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Posted to user@spark.apache.org by jane thorpe <ja...@aol.com.INVALID> on 2020/04/13 07:31:36 UTC
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 <ja...@aol.com.INVALID>
To: mich.talebzadeh <mi...@gmail.com>; liruijing09 <li...@gmail.com>; user <us...@spark.apache.org>
CC: user <us...@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 <mi...@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 http://talebzadehmich.wordpress.com
Disclaimer: Use it at your own risk. Any and all responsibility for any loss, damage or destructionof 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 suchloss, damage or destruction.
On Fri, 10 Apr 2020 at 17:37, Ruijing Li <li...@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
Re: Spark hangs while reading from jdbc - does nothing Removing Guess
work from trouble shooting
Posted by Ruijing Li <li...@gmail.com>.
Wanted to update everyone on this, thanks for all the responses. I was able
to solve this issue after doing a jstack dump - I found out this was the
cause
https://github.com/scala/bug/issues/10436
Lesson learned - I’ll use a safer json parser like json4s, seems like that
one should be able to be thread-safe hopefully.
On Fri, Apr 24, 2020 at 4:34 AM Waleed Fateem <wa...@gmail.com>
wrote:
> Are you running this in local mode? If not, are you even sure that the
> hanging is occurring on the driver's side?
>
> Did you check the Spark UI to see if there is a straggler task or not? If
> you do have a straggler/hanging task, and in case this is not an
> application running in local mode then you need to get the Java thread dump
> of the executor's JVM process. Once you do, you'll want to review the "Executor
> task launch worker for task XYZ" thread, whee XYZ is some integer value
> representing the task ID that was launched on that executor. In case you're running
> this is local mode that thread would be located in the same Java thread
> dump that you have already collected.
>
>
> On Tue, Apr 21, 2020 at 9:51 PM Ruijing Li <li...@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.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 <li...@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 <li...@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 <li...@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 <we...@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 <ka...@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 <li...@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
>>>>>>> <ja...@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 <ja...@aol.com.INVALID>
>>>>>>> > >>> To: janethorpe1 <ja...@aol.com>; mich.talebzadeh <
>>>>>>> > >>> mich.talebzadeh@gmail.com>; liruijing09 <li...@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 <ja...@aol.com.INVALID>
>>>>>>> > >>> To: mich.talebzadeh <mi...@gmail.com>; liruijing09 <
>>>>>>> > >>> liruijing09@gmail.com>; user <us...@spark.apache.org>
>>>>>>> > >>> CC: user <us...@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
>>
> --
Cheers,
Ruijing Li
Re: Spark hangs while reading from jdbc - does nothing Removing Guess
work from trouble shooting
Posted by Waleed Fateem <wa...@gmail.com>.
Are you running this in local mode? If not, are you even sure that the
hanging is occurring on the driver's side?
Did you check the Spark UI to see if there is a straggler task or not? If
you do have a straggler/hanging task, and in case this is not an
application running in local mode then you need to get the Java thread dump
of the executor's JVM process. Once you do, you'll want to review the "Executor
task launch worker for task XYZ" thread, whee XYZ is some integer value
representing the task ID that was launched on that executor. In case
you're running
this is local mode that thread would be located in the same Java thread
dump that you have already collected.
On Tue, Apr 21, 2020 at 9:51 PM Ruijing Li <li...@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 <ka...@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 <li...@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 <li...@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 <li...@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 <we...@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 <ka...@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 <li...@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
>>>>>> <ja...@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 <ja...@aol.com.INVALID>
>>>>>> > >>> To: janethorpe1 <ja...@aol.com>; mich.talebzadeh <
>>>>>> > >>> mich.talebzadeh@gmail.com>; liruijing09 <li...@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 <ja...@aol.com.INVALID>
>>>>>> > >>> To: mich.talebzadeh <mi...@gmail.com>; liruijing09 <
>>>>>> > >>> liruijing09@gmail.com>; user <us...@spark.apache.org>
>>>>>> > >>> CC: user <us...@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 <li...@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
>
Re: Spark hangs while reading from jdbc - does nothing Removing Guess
work from trouble shooting
Posted by ZHANG Wei <we...@outlook.com>.
