Dear Mark,
I think the issue have nothing to do with the network, because a simple reason after restarting omero service everything will work fine and after a while issue appears again.
Regards
Saleh
-Dcom.sun.jndi.ldap.read.timeout=5000
-Dcom.sun.jndi.ldap.connect.pool=false
-Dcom.sun.jndi.ldap.connect.pool.debug=all
-Dcom.sun.jndi.ldap.connect.pool.maxsize=1
$ bin/omero config set -- omero.jvmcfg.append -Dcom.sun.jndi.ldap.connect.pool=false
omero.data.dir=/data/OMERO
omero.db.name=omero_database
omero.db.pass=********
omero.db.user=db_user
omero.jvmcfg.append=-Dcom.sun.jndi.ldap.connect.pool=false
omero.jvmcfg.remove=-Dcom.sun.jndi.ldap.read.timeout=5000
omero.ldap.base=dc=ad,dc=hhu,dc=de
omero.ldap.config=true
omero.ldap.new_user_group=default
omero.ldap.password=********
omero.ldap.referral=ignore
omero.ldap.urls=ldap://ldaps.ad.hhu.de:3268
omero.ldap.user_mapping=omeName=sAMAccountName,firstName=givenName,lastName=sn,email=mail
omero.ldap.username=SVC_Omero
omero.security.ignore_case=true
omero.web.wsgi_timeout=60
omero.web.wsgi_workers=5
omero.jvmcfg.append=-Dcom.sun.jndi.ldap.connect.pool=false
omero.jvmcfg.append=-Dcom.sun.jndi.ldap.connect.pool=false
ps awux | grep Blitz | grep ldap
-Dcom.sun.jndi.ldap.connect.pool=false
-Dcom.sun.jndi.ldap.connect.pool.debug=all
-Dcom.sun.jndi.ldap.connect.pool.maxsize=1
Full thread dump OpenJDK 64-Bit Server VM (25.131-b12 mixed mode):
"Attach Listener" #25 daemon prio=9 os_prio=0 tid=0x00007f7990003800 nid=0xd9b waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"pool-2-thread-5" #24 prio=5 os_prio=0 tid=0x00007f7970009800 nid=0xb6d waiting on condition [0x00007f796dbd9000]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x00000000bdfe6c40> (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 java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:442)
at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1067)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:748)
"pool-2-thread-4" #23 prio=5 os_prio=0 tid=0x00007f7970008000 nid=0xb6b waiting on condition [0x00007f796dcda000]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x00000000bdfe6c40> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039)
at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:442)
at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1067)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:748)
"pool-2-thread-3" #22 prio=5 os_prio=0 tid=0x00007f7970005800 nid=0xb69 waiting on condition [0x00007f796dddb000]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x00000000bdfe6c40> (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 java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:442)
at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1067)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:748)
"PixelData-0-Ice.Timer" #21 prio=5 os_prio=0 tid=0x00007f79c5274000 nid=0xb65 waiting on condition [0x00007f796e0dc000]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x00000000f1f08b20> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039)
at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1081)
at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:809)
at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1067)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:748)
"PixelData-0-Ice.ThreadPool.Server-0" #20 prio=5 os_prio=0 tid=0x00007f79c5254000 nid=0xb64 runnable [0x00007f796e1dd000]
java.lang.Thread.State: RUNNABLE
at sun.nio.ch.EPollArrayWrapper.epollWait(Native Method)
at sun.nio.ch.EPollArrayWrapper.poll(EPollArrayWrapper.java:269)
at sun.nio.ch.EPollSelectorImpl.doSelect(EPollSelectorImpl.java:93)
at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:86)
- locked <0x00000000f204e7d0> (a sun.nio.ch.Util$3)
- locked <0x00000000f204e7c0> (a java.util.Collections$UnmodifiableSet)
- locked <0x00000000f204e6a8> (a sun.nio.ch.EPollSelectorImpl)
at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:97)
at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:101)
at IceInternal.Selector.select(Selector.java:201)
