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Posted to users@jena.apache.org by Jean-Marc Vanel <je...@gmail.com> on 2020/03/24 17:56:09 UTC
TDB blocked
Hi Jena users!
After changing my test suite in* semantic_forms
<http://semantic-forms.cc:9112/ldp/semantic_forms>* , I get consistently a
thread blocked forever. I upgraded to latest Jena Version = "3.14.0" , and
happily my Web application seems to be working fine on my laptop, and the
test suite sort of works, that is running tests one by one.
In my test suite I used to recursively delete the TDB directories after
each test. What changed is that instead I kept the same TDB directories for
each test, calling close() after each test.
This is with TDB 1. Is another unended transaction the issue? Then how to
discover that ?
Thread [pool-1-thread-1-ScalaTest-running-TestRDFCache] (Suspended)
Unsafe.park(boolean, long) line: not available [native method]
LockSupport.park(Object) line: 175
Semaphore$FairSync(AbstractQueuedSynchronizer).parkAndCheckInterrupt()
line: 836
Semaphore$FairSync(AbstractQueuedSynchronizer).doAcquireSharedInterruptibly(int)
line: 997
Semaphore$FairSync(AbstractQueuedSynchronizer).acquireSharedInterruptibly(int)
line: 1304
Semaphore.acquire() line: 312
* TransactionManager.acquireWriterLock(boolean) line: 616 *
TransactionManager.beginInternal(TxnType, TxnType, String) line: 358
TransactionManager.begin(TxnType, String) line: 343
StoreConnection.begin(TxnType, String) line: 128
StoreConnection.begin(TxnType) line: 108
DatasetGraphTransaction.begin(TxnType) line: 169
DatasetGraphTransaction.begin(ReadWrite) line: 162
DatasetImpl.begin(ReadWrite) line: 122
JenaDatasetStore.$anonfun$rw$1(Dataset, Function0) line: 23
Jean-Marc Vanel
<http://semantic-forms.cc:9112/display?displayuri=http://jmvanel.free.fr/jmv.rdf%23me>
+33 (0)6 89 16 29 52
Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui
Chroniques jardin
<http://semantic-forms.cc:1952/history?uri=http%3A%2F%2Fdbpedia.org%2Fresource%2FChronicle>
Re: TDB blocked
Posted by Andy Seaborne <an...@apache.org>.
Fork - what sort of fork? Java's Fork/join or OS process fork?
Doesn't forking (no exec) a JVM bypass all JVM related initialization,
e.g. classes. That will break a lot of things, TDB included. I don't
know if OS-fork clones everything anyway (e.g. threads and that means
ThreadLocal might be broken). [The scala doc is a little parsimonius]
---
There is no need to have one shared dataset/connection object anyway.
TDBFactory.create* is cheap after the dataset is first used in the JVM
process. It's little more than a cache lookup.
A test can be
TDBFactory.create*
<small test>
and be fast enough i.e push the dataset connect/create into the test or
test suite.
Bonus - create an in-memory TDB dataset so it leaves no on disk foot
print. Or the equivalent of a JUnit Temp folder but the create
in-memeory has lower start-up costs.
Andy
In-memory TDB dataset is not designed for production use - it is very
careful to be true TDB, just without peristent storage. It runs its own
copy-in/copy-out block cache so a lot of data copying to get proper
isolation of storage and usage.
Use DatasetFactory.createTxnMem() for a production in-memory database.
On 26/03/2020 08:24, Jean-Marc Vanel wrote:
> Le mer. 25 mars 2020 à 17:17, Andy Seaborne <an...@apache.org> a écrit :
>
>>
>> On 25/03/2020 14:36, Jean-Marc Vanel wrote:
>>> Le mer. 25 mars 2020 à 13:07, Andy Seaborne <an...@apache.org> a écrit :
>>
>
>
>> ...
>>
>
>
>>>> What's the full stack trace?
>>>> (What's the blocking thread?)
>> I was looking for the other thread that is blocking this one at
>> being(write). Same JVM.
>>
>
> See details below. Tell me if you still want it.
>
>
>>>> Yes, another unended W transaction in the same process might be the
>> cause.
>>>>
>>> I thought rather, another unended W transaction in *another* process,
>> since
>>> the tests execution was parallel.
>>
>> If I understand correctly,
>>
>> parallelExecution in Test := false
>>
>> means parallel in the same JVM.
>>
>
> Yes indeed, that's for taking advantage of multicore CPU's.
> The parameter that actually created the freeze problem in the original post
> was
>
> fork = true
>
> and it clear that calling TDBFactory.createDataset() and close() , and
> other calls, randomly from different JVM's on the same TDB directory is
> bound to fail.
>
> On the other hand, the combination
>
> fork := false
> parallelExecution in Test := true
>
> is not good for this kind of tests. My understanding is that TDB is made
> for multi-thread access in reading and writing (and it works perfectly in
> my Play Framework application for years), but not made for creating and
> closing.
> All tests pass, but one, with this stack (complete!):
>
> [info] TimeSeriesTestJena:
> [info] - notifyDataEvent + getTimeSeries
> [info] deductions.runtime.semlogs.TimeSeriesTestJena *** ABORTED ***
> [info] java.util.*ConcurrentModificationException*: Reader = 0, Writer = 2
> [info] at
> org.apache.jena.tdb.sys.DatasetControlMRSW.policyError(DatasetControlMRSW.java:147)
> [info] at
> org.apache.jena.tdb.sys.DatasetControlMRSW.policyError(DatasetControlMRSW.java:143)
> [info] at
> org.apache.jena.tdb.sys.DatasetControlMRSW.checkConcurrency(DatasetControlMRSW.java:75)
> [info] at
> org.apache.jena.tdb.sys.DatasetControlMRSW.startUpdate(DatasetControlMRSW.java:57)
> [info] at
> org.apache.jena.tdb.store.nodetupletable.NodeTupleTableConcrete.startWrite(NodeTupleTableConcrete.java:65)
> [info] at
> org.apache.jena.tdb.store.nodetupletable.NodeTupleTableConcrete.sync(NodeTupleTableConcrete.java:251)
> [info] at org.apache.jena.tdb.store.TableBase.sync(TableBase.java:51)
> [info] at
> org.apache.jena.tdb.store.DatasetGraphTDB.sync(DatasetGraphTDB.java:253)
> [info] at
> org.apache.jena.tdb.transaction.DatasetGraphTransaction.close(DatasetGraphTransaction.java:296)
> [info] at
> org.apache.jena.sparql.core.DatasetImpl.close(DatasetImpl.java:231)
>
>
>> Andy
>>
>>
>>>
>>> Test code:
>>>
>> https://github.com/jmvanel/semantic_forms/blob/master/scala/forms/src/test/scala/deductions/runtime/sparql_cache/TestRDFCache.scala
>>> =====
>>> Thread [pool-1-thread-1-ScalaTest-running-TestRDFCache] (Suspended)
>>> Unsafe.park(boolean, long) line: not available [native method]
>>> LockSupport.park(Object) line: 175
>>> Semaphore$FairSync(AbstractQueuedSynchronizer).parkAndCheckInterrupt()
>>> line: 836
>>>
>> Semaphore$FairSync(AbstractQueuedSynchronizer).doAcquireSharedInterruptibly(int)
