I apologize, but I cannot share it, even if it is just typical spark libraries. I definitely understand that limits debugging help, but wanted to understand if anyone has encountered a similar issue.
On Tue, Apr 21, 2020 at 7:12 PM Jungtaek Lim <kabhwan.opensou...@gmail.com> wrote: > If there's no third party libraries in the dump then why not share the > thread dump? (I mean, the output of jstack) > > stack trace would be more helpful to find which thing acquired lock and > which other things are waiting for acquiring lock, if we suspect deadlock. > > On Wed, Apr 22, 2020 at 2:38 AM Ruijing Li <liruijin...@gmail.com> wrote: > >> After refreshing a couple of times, I notice the lock is being swapped >> between these 3. The other 2 will be blocked by whoever gets this lock, in >> a cycle of 160 has lock -> 161 -> 159 -> 160 >> >> On Tue, Apr 21, 2020 at 10:33 AM Ruijing Li <liruijin...@gmail.com> >> wrote: >> >>> In thread dump, I do see this >>> - SparkUI-160- acceptor-id-ServerConnector@id(HTTP/1.1) | RUNNABLE | >>> Monitor >>> - SparkUI-161-acceptor-id-ServerConnector@id(HTTP/1.1) | BLOCKED | >>> Blocked by Thread(Some(160)) Lock >>> - SparkUI-159-acceptor-id-ServerConnector@id(HTTP/1.1) | BLOCKED | >>> Blocked by Thread(Some(160)) Lock >>> >>> Could the fact that 160 has the monitor but is not running be causing a >>> deadlock preventing the job from finishing? >>> >>> I do see my Finalizer and main method are waiting. I don’t see any other >>> threads from 3rd party libraries or my code in the dump. I do see spark >>> context cleaner has timed waiting. >>> >>> Thanks >>> >>> >>> On Tue, Apr 21, 2020 at 9:58 AM Ruijing Li <liruijin...@gmail.com> >>> 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 <wezh...@outlook.com> wrote: >>>> >>>>> The Thread dump result table of Spark UI can provide some clues to >>>>> find out thread locks issue, such as: >>>>> >>>>> Thread ID | Thread Name | Thread State | Thread >>>>> Locks >>>>> 13 | NonBlockingInputStreamThread | WAITING | Blocked by >>>>> Thread Some(48) Lock(jline.internal.NonBlockingInputStream@103008951}) >>>>> 48 | Thread-16 | RUNNABLE | >>>>> Monitor(jline.internal.NonBlockingInputStream@103008951}) >>>>> >>>>> And echo thread row can show the call stacks after being clicked, then >>>>> you can check the root cause of holding locks like this(Thread 48 of >>>>> above): >>>>> >>>>> org.fusesource.jansi.internal.Kernel32.ReadConsoleInputW(Native >>>>> Method) >>>>> >>>>> org.fusesource.jansi.internal.Kernel32.readConsoleInputHelper(Kernel32.java:811) >>>>> >>>>> org.fusesource.jansi.internal.Kernel32.readConsoleKeyInput(Kernel32.java:842) >>>>> >>>>> org.fusesource.jansi.internal.WindowsSupport.readConsoleInput(WindowsSupport.java:97) >>>>> jline.WindowsTerminal.readConsoleInput(WindowsTerminal.java:222) >>>>> <snip...> >>>>> >>>>> Hope it can help you. >>>>> >>>>> -- >>>>> Cheers, >>>>> -z >>>>> >>>>> On Thu, 16 Apr 2020 16:36:42 +0900 >>>>> Jungtaek Lim <kabhwan.opensou...