at IceInternal.ThreadPool.run(ThreadPool.java:414)
at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)
at java.lang.Thread.run(Thread.java:748)
"pool-2-thread-2" #19 prio=5 os_prio=0 tid=0x00007f7970004800 nid=0xb63 waiting on condition [0x00007f796e2de000]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x00000000bdfe6c40> (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 java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:442)
at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1067)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:748)
"PixelData-0-Ice.ThreadPool.Client-0" #18 prio=5 os_prio=0 tid=0x00007f79c5235800 nid=0xb62 runnable [0x00007f796e3df000]
java.lang.Thread.State: RUNNABLE
at sun.nio.ch.EPollArrayWrapper.epollWait(Native Method)
at sun.nio.ch.EPollArrayWrapper.poll(EPollArrayWrapper.java:269)
at sun.nio.ch.EPollSelectorImpl.doSelect(EPollSelectorImpl.java:93)
at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:86)
- locked <0x00000000f1f092a0> (a sun.nio.ch.Util$3)
- locked <0x00000000f1f09290> (a java.util.Collections$UnmodifiableSet)
- locked <0x00000000f1f09178> (a sun.nio.ch.EPollSelectorImpl)
at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:97)
at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:101)
at IceInternal.Selector.select(Selector.java:201)
at IceInternal.ThreadPool.run(ThreadPool.java:414)
at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)
at java.lang.Thread.run(Thread.java:748)
"pool-2-thread-1" #17 prio=5 os_prio=0 tid=0x00007f7970001800 nid=0xb61 waiting on condition [0x00007f796e4e0000]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x00000000bdfe6c40> (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 java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:442)
at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1067)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:748)
"OMERO.scheduler_QuartzSchedulerThread" #16 prio=5 os_prio=0 tid=0x00007f79c4ddc000 nid=0xb5f waiting on condition [0x00007f796e7e1000]
java.lang.Thread.State: TIMED_WAITING (sleeping)
at java.lang.Thread.sleep(Native Method)
at org.quartz.core.QuartzSchedulerThread.run(QuartzSchedulerThread.java:272)
"metrics-logger-reporter-thread-1" #14 daemon prio=5 os_prio=0 tid=0x00007f79c508b000 nid=0xb39 waiting on condition [0x00007f796f1bc000]
java.lang.Thread.State: TIMED_WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x00000000bdfddff8> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$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$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:809)
at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1067)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:748)
"Ice.ThreadPool.Client-0" #13 prio=5 os_prio=0 tid=0x00007f79c4c55800 nid=0xb2e runnable [0x00007f799457f000]
java.lang.Thread.State: RUNNABLE
at sun.nio.ch.EPollArrayWrapper.epollWait(Native Method)
at sun.nio.ch.EPollArrayWrapper.poll(EPollArrayWrapper.java:269)
at sun.nio.ch.EPollSelectorImpl.doSelect(EPollSelectorImpl.java:93)
at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:86)
- locked <0x00000000b333fe38> (a sun.nio.ch.Util$3)
- locked <0x00000000b333fe28> (a java.util.Collections$UnmodifiableSet)
- locked <0x00000000b333fd00> (a sun.nio.ch.EPollSelectorImpl)
at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:97)
at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:101)
at IceInternal.Selector.select(Selector.java:201)
at IceInternal.ThreadPool.run(ThreadPool.java:414)
at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)
at java.lang.Thread.run(Thread.java:748)
"net.sf.ehcache.CacheManager@3a5ecce3" #12 daemon prio=5 os_prio=0 tid=0x00007f79c431d000 nid=0xb2b in Object.wait() [0x00007f7994680000]
java.lang.Thread.State: TIMED_WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x00000000b3343408> (a java.util.TaskQueue)
at java.util.TimerThread.mainLoop(Timer.java:552)
- locked <0x00000000b3343408> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:505)
