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From Karl Wright <daddy...@gmail.com>
Subject Re: Web crawling causes Socket Timeout after Database Exception
Date Wed, 28 Nov 2012 11:37:35 GMT
Yes, the SQL code will be output to the manifoldcf.log as part of the
exception text.

However I hope that this checkin will already fix your problem.

Thanks,
Karl

On Wed, Nov 28, 2012 at 3:44 AM, Shigeki Kobayashi
<shigeki.kobayashi3@g.softbank.co.jp> wrote:
>
> Hi Karl,
>
> I can try. To obtain the error code, could you let me know what to code to
> put in what line of what file? I suppose the error code will be output into
> manifoldcf.log, is this right?
>
>
> Regards,
>
>
> Shigeki
>
>
>
> 2012/11/28 Karl Wright <daddywri@gmail.com>
>>
>> Hi Shigeki,
>>
>> This confirms my theory that our MySQL driver is not detecting all
>> cases where MySQL gives up on a transaction.  We need to correct this,
>> but in order to do that we need the SQL error code that MySQL throws
>> in this case:
>>
>> Caused by: java.sql.SQLException: Lock wait timeout exceeded; try
>> restarting transaction
>>
>> It looks like somebody actually posted the SQL error code that MYSQL
>> sends out with this online:
>>
>> ERROR 1205 (HY000): Lock wait timeout exceeded; try restarting transaction
>>
>> Are you able to build ManifoldCF?  I will check in a fix to trunk for
>> this problem shortly; it would be great if you could try it out.
>>
>> Thanks,
>> Karl
>>
>> On Wed, Nov 28, 2012 at 2:30 AM, Shigeki Kobayashi
>> <shigeki.kobayashi3@g.softbank.co.jp> wrote:
>> > Hi Karl,
>> >
>> >
>> > Here is a log of Database Exception that is occurred while crawling Web.
>> > This time, socket timeout exception did not happen so it might be a
>> > different matter.
>> > Even though the job status remain "Running", it seems that MCF stopped
>> > crawling (The job was not aborted).
>> > --------------------------------
>> > ERROR 2012-11-22 19:36:28,593 (Worker thread '16') - Worker thread
>> > aborting
>> > and restarting due to database connection reset: Database exception:
>> > Exception doing query: Lock wait timeout exceeded; try restarting
>> > transaction
>> > org.apache.manifoldcf.core.interfaces.ManifoldCFException: Database
>> > exception: Exception doing query: Lock wait timeout exceeded; try
>> > restarting
>> > transaction
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:681)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:709)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1394)
>> >         at
>> >
>> > org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:144)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:186)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.DBInterfaceMySQL.performModification(DBInterfaceMySQL.java:678)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.DBInterfaceMySQL.performUpdate(DBInterfaceMySQL.java:275)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.BaseTable.performUpdate(BaseTable.java:80)
>> >         at
>> >
>> > org.apache.manifoldcf.crawler.jobs.HopCount.markForDelete(HopCount.java:1426)
>> >         at
>> >
>> > org.apache.manifoldcf.crawler.jobs.HopCount.doDeleteInvalidation(HopCount.java:1356)
>> >         at
>> > org.apache.manifoldcf.crawler.jobs.HopCount.doFinish(HopCount.java:1057)
>> >         at
>> >
>> > org.apache.manifoldcf.crawler.jobs.HopCount.finishParents(HopCount.java:389)
>> >         at
>> >
>> > org.apache.manifoldcf.crawler.jobs.JobManager.finishDocuments(JobManager.java:4309)
>> >         at
>> >
>> > org.apache.manifoldcf.crawler.system.WorkerThread.run(WorkerThread.java:557)
>> > Caused by: java.sql.SQLException: Lock wait timeout exceeded; try
>> > restarting
>> > transaction
>> >         at
>> > com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
>> >         at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3609)
>> >         at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3541)
>> >         at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2002)
>> >         at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2163)
>> >         at
>> > com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
>> >         at
>> >
>> > com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
>> >         at
>> >
>> > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2427)
>> >         at
>> >
>> > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2345)
>> >         at
>> >
>> > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2330)
>> >         at
>> > org.apache.manifoldcf.core.database.Database.execute(Database.java:840)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:641)
>> >
>> > --------------------------------
>> >
>> >
>> > Here is a log of Database Exception that is occurred while crawling
>> > files
>> > using Windows shares connection:
>> >
>> >
>> > --------------------------------
>> > 2012/11/22 23:39:28 ERROR (Job start thread) - Job start thread aborting
>> > and
>> > restarting due to database connection reset: Database exception:
>> > Exception
>> > doing query: Lock wait timeout exceeded; try restarting transaction
>> > org.apache.manifoldcf.core.interfaces.ManifoldCFException: Database
>> > exception: Exception doing query: Lock wait timeout exceeded; try
>> > restarting
>> > transaction
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:681)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:709)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1394)
>> >         at
>> >
>> > org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:144)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:186)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.DBInterfaceMySQL.performQuery(DBInterfaceMySQL.java:852)
>> >         at
>> >
>> > org.apache.manifoldcf.crawler.jobs.JobManager.startJobs(JobManager.java:4711)
>> >         at
>> >
>> > org.apache.manifoldcf.crawler.system.JobStartThread.run(JobStartThread.java:68)
>> > Caused by: java.sql.SQLException: Lock wait timeout exceeded; try
>> > restarting
>> > transaction
>> >         at
>> > com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
>> >         at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3609)
>> >         at com.mysql.jdbc.MysqlIO.nextRowFast(MysqlIO.java:1578)
>> >         at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:1434)
>> >         at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java:2925)
>> >         at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:477)
>> >         at