>>> line: 997
>>>
>> Semaphore$FairSync(AbstractQueuedSynchronizer).acquireSharedInterruptibly(int)
>>> line: 1304
>>> Semaphore.acquire() line: 312
>>> TransactionManager.acquireWriterLock(boolean) line: 616
>>> TransactionManager.beginInternal(TxnType, TxnType, String) line: 358
>>> TransactionManager.begin(TxnType, String) line: 343
>>> StoreConnection.begin(TxnType, String) line: 128
>>> StoreConnection.begin(TxnType) line: 108
>>> DatasetGraphTransaction.begin(TxnType) line: 169
>>> DatasetGraphTransaction.begin(ReadWrite) line: 162
>>> DatasetImpl.begin(ReadWrite) line: 122
>>> JenaDatasetStore.$anonfun$rw$1(Dataset, Function0) line: 23
>>> 52027729.apply() line: not available
>>> Try$.apply(Function0<T>) line: 213
>>> JenaDatasetStore.rw(Dataset, Function0<T>) line: 22
>>> JenaDatasetStore.rw(Object, Function0) line: 10
>>> TestRDFCache(RDFCacheAlgo<Rdf,DATASET>).readStoreURI(Object, Object,
>>> DATASET) line: 368
>>> RDFCacheAlgo<Rdf,DATASET>.readStoreURI$(RDFCacheAlgo, Object, Object,
>>> Object) line: 366
>>> TestRDFCache.readStoreURI(Object, Object, Object) line: 10
>>> TestRDFCache(RDFCacheAlgo<Rdf,DATASET>).readStoreURIinOwnGraph(Object)
>>> line: 334
>>> TestRDFCache(RDFCacheAlgo<Rdf,DATASET>).readStoreUriInNamedGraph(Object)
>>> line: 326
>>> RDFCacheAlgo<Rdf,DATASET>.readStoreUriInNamedGraph$(RDFCacheAlgo, Object)
>>> line: 325
>>> TestRDFCache.readStoreUriInNamedGraph(Object) line: 10
>>> TestRDFCache.$anonfun$new$4(TestRDFCache) line: 63
>>> 1708361043.apply$mcV$sp() line: not available
>>> 1708361043(JFunction0$mcV$sp).apply() line: 23
>>> OutcomeOf$(OutcomeOf).outcomeOf(Function0<Object>) line: 85
>>> OutcomeOf.outcomeOf$(OutcomeOf, Function0) line: 83
>>> OutcomeOf$.outcomeOf(Function0<Object>) line: 104
>>> Transformer<FixtureParam>.apply() line: 22
>>> Transformer<FixtureParam>.apply() line: 20
>>> AnyFunSuiteLike$$anon$1.apply() line: 189
>>> TestRDFCache(TestSuite).withFixture(TestSuite$NoArgTest) line: 196
>>> TestSuite.withFixture$(TestSuite, TestSuite$NoArgTest) line: 195
>>> TestRDFCache(AnyFunSuite).withFixture(TestSuite$NoArgTest) line: 1562
>>> TestRDFCache(AnyFunSuiteLike).invokeWithFixture$1(SuperEngine$TestLeaf,
>>> Args, String) line: 187
>>> AnyFunSuiteLike.$anonfun$runTest$1(AnyFunSuiteLike, Args, String,
>>> SuperEngine$TestLeaf) line: 199
>>> 1593480726.apply(Object) line: not available
>>> Engine(SuperEngine<T>).runTestImpl(Suite, String, Args, boolean,
>>> Function1<SuperEngine<TestLea>,Outcome>) line: 306
>>> TestRDFCache(AnyFunSuiteLike).runTest(String, Args) line: 199
>>> AnyFunSuiteLike.runTest$(AnyFunSuiteLike, String, Args) line: 181
>>> TestRDFCache(AnyFunSuite).runTest(String, Args) line: 1562
>>> AnyFunSuiteLike.$anonfun$runTests$1(AnyFunSuiteLike, String, Args) line:
>>> 232
>>> 438507753.apply(Object, Object) line: not available
>>> SuperEngine<T>.$anonfun$runTestsInBranch$1(SuperEngine, Args, Suite,
>>> SuperEngine$Branch, ListBuffer, Function2, boolean, SuperEngine$Node)
>> line:
>>> 413
>>> 855709148.apply(Object) line: not available
>>> $colon$colon<B>(List<A>).foreach(Function1<A,U>) line: 392
>>> Engine(SuperEngine<T>).traverseSubNodes$1(SuperEngine$Branch, Args,
>> Suite,
>>> ListBuffer, Function2, boolean) line: 401
>>> Engine(SuperEngine<T>).runTestsInBranch(Suite, SuperEngine<Branc>, Args,
>>> boolean, Function2<String,Args,Status>) line: 396
>>> Engine(SuperEngine<T>).runTestsImpl(Suite, Option<String>, Args,
>> Informer,
>>> boolean, Function2<String,Args,Status>) line: 475
>>> TestRDFCache(AnyFunSuiteLike).runTests(Option<String>, Args) line: 232
>>> AnyFunSuiteLike.runTests$(AnyFunSuiteLike, Option, Args) line: 231
>>> TestRDFCache(AnyFunSuite).runTests(Option<String>, Args) line: 1562
>>> TestRDFCache(Suite).run(Option<String>, Args) line: 1112
>>> Suite.run$(Suite, Option, Args) line: 1094
>>>
>> TestRDFCache(AnyFunSuite).org$scalatest$funsuite$AnyFunSuiteLike$$super$run(Option,
>>> Args) line: 1562
>>> AnyFunSuiteLike.$anonfun$run$1(AnyFunSuiteLike, Option, Args) line: 236
>>> 113821125.apply(Object, Object) line: not available
>>> Engine(SuperEngine<T>).runImpl(Suite, Option<String>, Args,
>>> Function2<Option<String>,Args,Status>) line: 535
>>> TestRDFCache(AnyFunSuiteLike).run(Option<String>, Args) line: 236
>>> AnyFunSuiteLike.run$(AnyFunSuiteLike, Option, Args) line: 235
>>> TestRDFCache.org$scalatest$BeforeAndAfterAll$$super$run(Option, Args)
>> line:
>>> 10
>>> TestRDFCache(BeforeAndAfterAll).liftedTree1$1(Args, Option) line: 213
>>> TestRDFCache(BeforeAndAfterAll).run(Option<String>, Args) line: 210
>>> BeforeAndAfterAll.run$(BeforeAndAfterAll, Option, Args) line: 208
>>> TestRDFCache.run(Option<String>, Args) line: 10
>>> Framework.org$scalatest$tools$Framework$$runSuite(TaskDef, String, Suite,
>>> ClassLoader, SuiteSortingReporter, Tracker, EventHandler, Set<String>,
>>> Set<String>, Selector[], boolean, ConfigMap, SummaryCounter,
>>> Option<ScalaTestStatefulStatus>, LinkedBlockingQueue<Status>, Logger[],
>>> boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean,
>>> boolean, boolean, ExecutorService) line: 318
>>> Framework$ScalaTestTask.execute(EventHandler, Logger[]) line: 513
>>> ForkMain$Run.lambda$runTest$1(Task, ObjectOutputStream, Logger[]) line:
>> 304
>>> 1574877131.call() line: not available
>>> FutureTask<V>.run() line: 266
>>> ThreadPoolExecutor.runWorker(ThreadPoolExecutor$Worker) line: 1149
>>> ThreadPoolExecutor$Worker.run() line: 624
>>> Thread.run() line: 748
>>> =====
>>>
>>>
>>>
>>>> Andy
>>>>
>>>>
>>>> On 25/03/2020 11:08, Jean-Marc Vanel wrote:
>>>>> I investigated on that.
>>>>> Now my test suite passes without Jena TDB trouble. I just added this in
>>>>> Scala SBT :
>>>>> parallelExecution in Test := false
>>>>>
>>>>> I didn't know that parallel execution was the default.
>>>>> So apparently this was an issue with 2 processes accessing the same
>> TDB .
>>>>> Normally this is detected and an explicit Jena TDB message appears, but
>>>> not
>>>>> this time.
>>>>>
>>>>> Jean-Marc Vanel
>>>>> <
>>>>
>> http://semantic-forms.cc:9112/display?displayuri=http://jmvanel.free.fr/jmv.rdf%23me
>>>>>
>>>>> +33 (0)6 89 16 29 52
>>>>> Twitter: @jmvanel , @jmvanel_fr ; chat: irc://
>> irc.freenode.net#eulergui
>>>>> Chroniques jardin
>>>>> <
>>>>
>> http://semantic-forms.cc:1952/history?uri=http%3A%2F%2Fdbpedia.org%2Fresource%2FChronicle
>>>>>
>>>>>
>>>>>
>>>>> Le mar. 24 mars 2020 à 18:56, Jean-Marc Vanel <
>> jeanmarc.vanel@gmail.com>
>>>> a
>>>>> écrit :
>>>>>
>>>>>> Hi Jena users!
