContext.allocate(AllocationContext.java:169) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.rwstore.sector.AllocationContext.allocate(AllocationContext.java:159) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.rwstore.sector.AllocationContext.alloc(AllocationContext.java:359) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.rwstore.PSOutputStream.save(PSOutputStream.java:335) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.rwstore.PSOutputStream.getAddr(PSOutputStream.java:416) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.bop.solutions.SolutionSetStream.put(SolutionSetStream.java:297) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at com.bigdata.bop.engine.LocalNativeChunkMessage.(LocalNativeChunkMessage.java:213) ~[bigdata-core-2.1.5-SNAPSHOT.jar:na]
at

[Wikidata-bugs] [Maniphest] [Commented On] T164773: Error replicating wikidata blazegraph setup

2017-09-02 Thread Yurik 
Yurik added a comment.
I just finished full re-import with -Xmx=16GB , and it worked fine. I am not sure what has caused the original issue.  For future reference, here are the import stats (importing both Wikidata and OSM data from the same dir - 33GB total, 683 files of about the same size.  Total time was about 36 hours.  First 329 files were OSM, second 354 - wikidata (note how the graph starts jumping, possibly due to per-file statement distribution in WD.  OSM data is much more uniform in terms of statement per osm object)

F9290936: image.png

raw datastatements	time	rate	sets
107,179,984	640	167,220	6
189,557,036	1,260	150,378	11
255,343,483	1,884	135,523	15
323,230,658	2,533	127,587	19
389,362,380	3,231	120,504	23
454,181,776	3,971	114,351	27
519,770,290	4,654	111,667	31
585,537,711	5,358	109,275	35
669,713,329	6,025	111,138	40
753,727,112	6,704	112,415	45
835,803,507	7,485	111,656	50
901,307,143	8,218	109,668	54
966,655,528	8,963	107,845	58
1,015,648,545	9,570	106,123	61
1,080,889,536	10,310	104,829	65
1,147,921,605	11,098	103,427	69
1,218,376,248	11,800	103,245	73
1,288,894,078	12,464	103,401	77
1,340,627,982	13,252	101,158	80
1,374,208,625	13,948	98,521	82
1,408,174,205	14,568	96,659	84
1,459,277,475	15,389	94,824	87
1,510,100,090	16,207	93,174	90
1,560,517,757	16,986	91,866	93
1,627,435,035	17,713	91,877	97
1,693,942,260	18,401	92,053	101
1,760,534,757	19,151	91,927	105
1,827,353,450	19,934	91,669	109
1,877,349,669	20,571	91,260	112
1,927,029,732	21,190	90,937	115
1,976,839,801	21,803	90,665	118
2,043,621,669	22,602	90,417	122
2,093,614,307	23,222	90,153	125
2,143,530,955	23,884	89,744	128
2,193,300,587	24,504	89,506	131
2,259,768,850	25,281	89,382	135
2,309,402,067	25,896	89,178	138
2,359,045,834	26,524	88,937	141
2,408,813,042	27,193	88,582	144
2,458,534,137	27,866	88,224	147
2,508,173,248	28,587	87,736	150
2,557,695,348	29,236	87,481	153
2,607,093,365	29,879	87,254	156
2,672,980,080	30,659	87,181	160
2,722,486,059	31,293	86,997	163
2,771,962,432	31,913	86,859	166
2,837,660,998	32,616	87,001	170
2,887,208,486	33,270	86,779	173
2,936,799,169	33,925	86,567	176
2,986,273,795	34,593	86,325	179
3,035,728,568	35,243	86,136	182
3,085,184,315	35,859	86,035	185
3,151,468,039	36,608	86,086	189
3,201,011,063	37,213	86,017	192
3,267,535,396	37,935	86,134	196
3,334,686,516	38,576	86,443	200
3,401,886,904	39,240	86,692	204
3,468,645,120	39,954	86,814	208
3,534,648,676	40,730	86,781	212
3,600,523,802	41,492	86,775	216
3,666,138,573	42,282	86,706	220
3,731,829,153	43,077	86,629	224
3,797,535,576	43,829	86,643	228
3,863,523,948	44,582	86,659	232
3,928,985,444	45,258	86,812	236
3,994,209,028	45,921	86,979	240
4,059,507,043	46,604	87,104	244
4,125,187,426	47,359	87,104	248
4,190,652,309	48,108	87,108	252
4,256,123,933	48,782	87,246	256
4,321,507,795	49,466	87,362	260
4,386,987,648	50,120	87,528	264
4,452,442,948	50,739	87,750	268
4,517,769,637	51,363	87,956	272
4,583,567,763	52,006	88,133	276
4,649,357,008	52,705	88,213	280
4,715,013,078	53,387	88,316	284
4,780,538,748	54,036	88,468	288
4,845,958,188	54,701	88,588	292
4,912,126,601	55,324	88,787	296
4,977,535,397	55,951	88,961	300
5,042,533,501	56,599	89,091	304
5,107,487,478	57,217	89,264	308
5,172,445,286	57,824	89,450	312
5,253,524,269	58,545	89,734	317
5,305,784,367	59,194	89,633	320
5,343,676,632	60,030	89,016	322
5,381,274,598	60,966	88,265	324
5,418,420,058	61,807	87,665	326
5,468,584,289	62,692	87,228	329
5,518,098,321	63,442	86,977	333
5,564,009,469	64,131	86,759	339
5,619,110,296	64,763	86,763	345
5,673,559,079	65,380	86,777	354
5,715,132,031	65,986	86,610	360
5,756,082,773	66,616	86,406	368
5,812,130,630	67,248	86,428	376
5,858,211,979	67,888	86,291	382
5,917,602,276	68,563	86,308	390
5,972,627,425	69,255	86,241	396
6,033,689,471	70,387	85,720	400
6,061,126,737	71,089	85,260	402
6,090,631,401	71,841	84,778	405
6,120,734,012	72,539	84,377	409
6,153,355,223	73,182	84,082	413
6,207,067,286	73,873	84,023	420
6,253,755,885	74,611	83,817	427
6,284,713,321	75,280	83,484	432
6,319,282,922	76,000	83,147	439
6,355,867,878	76,609	82,964	444
6,399,714,387	77,288	82,803	450
6,436,640,839	78,036	82,482	455
6,481,234,379	78,650	82,405	461
6,526,759,664	79,391	82,209	466
6,579,995,114	80,501	81,737	470
6,599,378,396	81,211	81,261	471
6,625,131,210	82,089	80,705	473
6,645,098,333	82,772	80,281	475
6,669,624,733	83,502	79,873	478
6,699,812,271	84,314	79,462	482
6,738,122,743	84,990	79,281	486
6,774,046,102	85,662	79,078	492
6,808,866,336	86,267	78,927	497
6,833,736,316	86,915	78,625	501
6,860,334,945	87,592	78,320	506
6,887,971,112	88,315	77,992	511
6,919,244,750	88,952	77,786	515
6,953,331,447	89,571	77,628	520
6,978,517,812	90,206	77,361	523
7,007,112,877	90,843	77,134	527
7,044,596,712	91,468	77,016	532
7,080,015,049	92,212	76,779	536
7,124,088,113	93,041	76,569	540
7,145,384,434	94,007	76,008	541
7,163,582,483	94,892	75,491	542
7,177,490,061	95,537	75,127	543
7,198,819,202	96,483	74,611	545
7,217,160,866	97,276	74,191	547
7,239,559,213	98,115	73,786	550