>> > com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:2631)
>> >         at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:1800)
>> >         at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2221)
>> >         at
>> > com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
>> >         at
>> >
>> > com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
>> >         at
>> >
>> > com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2293)
>> >         at
>> > org.apache.manifoldcf.core.database.Database.execute(Database.java:826)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:641)
>> > 2012/11/22 23:39:28 ERROR (Finisher thread) - Finisher thread aborting
>> > and
>> > restarting due to database connection reset: Database exception:
>> > Exception
>> > doing query: Lock wait timeout exceeded; try restarting transaction
>> > org.apache.manifoldcf.core.interfaces.ManifoldCFException: Database
>> > exception: Exception doing query: Lock wait timeout exceeded; try
>> > restarting
>> > transaction
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:681)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:709)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1394)
>> >         at
>> >
>> > org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:144)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:186)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.DBInterfaceMySQL.performQuery(DBInterfaceMySQL.java:852)
>> >         at
>> >
>> > org.apache.manifoldcf.crawler.jobs.JobManager.finishJobs(JobManager.java:6469)
>> >         at
>> >
>> > org.apache.manifoldcf.crawler.system.FinisherThread.run(FinisherThread.java:64)
>> > Caused by: java.sql.SQLException: Lock wait timeout exceeded; try
>> > restarting
>> > transaction
>> >         at
>> > com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
>> >         at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3609)
>> >         at com.mysql.jdbc.MysqlIO.nextRowFast(MysqlIO.java:1578)
>> >         at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:1434)
>> >         at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java:2925)
>> >         at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:477)
>> >         at
>> > com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:2631)
>> >         at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:1800)
>> >         at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2221)
>> >         at
>> > com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
>> >         at
>> >
>> > com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
>> >         at
>> >
>> > com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2293)
>> >         at
>> > org.apache.manifoldcf.core.database.Database.execute(Database.java:826)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:641)
>> > 2012/11/22 23:39:30 ERROR (Worker thread '253') - Worker thread aborting
>> > and
>> > restarting due to database connection reset: Database exception:
>> > Exception
>> > doing query: Lock wait timeout exceeded; try restarting transaction
>> > org.apache.manifoldcf.core.interfaces.ManifoldCFException: Database
>> > exception: Exception doing query: Lock wait timeout exceeded; try
>> > restarting
>> > transaction
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:681)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:709)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1394)
>> >         at
>> >
>> > org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:144)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:186)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.DBInterfaceMySQL.performModification(DBInterfaceMySQL.java:678)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.DBInterfaceMySQL.performUpdate(DBInterfaceMySQL.java:275)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.BaseTable.performUpdate(BaseTable.java:80)
>> >         at
>> >
>> > org.apache.manifoldcf.crawler.jobs.JobQueue.updateCompletedRecord(JobQueue.java:722)
>> >         at
>> >
>> > org.apache.manifoldcf.crawler.jobs.JobManager.markDocumentCompletedMultiple(JobManager.java:2435)
>> >         at
>> >
>> > org.apache.manifoldcf.crawler.system.WorkerThread.run(WorkerThread.java:765)
>> > Caused by: java.sql.SQLException: Lock wait timeout exceeded; try
>> > restarting
>> > transaction
>> >         at
>> > com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
>> >         at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3609)
>> >         at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3541)
>> >         at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2002)
>> >         at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2163)
>> >         at
>> > com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
>> >         at
>> >
>> > com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
>> >         at
>> >
>> > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2427)
>> >         at
>> >
>> > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2345)
>> >         at
>> >
>> > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2330)
>> >         at
>> > org.apache.manifoldcf.core.database.Database.execute(Database.java:840)
>> >         at
>> >
>> > org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:641)
>> > --------------------------------
>> > Regards,
>> >
>> > Shigeki
>> >
>> >
>> > 2012/11/27 Karl Wright <daddywri@gmail.com>
>> >>
>> >> Hi Shigeki,
>> >>
>> >> Deadlocks are a fact of life in a very multithreaded application.
>> >> They are supposed to be caught by ManifoldCF, and the transactions
>> >> retried.  I can believe, though, that MySQL might set different
>> >> sqlexception status codes for different kinds of deadlock - if instead
>> >> of a sqlexception with a deadlock code, MySQL sometimes just drops the
>> >> JDBC connection, that might explain the problem.
>> >>
>> >> Can you refresh my memory and please send the ManifoldCF log part that
>> >> includes the socket timeout exception?  I can then see if it is coming
>> >> from the same place.
>> >>
>> >> Karl
>> >>
>> >> On Tue, Nov 27, 2012 at 12:50 AM, Shigeki Kobayashi
>> >> <shigeki.kobayashi3@g.softbank.co.jp> wrote:
>> >> > Hi Karl,
>> >> >
>> >> > According to INNODB STATUS in MySQL, while crawling web, the
>> >> > following
>> >> > DEADLOCK occurred.
>> >> > A few minutes later, database exception occurred in MCF.
>> >> > So do you think probably this DEADLOCK could cause the exception?