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 <ka...@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 <li...@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 <ka...@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 <li...@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 <li...@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 <li...@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 <we...@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 <ka...@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 <li...@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 <ga...@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 <ja...@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
> >>> janethorpe1@aol.com<ma...@aol.com>
> >>>
> >>>
> >>> -----Original Message-----
> >>> From: jane thorpe <ja...@aol.com.INVALID>
> >>> To: janethorpe1 <ja...@aol.com>>; mich.talebzadeh <
> >>> mich.talebzadeh@gmail.com<ma...@gmail.com>>; liruijing09 <li...@gmail.com>>; user <
> >>> user@spark.apache.org<ma...@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
> >>> janethorpe1@aol.com<ma...@aol.com>
> >>>
> >>>
> >>> -----Original Message-----
> >>> From: jane thorpe <ja...@aol.com.INVALID>
> >>> To: mich.talebzadeh <mi...@gmail.com>>; liruijing09 <
> >>> liruijing09@gmail.com<ma...@gmail.com>>; user <us...@spark.apache.org>>
> >>> CC: user <us...@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 <mi...@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 <li...@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-unsubscribe@spark.apache.org
Re: Spark hangs while reading from jdbc - does nothing Removing Guess
work from trouble shooting
Posted by Jungtaek Lim <ka...@gmail.com>.
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 <li...@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 <ka...@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 <li...@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 <li...@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 <li...@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 <we...@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 <ka...@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 <li...@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
>>>>>> <ja...@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 <ja...@aol.com.INVALID>
>>>>>> > >>> To: janethorpe1 <ja...@aol.com>; mich.talebzadeh <
>>>>>> > >>> mich.talebzadeh@gmail.com>; liruijing09 <li...@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 <ja...@aol.com.INVALID>
>>>>>> > >>> To: mich.talebzadeh <mi...@gmail.com>; liruijing09 <
>>>>>> > >>> liruijing09@gmail.com>; user <us...@spark.apache.org>
>>>>>> > >>> CC: user <us...@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 <li...@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
>
Re: Spark hangs while reading from jdbc - does nothing Removing Guess
work from trouble shooting
Posted by Ruijing Li <li...@gmail.com>.
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 <ka...@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 <li...@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 <li...@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 <li...@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 <we...@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 <ka...@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 <li...@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
>>>>> <ja...@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 <ja...@aol.com.INVALID>
>>>>> > >>> To: janethorpe1 <ja...@aol.com>; mich.talebzadeh <
>>>>> > >>> mich.talebzadeh@gmail.com>; liruijing09 <li...@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 <ja...@aol.com.INVALID>
>>>>> > >>> To: mich.talebzadeh <mi...@gmail.com>; liruijing09 <
>>>>> > >>> liruijing09@gmail.com>; user <us...@spark.apache.org>
>>>>> > >>> CC: user <us...@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 <li...@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
Re: Spark hangs while reading from jdbc - does nothing Removing Guess
work from trouble shooting
Posted by Jungtaek Lim <ka...@gmail.com>.
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 <li...@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 <li...@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 <li...@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 <we...@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 <ka...@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 <li...@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
>>>> <ja...@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 <ja...@aol.com.INVALID>
>>>> > >>> To: janethorpe1 <ja...@aol.com>; mich.talebzadeh <
>>>> > >>> mich.talebzadeh@gmail.com>; liruijing09 <li...@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 <ja...@aol.com.INVALID>
>>>> > >>> To: mich.talebzadeh <mi...@gmail.com>; liruijing09 <
>>>> > >>> liruijing09@gmail.com>; user <us...@spark.apache.org>
>>>> > >>> CC: user <us...@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 <li...@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
>
Re: Spark hangs while reading from jdbc - does nothing Removing Guess
work from trouble shooting
Posted by Ruijing Li <li...@gmail.com>.
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 <li...@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 <li...@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 <we...@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 <ka...@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 <li...@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
>>> <ja...@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 <ja...@aol.com.INVALID>
>>> > >>> To: janethorpe1 <ja...@aol.com>; mich.talebzadeh <
>>> > >>> mich.talebzadeh@gmail.com>; liruijing09 <li...@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 <ja...@aol.com.INVALID>
>>> > >>> To: mich.talebzadeh <mi...@gmail.com>; liruijing09 <
>>> > >>> liruijing09@gmail.com>; user <us...@spark.apache.org>
>>> > >>> CC: user <us...@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 <li...@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
Re: Spark hangs while reading from jdbc - does nothing Removing Guess
work from trouble shooting
Posted by Ruijing Li <li...@gmail.com>.
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 <li...@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 <we...@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 <ka...@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 <li...@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
>> <ja...@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 <ja...@aol.com.INVALID>
>> > >>> To: janethorpe1 <ja...@aol.com>; mich.talebzadeh <
>> > >>> mich.talebzadeh@gmail.com>; liruijing09 <li...@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 <ja...@aol.com.INVALID>
>> > >>> To: mich.talebzadeh <mi...@gmail.com>; liruijing09 <
>> > >>> liruijing09@gmail.com>; user <us...@spark.apache.org>
>> > >>> CC: user <us...@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 <li...@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
Re: Spark hangs while reading from jdbc - does nothing Removing Guess
work from trouble shooting
Posted by Ruijing Li <li...@gmail.com>.
