JS Error: uncaught exception: error: { "$err" : "assertion db/pdfile.h:223" }

[Fathi Ghroul]

Hello,

I've just started to learn MongoDb using RockMongo. I added a database
and I'm receiving the following message whenever I'm trying to access
the database through Rockmongo.

Execute failed:db assertion failure
function (){ return db.getCollectionNames(); }

Thanks,
Fathi

[Nat]

It could be that database is corrupted. Try to repairDatabase() to see whether it helps or not.

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[Fathi Ghroul]

I tried but it not improve.

2012/6/8 Nat <nat....@gmail.com>

[Eliot Horowitz]

Can you send the full mongo log?

[Markku]

We are using large ec2 instance and been importing (.update()) open street map places to mongodb. Suddenly mongodb hanged. Only find().count() operation seems to work. Everything else gives error.

> db.repairDatabase();

{

        "errmsg" : "clone failed for trivian with error: query failed trivian.system.namespaces",

        "ok" : 0

}

> db.places.validate()

{

        "ns" : "trivian.places",

        "errmsg" : "exception: assertion db/pdfile.h:300",

        "code" : 0,

        "ok" : 0,

        "valid" : false

}

> db.places.find().count()

6706729

root@ip-10-144-73-149:/ebs/trivian/scripts# sudo mongo --version

MongoDB shell version: 2.0.3

/ebs/trivian/mongodb/logs/mongodb.log

Tue Jul  3 11:24:45 [snapshotthread] cpu: elapsed:4000  writelock: 0%

Tue Jul  3 11:24:46 [conn17]  trivian.system.namespaces Assertion failure isOk() db/pdfile.h 300

0x57a636 0x5854eb 0x8a7b2a 0x8a7ed6 0x8cf301 0x94c093 0x8cbc7a 0x8cc093 0x8cc59c 0x8d5d2e 0x8dd7be 0x8df1d3 0x8e04a7 0x943a49 0x8869d7 0x88df49 0xaa37d6 0x637497 0x7fe1702cfe9a 0x7fe16f7ed4bd

 mongod(_ZN5mongo12sayDbContextEPKc+0x96) [0x57a636]

 mongod(_ZN5mongo8assertedEPKcS1_j+0xfb) [0x5854eb]

 mongod(_ZN5mongo11DataFileMgr7findAllEPKcRKNS_7DiskLocE+0x5fa) [0x8a7b2a]

 mongod(_ZN5mongo13findTableScanEPKcRKNS_7BSONObjERKNS_7DiskLocE+0xe6) [0x8a7ed6]

 mongod(_ZNK5mongo9QueryPlan9newCursorERKNS_7DiskLocEi+0x3a1) [0x8cf301]

 mongod(_ZN5mongo11UserQueryOp5_initEv+0x763) [0x94c093]

 mongod(_ZN5mongo7QueryOp4initEv+0x11a) [0x8cbc7a]

 mongod(_ZN5mongo12QueryPlanSet6Runner6initOpERNS_7QueryOpE+0x23) [0x8cc093]

 mongod(_ZN5mongo12QueryPlanSet6Runner4initEv+0x2ec) [0x8cc59c]

 mongod(_ZN5mongo12QueryPlanSet6Runner22runUntilFirstCompletesEv+0x1e) [0x8d5d2e]

 mongod(_ZN5mongo12QueryPlanSet5runOpERNS_7QueryOpE+0x11e) [0x8dd7be]

 mongod(_ZN5mongo16MultiPlanScanner9runOpOnceERNS_7QueryOpE+0x523) [0x8df1d3]

 mongod(_ZN5mongo16MultiPlanScanner5runOpERNS_7QueryOpE+0x17) [0x8e04a7]

 mongod(_ZN5mongo8runQueryERNS_7MessageERNS_12QueryMessageERNS_5CurOpES1_+0xa79) [0x943a49]

 mongod() [0x8869d7]

 mongod(_ZN5mongo16assembleResponseERNS_7MessageERNS_10DbResponseERKNS_11HostAndPortE+0x559) [0x88df49]

 mongod(_ZN5mongo16MyMessageHandler7processERNS_7MessageEPNS_21AbstractMessagingPortEPNS_9LastErrorE+0x76) [0xaa37d6]

 mongod(_ZN5mongo3pms9threadRunEPNS_13MessagingPortE+0x287) [0x637497]

