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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 Tue, 21 Apr 2020 17:33:24 GMT
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

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