>>>>>>
>>>>>> After changing my test suite in* semantic_forms
>>>>>> <http://semantic-forms.cc:9112/ldp/semantic_forms>* , I get
>>>>>> consistently a thread blocked forever. I upgraded to latest Jena
>>>> Version =
>>>>>> "3.14.0" , and happily my Web application seems to be working fine on
>> my
>>>>>> laptop, and the test suite sort of works, that is running tests one by
>>>> one.
>>>>>> In my test suite I used to recursively delete the TDB directories
>> after
>>>>>> each test. What changed is that instead I kept the same TDB
>> directories
>>>> for
>>>>>> each test, calling close() after each test.
>>>>>> This is with TDB 1. Is another unended transaction the issue? Then how
>>>> to
>>>>>> discover that ?
>>>>>>
>>>>>> Thread [pool-1-thread-1-ScalaTest-running-TestRDFCache] (Suspended)
>>>>>> Unsafe.park(boolean, long) line: not available [native method]
>>>>>> LockSupport.park(Object) line: 175
>>>>>> Semaphore$FairSync(AbstractQueuedSynchronizer).parkAndCheckInterrupt()
>>>>>> line: 836
>>>>>>
>>>>
>> Semaphore$FairSync(AbstractQueuedSynchronizer).doAcquireSharedInterruptibly(int)
>>>>>> line: 997
>>>>>>
>>>>
>> Semaphore$FairSync(AbstractQueuedSynchronizer).acquireSharedInterruptibly(int)
>>>>>> line: 1304
>>>>>> Semaphore.acquire() line: 312
>>>>>>
>>>>>> * TransactionManager.acquireWriterLock(boolean) line: 616 *
>>>>>> TransactionManager.beginInternal(TxnType, TxnType, String) line: 358
>>>>>> TransactionManager.begin(TxnType, String) line: 343
>>>>>> StoreConnection.begin(TxnType, String) line: 128
>>>>>> StoreConnection.begin(TxnType) line: 108
>>>>>> DatasetGraphTransaction.begin(TxnType) line: 169
>>>>>> DatasetGraphTransaction.begin(ReadWrite) line: 162
>>>>>> DatasetImpl.begin(ReadWrite) line: 122
>>>>>> JenaDatasetStore.$anonfun$rw$1(Dataset, Function0) line: 23
>>>>>>
>>>>>>
>>>>>> Jean-Marc Vanel
>>>>>> <
>>>>
>> http://semantic-forms.cc:9112/display?displayuri=http://jmvanel.free.fr/jmv.rdf%23me
>>>>>
>>>>>> +33 (0)6 89 16 29 52
>>>>>> Twitter: @jmvanel , @jmvanel_fr ; chat: irc://
>> irc.freenode.net#eulergui
>>>>>> Chroniques jardin
>>>>>> <
>>>>
>> http://semantic-forms.cc:1952/history?uri=http%3A%2F%2Fdbpedia.org%2Fresource%2FChronicle
>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
Re: TDB blocked
Posted by Jean-Marc Vanel <je...@gmail.com>.
Le mer. 25 mars 2020 à 17:17, Andy Seaborne <an...@apache.org> a écrit :
>
> On 25/03/2020 14:36, Jean-Marc Vanel wrote:
> > Le mer. 25 mars 2020 à 13:07, Andy Seaborne <an...@apache.org> a écrit :
>
> ...
>
> >> What's the full stack trace?
> >> (What's the blocking thread?)
> I was looking for the other thread that is blocking this one at
> being(write). Same JVM.
>
See details below. Tell me if you still want it.
> >> Yes, another unended W transaction in the same process might be the
> cause.
> >>
> > I thought rather, another unended W transaction in *another* process,
> since
> > the tests execution was parallel.
>
> If I understand correctly,
>
> parallelExecution in Test := false
>
> means parallel in the same JVM.
>
Yes indeed, that's for taking advantage of multicore CPU's.
The parameter that actually created the freeze problem in the original post
was
fork = true
and it clear that calling TDBFactory.createDataset() and close() , and
other calls, randomly from different JVM's on the same TDB directory is
bound to fail.
On the other hand, the combination
fork := false
parallelExecution in Test := true
is not good for this kind of tests. My understanding is that TDB is made
for multi-thread access in reading and writing (and it works perfectly in
my Play Framework application for years), but not made for creating and
closing.
All tests pass, but one, with this stack (complete!):
[info] TimeSeriesTestJena:
[info] - notifyDataEvent + getTimeSeries
[info] deductions.runtime.semlogs.TimeSeriesTestJena *** ABORTED ***
[info] java.util.*ConcurrentModificationException*: Reader = 0, Writer = 2
[info] at
org.apache.jena.tdb.sys.DatasetControlMRSW.policyError(DatasetControlMRSW.java:147)
[info] at
org.apache.jena.tdb.sys.DatasetControlMRSW.policyError(DatasetControlMRSW.java:143)
[info] at
org.apache.jena.tdb.sys.DatasetControlMRSW.checkConcurrency(DatasetControlMRSW.java:75)
[info] at
org.apache.jena.tdb.sys.DatasetControlMRSW.startUpdate(DatasetControlMRSW.java:57)
[info] at
org.apache.jena.tdb.store.nodetupletable.NodeTupleTableConcrete.startWrite(NodeTupleTableConcrete.java:65)
[info] at
org.apache.jena.tdb.store.nodetupletable.NodeTupleTableConcrete.sync(NodeTupleTableConcrete.java:251)
[info] at org.apache.jena.tdb.store.TableBase.sync(TableBase.java:51)
[info] at
org.apache.jena.tdb.store.DatasetGraphTDB.sync(DatasetGraphTDB.java:253)
[info] at
org.apache.jena.tdb.transaction.DatasetGraphTransaction.close(DatasetGraphTransaction.java:296)
[info] at
org.apache.jena.sparql.core.DatasetImpl.close(DatasetImpl.java:231)
> Andy
>
>
> >
> > Test code:
> >
> https://github.com/jmvanel/semantic_forms/blob/master/scala/forms/src/test/scala/deductions/runtime/sparql_cache/TestRDFCache.scala
> > =====
> > Thread [pool-1-thread-1-ScalaTest-running-TestRDFCache] (Suspended)
> > Unsafe.park(boolean, long) line: not available [native method]
> > LockSupport.park(Object) line: 175
> > Semaphore$FairSync(AbstractQueuedSynchronizer).parkAndCheckInterrupt()
> > line: 836
> >
> Semaphore$FairSync(AbstractQueuedSynchronizer).doAcquireSharedInterruptibly(int)
> > line: 997
> >
> Semaphore$FairSync(AbstractQueuedSynchronizer).acquireSharedInterruptibly(int)
> > line: 1304
> > Semaphore.acquire() line: 312
> > TransactionManager.acquireWriterLock(boolean) line: 616
> > TransactionManager.beginInternal(TxnType, TxnType, String) line: 358
> > TransactionManager.begin(TxnType, String) line: 343
> > StoreConnection.begin(TxnType, String) line: 128
> > StoreConnection.begin(TxnType) line: 108
> > DatasetGraphTransaction.begin(TxnType) line: 169
> > DatasetGraphTransaction.begin(ReadWrite) line: 162
> > DatasetImpl.begin(ReadWrite) line: 122
> > JenaDatasetStore.$anonfun$rw$1(Dataset, Function0) line: 23
> > 52027729.apply() line: not available
> > Try$.apply(Function0<T>) line: 213
> > JenaDatasetStore.rw(Dataset, Function0<T>) line: 22
> > JenaDatasetStore.rw(Object, Function0) line: 10