 /lib/x86_64-linux-gnu/libpthread.so.0(+0x7e9a) [0x7fe1702cfe9a]

 /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d) [0x7fe16f7ed4bd]

Tue Jul  3 11:24:46 [conn17] assertion 0 assertion db/pdfile.h:300 ns:trivian.system.namespaces query:{}

Tue Jul  3 11:24:46 [conn17] profile: warning ns trivian.system.profile does not exist

Tue Jul  3 11:24:49 [snapshotthread] cpu: elapsed:4000  writelock: 0%

Tue Jul  3 11:24:51 [conn16] Assertion: 10320:BSONElement: bad type 96

0x584432 0x5072bd 0x502112 0x502329 0x8d0da5 0x8d3fdb 0x8db769 0x8ddac7 0x8e0968 0x943692 0x8869d7 0x88df49 0xaa37d6 0x637497 0x7fe1702cfe9a 0x7fe16f7ed4bd

 mongod(_ZN5mongo11msgassertedEiPKc+0x112) [0x584432]

 mongod(_ZNK5mongo11BSONElement4sizeEv+0x1bd) [0x5072bd]

 mongod(_ZN5mongo20anyElementNamesMatchERKNS_7BSONObjES2_+0x92) [0x502112]

 mongod(_ZNK5mongo9IndexSpec12_suitabilityERKNS_7BSONObjES3_+0x19) [0x502329]

 mongod(_ZN5mongo16QueryUtilIndexed11indexUsefulERKNS_17FieldRangeSetPairEPNS_16NamespaceDetailsEiRKNS_7BSONObjE+0x165) [0x8d0da5]

 mongod(_ZN5mongo12QueryPlanSet13addOtherPlansEb+0x1fb) [0x8d3fdb]

 mongod(_ZN5mongo12QueryPlanSet4initEv+0x14b9) [0x8db769]

 mongod(_ZN5mongo12QueryPlanSetC1EPKcSt8auto_ptrINS_17FieldRangeSetPairEES5_RKNS_7BSONObjES8_bPKNS_11BSONElementEbS8_S8_bb+0x1f7) [0x8ddac7]

 mongod(_ZN5mongo16MultiPlanScannerC1EPKcRKNS_7BSONObjES5_PKNS_11BSONElementEbS5_S5_bb+0x2c8) [0x8e0968]

 mongod(_ZN5mongo8runQueryERNS_7MessageERNS_12QueryMessageERNS_5CurOpES1_+0x6c2) [0x943692]

 mongod() [0x8869d7]

 mongod(_ZN5mongo16assembleResponseERNS_7MessageERNS_10DbResponseERKNS_11HostAndPortE+0x559) [0x88df49]

 mongod(_ZN5mongo16MyMessageHandler7processERNS_7MessageEPNS_21AbstractMessagingPortEPNS_9LastErrorE+0x76) [0xaa37d6]

 mongod(_ZN5mongo3pms9threadRunEPNS_13MessagingPortE+0x287) [0x637497]

 /lib/x86_64-linux-gnu/libpthread.so.0(+0x7e9a) [0x7fe1702cfe9a]

 /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d) [0x7fe16f7ed4bd]

root@ip-10-144-73-149:/ebs/trivian/scripts# ls -la /ebs/trivian/mongodb/data

total 4242472

drwxr-xr-x 4 root root       4096 Jul  3 11:35 .

drwxr-xr-x 4 root root       4096 Jul  2 11:38 ..

