That's not dead locked. They are just trying acqure the same Monitor lock, and
there are 3 threads. One acquired, and others are waiting for the lock being
released. It's a common senario. You have to check the monitor lock object from
callstack source code. There should be some operations after holding the lock,
and a cause to wait for something, which could be a hint.
> After refreshing a couple of times, I notice the lock is being swapped
> between these 3. The other 2 will be blocked by whoever gets this lock, in a
> cycle of 160 has lock -> 161 -> 159 -> 160
But back to your case, those are normal SparkUI HTTP service behaviors:
> - SparkUI-160- acceptor-id-ServerConnector@id(HTTP/1.1) | RUNNABLE | Monitor
> - SparkUI-161-acceptor-id-ServerConnector@id(HTTP/1.1) | BLOCKED | Blocked by
> Thread(Some(160)) Lock
> - SparkUI-159-acceptor-id-ServerConnector@id(HTTP/1.1) | BLOCKED | Blocked
> by Thread(Some(160)) Lock
Since I have no your core dump, just use my local environment dump as a demo,
and comment in line:
29
SparkUI-29-acceptor-0@105d657c-ServerConnector@1e9a8907{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
RUNNABLE Monitor(java.lang.Object@1195548344})
sun.nio.ch.ServerSocketChannelImpl.accept0(Native Method)
^^^^^^^^^^^^^^ The native accept0()
can be understanded as Linux accept() [1], this can block.
sun.nio.ch.ServerSocketChannelImpl.accept(ServerSocketChannelImpl.java:422)
sun.nio.ch.ServerSocketChannelImpl.accept(ServerSocketChannelImpl.java:250)
=> holding Monitor(java.lang.Object@1195548344})
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ I can find
`synchronized(this.lock)` in this source localtion context
org.spark_project.jetty.server.ServerConnector.accept(ServerConnector.java:397)
org.spark_project.jetty.server.AbstractConnector$Acceptor.run(AbstractConnector.java:601)
org.spark_project.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:671)
org.spark_project.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:589)
java.lang.Thread.run(Thread.java:748)
So, you might have to find another clues, just let those "SparkUI-" go, or
check the log to see if someone is working on something.
Just my 2 cents.
--
Cheers,
-z
[1] -- https://linux.die.net/man/2/accept
________________________________________
From: Jungtaek Lim <kabhwan.opensou...@gmail.com>
Sent: Wednesday, April 22, 2020 11:21
To: Ruijing Li
Cc: Gabor Somogyi; Mich Talebzadeh; ZHANG Wei; user
Subject: Re: Spark hangs while reading from jdbc - does nothing Removing Guess
work from trouble shooting
No, that's not a thing to apologize for. It's just your call - less context
would bring less reaction and interest.
On Wed, Apr 22, 2020 at 11:50 AM Ruijing Li
<liruijin...@gmail.com<mailto:liruijin...@gmail.com>> wrote:
I apologize, but I cannot share it, even if it is just typical spark libraries.
I definitely understand that limits debugging help, but wanted to understand if
anyone has encountered a similar issue.
On Tue, Apr 21, 2020 at 7:12 PM Jungtaek Lim
<kabhwan.opensou...@gmail.com<mailto:kabhwan.opensou...@gmail.com>> wrote:
If there's no third party libraries in the dump then why not share the thread
dump? (I mean, the output of jstack)
stack trace would be more helpful to find which thing acquired lock and which
other things are waiting for acquiring lock, if we suspect deadlock.