[Wikidata-bugs] [Maniphest] [Commented On] T164773: Error replicating wikidata blazegraph setup

2017-08-31 Thread Yurik 
Yurik added a comment.
I'm re-running the import with the default settings (mmx=16gb), almost 700 gz files (127GB). This time, all of the OSM data uses integer storage instead of the original strings ("osmnode:123" treats 123 as a prefix + an int). Will know the results in 2 days.TASK DETAILhttps://phabricator.wikimedia.org/T164773EMAIL PREFERENCEShttps://phabricator.wikimedia.org/settings/panel/emailpreferences/To: YurikCc: Gehel, Smalyshev, Aklapper, Yurik, Lucas_Werkmeister_WMDE, GoranSMilovanovic, QZanden, EBjune, merbst, Avner, debt, Jonas, FloNight, Xmlizer, Izno, jkroll, Wikidata-bugs, Jdouglas, aude, Tobias1984, Manybubbles, Mbch331___
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[Wikidata-bugs] [Maniphest] [Commented On] T164773: Error replicating wikidata blazegraph setup

2017-08-31 Thread Smalyshev 
Smalyshev added a comment.
MemoryManagerClosedException by itself is not a big issue as far as I can see, it may be query timeout or something like that. That shouldn't happen on data loading though (that one should not time out).TASK DETAILhttps://phabricator.wikimedia.org/T164773EMAIL PREFERENCEShttps://phabricator.wikimedia.org/settings/panel/emailpreferences/To: SmalyshevCc: Gehel, Smalyshev, Aklapper, Yurik, Lucas_Werkmeister_WMDE, GoranSMilovanovic, QZanden, EBjune, merbst, Avner, debt, Jonas, FloNight, Xmlizer, Izno, jkroll, Wikidata-bugs, Jdouglas, aude, Tobias1984, Manybubbles, Mbch331___
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[Wikidata-bugs] [Maniphest] [Commented On] T164773: Error replicating wikidata blazegraph setup

2017-06-23 Thread Smalyshev 
Smalyshev added a comment.
Didn't see it happen on my side, is it reproducible?TASK DETAILhttps://phabricator.wikimedia.org/T164773EMAIL PREFERENCEShttps://phabricator.wikimedia.org/settings/panel/emailpreferences/To: SmalyshevCc: Smalyshev, Aklapper, Yurik, GoranSMilovanovic, QZanden, EBjune, merbst, Avner, debt, Gehel, Jonas, FloNight, Xmlizer, Izno, jkroll, Wikidata-bugs, Jdouglas, aude, Tobias1984, Manybubbles, Mbch331___
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