@gmail.com> wrote: >>>>> >>>>> > Do thread dump continuously, per specific period (like 1s) and see >>>>> the >>>>> > change of stack / lock for each thread. (This is not easy to be done >>>>> in UI >>>>> > so maybe doing manually would be the only option. Not sure Spark UI >>>>> will >>>>> > provide the same, haven't used at all.) >>>>> > >>>>> > It will tell which thread is being blocked (even it's shown as >>>>> running) and >>>>> > which point to look at. >>>>> > >>>>> > On Thu, Apr 16, 2020 at 4:29 PM Ruijing Li <liruijin...@gmail.com> >>>>> wrote: >>>>> > >>>>> > > Once I do. thread dump, what should I be looking for to tell where >>>>> it is >>>>> > > hanging? Seeing a lot of timed_waiting and waiting on driver. >>>>> Driver is >>>>> > > also being blocked by spark UI. If there are no tasks, is there a >>>>> point to >>>>> > > do thread dump of executors? >>>>> > > >>>>> > > On Tue, Apr 14, 2020 at 4:49 AM Gabor Somogyi < >>>>> gabor.g.somo...@gmail.com> >>>>> > > wrote: >>>>> > > >>>>> > >> The simplest way is to do thread dump which doesn't require any >>>>> fancy >>>>> > >> tool (it's available on Spark UI). >>>>> > >> Without thread dump it's hard to say anything... >>>>> > >> >>>>> > >> >>>>> > >> On Tue, Apr 14, 2020 at 11:32 AM jane thorpe >>>>> <janethor...@aol.com.invalid> >>>>> > >> wrote: >>>>> > >> >>>>> > >>> Here a is another tool I use Logic Analyser 7:55 >>>>> > >>> https://youtu.be/LnzuMJLZRdU >>>>> > >>> >>>>> > >>> 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 >>>>> > >>> janethor...@aol.com >>>>> > >>> >>>>> > >>> >>>>> > >>> -----Original Message----- >>>>> > >>> From: jane thorpe <janethor...@aol.com.INVALID> >>>>> > >>> To: janethorpe1 <janethor...@aol.com>; mich.talebzadeh < >>>>> > >>> mich.talebza...@gmail.com>; liruijing09 <liruijin...@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 >>>>> > >>> janethor...@aol.com >>>>> > >>> >>>>> > >>> >>>>> > >>> -----Original Message----- >>>>> > >>> From: jane thorpe <janethor...@aol.com.INVALID> >>>>> > >>> To: mich.talebzadeh <mich.talebza...@gmail.com>; liruijing09 < >>>>> > >>> liruijin...@gmail.com>; user <user@spark.apache.org> >>>>> > >>> CC: user <user@spark.apache.org> >>>>> > >>> Sent: Sun, 12 Apr 2020 4:35 >>>>> > >>> Subject: Re: Spark hangs while reading from jdbc - does nothing >>>>> > >>> >>>>> > >>> You seem to be implying the error is intermittent. >>>>> > >>> You seem to be implying data is being ingested via JDBC. So the >>>>> > >>> connection has proven itself to be working unless no data is >>>>> arriving from >>>>> > >>> the JDBC channel at all. If no data is arriving then one could >>>>> say it >>>>> > >>> could be the JDBC. >>>>> > >>> If the error is intermittent then it is likely a resource >>>>> involved in >>>>> > >>> processing is filling to capacity. >>>>> > >>> Try reducing the data ingestion volume and see if that >>>>> completes, then >>>>> > >>> increase the data ingested incrementally. >>>>> > >>> I assume you have run the job on small amount of data so you >>>>> have >>>>> > >>> completed your prototype stage successfully. >>>>> > >>> >>>>> > >>> ------------------------------ >>>>> > >>> On Saturday, 11 April 2020 Mich Talebzadeh < >>>>> mich.talebza...