"PostgreSQL-JDBC-SharedTimer-1" #11 daemon prio=5 os_prio=0 tid=0x00007f79c4b90000 nid=0xb26 in Object.wait() [0x00007f7994981000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x00000000b3344998> (a java.util.TaskQueue)
at java.lang.Object.wait(Object.java:502)
at java.util.TimerThread.mainLoop(Timer.java:526)
- locked <0x00000000b3344998> (a java.util.TaskQueue)
at java.util.TimerThread.run(Timer.java:505)
"bitronix-task-scheduler" #10 daemon prio=5 os_prio=0 tid=0x00007f79c4b47000 nid=0xb24 waiting on condition [0x00007f7994a82000]
java.lang.Thread.State: TIMED_WAITING (sleeping)
at java.lang.Thread.sleep(Native Method)
at bitronix.tm.timer.TaskScheduler.run(TaskScheduler.java:245)
"perf4j-async-stats-appender-sink-CoalescingStatistics" #9 daemon prio=5 os_prio=0 tid=0x00007f79c487f800 nid=0xad4 waiting on condition [0x00007f79b015b000]
java.lang.Thread.State: TIMED_WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x00000000b333d790> (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.ArrayBlockingQueue.poll(ArrayBlockingQueue.java:418)
at org.perf4j.helpers.GenericAsyncCoalescingStatisticsAppender$StopWatchesFromQueueIterator.getNext(GenericAsyncCoalescingStatisticsAppender.java:388)
at org.perf4j.helpers.GenericAsyncCoalescingStatisticsAppender$StopWatchesFromQueueIterator.hasNext(GenericAsyncCoalescingStatisticsAppender.java:349)
at org.perf4j.helpers.GroupingStatisticsIterator.getNext(GroupingStatisticsIterator.java:149)
at org.perf4j.helpers.GroupingStatisticsIterator.hasNext(GroupingStatisticsIterator.java:102)
at org.perf4j.helpers.GenericAsyncCoalescingStatisticsAppender$Dispatcher.run(GenericAsyncCoalescingStatisticsAppender.java:314)
at java.lang.Thread.run(Thread.java:748)
"Service Thread" #7 daemon prio=9 os_prio=0 tid=0x00007f79c4154800 nid=0xab0 runnable [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"C1 CompilerThread1" #6 daemon prio=9 os_prio=0 tid=0x00007f79c4150000 nid=0xaae waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"C2 CompilerThread0" #5 daemon prio=9 os_prio=0 tid=0x00007f79c4142800 nid=0xaac waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Signal Dispatcher" #4 daemon prio=9 os_prio=0 tid=0x00007f79c4140000 nid=0xaab runnable [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"Finalizer" #3 daemon prio=8 os_prio=0 tid=0x00007f79c4116000 nid=0xaa5 in Object.wait() [0x00007f79b1a87000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x00000000b3659cd0> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
- locked <0x00000000b3659cd0> (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=0x00007f79c4111800 nid=0xaa1 in Object.wait() [0x00007f79b1b88000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x00000000b3659d68> (a java.lang.ref.Reference$Lock)
at java.lang.Object.wait(Object.java:502)
at java.lang.ref.Reference.tryHandlePending(Reference.java:191)
- locked <0x00000000b3659d68> (a java.lang.ref.Reference$Lock)
at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:153)
"main" #1 prio=5 os_prio=0 tid=0x00007f79c4009000 nid=0xa94 in Object.wait() [0x00007f79cc274000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x00000000f19c4800> (a IceInternal.ObjectAdapterFactory)
at java.lang.Object.wait(Object.java:502)
at IceInternal.ObjectAdapterFactory.waitForShutdown(ObjectAdapterFactory.java:63)
- locked <0x00000000f19c4800> (a IceInternal.ObjectAdapterFactory)
at Ice.CommunicatorI.waitForShutdown(CommunicatorI.java:32)
at ome.services.blitz.Entry.start(Entry.java:202)
at ome.services.blitz.Entry.main(Entry.java:146)
"VM Thread" os_prio=0 tid=0x00007f79c4108000 nid=0xa9e runnable
"GC task thread#0 (ParallelGC)" os_prio=0 tid=0x00007f79c401e800 nid=0xa98 runnable
"GC task thread#1 (ParallelGC)" os_prio=0 tid=0x00007f79c4020000 nid=0xa9b runnable
"VM Periodic Task Thread" os_prio=0 tid=0x00007f79c4157000 nid=0xab1 waiting on condition
JNI global references: 299
bin/omero config set -- omero.jvmcfg.append -Dcom.sun.jndi.ldap.connect.pool.timeout=500
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