drwxr-xr-x 2 root root       4096 Jul  3 11:36 journal

-rw------- 1 root root   67108864 Jul  2 11:40 local.0

-rw------- 1 root root   16777216 Jul  2 11:40 local.ns

-rwxr-xr-x 1 root root          5 Jul  3 09:52 mongod.lock

-rw------- 1 root root   16777216 Jul  3 10:05 test.ns

drwxr-xr-x 2 root root       4096 Jul  3 10:09 _tmp

-rw------- 1 root root   67108759 Jul  3 11:22 trivian.0

-rw------- 1 root root  134217728 Jul  3 10:17 trivian.1

-rw------- 1 root root  268435456 Jul  3 10:17 trivian.2

-rw------- 1 root root  536870676 Jul  3 11:23 trivian.3

-rw------- 1 root root 1073741824 Jul  3 10:17 trivian.4

-rw------- 1 root root 2146435072 Jul  3 10:09 trivian.5

-rw------- 1 root root   16777216 Jul  3 11:37 trivian.ns

-Markku

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>
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[Markku]

MongoDb does not startup anymore.

root@ip-10-144-73-149:/ebs/trivian/scripts# sudo mongod --dbpath=/ebs/trivian/mongodb/data --quiet --nohttpinterface --profile=2 --slowms=100 --journal --cpu --fork --bind_ip 127.0.0.1,10.144.73.149 --logpath=/ebs/trivian/mongodb/logs/mongodb.log

root@ip-10-144-73-149:/ebs/trivian/scripts# forked process: 5054

all output going to: /ebs/trivian/mongodb/logs/mongodb.log

root@ip-10-144-73-149:/ebs/trivian/scripts# cat /ebs/trivian/mongodb/logs/mongodb.log

Tue Jul  3 11:50:14 [initandlisten] MongoDB starting : pid=5054 port=27017 dbpath=/ebs/trivian/mongodb/data 64-bit host=ip-10-144-73-149

Tue Jul  3 11:50:14 [initandlisten] db version v2.0.3, pdfile version 4.5

Tue Jul  3 11:50:14 [initandlisten] git version: 05bb8aa793660af8fce7e36b510ad48c27439697

Tue Jul  3 11:50:14 [initandlisten] build info: Linux ip-10-110-9-236 2.6.21.7-2.ec2.v1.2.fc8xen #1 SMP Fri Nov 20 17:48:28 EST 2009 x86_64 BOOST_LIB_VERSION=1_41

Tue Jul  3 11:50:14 [initandlisten] options: { bind_ip: "127.0.0.1,10.144.73.149", cpu: true, dbpath: "/ebs/trivian/mongodb/data", fork: true, journal: true, logpath: "/ebs/trivian/mongodb/logs/mongodb.log", nohttpinterface: true, profile: 2, quiet: true, slowms: 100 }

Tue Jul  3 11:50:14 [initandlisten] journal dir=/ebs/trivian/mongodb/data/journal

Tue Jul  3 11:50:14 [initandlisten] recover : no journal files present, no recovery needed

Tue Jul  3 11:50:14 [initandlisten] profile: warning ns local.system.profile does not exist

Tue Jul  3 11:50:14 [initandlisten] ****

Tue Jul  3 11:50:14 [initandlisten] ****

Tue Jul  3 11:50:14 [initandlisten] need to upgrade database trivian with pdfile version 5.67108864, new version: 4.5

Tue Jul  3 11:50:14 [initandlisten]      Not upgrading, exiting

Tue Jul  3 11:50:14 [initandlisten]      run --upgrade to upgrade dbs, then start again

Tue Jul  3 11:50:14 [initandlisten] ****

Tue Jul  3 11:50:14 dbexit:

Tue Jul  3 11:50:14 [initandlisten] shutdown: going to close listening sockets...

Tue Jul  3 11:50:14 [initandlisten] shutdown: going to flush diaglog...

Tue Jul  3 11:50:14 [initandlisten] shutdown: going to close sockets...

Tue Jul  3 11:50:14 [initandlisten] shutdown: waiting for fs preallocator...

Tue Jul  3 11:50:14 [initandlisten] shutdown: lock for final commit...

Tue Jul  3 11:50:14 [initandlisten] shutdown: final commit...

Tue Jul  3 11:50:14 [initandlisten] shutdown: closing all files...

Tue Jul  3 11:50:14 [initandlisten] closeAllFiles() finished

Tue Jul  3 11:50:14 [initandlisten] journalCleanup...

Tue Jul  3 11:50:14 [initandlisten] removeJournalFiles

Tue Jul  3 11:50:14 [initandlisten] shutdown: removing fs lock...