> > TestRDFCache(RDFCacheAlgo<Rdf,DATASET>).readStoreURI(Object, Object,
> > DATASET) line: 368
> > RDFCacheAlgo<Rdf,DATASET>.readStoreURI$(RDFCacheAlgo, Object, Object,
> > Object) line: 366
> > TestRDFCache.readStoreURI(Object, Object, Object) line: 10
> > TestRDFCache(RDFCacheAlgo<Rdf,DATASET>).readStoreURIinOwnGraph(Object)
> > line: 334
> > TestRDFCache(RDFCacheAlgo<Rdf,DATASET>).readStoreUriInNamedGraph(Object)
> > line: 326
> > RDFCacheAlgo<Rdf,DATASET>.readStoreUriInNamedGraph$(RDFCacheAlgo, Object)
> > line: 325
> > TestRDFCache.readStoreUriInNamedGraph(Object) line: 10
> > TestRDFCache.$anonfun$new$4(TestRDFCache) line: 63
> > 1708361043.apply$mcV$sp() line: not available
> > 1708361043(JFunction0$mcV$sp).apply() line: 23
> > OutcomeOf$(OutcomeOf).outcomeOf(Function0<Object>) line: 85
> > OutcomeOf.outcomeOf$(OutcomeOf, Function0) line: 83
> > OutcomeOf$.outcomeOf(Function0<Object>) line: 104
> > Transformer<FixtureParam>.apply() line: 22
> > Transformer<FixtureParam>.apply() line: 20
> > AnyFunSuiteLike$$anon$1.apply() line: 189
> > TestRDFCache(TestSuite).withFixture(TestSuite$NoArgTest) line: 196
> > TestSuite.withFixture$(TestSuite, TestSuite$NoArgTest) line: 195
> > TestRDFCache(AnyFunSuite).withFixture(TestSuite$NoArgTest) line: 1562
> > TestRDFCache(AnyFunSuiteLike).invokeWithFixture$1(SuperEngine$TestLeaf,
> > Args, String) line: 187
> > AnyFunSuiteLike.$anonfun$runTest$1(AnyFunSuiteLike, Args, String,
> > SuperEngine$TestLeaf) line: 199
> > 1593480726.apply(Object) line: not available
> > Engine(SuperEngine<T>).runTestImpl(Suite, String, Args, boolean,
> > Function1<SuperEngine<TestLea>,Outcome>) line: 306
> > TestRDFCache(AnyFunSuiteLike).runTest(String, Args) line: 199
> > AnyFunSuiteLike.runTest$(AnyFunSuiteLike, String, Args) line: 181
> > TestRDFCache(AnyFunSuite).runTest(String, Args) line: 1562
> > AnyFunSuiteLike.$anonfun$runTests$1(AnyFunSuiteLike, String, Args) line:
> > 232
> > 438507753.apply(Object, Object) line: not available
> > SuperEngine<T>.$anonfun$runTestsInBranch$1(SuperEngine, Args, Suite,
> > SuperEngine$Branch, ListBuffer, Function2, boolean, SuperEngine$Node)
> line:
> > 413
> > 855709148.apply(Object) line: not available
> > $colon$colon<B>(List<A>).foreach(Function1<A,U>) line: 392
> > Engine(SuperEngine<T>).traverseSubNodes$1(SuperEngine$Branch, Args,
> Suite,
> > ListBuffer, Function2, boolean) line: 401
> > Engine(SuperEngine<T>).runTestsInBranch(Suite, SuperEngine<Branc>, Args,
> > boolean, Function2<String,Args,Status>) line: 396
> > Engine(SuperEngine<T>).runTestsImpl(Suite, Option<String>, Args,
> Informer,
> > boolean, Function2<String,Args,Status>) line: 475
> > TestRDFCache(AnyFunSuiteLike).runTests(Option<String>, Args) line: 232
> > AnyFunSuiteLike.runTests$(AnyFunSuiteLike, Option, Args) line: 231
> > TestRDFCache(AnyFunSuite).runTests(Option<String>, Args) line: 1562
> > TestRDFCache(Suite).run(Option<String>, Args) line: 1112
> > Suite.run$(Suite, Option, Args) line: 1094
> >
> TestRDFCache(AnyFunSuite).org$scalatest$funsuite$AnyFunSuiteLike$$super$run(Option,
> > Args) line: 1562
> > AnyFunSuiteLike.$anonfun$run$1(AnyFunSuiteLike, Option, Args) line: 236
> > 113821125.apply(Object, Object) line: not available
> > Engine(SuperEngine<T>).runImpl(Suite, Option<String>, Args,
> > Function2<Option<String>,Args,Status>) line: 535
> > TestRDFCache(AnyFunSuiteLike).run(Option<String>, Args) line: 236
> > AnyFunSuiteLike.run$(AnyFunSuiteLike, Option, Args) line: 235
> > TestRDFCache.org$scalatest$BeforeAndAfterAll$$super$run(Option, Args)
> line:
> > 10
> > TestRDFCache(BeforeAndAfterAll).liftedTree1$1(Args, Option) line: 213
> > TestRDFCache(BeforeAndAfterAll).run(Option<String>, Args) line: 210
> > BeforeAndAfterAll.run$(BeforeAndAfterAll, Option, Args) line: 208
> > TestRDFCache.run(Option<String>, Args) line: 10
> > Framework.org$scalatest$tools$Framework$$runSuite(TaskDef, String, Suite,
> > ClassLoader, SuiteSortingReporter, Tracker, EventHandler, Set<String>,
> > Set<String>, Selector[], boolean, ConfigMap, SummaryCounter,
> > Option<ScalaTestStatefulStatus>, LinkedBlockingQueue<Status>, Logger[],
> > boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean,
> > boolean, boolean, ExecutorService) line: 318
> > Framework$ScalaTestTask.execute(EventHandler, Logger[]) line: 513
> > ForkMain$Run.lambda$runTest$1(Task, ObjectOutputStream, Logger[]) line:
> 304
> > 1574877131.call() line: not available
> > FutureTask<V>.run() line: 266
> > ThreadPoolExecutor.runWorker(ThreadPoolExecutor$Worker) line: 1149
> > ThreadPoolExecutor$Worker.run() line: 624
> > Thread.run() line: 748
> > =====
> >
> >
> >
> >> Andy
> >>
> >>
> >> On 25/03/2020 11:08, Jean-Marc Vanel wrote:
> >>> I investigated on that.
> >>> Now my test suite passes without Jena TDB trouble. I just added this in
> >>> Scala SBT :
> >>> parallelExecution in Test := false
> >>>
> >>> I didn't know that parallel execution was the default.
> >>> So apparently this was an issue with 2 processes accessing the same
> TDB .
> >>> Normally this is detected and an explicit Jena TDB message appears, but
> >> not
> >>> this time.
> >>>
> >>> Jean-Marc Vanel
> >>> <
> >>
> http://semantic-forms.cc:9112/display?displayuri=http://jmvanel.free.fr/jmv.rdf%23me
> >>>
> >>> +33 (0)6 89 16 29 52
> >>> Twitter: @jmvanel , @jmvanel_fr ; chat: irc://
> irc.freenode.net#eulergui
> >>> Chroniques jardin
> >>> <
> >>
> http://semantic-forms.cc:1952/history?uri=http%3A%2F%2Fdbpedia.org%2Fresource%2FChronicle
> >>>
> >>>
> >>>
> >>> Le mar. 24 mars 2020 à 18:56, Jean-Marc Vanel <
> jeanmarc.vanel@gmail.com>
> >> a
> >>> écrit :
> >>>
> >>>> Hi Jena users!
> >>>>
> >>>> After changing my test suite in* semantic_forms
> >>>> <http://semantic-forms.cc:9112/ldp/semantic_forms>* , I get
> >>>> consistently a thread blocked forever. I upgraded to latest Jena
> >> Version =
> >>>> "3.14.0" , and happily my Web application seems to be working fine on
> my
> >>>> laptop, and the test suite sort of works, that is running tests one by
> >> one.
> >>>> In my test suite I used to recursively delete the TDB directories
> after
> >>>> each test. What changed is that instead I kept the same TDB
> directories
> >> for
> >>>> each test, calling close() after each test.