>> >> >
>> >> > I do not know the error code from MySQL yet, but maybe I could obtain
>> >> > it
>> >> > if
>> >> > you could let me
>> >> > know what code in what file should be added in order to output the
>> >> > error
>> >> > code into manifold.log
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > ------------------------------------------------------------------------------
>> >> > INNODB STATUS:
>> >> > =====================================
>> >> > 121127 11:17:49 INNODB MONITOR OUTPUT
>> >> > =====================================
>> >> > Per second averages calculated from the last 60 seconds
>> >> > -----------------
>> >> > BACKGROUND THREAD
>> >> > -----------------
>> >> > srv_master_thread loops: 401163 1_second, 401162 sleeps, 40049
>> >> > 10_second,
>> >> > 674 background, 674 flush
>> >> > srv_master_thread log flush and writes: 401182
>> >> > ----------
>> >> > SEMAPHORES
>> >> > ----------
>> >> > OS WAIT ARRAY INFO: reservation count 7319, signal count 6842
>> >> > Mutex spin waits 3702, rounds 111120, OS waits 3626
>> >> > RW-shared spins 2189, rounds 63516, OS waits 1767
>> >> > RW-excl spins 255, rounds 57147, OS waits 1897
>> >> > Spin rounds per wait: 30.02 mutex, 29.02 RW-shared, 224.11 RW-excl
>> >> > ------------------------
>> >> > LATEST DETECTED DEADLOCK
>> >> > ------------------------
>> >> > 121122 19:31:55
>> >> > *** (1) TRANSACTION:
>> >> > TRANSACTION 3021A0, ACTIVE 32 sec starting index read
>> >> > mysql tables in use 1, locked 1
>> >> > LOCK WAIT 64 lock struct(s), heap size 14776, 110 row lock(s), undo
>> >> > log
>> >> > entries 51
>> >> > MySQL thread id 24, OS thread handle 0x7ff8ffe06700, query id 41385
>> >> > 10.249.23.9 manifoldcf Sending data
>> >> > SELECT parentidhash,linktype,distance FROM hopcount WHERE
>> >> > jobid=1351139121625 AND parentidhash IN
>> >> >
>> >> >
>> >> > ('A0ED08F9D45547FF54B72869FE5E7C3C5B0E910A','F5E2F6C6B43FB5D030C4F0AE8E22AD07536475A8','C0856A1AFF55F7BB20BCAE317E18F588EEFB806D','019253D99FCB265A20A3CFF11D0443937FE2D4D0','21A979F9BB9120F747B0B605EDABA71EB364A584','A8B5B7245D0810584B764470B42CFDF71C33A7E5','6FE272988943D3BD64E285951A1A6739011FC15E','1E1CA954A3E31BFC28FFE1BE70757408341CDB6A','8DAE8B4734A30FE2D346EEBD1CCC3A16468F7B7B','028CD3E7FF7F493E3EC3980FF303DB05DC42404E','924E0608A5C4505C9272A69B8C1F82C7B883A11F','13F6402C96E0979EF5F17338DFF96BD9912125D9','43174E34AA07C34237D622A43A82AFE3825C3870','32892282A6866BD181BDA0BA85801192370C84F3','0311197289655163E1452E90D43A5D96D9A4E751','178C8BE84AEDC9F362CE3A2CC2702F6C2CD9CBA1','7CF15B193B3BDA097BEB437272FC5E413B86B63D')
>> >> > AND linktype IN ('link','redirect')
>> >> > *** (1) WAITING FOR THIS LOCK TO BE GRANTED:
>> >> > RECORD LOCKS space id 0 page no 2449 n bits 192 index `PRIMARY` of
>> >> > table
>> >> > `manifoldcf`.`hopcount` trx id 3021A0 lock mode S locks rec but not
>> >> > gap
>> >> > waiting
>> >> > Record lock, heap no 28 PHYSICAL RECORD: n_fields 8; compact format;
>> >> > info
>> >> > bits 0
>> >> >  0: len 8; hex 8000013b261c6d8a; asc    ;& m ;;
>> >> >  1: len 6; hex 0000002f4e47; asc    /NG;;
>> >> >  2: len 7; hex 900000021b06ec; asc        ;;
>> >> >  3: len 1; hex 4e; asc N;;
>> >> >  4: len 30; hex
>> >> > 384441453842343733344133304645324433343645454244314343433341; asc
>> >> > 8DAE8B4734A30FE2D346EEBD1CCC3A; (total 40 bytes);
>> >> >  5: len 8; hex 8000000000000001; asc         ;;
>> >> >  6: len 8; hex 8000013a962ad9d9; asc    : *  ;;
>> >> >  7: len 4; hex 6c696e6b; asc link;;
>> >> >
>> >> > *** (2) TRANSACTION:
>> >> > TRANSACTION 302208, ACTIVE 3 sec fetching rows
>> >> > mysql tables in use 3, locked 3
>> >> > 1436 lock struct(s), heap size 145848, 122906 row lock(s)
>> >> > MySQL thread id 39, OS thread handle 0x7ff8ffa37700, query id 40699
>> >> > 10.249.23.9 manifoldcf preparing
>> >> > UPDATE hopcount SET deathmark='D',distance=-1 WHERE id IN(SELECT
>> >> > ownerid
>> >> > FROM hopdeletedeps t0 WHERE t0.jobid=1351139121625 AND
>> >> > t0.childidhash='D573BDC6D59C7A7CC2862646322F69EA5574C36D' AND
>> >> > EXISTS(SELECT
>> >> > 'x' FROM intrinsiclink t1 WHERE t1.jobid=t0.jobid AND
>> >> > t1.linktype=t0.linktype AND t1.parentidhash=t0.parentidhash AND
>> >> > t1.childidhash=t0.childidhash AND t1.isnew='B'))
>> >> > *** (2) HOLDS THE LOCK(S):
>> >> > RECORD LOCKS space id 0 page no 2449 n bits 192 index `PRIMARY` of
>> >> > table
>> >> > `manifoldcf`.`hopcount` trx id 302208 lock_mode X
>> >> > Record lock, heap no 1 PHYSICAL RECORD: n_fields 1; compact format;
>> >> > info
>> >> > bits 0
>> >> >  0: len 8; hex 73757072656d756d; asc supremum;;
>> >> >
>> >> > ...