Tue Jul  3 11:50:14 dbexit: really exiting now

Logstream::get called in uninitialized state

Tue Jul  3 11:50:14 ERROR: Client::~Client _context should be null but is not; client:initandlisten

root@ip-10-144-73-149:/ebs/trivian/scripts# ps -ef | grep mongo

root      4990  4793  0 11:28 pts/2    00:00:00 sudo mongo

root      4991  4990  0 11:28 pts/2    00:00:00 mongo

root      5062  4436  0 11:50 pts/0    00:00:00 grep --color=auto mongo

[Markku]

Repair does not work

sudo mongod --repair --dbpath=/ebs/trivian/mongodb/data

Tue Jul  3 11:55:07 [initandlisten] MongoDB starting : pid=5096 port=27017 dbpath=/ebs/trivian/mongodb/data 64-bit host=ip-10-144-73-149

Tue Jul  3 11:55:07 [initandlisten] db version v2.0.3, pdfile version 4.5

Tue Jul  3 11:55:07 [initandlisten] git version: 05bb8aa793660af8fce7e36b510ad48c27439697

Tue Jul  3 11:55:07 [initandlisten] build info: Linux ip-10-110-9-236 2.6.21.7-2.ec2.v1.2.fc8xen #1 SMP Fri Nov 20 17:48:28 EST 2009 x86_64 BOOST_LIB_VERSION=1_41

Tue Jul  3 11:55:07 [initandlisten] options: { dbpath: "/ebs/trivian/mongodb/data", repair: true }

Tue Jul  3 11:55:07 [initandlisten] journal dir=/ebs/trivian/mongodb/data/journal

Tue Jul  3 11:55:07 [initandlisten] recover : no journal files present, no recovery needed

Tue Jul  3 11:55:07 [initandlisten] ****

Tue Jul  3 11:55:07 [initandlisten] ****

Tue Jul  3 11:55:07 [initandlisten] need to upgrade database trivian with pdfile version 5.67108864, new version: 4.5

Tue Jul  3 11:55:07 [initandlisten]      starting upgrade

Tue Jul  3 11:55:07 [initandlisten]  trivian repairDatabase trivian

Tue Jul  3 11:55:07 [initandlisten] removeJournalFiles

Tue Jul  3 11:55:07 [initandlisten]  trivian.system.namespaces Assertion failure isOk() db/pdfile.h 300

0x57a636 0x5854eb 0x8a7b2a 0x8a7ed6 0x8cf301 0x94c093 0x8cbc7a 0x8cc093 0x8cc59c 0x8d5d2e 0x8dd7be 0x8df1d3 0x8e04a7 0x943a49 0x8869d7 0x88df49 0x88f851 0x5e2add 0x5b579

c 0x851341

 mongod(_ZN5mongo12sayDbContextEPKc+0x96) [0x57a636]

 mongod(_ZN5mongo8assertedEPKcS1_j+0xfb) [0x5854eb]

 mongod(_ZN5mongo11DataFileMgr7findAllEPKcRKNS_7DiskLocE+0x5fa) [0x8a7b2a]

 mongod(_ZN5mongo13findTableScanEPKcRKNS_7BSONObjERKNS_7DiskLocE+0xe6) [0x8a7ed6]

 mongod(_ZNK5mongo9QueryPlan9newCursorERKNS_7DiskLocEi+0x3a1) [0x8cf301]

 mongod(_ZN5mongo11UserQueryOp5_initEv+0x763) [0x94c093]

 mongod(_ZN5mongo7QueryOp4initEv+0x11a) [0x8cbc7a]

 mongod(_ZN5mongo12QueryPlanSet6Runner6initOpERNS_7QueryOpE+0x23) [0x8cc093]

 mongod(_ZN5mongo12QueryPlanSet6Runner4initEv+0x2ec) [0x8cc59c]

 mongod(_ZN5mongo12QueryPlanSet6Runner22runUntilFirstCompletesEv+0x1e) [0x8d5d2e]

 mongod(_ZN5mongo12QueryPlanSet5runOpERNS_7QueryOpE+0x11e) [0x8dd7be]

