Re: TDB blocked

Andy Seaborne Wed, 25 Mar 2020 09:17:21 -0700



On 25/03/2020 14:36, Jean-Marc Vanel wrote:

Le mer. 25 mars 2020 à 13:07, Andy Seaborne <a...@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 atbeing(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
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Le mar. 24 mars 2020 à 18:56, Jean-Marc Vanel <jeanmarc.va...@gmail.com>

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
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http://semantic-forms.cc:1952/history?uri=http%3A%2F%2Fdbpedia.org%2Fresource%2FChronicle

Re: TDB blocked

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