On Wed, Apr 22, 2020 at 2:38 AM Ruijing Li
<liruijin...@gmail.com<mailto:liruijin...@gmail.com>> wrote:
After refreshing a couple of times, I notice the lock is being swapped between
these 3. The other 2 will be blocked by whoever gets this lock, in a cycle of
160 has lock -> 161 -> 159 -> 160
On Tue, Apr 21, 2020 at 10:33 AM Ruijing Li
<liruijin...@gmail.com<mailto:liruijin...@gmail.com>> wrote:
In thread dump, I do see this
- SparkUI-160- acceptor-id-ServerConnector@id(HTTP/1.1) | RUNNABLE | Monitor
- SparkUI-161-acceptor-id-ServerConnector@id(HTTP/1.1) | BLOCKED | Blocked by
Thread(Some(160)) Lock
- SparkUI-159-acceptor-id-ServerConnector@id(HTTP/1.1) | BLOCKED | Blocked by
Thread(Some(160)) Lock
Could the fact that 160 has the monitor but is not running be causing a
deadlock preventing the job from finishing?
I do see my Finalizer and main method are waiting. I don’t see any other
threads from 3rd party libraries or my code in the dump. I do see spark context
cleaner has timed waiting.
Thanks
On Tue, Apr 21, 2020 at 9:58 AM Ruijing Li
<liruijin...@gmail.com<mailto:liruijin...@gmail.com>> wrote:
Strangely enough I found an old issue that is the exact same issue as mine
https://issues.apache.org/jira/plugins/servlet/mobile#issue/SPARK-18343<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fissues.apache.org%2Fjira%2Fplugins%2Fservlet%2Fmobile%23issue%2FSPARK-18343&data=02%7C01%7C%7Caffcf245a3b94e07c40408d7e66c566a%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637231225280613776&sdata=NdPXb2Qdw6S5Tuqs1eRFfyHQoppi8JKI%2F2hTED%2BxOy8%3D&reserved=0>
However I’m using spark 2.4.4 so the issue should have been solved by now.
Like the user in the jira issue I am using mesos, but I am reading from oracle
instead of writing to Cassandra and S3.
On Thu, Apr 16, 2020 at 1:54 AM ZHANG Wei
<wezh...@outlook.com<mailto:wezh...@outlook.com>> wrote:
The Thread dump result table of Spark UI can provide some clues to find out
thread locks issue, such as:
Thread ID | Thread Name | Thread State | Thread Locks
13 | NonBlockingInputStreamThread | WAITING | Blocked by Thread
Some(48) Lock(jline.internal.NonBlockingInputStream@103008951})
48 | Thread-16 | RUNNABLE |
Monitor(jline.internal.NonBlockingInputStream@103008951})
And echo thread row can show the call stacks after being clicked, then you can
check the root cause of holding locks like this(Thread 48 of above):
org.fusesource.jansi.internal.Kernel32.ReadConsoleInputW(Native Method)
org.fusesource.jansi.internal.Kernel32.readConsoleInputHelper(Kernel32.java:811)
org.fusesource.jansi.internal.Kernel32.readConsoleKeyInput(Kernel32.java:842)
org.fusesource.jansi.internal.WindowsSupport.readConsoleInput(WindowsSupport.java:97)
jline.WindowsTerminal.readConsoleInput(WindowsTerminal.java:222)
<snip...>
Hope it can help you.
--
Cheers,
-z
On Thu, 16 Apr 2020 16:36:42 +0900
Jungtaek Lim
<kabhwan.opensou...@gmail.com<mailto:kabhwan.opensou...@gmail.com>> wrote:
> Do thread dump continuously, per specific period (like 1s) and see the
> change of stack / lock for each thread. (This is not easy to be done in UI
> so maybe doing manually would be the only option. Not sure Spark UI will
> provide the same, haven't used at all.)
>
> It will tell which thread is being blocked (even it's shown as running) and
> which point to look at.
>
> On Thu, Apr 16, 2020 at 4:29 PM Ruijing Li
> <liruijin...@gmail.com<mailto:liruijin...@gmail.com>> wrote:
>
> > Once I do. thread dump, what should I be looking for to tell where it is
> > hanging? Seeing a lot of timed_waiting and waiting on driver. Driver is
> > also being blocked by spark UI. If there are no tasks, is there a point to
> > do thread dump of executors?