> >>>> This is with TDB 1. Is another unended transaction the issue? Then how
> >> to
> >>>> discover that ?
> >>>>
> >>>> Thread [pool-1-thread-1-ScalaTest-running-TestRDFCache] (Suspended)
> >>>> Unsafe.park(boolean, long) line: not available [native method]
> >>>> LockSupport.park(Object) line: 175
> >>>> Semaphore$FairSync(AbstractQueuedSynchronizer).parkAndCheckInterrupt()
> >>>> line: 836
> >>>>
> >>
> Semaphore$FairSync(AbstractQueuedSynchronizer).doAcquireSharedInterruptibly(int)
> >>>> line: 997
> >>>>
> >>
> Semaphore$FairSync(AbstractQueuedSynchronizer).acquireSharedInterruptibly(int)
> >>>> line: 1304
> >>>> Semaphore.acquire() line: 312
> >>>>
> >>>> * TransactionManager.acquireWriterLock(boolean) line: 616 *
> >>>> TransactionManager.beginInternal(TxnType, TxnType, String) line: 358
> >>>> TransactionManager.begin(TxnType, String) line: 343
> >>>> StoreConnection.begin(TxnType, String) line: 128
> >>>> StoreConnection.begin(TxnType) line: 108
> >>>> DatasetGraphTransaction.begin(TxnType) line: 169
> >>>> DatasetGraphTransaction.begin(ReadWrite) line: 162
> >>>> DatasetImpl.begin(ReadWrite) line: 122
> >>>> JenaDatasetStore.$anonfun$rw$1(Dataset, Function0) line: 23
> >>>>
> >>>>
> >>>> Jean-Marc Vanel
> >>>> <
> >>
> http://semantic-forms.cc:9112/display?displayuri=http://jmvanel.free.fr/jmv.rdf%23me
> >>>
> >>>> +33 (0)6 89 16 29 52
> >>>> Twitter: @jmvanel , @jmvanel_fr ; chat: irc://
> irc.freenode.net#eulergui
> >>>> Chroniques jardin
> >>>> <
> >>
> http://semantic-forms.cc:1952/history?uri=http%3A%2F%2Fdbpedia.org%2Fresource%2FChronicle
> >>>
> >>>>
> >>>
> >>
> >
>
Re: TDB blocked
Posted by Andy Seaborne <an...@apache.org>.
On 25/03/2020 14:36, Jean-Marc Vanel wrote:
> Le mer. 25 mars 2020 à 13:07, Andy Seaborne <an...@apache.org> a écrit :
>
>> What's the full stack trace?
>> (What's the blocking thread?)
>>
>
> See below.
I was looking for the other thread that is blocking this one at
being(write). Same JVM.
There is no across different JVM locking in TDB.
>
>
>> Yes, another unended W transaction in the same process might be the cause.
>>
>
> I thought rather, another unended W transaction in *another* process, since
> the tests execution was parallel.
If I understand correctly,
parallelExecution in Test := false
means parallel in the same JVM.
Andy
>
> Test code:
> https://github.com/jmvanel/semantic_forms/blob/master/scala/forms/src/test/scala/deductions/runtime/sparql_cache/TestRDFCache.scala
> =====
> Thread [pool-1-thread-1-ScalaTest-running-TestRDFCache] (Suspended)
> Unsafe.park(boolean, long) line: not available [native method]
> LockSupport.park(Object) line: 175
> Semaphore$FairSync(AbstractQueuedSynchronizer).parkAndCheckInterrupt()
> line: 836
> Semaphore$FairSync(AbstractQueuedSynchronizer).doAcquireSharedInterruptibly(int)
> line: 997
> Semaphore$FairSync(AbstractQueuedSynchronizer).acquireSharedInterruptibly(int)
> line: 1304
> Semaphore.acquire() line: 312
> TransactionManager.acquireWriterLock(boolean) line: 616
> TransactionManager.beginInternal(TxnType, TxnType, String) line: 358
> TransactionManager.begin(TxnType, String) line: 343
> StoreConnection.begin(TxnType, String) line: 128
> StoreConnection.begin(TxnType) line: 108
> DatasetGraphTransaction.begin(TxnType) line: 169
> DatasetGraphTransaction.begin(ReadWrite) line: 162
> DatasetImpl.begin(ReadWrite) line: 122
> JenaDatasetStore.$anonfun$rw$1(Dataset, Function0) line: 23
> 52027729.apply() line: not available
> Try$.apply(Function0<T>) line: 213
> JenaDatasetStore.rw(Dataset, Function0<T>) line: 22
> JenaDatasetStore.rw(Object, Function0) line: 10
> TestRDFCache(RDFCacheAlgo<Rdf,DATASET>).readStoreURI(Object, Object,
> DATASET) line: 368
> RDFCacheAlgo<Rdf,DATASET>.readStoreURI$(RDFCacheAlgo, Object, Object,
> Object) line: 366
> TestRDFCache.readStoreURI(Object, Object, Object) line: 10
> TestRDFCache(RDFCacheAlgo<Rdf,DATASET>).readStoreURIinOwnGraph(Object)
> line: 334
> TestRDFCache(RDFCacheAlgo<Rdf,DATASET>).readStoreUriInNamedGraph(Object)
> line: 326
> RDFCacheAlgo<Rdf,DATASET>.readStoreUriInNamedGraph$(RDFCacheAlgo, Object)
> line: 325
> TestRDFCache.readStoreUriInNamedGraph(Object) line: 10
> TestRDFCache.$anonfun$new$4(TestRDFCache) line: 63
> 1708361043.apply$mcV$sp() line: not available
> 1708361043(JFunction0$mcV$sp).apply() line: 23
> OutcomeOf$(OutcomeOf).outcomeOf(Function0<Object>) line: 85
> OutcomeOf.outcomeOf$(OutcomeOf, Function0) line: 83
> OutcomeOf$.outcomeOf(Function0<Object>) line: 104
> Transformer<FixtureParam>.apply() line: 22
> Transformer<FixtureParam>.apply() line: 20
> AnyFunSuiteLike$$anon$1.apply() line: 189
> TestRDFCache(TestSuite).withFixture(TestSuite$NoArgTest) line: 196
> TestSuite.withFixture$(TestSuite, TestSuite$NoArgTest) line: 195
> TestRDFCache(AnyFunSuite).withFixture(TestSuite$NoArgTest) line: 1562
> TestRDFCache(AnyFunSuiteLike).invokeWithFixture$1(SuperEngine$TestLeaf,
> Args, String) line: 187
> AnyFunSuiteLike.$anonfun$runTest$1(AnyFunSuiteLike, Args, String,
> SuperEngine$TestLeaf) line: 199
> 1593480726.apply(Object) line: not available
> Engine(SuperEngine<T>).runTestImpl(Suite, String, Args, boolean,
> Function1<SuperEngine<TestLea>,Outcome>) line: 306
> TestRDFCache(AnyFunSuiteLike).runTest(String, Args) line: 199
> AnyFunSuiteLike.runTest$(AnyFunSuiteLike, String, Args) line: 181
> TestRDFCache(AnyFunSuite).runTest(String, Args) line: 1562
> AnyFunSuiteLike.$anonfun$runTests$1(AnyFunSuiteLike, String, Args) line:
> 232
> 438507753.apply(Object, Object) line: not available
> SuperEngine<T>.$anonfun$runTestsInBranch$1(SuperEngine, Args, Suite,
> SuperEngine$Branch, ListBuffer, Function2, boolean, SuperEngine$Node) line:
> 413
> 855709148.apply(Object) line: not available