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 <we...@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 <ka...@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 <li...@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
> <ja...@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 <ja...@aol.com.INVALID>
> > >>> To: janethorpe1 <ja...@aol.com>; mich.talebzadeh <
> > >>> mich.talebzadeh@gmail.com>; liruijing09 <li...@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 <ja...@aol.com.INVALID>
> > >>> To: mich.talebzadeh <mi...@gmail.com>; liruijing09 <
> > >>> liruijing09@gmail.com>; user <us...@spark.apache.org>
> > >>> CC: user <us...@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 <li...@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
Re: Spark hangs while reading from jdbc - does nothing Removing
Guess work from trouble shooting
Posted by ZHANG Wei <we...@outlook.com>.
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 <ka...@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 <li...@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 <ga...@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 <ja...@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 <ja...@aol.com.INVALID>
> >>> To: janethorpe1 <ja...@aol.com>; mich.talebzadeh <
> >>> mich.talebzadeh@gmail.com>; liruijing09 <li...@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 <ja...@aol.com.INVALID>
> >>> To: mich.talebzadeh <mi...@gmail.com>; liruijing09 <
> >>> liruijing09@gmail.com>; user <us...@spark.apache.org>
> >>> CC: user <us...@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 <mi...@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 <li...@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
> >
---------------------------------------------------------------------
To unsubscribe e-mail: user-unsubscribe@spark.apache.org
Re: Spark hangs while reading from jdbc - does nothing Removing Guess
work from trouble shooting
Posted by Jungtaek Lim <ka...@gmail.com>.
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 <li...@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 <ga...@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 <ja...@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 <ja...@aol.com.INVALID>
>>> To: janethorpe1 <ja...@aol.com>; mich.talebzadeh <
>>> mich.talebzadeh@gmail.com>; liruijing09 <li...@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 <ja...@aol.com.INVALID>
>>> To: mich.talebzadeh <mi...@gmail.com>; liruijing09 <
>>> liruijing09@gmail.com>; user <us...@spark.apache.org>
>>> CC: user <us...@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 <mi...@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 <li...@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
>
Re: Spark hangs while reading from jdbc - does nothing Removing Guess
work from trouble shooting
Posted by Ruijing Li <li...@gmail.com>.
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 <ga...@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 <ja...@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 <ja...@aol.com.INVALID>
>> To: janethorpe1 <ja...@aol.com>; mich.talebzadeh <
>> mich.talebzadeh@gmail.com>; liruijing09 <li...@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 <ja...@aol.com.INVALID>
>> To: mich.talebzadeh <mi...@gmail.com>; liruijing09 <
>> liruijing09@gmail.com>; user <us...@spark.apache.org>
>> CC: user <us...@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 <mi...@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 <li...@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
Re: Spark hangs while reading from jdbc - does nothing Removing Guess
work from trouble shooting
Posted by Gabor Somogyi <ga...@gmail.com>.
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 <ja...@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 <ja...@aol.com.INVALID>
> To: janethorpe1 <ja...@aol.com>; mich.talebzadeh <
> mich.talebzadeh@gmail.com>; liruijing09 <li...@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 <ja...@aol.com.INVALID>
> To: mich.talebzadeh <mi...@gmail.com>; liruijing09 <
> liruijing09@gmail.com>; user <us...@spark.apache.org>
> CC: user <us...@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 <mi...@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 <li...@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
>
>
Re: Spark hangs while reading from jdbc - does nothing Removing
Guess work from trouble shooting
Posted by jane thorpe <ja...@aol.com.INVALID>.
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 <ja...@aol.com.INVALID>
To: janethorpe1 <ja...@aol.com>; mich.talebzadeh <mi...@gmail.com>; liruijing09 <li...@gmail.com>; user <us...@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 <ja...@aol.com.INVALID>
To: mich.talebzadeh <mi...@gmail.com>; liruijing09 <li...@gmail.com>; user <us...@spark.apache.org>
CC: user <us...@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 <mi...@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 http://talebzadehmich.wordpress.com
Disclaimer: Use it at your own risk. Any and all responsibility for any loss, damage or destructionof 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 suchloss, damage or destruction.
On Fri, 10 Apr 2020 at 17:37, Ruijing Li <li...@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