>> >> > ...
>> >> > ...
>> >> >
>> >> > *** WE ROLL BACK TRANSACTION (1)
>> >> > ------------
>> >> > TRANSACTIONS
>> >> > ------------
>> >> > Trx id counter 38375F
>> >> > Purge done for trx's n:o < 3024F7 undo n:o < 0
>> >> > History list length 652
>> >> > LIST OF TRANSACTIONS FOR EACH SESSION:
>> >> > ---TRANSACTION 0, not started
>> >> > MySQL thread id 110, OS thread handle 0x7ff914113700, query id
>> >> > 1436936
>> >> > localhost root
>> >> > SHOW ENGINE INNODB STATUS
>> >> > ---TRANSACTION 0, not started
>> >> > MySQL thread id 106, OS thread handle 0x7ff9035b3700, query id
>> >> > 1435785
>> >> > localhost root
>> >> > ---TRANSACTION 38375E, not started
>> >> > MySQL thread id 99, OS thread handle 0x7ff8ff72b700, query id 1436934
>> >> > 10.249.23.9 manifoldcf
>> >> > --------
>> >> > ...
>> >> >
>> >> >
>> >> > ------------------------------------------------------------------------------
>> >> >
>> >> >
>> >> > Likewise, file crawling using Windows shares faced similar matter.
>> >> > DEADLOCK
>> >> > occured in MySQL and
>> >> > Database Exception occured in MCF as well:
>> >> >
>> >> >
>> >> >
>> >> > ------------------------------------------------------------------------------
>> >> >
>> >> > | InnoDB |      |
>> >> > =====================================
>> >> > 121126 16:05:21 INNODB MONITOR OUTPUT
>> >> > =====================================
>> >> > Per second averages calculated from the last 48 seconds
>> >> > -----------------
>> >> > BACKGROUND THREAD
>> >> > -----------------
>> >> > srv_master_thread loops: 327427 1_second, 327300 sleeps, 32438
>> >> > 10_second,
>> >> > 3544 background, 3544 flush
>> >> > srv_master_thread log flush and writes: 327670
>> >> > ----------
>> >> > SEMAPHORES
>> >> > ----------
>> >> > OS WAIT ARRAY INFO: reservation count 1808090, signal count 2140762
>> >> > Mutex spin waits 18194682, rounds 103331992, OS waits 842070
>> >> > RW-shared spins 1311114, rounds 25796436, OS waits 457767
>> >> > RW-excl spins 577964, rounds 15904805, OS waits 333210
>> >> > Spin rounds per wait: 5.68 mutex, 19.68 RW-shared, 27.52 RW-excl
>> >> > ------------------------
>> >> > LATEST DETECTED DEADLOCK
>> >> > ------------------------
>> >> > 121122 23:38:46
>> >> > *** (1) TRANSACTION:
>> >> > TRANSACTION 674749, ACTIVE 7 sec inserting
>> >> > mysql tables in use 1, locked 1
>> >> > LOCK WAIT 4 lock struct(s), heap size 1248, 3 row lock(s), undo log
>> >> > entries
>> >> > 1
>> >> > MySQL thread id 99, OS thread handle 0x7f7d4a356700, query id
>> >> > 23942404
>> >> > localhost 127.0.0.1 manifoldcf update
>> >> > INSERT INTO jobqueue
>> >> >
>> >> >
>> >> > (docpriority,id,priorityset,docid,status,dochash,checktime,checkaction,jobid)
>> >> > VALUES
>> >> >
>> >> >
>> >> > (13.830866056523654,1353595119848,1353595119385,'smb://xxx/xxx','P','88517951DB2E0666151E7B5308C9FDCB16F062AD',0,'R',1353575409046)
>> >> > *** (1) WAITING FOR THIS LOCK TO BE GRANTED:
>> >> > RECORD LOCKS space id 0 page no 221894 n bits 208 index
>> >> > `I1352346865065`
>> >> > of
>> >> > table `manifoldcf`.`jobqueue` trx id 674749 lock_mode X locks gap
>> >> > before
>> >> > rec
>> >> > insert intention waiting
>> >> > Record lock, heap no 134 PHYSICAL RECORD: n_fields 3; compact format;
>> >> > info
>> >> > bits 0
>> >> >  0: len 30; hex
>> >> > 383835313838444433453134444134354242384531383433424330393444; asc
>> >> > 885188DD3E14DA45BB8E1843BC094D; (total 40 bytes);
>> >> >  1: len 8; hex 8000013b2761a596; asc    ;'a  ;;
>> >> >  2: len 8; hex 8000013b287bd5c9; asc    ;({  ;;
>> >> >
>> >> > *** (2) TRANSACTION:
>> >> > TRANSACTION 6740DF, ACTIVE 9 sec fetching rows
>> >> > mysql tables in use 5, locked 5
>> >> > 23571 lock struct(s), heap size 2439608, 1058037 row lock(s)
>> >> > MySQL thread id 45, OS thread handle 0x7f7d21231700, query id
>> >> > 23937374
>> >> > localhost 127.0.0.1 manifoldcf Sending data
>> >> > SELECT
>> >> >
>> >> >
>> >> > t0.id,t0.jobid,t0.dochash,t0.docid,t0.status,t0.failtime,t0.failcount,t0.priorityset
>> >> > FROM jobqueue t0 WHERE t0.status IN ('P','G') AND t0.checkaction='R'
>> >> > AND
>> >> > t0.checktime<=1353595117855 AND EXISTS(SELECT 'x' FROM jobs t1 WHERE
>> >> > t1.status IN ('A','a') AND t1.id=t0.jobid AND t1.priority=5) AND NOT
>> >> > EXISTS(SELECT 'x' FROM jobqueue t2 WHERE t2.dochash=t0.dochash AND
