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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 16:58:20 GMT
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

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