> >
> > On Tue, Apr 14, 2020 at 4:49 AM Gabor Somogyi
> > <gabor.g.somo...@gmail.com<mailto:gabor.g.somo...@gmail.com>>
> > wrote:
> >
> >> The simplest way is to do thread dump which doesn't require any fancy
> >> tool (it's available on Spark UI).
> >> Without thread dump it's hard to say anything...
> >>
> >>
> >> On Tue, Apr 14, 2020 at 11:32 AM jane thorpe <janethor...@aol.com.invalid>
> >> wrote:
> >>
> >>> Here a is another tool I use Logic Analyser 7:55
> >>> https://youtu.be/LnzuMJLZRdU<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fyoutu.be%2FLnzuMJLZRdU&data=02%7C01%7C%7Caffcf245a3b94e07c40408d7e66c566a%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637231225280613776&sdata=7EiRropY7J%2Fyl7xmA6tk2H6hHDmw%2B3OMZaAW46vK9SY%3D&reserved=0>
> >>>
> >>> you could take some suggestions for improving performance queries.
> >>> https://dzone.com/articles/why-you-should-not-use-select-in-sql-query-1<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdzone.com%2Farticles%2Fwhy-you-should-not-use-select-in-sql-query-1&data=02%7C01%7C%7Caffcf245a3b94e07c40408d7e66c566a%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637231225280623770&sdata=NE1d2MrZEQi6rpRZcBaX7jAEF71CEPejWsuhEs6%2FYrg%3D&reserved=0>
> >>>
> >>>
> >>> Jane thorpe
> >>> janethor...@aol.com<mailto:janethor...@aol.com>
> >>>
> >>>
> >>> -----Original Message-----
> >>> From: jane thorpe <janethor...@aol.com.INVALID>
> >>> To: janethorpe1 <janethor...@aol.com<mailto:janethor...@aol.com>>;
> >>> mich.talebzadeh <
> >>> mich.talebza...@gmail.com<mailto:mich.talebza...@gmail.com>>; liruijing09
> >>> <liruijin...@gmail.com<mailto:liruijin...@gmail.com>>; user <
> >>> user@spark.apache.org<mailto:user@spark.apache.org>>
> >>> Sent: Mon, 13 Apr 2020 8:32
> >>> Subject: Re: Spark hangs while reading from jdbc - does nothing Removing
> >>> Guess work from trouble shooting
> >>>
> >>>
> >>>
> >>> This tool may be useful for you to trouble shoot your problems away.
> >>>
> >>>
> >>> https://www.javacodegeeks.com/2020/04/simplifying-apm-remove-the-guesswork-from-troubleshooting.html<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.javacodegeeks.com%2F2020%2F04%2Fsimplifying-apm-remove-the-guesswork-from-troubleshooting.html&data=02%7C01%7C%7Caffcf245a3b94e07c40408d7e66c566a%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637231225280623770&sdata=LB3uy3fnFruTTsJx%2B7kertajJEknhklgCnLOkLw%2FnAI%3D&reserved=0>
> >>>
> >>>
> >>> "APM tools typically use a waterfall-type view to show the blocking
> >>> time of different components cascading through the control flow within an
> >>> application.
> >>> These types of visualizations are useful, and AppOptics has them, but
> >>> they can be difficult to understand for those of us without a PhD."
> >>>
> >>> Especially helpful if you want to understand through visualisation and
> >>> you do not have a phD.
> >>>
> >>>
> >>> Jane thorpe
> >>> janethor...@aol.com<mailto:janethor...@aol.com>
> >>>
> >>>
> >>> -----Original Message-----
> >>> From: jane thorpe <janethor...@aol.com.INVALID>
> >>> To: mich.talebzadeh
> >>> <mich.talebza...@gmail.com<mailto:mich.talebza...@gmail.com>>;
> >>> liruijing09 <
> >>> liruijin...@gmail.com<mailto:liruijin...@gmail.com>>; user
> >>> <user@spark.apache.org<mailto:user@spark.apache.org>>
> >>> CC: user <user@spark.apache.org<mailto:user@spark.apache.org>>
> >>> Sent: Sun, 12 Apr 2020 4:35
> >>> Subject: Re: Spark hangs while reading from jdbc - does nothing
> >>>
> >>> You seem to be implying the error is intermittent.