>> >> > t2.status
>> >> > IN ('A','F','a','f','D','d') AND t2.jobid!=t0.jobid) AND NOT
>> >> > EXISTS(SELECT
>> >> > 'x' FROM prereqevents t3,events t4 WHERE t0.id=t3.owner AND
>> >> > t3.eventname=t4.name) ORDER BY t0.docpriority ASC,t0.status
>> >> > ASC,t0.checkaction ASC,t0.checktime ASC LIMIT 1200
>> >> > *** (2) HOLDS THE LOCK(S):
>> >> > RECORD LOCKS space id 0 page no 221894 n bits 208 index
>> >> > `I1352346865065`
>> >> > of
>> >> > table `manifoldcf`.`jobqueue` trx id 6740DF lock mode S locks gap
>> >> > before
>> >> > rec
>> >> > Record lock, heap no 8 PHYSICAL RECORD: n_fields 3; compact format;
>> >> > info
>> >> > bits 0
>> >> >  0: len 30; hex
>> >> > 383834464239393738383632333242323331353041343031303337424444; asc
>> >> > 884FB997886232B23150A401037BDD; (total 40 bytes);
>> >> >  1: len 8; hex 8000013b2761a596; asc    ;'a  ;;
>> >> >  2: len 8; hex 8000013b27c4823b; asc    ;'  ;;;
>> >> >
>> >> > ...
>> >> > ...
>> >> > ...
>> >> >
>> >> > *** WE ROLL BACK TRANSACTION (1)
>> >> > ------------
>> >> > TRANSACTIONS
>> >> > ------------
>> >> > Trx id counter 6ACDF6
>> >> > Purge done for trx's n:o < 6752D1 undo n:o < 0
>> >> > History list length 485
>> >> > LIST OF TRANSACTIONS FOR EACH SESSION:
>> >> > ---TRANSACTION 0, not started
>> >> > MySQL thread id 5505, OS thread handle 0x7f7d210ec700, query id
>> >> > 25071245
>> >> > localhost root
>> >> > SHOW ENGINE INNODB STATUS
>> >> > ---TRANSACTION 6ACDF5, not started
>> >> > MySQL thread id 99, OS thread handle 0x7f7d4a356700, query id
>> >> > 25071244
>> >> > localhost 127.0.0.1 manifoldcf
>> >> > ...
>> >> >
>> >> >
>> >> > ------------------------------------------------------------------------------
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > Regards,
>> >> >
>> >> > Shigeki
>> >> >
>> >> >
>> >> > 2012/10/19 Shigeki Kobayashi <shigeki.kobayashi3@g.softbank.co.jp>
>> >> >>
>> >> >> Due to the error, I had to downgrade to a lower version so I haven't
>> >> >> found
>> >> >> the MySQL error code yet.
>> >> >>
>> >> >> I installed MCF1.0 in a different environment where crawlable
>> >> >> contents
>> >> >> are
>> >> >> different from the above environment.
>> >> >> I could not reproduce the Database exception but socket timeout
>> >> >> occurred
>> >> >> In the same environment, I ran MCF0.6 and it completed crawling
>> >> >> without
>> >> >> socket timeout.
>> >> >> Like you said, socket timeout seems to be a different problem from
>> >> >> the
>> >> >> Database exception .
>> >> >>
>> >> >> 2012/10/18 Karl Wright <daddywri@gmail.com>
>> >> >>>
>> >> >>> So, what was the resolution of this problem?  Any news?
>> >> >>> Karl
>> >> >>>
>> >> >>> On Thu, Oct 11, 2012 at 2:28 AM, Karl Wright <daddywri@gmail.com>
>> >> >>> wrote:
>> >> >>> > The only change is that the MySQL driver now performs ANALYZE
>> >> >>> > operations on the fly in order to keep the database operating at
>> >> >>> > high
>> >> >>> > efficiency.  This is CONNECTORS-510.  It is possible that, on a
>> >> >>> > large
>> >> >>> > database table, these operations will cause others to wait long
>> >> >>> > enough
>> >> >>> > so that their timeout is exceeded.  Such an event does not take
>> >> >>> > place
>> >> >>> > while the load tests run, however.  If you want to turn off the
>> >> >>> > analyze operation, you can do that by setting a per-table
>> >> >>> > property
>> >> >>> > to
>> >> >>> > override the analyze default of 10000 operations:
>> >> >>> >
>> >> >>> > analyzeThreshold =
>> >> >>> >
>> >> >>> >
>> >> >>> >
>> >> >>> > ManifoldCF.getIntProperty("org.apache.manifold.db.mysql.analyze."+tableName,10000);
>> >> >>> >
>> >> >>> > The table in question is "jobqueue".  If you set this value to
>> >> >>> > something like 1000000000 and you still see MySQL timeouts, then
>> >> >>> > this
>> >> >>> > new code is not the problem.  And, like I said, the best solution
>> >> >>> > is
>> >> >>> > to recognize the error and retry, but first I would need the
>> >> >>> > error
>> >> >>> > code.  Adding an appropriate output of sqlState around line 123
>> >> >>> > of
>> >> >>> >
>> >> >>> >
>> >> >>> >
>> >> >>> > framework/core/src/main/java/org/apache/manifoldcf/core/database/DBInterfaceMySQL.java
>> >> >>> > would allow us to see what code to catch, when it happened again.