> $colon$colon<B>(List<A>).foreach(Function1<A,U>) line: 392
> Engine(SuperEngine<T>).traverseSubNodes$1(SuperEngine$Branch, Args, Suite,
> ListBuffer, Function2, boolean) line: 401
> Engine(SuperEngine<T>).runTestsInBranch(Suite, SuperEngine<Branc>, Args,
> boolean, Function2<String,Args,Status>) line: 396
> Engine(SuperEngine<T>).runTestsImpl(Suite, Option<String>, Args, Informer,
> boolean, Function2<String,Args,Status>) line: 475
> TestRDFCache(AnyFunSuiteLike).runTests(Option<String>, Args) line: 232
> AnyFunSuiteLike.runTests$(AnyFunSuiteLike, Option, Args) line: 231
> TestRDFCache(AnyFunSuite).runTests(Option<String>, Args) line: 1562
> TestRDFCache(Suite).run(Option<String>, Args) line: 1112
> Suite.run$(Suite, Option, Args) line: 1094
> TestRDFCache(AnyFunSuite).org$scalatest$funsuite$AnyFunSuiteLike$$super$run(Option,
> Args) line: 1562
> AnyFunSuiteLike.$anonfun$run$1(AnyFunSuiteLike, Option, Args) line: 236
> 113821125.apply(Object, Object) line: not available
> Engine(SuperEngine<T>).runImpl(Suite, Option<String>, Args,
> Function2<Option<String>,Args,Status>) line: 535
> TestRDFCache(AnyFunSuiteLike).run(Option<String>, Args) line: 236
> AnyFunSuiteLike.run$(AnyFunSuiteLike, Option, Args) line: 235
> TestRDFCache.org$scalatest$BeforeAndAfterAll$$super$run(Option, Args) line:
> 10
> TestRDFCache(BeforeAndAfterAll).liftedTree1$1(Args, Option) line: 213
> TestRDFCache(BeforeAndAfterAll).run(Option<String>, Args) line: 210
> BeforeAndAfterAll.run$(BeforeAndAfterAll, Option, Args) line: 208
> TestRDFCache.run(Option<String>, Args) line: 10
> Framework.org$scalatest$tools$Framework$$runSuite(TaskDef, String, Suite,
> ClassLoader, SuiteSortingReporter, Tracker, EventHandler, Set<String>,
> Set<String>, Selector[], boolean, ConfigMap, SummaryCounter,
> Option<ScalaTestStatefulStatus>, LinkedBlockingQueue<Status>, Logger[],
> boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean,
> boolean, boolean, ExecutorService) line: 318
> Framework$ScalaTestTask.execute(EventHandler, Logger[]) line: 513
> ForkMain$Run.lambda$runTest$1(Task, ObjectOutputStream, Logger[]) line: 304
> 1574877131.call() line: not available
> FutureTask<V>.run() line: 266
> ThreadPoolExecutor.runWorker(ThreadPoolExecutor$Worker) line: 1149
> ThreadPoolExecutor$Worker.run() line: 624
> Thread.run() line: 748
> =====
>
>
>
>> Andy
>>
>>
>> On 25/03/2020 11:08, Jean-Marc Vanel wrote:
>>> I investigated on that.
>>> Now my test suite passes without Jena TDB trouble. I just added this in
>>> Scala SBT :
>>> parallelExecution in Test := false
>>>
>>> I didn't know that parallel execution was the default.
>>> So apparently this was an issue with 2 processes accessing the same TDB .
>>> Normally this is detected and an explicit Jena TDB message appears, but
>> not
>>> this time.
>>>
>>> Jean-Marc Vanel
>>> <
>> http://semantic-forms.cc:9112/display?displayuri=http://jmvanel.free.fr/jmv.rdf%23me
>>>
>>> +33 (0)6 89 16 29 52
>>> Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui
>>> Chroniques jardin
>>> <
>> http://semantic-forms.cc:1952/history?uri=http%3A%2F%2Fdbpedia.org%2Fresource%2FChronicle
>>>
>>>
>>>
>>> Le mar. 24 mars 2020 à 18:56, Jean-Marc Vanel <je...@gmail.com>
>> a
>>> écrit :
>>>
>>>> Hi Jena users!
>>>>
>>>> After changing my test suite in* semantic_forms
>>>> <http://semantic-forms.cc:9112/ldp/semantic_forms>* , I get
>>>> consistently a thread blocked forever. I upgraded to latest Jena
>> Version =
>>>> "3.14.0" , and happily my Web application seems to be working fine on my
>>>> laptop, and the test suite sort of works, that is running tests one by
>> one.
>>>> In my test suite I used to recursively delete the TDB directories after
>>>> each test. What changed is that instead I kept the same TDB directories
>> for
>>>> each test, calling close() after each test.
>>>> This is with TDB 1. Is another unended transaction the issue? Then how
>> to
>>>> discover that ?
>>>>
>>>> Thread [pool-1-thread-1-ScalaTest-running-TestRDFCache] (Suspended)
>>>> Unsafe.park(boolean, long) line: not available [native method]
>>>> LockSupport.park(Object) line: 175
>>>> Semaphore$FairSync(AbstractQueuedSynchronizer).parkAndCheckInterrupt()
>>>> line: 836
>>>>
>> Semaphore$FairSync(AbstractQueuedSynchronizer).doAcquireSharedInterruptibly(int)
>>>> line: 997
>>>>
>> Semaphore$FairSync(AbstractQueuedSynchronizer).acquireSharedInterruptibly(int)
>>>> line: 1304
>>>> Semaphore.acquire() line: 312
>>>>
>>>> * TransactionManager.acquireWriterLock(boolean) line: 616 *
>>>> TransactionManager.beginInternal(TxnType, TxnType, String) line: 358
>>>> TransactionManager.begin(TxnType, String) line: 343
>>>> StoreConnection.begin(TxnType, String) line: 128
>>>> StoreConnection.begin(TxnType) line: 108
>>>> DatasetGraphTransaction.begin(TxnType) line: 169
>>>> DatasetGraphTransaction.begin(ReadWrite) line: 162
>>>> DatasetImpl.begin(ReadWrite) line: 122
>>>> JenaDatasetStore.$anonfun$rw$1(Dataset, Function0) line: 23
>>>>
>>>>
>>>> Jean-Marc Vanel
>>>> <
>> http://semantic-forms.cc:9112/display?displayuri=http://jmvanel.free.fr/jmv.rdf%23me
>>>
>>>> +33 (0)6 89 16 29 52
>>>> Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui
>>>> Chroniques jardin
>>>> <
>> http://semantic-forms.cc:1952/history?uri=http%3A%2F%2Fdbpedia.org%2Fresource%2FChronicle
>>>
>>>>
>>>
>>
>
Re: TDB blocked
Posted by Jean-Marc Vanel <je...@gmail.com>.
Le mer. 25 mars 2020 à 13:07, Andy Seaborne <an...@apache.org> a écrit :
> What's the full stack trace?
> (What's the blocking thread?)
>
See below.
> Yes, another unended W transaction in the same process might be the cause.
>
I thought rather, another unended W transaction in *another* process, since
the tests execution was parallel.