> >>> You seem to be implying data is being ingested via JDBC. So the
> >>> connection has proven itself to be working unless no data is arriving from
> >>> the JDBC channel at all. If no data is arriving then one could say it
> >>> could be the JDBC.
> >>> If the error is intermittent then it is likely a resource involved in
> >>> processing is filling to capacity.
> >>> Try reducing the data ingestion volume and see if that completes, then
> >>> increase the data ingested incrementally.
> >>> I assume you have run the job on small amount of data so you have
> >>> completed your prototype stage successfully.
> >>>
> >>> ------------------------------
> >>> On Saturday, 11 April 2020 Mich Talebzadeh
> >>> <mich.talebza...@gmail.com<mailto:mich.talebza...@gmail.com>>
> >>> wrote:
> >>> Hi,
> >>>
> >>> Have you checked your JDBC connections from Spark to Oracle. What is
> >>> Oracle saying? Is it doing anything or hanging?
> >>>
> >>> set pagesize 9999
> >>> set linesize 140
> >>> set heading off
> >>> select SUBSTR(name,1,8) || ' sessions as on '||TO_CHAR(CURRENT_DATE,
> >>> 'MON DD YYYY HH:MI AM') from v$database;
> >>> set heading on
> >>> column spid heading "OS PID" format a6
> >>> column process format a13 heading "Client ProcID"
> >>> column username format a15
> >>> column sid format 999
> >>> column serial# format 99999
> >>> column STATUS format a3 HEADING 'ACT'
> >>> column last format 9,999.99
> >>> column TotGets format 999,999,999,999 HEADING 'Logical I/O'
> >>> column phyRds format 999,999,999 HEADING 'Physical I/O'
> >>> column total_memory format 999,999,999 HEADING 'MEM/KB'
> >>> --
> >>> SELECT
> >>> substr(a.username,1,15) "LOGIN"
> >>> , substr(a.sid,1,5) || ','||substr(a.serial#,1,5) AS
> >>> "SID/serial#"
> >>> , TO_CHAR(a.logon_time, 'DD/MM HH:MI') "LOGGED IN SINCE"
> >>> , substr(a.machine,1,10) HOST
> >>> , substr(p.username,1,8)||'/'||substr(p.spid,1,5) "OS PID"
> >>> , substr(a.osuser,1,8)||'/'||substr(a.process,1,5) "Client PID"
> >>> , substr(a.program,1,15) PROGRAM
> >>> --,ROUND((CURRENT_DATE-a.logon_time)*24) AS "Logged/Hours"
> >>> , (
> >>> select round(sum(ss.value)/1024) from v$sesstat ss,
> >>> v$statname sn
> >>> where ss.sid = a.sid and
> >>> sn.statistic# = ss.statistic# and
> >>> --
> >>> sn.name<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsn.name%2F&data=02%7C01%7C%7Caffcf245a3b94e07c40408d7e66c566a%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637231225280633763&sdata=cVdKW1uCKIITq9TyF%2FTJHYCX3hJflpHLVL9h57i2wvw%3D&reserved=0>
> >>> in ('session pga memory')
> >>>
> >>> sn.name<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsn.name%2F&data=02%7C01%7C%7Caffcf245a3b94e07c40408d7e66c566a%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637231225280633763&sdata=cVdKW1uCKIITq9TyF%2FTJHYCX3hJflpHLVL9h57i2wvw%3D&reserved=0>
> >>> in ('session pga memory','session uga
> >>> memory')
> >>> ) AS total_memory
> >>> , (b.block_gets + b.consistent_gets) TotGets
> >>> , b.physical_reads phyRds
> >>> , decode(a.status, 'ACTIVE', 'Y','INACTIVE', 'N') STATUS
> >>> , CASE WHEN a.sid in (select sid from v$mystat where rownum = 1)