>> >> >>> >
>> >> >>> > For the Web connector, the only modifications have been in
>> >> >>> > regards
>> >> >>> > to
>> >> >>> > how it handles 500 errors, which now correctly code to avoid an
>> >> >>> > IndexExceptionOutOfBounds exception.  This has nothing to do with
>> >> >>> > socket exceptions, which are caused for external reasons only.
>> >> >>> >
>> >> >>> > Karl
>> >> >>> >
>> >> >>> >
>> >> >>> > On Wed, Oct 10, 2012 at 10:32 PM, Shigeki Kobayashi
>> >> >>> > <shigeki.kobayashi3@g.softbank.co.jp> wrote:
>> >> >>> >> Hi Karl,
>> >> >>> >>
>> >> >>> >>
>> >> >>> >> I was comparing version 1.0 with old trunk based on version 0.6
>> >> >>> >> implementing
>> >> >>> >> CONNECTORS-501(
>> >> >>> >> Medium-scale web crawl with hopcount-based filtering fails to
>> >> >>> >> find
>> >> >>> >> correct
>> >> >>> >> number of documents).
>> >> >>> >>
>> >> >>> >> Running each version with the same MySQL setting and the same
>> >> >>> >> throttling,
>> >> >>> >> somehow the version 1.0 hangs with the error.
>> >> >>> >> Since the old trunk completes crawling, I wonder if something
>> >> >>> >> has
>> >> >>> >> changed.
>> >> >>> >>
>> >> >>> >> Just to make sure I will recheck if there are any wrong settings
>> >> >>> >> in
>> >> >>> >> MCF.
>> >> >>> >>
>> >> >>> >> Thanks.
>> >> >>> >>
>> >> >>> >> Regards,
>> >> >>> >>
>> >> >>> >> Shigeki
>> >> >>> >>
>> >> >>> >> 2012/10/10 Karl Wright <daddywri@gmail.com>
>> >> >>> >>>
>> >> >>> >>> Hi Shigeki,
>> >> >>> >>>
>> >> >>> >>> The socket timeout exception is only a warning.  It means that
>> >> >>> >>> some
>> >> >>> >>> site you are crawling did not accept a socket connection within
>> >> >>> >>> the
>> >> >>> >>> allowed time (5 minutes I think).  The Web Connector will retry
>> >> >>> >>> the
>> >> >>> >>> connection a few times, and if it is still rejected, it will
>> >> >>> >>> eventually give up on that page.  One thing you want to check,
>> >> >>> >>> though,
>> >> >>> >>> is that you are using proper throttling, because if you aren't
>> >> >>> >>> then
>> >> >>> >>> one cause of this problem is that the webmaster of the site you
>> >> >>> >>> are
>> >> >>> >>> trying to crawl may have blocked you from accessing it.
>> >> >>> >>>
>> >> >>> >>> The database exception is more problematic.  It means that
>> >> >>> >>> MySQL
>> >> >>> >>> thinks it took too long for a specific transaction to complete,
>> >> >>> >>> and
>> >> >>> >>> the database aborted the transaction due to a timeout.  There
>> >> >>> >>> are
>> >> >>> >>> two
>> >> >>> >>> ways of dealing with this issue.  One way is to modify your
>> >> >>> >>> MySQL
>> >> >>> >>> configuration to increase the transaction timeout value to some
>> >> >>> >>> high
>> >> >>> >>> number.  The second way is to modify ManifoldCF to recognize
>> >> >>> >>> the
>> >> >>> >>> timeout error specifically, and cause a retry.  But in order to
>> >> >>> >>> do
>> >> >>> >>> the
>> >> >>> >>> latter, I would need to know what SQL error code MySQL returns
>> >> >>> >>> for
>> >> >>> >>> this situation, which will mean we either need to look it up
>> >> >>> >>> (if
>> >> >>> >>> we
>> >> >>> >>> can), or modify a ManifoldCF instance to log it when this
>> >> >>> >>> problem
>> >> >>> >>> occurs.
>> >> >>> >>>
>> >> >>> >>> Please let me know how you would like to proceed.
>> >> >>> >>>
>> >> >>> >>> Karl
>> >> >>> >>>
>> >> >>> >>> On Wed, Oct 10, 2012 at 3:51 AM, Shigeki Kobayashi
>> >> >>> >>> <shigeki.kobayashi3@g.softbank.co.jp> wrote:
>> >> >>> >>> >
>> >> >>> >>> > Hi
>> >> >>> >>> >
>> >> >>> >>> > I am having a trouble with crawling web using MCF1.0.
>> >> >>> >>> > I run MCF with MySQL 5.5 and Tomcat 6.0.