Test code:
https://github.com/jmvanel/semantic_forms/blob/master/scala/forms/src/test/scala/deductions/runtime/sparql_cache/TestRDFCache.scala
=====
Thread [pool-1-thread-1-ScalaTest-running-TestRDFCache] (Suspended)
Unsafe.park(boolean, long) line: not available [native method]
LockSupport.park(Object) line: 175
Semaphore$FairSync(AbstractQueuedSynchronizer).parkAndCheckInterrupt()
line: 836
Semaphore$FairSync(AbstractQueuedSynchronizer).doAcquireSharedInterruptibly(int)
line: 997
Semaphore$FairSync(AbstractQueuedSynchronizer).acquireSharedInterruptibly(int)
line: 1304
Semaphore.acquire() line: 312
TransactionManager.acquireWriterLock(boolean) line: 616
TransactionManager.beginInternal(TxnType, TxnType, String) line: 358
TransactionManager.begin(TxnType, String) line: 343
StoreConnection.begin(TxnType, String) line: 128
StoreConnection.begin(TxnType) line: 108
DatasetGraphTransaction.begin(TxnType) line: 169
DatasetGraphTransaction.begin(ReadWrite) line: 162
DatasetImpl.begin(ReadWrite) line: 122
JenaDatasetStore.$anonfun$rw$1(Dataset, Function0) line: 23
52027729.apply() line: not available
Try$.apply(Function0<T>) line: 213
JenaDatasetStore.rw(Dataset, Function0<T>) line: 22
JenaDatasetStore.rw(Object, Function0) line: 10
TestRDFCache(RDFCacheAlgo<Rdf,DATASET>).readStoreURI(Object, Object,
DATASET) line: 368
RDFCacheAlgo<Rdf,DATASET>.readStoreURI$(RDFCacheAlgo, Object, Object,
Object) line: 366
TestRDFCache.readStoreURI(Object, Object, Object) line: 10
TestRDFCache(RDFCacheAlgo<Rdf,DATASET>).readStoreURIinOwnGraph(Object)
line: 334
TestRDFCache(RDFCacheAlgo<Rdf,DATASET>).readStoreUriInNamedGraph(Object)
line: 326
RDFCacheAlgo<Rdf,DATASET>.readStoreUriInNamedGraph$(RDFCacheAlgo, Object)
line: 325
TestRDFCache.readStoreUriInNamedGraph(Object) line: 10
TestRDFCache.$anonfun$new$4(TestRDFCache) line: 63
1708361043.apply$mcV$sp() line: not available
1708361043(JFunction0$mcV$sp).apply() line: 23
OutcomeOf$(OutcomeOf).outcomeOf(Function0<Object>) line: 85
OutcomeOf.outcomeOf$(OutcomeOf, Function0) line: 83
OutcomeOf$.outcomeOf(Function0<Object>) line: 104
Transformer<FixtureParam>.apply() line: 22
Transformer<FixtureParam>.apply() line: 20
AnyFunSuiteLike$$anon$1.apply() line: 189
TestRDFCache(TestSuite).withFixture(TestSuite$NoArgTest) line: 196
TestSuite.withFixture$(TestSuite, TestSuite$NoArgTest) line: 195
TestRDFCache(AnyFunSuite).withFixture(TestSuite$NoArgTest) line: 1562
TestRDFCache(AnyFunSuiteLike).invokeWithFixture$1(SuperEngine$TestLeaf,
Args, String) line: 187
AnyFunSuiteLike.$anonfun$runTest$1(AnyFunSuiteLike, Args, String,
SuperEngine$TestLeaf) line: 199
1593480726.apply(Object) line: not available
Engine(SuperEngine<T>).runTestImpl(Suite, String, Args, boolean,
Function1<SuperEngine<TestLea>,Outcome>) line: 306
TestRDFCache(AnyFunSuiteLike).runTest(String, Args) line: 199
AnyFunSuiteLike.runTest$(AnyFunSuiteLike, String, Args) line: 181
TestRDFCache(AnyFunSuite).runTest(String, Args) line: 1562
AnyFunSuiteLike.$anonfun$runTests$1(AnyFunSuiteLike, String, Args) line:
232
438507753.apply(Object, Object) line: not available
SuperEngine<T>.$anonfun$runTestsInBranch$1(SuperEngine, Args, Suite,
SuperEngine$Branch, ListBuffer, Function2, boolean, SuperEngine$Node) line:
413
855709148.apply(Object) line: not available
$colon$colon<B>(List<A>).foreach(Function1<A,U>) line: 392
Engine(SuperEngine<T>).traverseSubNodes$1(SuperEngine$Branch, Args, Suite,
ListBuffer, Function2, boolean) line: 401
Engine(SuperEngine<T>).runTestsInBranch(Suite, SuperEngine<Branc>, Args,
boolean, Function2<String,Args,Status>) line: 396
Engine(SuperEngine<T>).runTestsImpl(Suite, Option<String>, Args, Informer,
boolean, Function2<String,Args,Status>) line: 475
TestRDFCache(AnyFunSuiteLike).runTests(Option<String>, Args) line: 232
AnyFunSuiteLike.runTests$(AnyFunSuiteLike, Option, Args) line: 231
TestRDFCache(AnyFunSuite).runTests(Option<String>, Args) line: 1562
TestRDFCache(Suite).run(Option<String>, Args) line: 1112
Suite.run$(Suite, Option, Args) line: 1094
TestRDFCache(AnyFunSuite).org$scalatest$funsuite$AnyFunSuiteLike$$super$run(Option,
Args) line: 1562
AnyFunSuiteLike.$anonfun$run$1(AnyFunSuiteLike, Option, Args) line: 236
113821125.apply(Object, Object) line: not available
Engine(SuperEngine<T>).runImpl(Suite, Option<String>, Args,
Function2<Option<String>,Args,Status>) line: 535
TestRDFCache(AnyFunSuiteLike).run(Option<String>, Args) line: 236
AnyFunSuiteLike.run$(AnyFunSuiteLike, Option, Args) line: 235
TestRDFCache.org$scalatest$BeforeAndAfterAll$$super$run(Option, Args) line:
10
TestRDFCache(BeforeAndAfterAll).liftedTree1$1(Args, Option) line: 213
TestRDFCache(BeforeAndAfterAll).run(Option<String>, Args) line: 210
BeforeAndAfterAll.run$(BeforeAndAfterAll, Option, Args) line: 208
TestRDFCache.run(Option<String>, Args) line: 10
Framework.org$scalatest$tools$Framework$$runSuite(TaskDef, String, Suite,
ClassLoader, SuiteSortingReporter, Tracker, EventHandler, Set<String>,
Set<String>, Selector[], boolean, ConfigMap, SummaryCounter,
Option<ScalaTestStatefulStatus>, LinkedBlockingQueue<Status>, Logger[],
boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean,
boolean, boolean, ExecutorService) line: 318
Framework$ScalaTestTask.execute(EventHandler, Logger[]) line: 513
ForkMain$Run.lambda$runTest$1(Task, ObjectOutputStream, Logger[]) line: 304
1574877131.call() line: not available
FutureTask<V>.run() line: 266
ThreadPoolExecutor.runWorker(ThreadPoolExecutor$Worker) line: 1149
ThreadPoolExecutor$Worker.run() line: 624
Thread.run() line: 748
=====
> Andy
>
>
> On 25/03/2020 11:08, Jean-Marc Vanel wrote:
> > I investigated on that.
> > Now my test suite passes without Jena TDB trouble. I just added this in
> > Scala SBT :
> > parallelExecution in Test := false
> >
> > I didn't know that parallel execution was the default.
> > So apparently this was an issue with 2 processes accessing the same TDB .
> > Normally this is detected and an explicit Jena TDB message appears, but
> not
> > this time.
> >
> > Jean-Marc Vanel
> > <
> http://semantic-forms.cc:9112/display?displayuri=http://jmvanel.free.fr/jmv.rdf%23me
> >
> > +33 (0)6 89 16 29 52
> > Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui
> > Chroniques jardin
> > <
> http://semantic-forms.cc:1952/history?uri=http%3A%2F%2Fdbpedia.org%2Fresource%2FChronicle
> >
> >
> >
> > Le mar. 24 mars 2020 à 18:56, Jean-Marc Vanel <je...@gmail.com>
> a
> > écrit :
> >
> >> Hi Jena users!
> >>
> >> After changing my test suite in* semantic_forms
> >> <http://semantic-forms.cc:9112/ldp/semantic_forms>* , I get
> >> consistently a thread blocked forever. I upgraded to latest Jena
> Version =
> >> "3.14.0" , and happily my Web application seems to be working fine on my
> >> laptop, and the test suite sort of works, that is running tests one by
> one.
> >> In my test suite I used to recursively delete the TDB directories after
> >> each test. What changed is that instead I kept the same TDB directories
> for
> >> each test, calling close() after each test.
> >> This is with TDB 1. Is another unended transaction the issue? Then how
> to
> >> discover that ?