> >>> THEN '<-- YOU' ELSE ' ' END "INFO"
> >>> FROM
> >>> v$process p
> >>> ,v$session a
> >>> ,v$sess_io b
> >>> WHERE
> >>> a.paddr = p.addr
> >>> AND p.background IS NULL
> >>> --AND a.sid NOT IN (select sid from v$mystat where rownum = 1)
> >>> AND a.sid = b.sid
> >>> AND a.username is not null
> >>> --AND (a.last_call_et < 3600 or a.status = 'ACTIVE')
> >>> --AND CURRENT_DATE - logon_time > 0
> >>> --AND a.sid NOT IN ( select sid from v$mystat where rownum=1) --
> >>> exclude me
> >>> --AND (b.block_gets + b.consistent_gets) > 0
> >>> ORDER BY a.username;
> >>> exit
> >>>
> >>> HTH
> >>>
> >>> Dr Mich Talebzadeh
> >>>
> >>> LinkedIn *
> >>> https://www.linkedin.com/profile/view?id=AAEAAAAWh2gBxianrbJd6zP6AcPCCdOABUrV8Pw<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linkedin.com%2Fprofile%2Fview%3Fid%3DAAEAAAAWh2gBxianrbJd6zP6AcPCCdOABUrV8Pw&data=02%7C01%7C%7Caffcf245a3b94e07c40408d7e66c566a%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637231225280633763&sdata=VS0zVNx0OVroU%2BegWJsQ8%2FwhXRFPwJSud43ATNCXFMM%3D&reserved=0>
> >>> <https://www.linkedin.com/profile/view?id=AAEAAAAWh2gBxianrbJd6zP6AcPCCdOABUrV8Pw<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linkedin.com%2Fprofile%2Fview%3Fid%3DAAEAAAAWh2gBxianrbJd6zP6AcPCCdOABUrV8Pw&data=02%7C01%7C%7Caffcf245a3b94e07c40408d7e66c566a%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637231225280643758&sdata=j9RDfn%2F3gppIvYlTfddih41ovBz12mQTJ1Jly2vwe9c%3D&reserved=0>>*
> >>>
> >>> http://talebzadehmich.wordpress.com<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftalebzadehmich.wordpress.com%2F&data=02%7C01%7C%7Caffcf245a3b94e07c40408d7e66c566a%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637231225280643758&sdata=OWyqEmpgy0x1gKGVntbEkycLwL6YjQXGCf3tNOcJIMA%3D&reserved=0>
> >>>
> >>> *Disclaimer:* Use it at your own risk. Any and all responsibility for
> >>> any loss, damage or destruction of data or any other property which may
> >>> arise from relying on this email's technical content is explicitly
> >>> disclaimed. The author will in no case be liable for any monetary damages
> >>> arising from such loss, damage or destruction.
> >>>
> >>>
> >>>
> >>> On Fri, 10 Apr 2020 at 17:37, Ruijing Li
> >>> <liruijin...@gmail.com<mailto:liruijin...@gmail.com>> wrote:
> >>>
> >>> Hi all,
> >>>
> >>> I am on spark 2.4.4 and using scala 2.11.12, and running cluster mode on
> >>> mesos. I am ingesting from an oracle database using spark.read.jdbc. I am
> >>> seeing a strange issue where spark just hangs and does nothing, not
> >>> starting any new tasks. Normally this job finishes in 30 stages but
> >>> sometimes it stops at 29 completed stages and doesn’t start the last
> >>> stage.
> >>> The spark job is idling and there is no pending or active task. What could
> >>> be the problem? Thanks.
> >>> --
> >>> Cheers,
> >>> Ruijing Li
> >>>
> >>> --
> > Cheers,
> > Ruijing Li
> >
--
Cheers,
Ruijing Li
--
Cheers,
Ruijing Li
--
Cheers,
Ruijing Li
--
Cheers,
Ruijing Li
---------------------------------------------------------------------
To unsubscribe e-mail: user-unsubscr...@spark.apache.org