>> >> >>> >>> > It should keep crawling contents, but MCF prints the
>> >> >>> >>> > following
>> >> >>> >>> > Database
>> >> >>> >>> > exception log, then hangs.
>> >> >>> >>> > After DB Exception, Socket Time Exception occurs.
>> >> >>> >>> >
>> >> >>> >>> > Anyone has faced this problem?
>> >> >>> >>> >
>> >> >>> >>> > --Database Exception log:
>> >> >>> >>> >
>> >> >>> >>> > ERROR 2012-10-10 16:11:05,787 (Worker thread '42') - Worker
>> >> >>> >>> > thread
>> >> >>> >>> > aborting
>> >> >>> >>> > and restarting due to database connection reset: Database
>> >> >>> >>> > exception:
>> >> >>> >>> > Exception doing query: Lock wait timeout exceeded; try
>> >> >>> >>> > restarting
>> >> >>> >>> > transaction
>> >> >>> >>> > org.apache.manifoldcf.core.interfaces.ManifoldCFException:
>> >> >>> >>> > Database
>> >> >>> >>> > exception: Exception doing query: Lock wait timeout exceeded;
>> >> >>> >>> > try
>> >> >>> >>> > restarting
>> >> >>> >>> > transaction
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:681)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:709)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1394)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:144)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:186)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.core.database.DBInterfaceMySQL.performQuery(DBInterfaceMySQL.java:852)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.jobs.JobManager.addDocuments(JobManager.java:4089)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.system.WorkerThread$ProcessActivity.processDocumentReferences(WorkerThread.java:1932)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.system.WorkerThread$ProcessActivity.addDocumentReference(WorkerThread.java:1487)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.connectors.webcrawler.WebcrawlerConnector$ProcessActivityLinkHandler.noteDiscoveredLink(WebcrawlerConnector.java:6049)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.connectors.webcrawler.WebcrawlerConnector$ProcessAcivityHTMLHandler.noteAHREF(WebcrawlerConnector.java:6159)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.connectors.webcrawler.LinkParseState.noteNonscriptTag(LinkParseState.java:44)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.connectors.webcrawler.FormParseState.noteNonscriptTag(FormParseState.java:52)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.connectors.webcrawler.ScriptParseState.noteTag(ScriptParseState.java:50)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.connectors.webcrawler.BasicParseState.dealWithCharacter(BasicParseState.java:225)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.connectors.webcrawler.WebcrawlerConnector.handleHTML(WebcrawlerConnector.java:7047)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.connectors.webcrawler.WebcrawlerConnector.extractLinks(WebcrawlerConnector.java:6011)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.connectors.webcrawler.WebcrawlerConnector.processDocuments(WebcrawlerConnector.java:1282)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.connectors.BaseRepositoryConnector.processDocuments(BaseRepositoryConnector.java:423)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.system.WorkerThread.run(WorkerThread.java:551)
>> >> >>> >>> > Caused by: java.sql.SQLException: Lock wait timeout exceeded;
>> >> >>> >>> > try
>> >> >>> >>> > restarting
>> >> >>> >>> > transaction
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> > com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
>> >> >>> >>> >         at
>> >> >>> >>> > com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3609)
>> >> >>> >>> >         at
>> >> >>> >>> > com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3541)
>> >> >>> >>> >         at
>> >> >>> >>> > com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2002)
>> >> >>> >>> >         at
>> >> >>> >>> > com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2163)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> > com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2293)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.core.database.Database.execute(Database.java:826)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:641)
>> >> >>> >>> > ERROR 2012-10-10 16:11:06,799 (Worker thread '9') - Worker
>> >> >>> >>> > thread
>> >> >>> >>> > aborting
>> >> >>> >>> > and restarting due to database connection reset: Database
>> >> >>> >>> > exception:
>> >> >>> >>> > Exception doing query: Lock wait timeout exceeded; try
>> >> >>> >>> > restarting
>> >> >>> >>> > transaction
>> >> >>> >>> > org.apache.manifoldcf.core.interfaces.ManifoldCFException:
>> >> >>> >>> > Database
>> >> >>> >>> > exception: Exception doing query: Lock wait timeout exceeded;
>> >> >>> >>> > try
>> >> >>> >>> > restarting
>> >> >>> >>> > transaction
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:681)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:709)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1394)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:144)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:186)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.core.database.DBInterfaceMySQL.performQuery(DBInterfaceMySQL.java:852)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.jobs.JobManager.addDocuments(JobManager.java:4089)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.system.WorkerThread$ProcessActivity.processDocumentReferences(WorkerThread.java:1932)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.system.WorkerThread$ProcessActivity.flush(WorkerThread.java:1863)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.system.WorkerThread.run(WorkerThread.java:554)
>> >> >>> >>> > Caused by: java.sql.SQLException: Lock wait timeout exceeded;
>> >> >>> >>> > try
>> >> >>> >>> > restarting
>> >> >>> >>> > transaction
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> > com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
>> >> >>> >>> >         at
>> >> >>> >>> > com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3609)
>> >> >>> >>> >         at
>> >> >>> >>> > com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3541)
>> >> >>> >>> >         at