> >>
> >> Thread [pool-1-thread-1-ScalaTest-running-TestRDFCache] (Suspended)
> >> Unsafe.park(boolean, long) line: not available [native method]
> >> LockSupport.park(Object) line: 175
> >> Semaphore$FairSync(AbstractQueuedSynchronizer).parkAndCheckInterrupt()
> >> line: 836
> >>
> Semaphore$FairSync(AbstractQueuedSynchronizer).doAcquireSharedInterruptibly(int)
> >> line: 997
> >>
> Semaphore$FairSync(AbstractQueuedSynchronizer).acquireSharedInterruptibly(int)
> >> line: 1304
> >> Semaphore.acquire() line: 312
> >>
> >> * TransactionManager.acquireWriterLock(boolean) line: 616 *
> >> TransactionManager.beginInternal(TxnType, TxnType, String) line: 358
> >> TransactionManager.begin(TxnType, String) line: 343
> >> StoreConnection.begin(TxnType, String) line: 128
> >> StoreConnection.begin(TxnType) line: 108
> >> DatasetGraphTransaction.begin(TxnType) line: 169
> >> DatasetGraphTransaction.begin(ReadWrite) line: 162
> >> DatasetImpl.begin(ReadWrite) line: 122
> >> JenaDatasetStore.$anonfun$rw$1(Dataset, Function0) line: 23
> >>
> >>
> >> Jean-Marc Vanel
> >> <
> http://semantic-forms.cc:9112/display?displayuri=http://jmvanel.free.fr/jmv.rdf%23me
> >
> >> +33 (0)6 89 16 29 52
> >> Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui
> >> Chroniques jardin
> >> <
> http://semantic-forms.cc:1952/history?uri=http%3A%2F%2Fdbpedia.org%2Fresource%2FChronicle
> >
> >>
> >
>
Re: TDB blocked
Posted by Andy Seaborne <an...@apache.org>.
What's the full stack trace?
(What's the blocking thread?)
Yes, another unended W transaction in the same process might be the cause.
Andy
On 25/03/2020 11:08, Jean-Marc Vanel wrote:
> I investigated on that.
> Now my test suite passes without Jena TDB trouble. I just added this in
> Scala SBT :
> parallelExecution in Test := false
>
> I didn't know that parallel execution was the default.
> So apparently this was an issue with 2 processes accessing the same TDB .
> Normally this is detected and an explicit Jena TDB message appears, but not
> this time.
>
> Jean-Marc Vanel
> <http://semantic-forms.cc:9112/display?displayuri=http://jmvanel.free.fr/jmv.rdf%23me>
> +33 (0)6 89 16 29 52
> Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui
> Chroniques jardin
> <http://semantic-forms.cc:1952/history?uri=http%3A%2F%2Fdbpedia.org%2Fresource%2FChronicle>
>
>
> Le mar. 24 mars 2020 à 18:56, Jean-Marc Vanel <je...@gmail.com> a
> écrit :
>
>> Hi Jena users!
>>
>> After changing my test suite in* semantic_forms
>> <http://semantic-forms.cc:9112/ldp/semantic_forms>* , I get
>> consistently a thread blocked forever. I upgraded to latest Jena Version =
>> "3.14.0" , and happily my Web application seems to be working fine on my
>> laptop, and the test suite sort of works, that is running tests one by one.
>> In my test suite I used to recursively delete the TDB directories after
>> each test. What changed is that instead I kept the same TDB directories for
>> each test, calling close() after each test.
>> This is with TDB 1. Is another unended transaction the issue? Then how to
>> discover that ?
>>
>> Thread [pool-1-thread-1-ScalaTest-running-TestRDFCache] (Suspended)
>> Unsafe.park(boolean, long) line: not available [native method]
>> LockSupport.park(Object) line: 175
>> Semaphore$FairSync(AbstractQueuedSynchronizer).parkAndCheckInterrupt()
>> line: 836
>> Semaphore$FairSync(AbstractQueuedSynchronizer).doAcquireSharedInterruptibly(int)
>> line: 997
>> Semaphore$FairSync(AbstractQueuedSynchronizer).acquireSharedInterruptibly(int)
>> line: 1304
>> Semaphore.acquire() line: 312
>>
>> * TransactionManager.acquireWriterLock(boolean) line: 616 *
>> TransactionManager.beginInternal(TxnType, TxnType, String) line: 358
>> TransactionManager.begin(TxnType, String) line: 343
>> StoreConnection.begin(TxnType, String) line: 128
>> StoreConnection.begin(TxnType) line: 108
>> DatasetGraphTransaction.begin(TxnType) line: 169
>> DatasetGraphTransaction.begin(ReadWrite) line: 162
>> DatasetImpl.begin(ReadWrite) line: 122
>> JenaDatasetStore.$anonfun$rw$1(Dataset, Function0) line: 23
>>
>>
>> Jean-Marc Vanel
>> <http://semantic-forms.cc:9112/display?displayuri=http://jmvanel.free.fr/jmv.rdf%23me>
>> +33 (0)6 89 16 29 52
>> Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui
>> Chroniques jardin
>> <http://semantic-forms.cc:1952/history?uri=http%3A%2F%2Fdbpedia.org%2Fresource%2FChronicle>
>>
>
Re: TDB blocked
Posted by Jean-Marc Vanel <je...@gmail.com>.
I investigated on that.
Now my test suite passes without Jena TDB trouble. I just added this in
Scala SBT :
parallelExecution in Test := false
I didn't know that parallel execution was the default.
So apparently this was an issue with 2 processes accessing the same TDB .
Normally this is detected and an explicit Jena TDB message appears, but not
this time.
Jean-Marc Vanel
<http://semantic-forms.cc:9112/display?displayuri=http://jmvanel.free.fr/jmv.rdf%23me>
+33 (0)6 89 16 29 52
Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui
Chroniques jardin
<http://semantic-forms.cc:1952/history?uri=http%3A%2F%2Fdbpedia.org%2Fresource%2FChronicle>
Le mar. 24 mars 2020 à 18:56, Jean-Marc Vanel <je...@gmail.com> a
écrit :
> Hi Jena users!
>
> After changing my test suite in* semantic_forms
> <http://semantic-forms.cc:9112/ldp/semantic_forms>* , I get
> consistently a thread blocked forever. I upgraded to latest Jena Version =
> "3.14.0" , and happily my Web application seems to be working fine on my
> laptop, and the test suite sort of works, that is running tests one by one.
> In my test suite I used to recursively delete the TDB directories after
> each test. What changed is that instead I kept the same TDB directories for
> each test, calling close() after each test.
> This is with TDB 1. Is another unended transaction the issue? Then how to
> discover that ?
>
> Thread [pool-1-thread-1-ScalaTest-running-TestRDFCache] (Suspended)
> Unsafe.park(boolean, long) line: not available [native method]
> LockSupport.park(Object) line: 175
> Semaphore$FairSync(AbstractQueuedSynchronizer).parkAndCheckInterrupt()
> line: 836
> Semaphore$FairSync(AbstractQueuedSynchronizer).doAcquireSharedInterruptibly(int)
> line: 997
> Semaphore$FairSync(AbstractQueuedSynchronizer).acquireSharedInterruptibly(int)
> line: 1304
> Semaphore.acquire() line: 312
>
> * TransactionManager.acquireWriterLock(boolean) line: 616 *
> TransactionManager.beginInternal(TxnType, TxnType, String) line: 358
> TransactionManager.begin(TxnType, String) line: 343
> StoreConnection.begin(TxnType, String) line: 128
> StoreConnection.begin(TxnType) line: 108
> DatasetGraphTransaction.begin(TxnType) line: 169
> DatasetGraphTransaction.begin(ReadWrite) line: 162
> DatasetImpl.begin(ReadWrite) line: 122
> JenaDatasetStore.$anonfun$rw$1(Dataset, Function0) line: 23
>
>
> Jean-Marc Vanel
> <http://semantic-forms.cc:9112/display?displayuri=http://jmvanel.free.fr/jmv.rdf%23me>
> +33 (0)6 89 16 29 52
> Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui
> Chroniques jardin
> <http://semantic-forms.cc:1952/history?uri=http%3A%2F%2Fdbpedia.org%2Fresource%2FChronicle>
>