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From Ruijing Li <liruijin...@gmail.com>
Subject Re: Spark hangs while reading from jdbc - does nothing Removing Guess work from trouble shooting
Date Wed, 22 Apr 2020 02:50:34 GMT
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.opensource@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 <liruijing09@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 <liruijing09@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 <liruijing09@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
>>>>
>>>> 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 <wezhang@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.opensource@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 <liruijing09@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.somogyi@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
>>>>> <janethorpe1@aol.com.invalid>
>>>>> > >> wrote:
>>>>> > >>
>>>>> > >>> Here a is another tool I use Logic Analyser  7:55
>>>>> > >>> https://youtu.be/LnzuMJLZRdU
>>>>> > >>>
>>>>> > >>> you could take some suggestions for improving performance
>>>>> queries.
>>>>> > >>>
>>>>> https://dzone.com/articles/why-you-should-not-use-select-in-sql-query-1
>>>>> > >>>
>>>>> > >>>
>>>>> > >>> Jane thorpe
>>>>> > >>> janethorpe1@aol.com
>>>>> > >>>
>>>>> > >>>
>>>>> > >>> -----Original Message-----
>>>>> > >>> From: jane thorpe <janethorpe1@aol.com.INVALID>
>>>>> > >>> To: janethorpe1 <janethorpe1@aol.com>; mich.talebzadeh
<
>>>>> > >>> mich.talebzadeh@gmail.com>; liruijing09 <liruijing09@gmail.com>;
>>>>> user <
>>>>> > >>> 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
>>>>> > >>>
>>>>> > >>>
>>>>> > >>> "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
>>>>> > >>> janethorpe1@aol.com
>>>>> > >>>
>>>>> > >>>
>>>>> > >>> -----Original Message-----
>>>>> > >>> From: jane thorpe <janethorpe1@aol.com.INVALID>
>>>>> > >>> To: mich.talebzadeh <mich.talebzadeh@gmail.com>;
liruijing09 <
>>>>> > >>> liruijing09@gmail.com>; user <user@spark.apache.org>
>>>>> > >>> CC: user <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.talebzadeh@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$statname sn
>>>>> > >>>                 where ss.sid = a.sid and
>>>>> > >>>                         sn.statistic# = ss.statistic#
and
>>>>> > >>>                         -- sn.name in ('session pga
memory')
>>>>> > >>>                         sn.name in ('session pga
>>>>> memory','session uga
>>>>> > >>> memory')
>>>>> > >>>           ) AS total_memory
>>>>> > >>>         , (b.block_gets + b.consistent_gets) TotGets
>>>>> > >>>         , b.physical_reads phyRds
>>>>> > >>>         , decode(a.status, 'ACTIVE', 'Y','INACTIVE',
'N') STATUS
>>>>> > >>>         , CASE WHEN a.sid in (select sid from v$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://www.linkedin.com/profile/view?id=AAEAAAAWh2gBxianrbJd6zP6AcPCCdOABUrV8Pw
>>>>> >*
>>>>> > >>>
>>>>> > >>> http://talebzadehmich.wordpress.com
>>>>> > >>>
>>>>> > >>> *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 <liruijing09@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

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