@gmail.com> >>>>> > >>> wrote: >>>>> > >>> Hi, >>>>> > >>> >>>>> > >>> Have you checked your JDBC connections from Spark to Oracle. >>>>> What is >>>>> > >>> Oracle saying? Is it doing anything or hanging? >>>>> > >>> >>>>> > >>> set pagesize 9999 >>>>> > >>> set linesize 140 >>>>> > >>> set heading off >>>>> > >>> select SUBSTR(name,1,8) || ' sessions as on >>>>> '||TO_CHAR(CURRENT_DATE, >>>>> > >>> 'MON DD YYYY HH:MI AM') from v$database; >>>>> > >>> set heading on >>>>> > >>> column spid heading "OS PID" format a6 >>>>> > >>> column process format a13 heading "Client ProcID" >>>>> > >>> column username format a15 >>>>> > >>> column sid format 999 >>>>> > >>> column serial# format 99999 >>>>> > >>> column STATUS format a3 HEADING 'ACT' >>>>> > >>> column last format 9,999.99 >>>>> > >>> column TotGets format 999,999,999,999 HEADING 'Logical I/O' >>>>> > >>> column phyRds format 999,999,999 HEADING 'Physical I/O' >>>>> > >>> column total_memory format 999,999,999 HEADING 'MEM/KB' >>>>> > >>> -- >>>>> > >>> SELECT >>>>> > >>> substr(a.username,1,15) "LOGIN" >>>>> > >>> , substr(a.sid,1,5) || ','||substr(a.serial#,1,5) AS >>>>> > >>> "SID/serial#" >>>>> > >>> , TO_CHAR(a.logon_time, 'DD/MM HH:MI') "LOGGED IN SINCE" >>>>> > >>> , substr(a.machine,1,10) HOST >>>>> > >>> , substr(p.username,1,8)||'/'||substr(p.spid,1,5) "OS >>>>> PID" >>>>> > >>> , substr(a.osuser,1,8)||'/'||substr(a.process,1,5) >>>>> "Client PID" >>>>> > >>> , substr(a.program,1,15) PROGRAM >>>>> > >>> --,ROUND((CURRENT_DATE-a.logon_time)*24) AS >>>>> "Logged/Hours" >>>>> > >>> , ( >>>>> > >>> select round(sum(ss.value)/1024) from v$sesstat >>>>> ss, >>>>> > >>> v$statname sn >>>>> > >>> where ss.sid = a.sid and >>>>> > >>> sn.statistic# = ss.statistic# and >>>>> > >>> -- sn.name in ('session pga memory') >>>>> > >>> sn.name in ('session pga >>>>> memory','session uga >>>>> > >>> memory') >>>>> > >>> ) AS total_memory >>>>> > >>> , (b.block_gets + b.consistent_gets) TotGets >>>>> > >>> , b.physical_reads phyRds >>>>> > >>> , decode(a.status, 'ACTIVE', 'Y','INACTIVE', 'N') STATUS >>>>> > >>> , CASE WHEN a.sid in (select sid from v$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 <liruijin...@gmail.com> >>>>> wrote: >>>>> > >>> >>>>> > >>> Hi all, >>>>> > >>> >>>>> > >>> I am on spark 2.4.4 and using scala 2.11.12, and running cluster >>>>> mode on >>>>> > >>> mesos. I am ingesting from an oracle database using >>>>> spark.read.jdbc. I am >>>>> > >>> seeing a strange issue where spark just hangs and does nothing, >>>>> not >>>>> > >>> starting any new tasks. Normally this job finishes in 30 stages >>>>> but >>>>> > >>> sometimes it stops at 29 completed stages and doesn’t start the >>>>> last stage. >>>>> > >>> The spark job is idling and there is no pending or active task. >>>>> What could >>>>> > >>> be the problem? Thanks. >>>>> > >>> -- >>>>> > >>> Cheers, >>>>> > >>> Ruijing Li >>>>> > >>> >>>>> > >>> -- >>>>> > > Cheers, >>>>> > > Ruijing Li >>>>> > > >>>>> >>>> -- >>>> Cheers, >>>> Ruijing Li >>>> >>> -- >>> Cheers, >>> Ruijing Li >>> >> -- >> Cheers, >> Ruijing Li >> > -- Cheers, Ruijing Li