>> >> >>> >>> > com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2002)
>> >> >>> >>> >         at
>> >> >>> >>> > com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2163)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> > com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2293)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.core.database.Database.execute(Database.java:826)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:641)
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > ---- Socket Timeout:
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > DEBUG 2012-10-10 16:16:27,256 (Worker thread '49') - Socket
>> >> >>> >>> > timeout
>> >> >>> >>> > exception trying to close connection: Read timed out
>> >> >>> >>> > java.net.SocketTimeoutException: Read timed out
>> >> >>> >>> >         at java.net.SocketInputStream.socketRead0(Native
>> >> >>> >>> > Method)
>> >> >>> >>> >         at
>> >> >>> >>> > java.net.SocketInputStream.read(SocketInputStream.java:129)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> > java.io.BufferedInputStream.fill(BufferedInputStream.java:218)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> > java.io.BufferedInputStream.read1(BufferedInputStream.java:258)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> > java.io.BufferedInputStream.read(BufferedInputStream.java:317)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.commons.httpclient.ContentLengthInputStream.read(Unknown
>> >> >>> >>> > Source)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.commons.httpclient.ContentLengthInputStream.read(Unknown
>> >> >>> >>> > Source)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.commons.httpclient.ChunkedInputStream.exhaustInputStream(Unknown
>> >> >>> >>> > Source)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.commons.httpclient.ContentLengthInputStream.close(Unknown
>> >> >>> >>> > Source)
>> >> >>> >>> >         at
>> >> >>> >>> > java.io.FilterInputStream.close(FilterInputStream.java:155)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.commons.httpclient.AutoCloseInputStream.notifyWatcher(Unknown
>> >> >>> >>> > Source)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> > org.apache.commons.httpclient.AutoCloseInputStream.close(Unknown
>> >> >>> >>> > Source)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.connectors.webcrawler.ThrottledFetcher$ThrottledInputstream.close(ThrottledFetcher.java:2082)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.connectors.webcrawler.DataCache.addData(DataCache.java:176)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.connectors.webcrawler.WebcrawlerConnector.getDocumentVersions(WebcrawlerConnector.java:745)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.system.WorkerThread.run(WorkerThread.java:321)
>> >> >>> >>> >  INFO 2012-10-10 16:16:27,273 (Worker thread '49') - WEB:
>> >> >>> >>> > FETCH
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > URL|http://xxxxxx/...|1349852786744+600514|-104|4125|org.apache.manifoldcf.core.interfaces.ManifoldCFException|
>> >> >>> >>> > Interrupted: Socket timeout: Read timed out
>> >> >>> >>> > DEBUG 2012-10-10 16:16:27,273 (Worker thread '49') - WEB:
>> >> >>> >>> > Fetch
>> >> >>> >>> > exception
>> >> >>> >>> > for 'http://xxxxxx/...'
>> >> >>> >>> > org.apache.manifoldcf.core.interfaces.ManifoldCFException:
>> >> >>> >>> > Interrupted:
>> >> >>> >>> > Socket timeout: Read timed out
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.connectors.webcrawler.ThrottledFetcher$ThrottledConnection.noteInterrupted(ThrottledFetcher.java:1818)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.connectors.webcrawler.WebcrawlerConnector.getDocumentVersions(WebcrawlerConnector.java:797)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.system.WorkerThread.run(WorkerThread.java:321)
>> >> >>> >>> > Caused by:
>> >> >>> >>> > org.apache.manifoldcf.agents.interfaces.ServiceInterruption:
>> >> >>> >>> > Socket timeout: Read timed out
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.connectors.webcrawler.DataCache.addData(DataCache.java:101)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.connectors.webcrawler.WebcrawlerConnector.getDocumentVersions(WebcrawlerConnector.java:745)
>> >> >>> >>> >         ... 1 more
>> >> >>> >>> > Caused by: java.net.SocketTimeoutException: Read timed out
>> >> >>> >>> >         at java.net.SocketInputStream.socketRead0(Native
>> >> >>> >>> > Method)
>> >> >>> >>> >         at
>> >> >>> >>> > java.net.SocketInputStream.read(SocketInputStream.java:129)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> > java.io.BufferedInputStream.read1(BufferedInputStream.java:256)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> > java.io.BufferedInputStream.read(BufferedInputStream.java:317)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.commons.httpclient.ContentLengthInputStream.read(Unknown
>> >> >>> >>> > Source)
>> >> >>> >>> >         at
>> >> >>> >>> > java.io.FilterInputStream.read(FilterInputStream.java:116)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> > org.apache.commons.httpclient.AutoCloseInputStream.read(Unknown
>> >> >>> >>> > Source)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.connectors.webcrawler.ThrottledFetcher$ThrottledInputstream.basicRead(ThrottledFetcher.java:2012)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.connectors.webcrawler.ThrottledFetcher$ThrottledInputstream.read(ThrottledFetcher.java:1976)
>> >> >>> >>> >         at
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > org.apache.manifoldcf.crawler.connectors.webcrawler.DataCache.addData(DataCache.java:95)
>> >> >>> >>> >         ... 2 more
>> >> >>> >>> >  WARN 2012-10-10 16:16:27,274 (Worker thread '49') -
>> >> >>> >>> > Pre-ingest
>> >> >>> >>> > service
>> >> >>> >>> > interruption reported for job 1349774325961 connection 'WEB':
>> >> >>> >>> > Socket
>> >> >>> >>> > timeout: Read timed out
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> >
>> >> >>> >>> > Regards,
>> >> >>> >>> >
>> >> >>> >>> > Shigeki
>> >> >>> >>
>> >> >>> >>
>> >> >>> >>
>> >> >>> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >
>> >> >
>> >> >
>> >
>> >
>> >
>> >
>
>
>

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