 mongod(_ZN5mongo16MultiPlanScanner9runOpOnceERNS_7QueryOpE+0x523) [0x8df1d3]

 mongod(_ZN5mongo16MultiPlanScanner5runOpERNS_7QueryOpE+0x17) [0x8e04a7]

 mongod(_ZN5mongo8runQueryERNS_7MessageERNS_12QueryMessageERNS_5CurOpES1_+0xa79) [0x943a49]

 mongod() [0x8869d7]

 mongod(_ZN5mongo16assembleResponseERNS_7MessageERNS_10DbResponseERKNS_11HostAndPortE+0x559) [0x88df49]

 mongod(_ZN5mongo14DBDirectClient4callERNS_7MessageES2_bPSs+0x81) [0x88f851]

 mongod(_ZN5mongo14DBClientCursor4initEv+0xad) [0x5e2add]

 mongod(_ZN5mongo12DBClientBase5queryERKSsNS_5QueryEiiPKNS_7BSONObjEii+0x3ac) [0x5b579c]

 mongod(_ZN5mongo6Cloner2goEPKcRSsRKSsbbbbbbPi+0x501) [0x851341]

Tue Jul  3 11:55:07 [initandlisten] assertion 0 assertion db/pdfile.h:300 ns:trivian.system.namespaces query:{}

Tue Jul  3 11:55:07 [initandlisten]  trivian clone failed for trivian with error: query failed trivian.system.namespaces

Tue Jul  3 11:55:07 [initandlisten] removeJournalFiles

Tue Jul  3 11:55:07 [initandlisten]  trivian Assertion failure doDBUpgrade( dbName , errmsg , h ) db/db.cpp 298

0x57a636 0x5854eb 0xa93382 0xa94c54 0xa9558d 0xa9f2ba 0x7f5a25c1c76d 0x501349

 mongod(_ZN5mongo12sayDbContextEPKc+0x96) [0x57a636]

 mongod(_ZN5mongo8assertedEPKcS1_j+0xfb) [0x5854eb]

 mongod() [0xa93382]

 mongod(_ZN5mongo14_initAndListenEi+0x404) [0xa94c54]

 mongod(_ZN5mongo13initAndListenEi+0x1d) [0xa9558d]

 mongod(main+0x9aaa) [0xa9f2ba]

 /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7f5a25c1c76d]

 mongod(__gxx_personality_v0+0x3f1) [0x501349]

Tue Jul  3 11:55:07 [initandlisten] exception in initAndListen: 0 assertion db/db.cpp:298, terminating

Tue Jul  3 11:55:07 dbexit:

Tue Jul  3 11:55:07 [initandlisten] shutdown: going to close listening sockets...

Tue Jul  3 11:55:07 [initandlisten] shutdown: going to flush diaglog...

Tue Jul  3 11:55:07 [initandlisten] shutdown: going to close sockets...

Tue Jul  3 11:55:07 [initandlisten] shutdown: waiting for fs preallocator...

Tue Jul  3 11:55:07 [initandlisten] shutdown: lock for final commit...

Tue Jul  3 11:55:07 [initandlisten] shutdown: final commit...

Tue Jul  3 11:55:07 [initandlisten] shutdown: closing all files...

Tue Jul  3 11:55:07 [initandlisten] closeAllFiles() finished

Tue Jul  3 11:55:07 [initandlisten] journalCleanup...

Tue Jul  3 11:55:07 [initandlisten] removeJournalFiles

Tue Jul  3 11:55:07 [initandlisten] shutdown: removing fs lock...

Tue Jul  3 11:55:07 dbexit: really exiting now

[Nat]

It looks fairly similar to https://jira.mongodb.org/browse/SERVER-4198

Did you ever run it without journaling option on?

---

From: Markku <markku....@gmail.com>

Sender: mongod...@googlegroups.com

Date: Tue, 3 Jul 2012 04:57:46 -0700 (PDT)

To: <mongod...@googlegroups.com>

ReplyTo: mongod...@googlegroups.com

Subject: Re: [mongodb-user] JS Error: uncaught exception: error: { "$err" : "assertion db/pdfile.h:223" }

mongodb-user...@googlegroups.com