I'm newbie to mongodb, my mongodb database was getting dropped automatically sometimes. I could not find the cause. We have not issued any drop command . but the database is missing and log file contains,
MongoDB - Version 2.4.6
dropDatabase test starting
removeJournalFiles
dropDatabase test finished
Assertion: 13347:local.oplog.rs missing. did you drop it? if so restart server
0x9877f6 0x94bfaa 0x7998e8 0x794d8c 0x6b909e 0x6b95bc 0x7a1549 0x7a4b03 0x75a530 0x5a08eb 0x973c82 0x33b8e07f33 0x33b86f4ded
/usr/bin/mongod(_ZN5mongo15printStackTraceERSo+0x26) [0x9877f6]
/usr/bin/mongod(_ZN5mongo11msgassertedEiPKc+0x9a) [0x94bfaa]
/usr/bin/mongod() [0x7998e8]
/usr/bin/mongod(_ZN5mongo5logOpEPKcS1_RKNS_7BSONObjEPS2_Pbb+0x3c) [0x794d8c]
/usr/bin/mongod(_ZN5mongo7Command11execCommandEPS0_RNS_6ClientEiPKcRNS_7BSONObjERNS_14BSONObjBuilderEb+0xb6e) [0x6b909e]
/usr/bin/mongod(_ZN5mongo12_runCommandsEPKcRNS_7BSONObjERNS_11_BufBuilderINS_16TrivialAllocatorEEERNS_14BSONObjBuilderEbi+0x22c) [0x6b95bc]
/usr/bin/mongod(_ZN5mongo11runCommandsEPKcRNS_7BSONObjERNS_5CurOpERNS_11_BufBuilderINS_16TrivialAllocatorEEERNS_14BSONObjBuilderEbi+0x29) [0x7a1549]
/usr/bin/mongod(_ZN5mongo8runQueryERNS_7MessageERNS_12QueryMessageERNS_5CurOpES1_+0x6c3) [0x7a4b03]
/usr/bin/mongod(_ZN5mongo16assembleResponseERNS_7MessageERNS_10DbResponseERKNS_11HostAndPortE+0x6f0) [0x75a530]
/usr/bin/mongod(_ZN5mongo16MyMessageHandler7processERNS_7MessageEPNS_21AbstractMessagingPortEPNS_9LastErrorE+0xbb) [0x5a08eb]
/usr/bin/mongod(_ZN5mongo17PortMessageServer17handleIncomingMsgEPv+0x432) [0x973c82]
/lib64/libpthread.so.0() [0x33b8e07f33]
/lib64/libc.so.6(clone+0x6d) [0x33b86f4ded]
Please anyone explain me the cause of automatic DB dropping .
Related
I had recently a bug with one collection among my databases. Tried to fix it by myself and then I ran dbmongo with --repair and it never worked with the most recent mongo (6.0 version) . One of the error i get is the following
"t":{"$date":"2022-10-23T10:34:56.814+03:00"},"s":"E", "c":"STORAGE", "id":22435, "ctx":"initandlisten","msg":"WiredTiger error","attr":{"error":0,"message":"[1666510496:814423][245805:0x7f99fc399c80], file:collection-591-2337122025107551252.wt, WT_CURSOR.next: __wt_block_read_off, 296: collection-591-2337122025107551252.wt: potential hardware corruption, read checksum error for 16384B block at offset 4537556992: calculated block checksum doesn't match expected checksum"}}
I tried to fix this error by removing the collection.
Then it produces another error "aborting after invariant() failure":
{"t":{"$date":"2022-10-23T11:13:48.644+03:00"},"s":"F", "c":"-", "id":23081, "ctx":"initandlisten","msg":"Invariant failure","attr":{"expr":"buildUUID","msg":"collection: mydatabase.birds_collection:_id_","file":"src/mongo/db/catalog/index_catalog_impl.cpp","line":169}}
{"t":{"$date":"2022-10-23T11:13:48.644+03:00"},"s":"F", "c":"-", "id":23082, "ctx":"initandlisten","msg":"\n\n***aborting after invariant() failure\n\n"}
{"t":{"$date":"2022-10-23T11:13:48.646+03:00"},"s":"F", "c":"CONTROL", "id":6384300, "ctx":"initandlisten","msg":"Writing fatal message","attr":{"message":"Got signal: 6 (Aborted).\n"}}
Then no matter how many time i run it i always get this error.
Everything i read online consists in running the --repair command
I would be glad is there any way to make it work again even with some broken collections. If there isn't any way how can I backup my collections ?
I tried mongodump but I cannot use since mongo will not start because of this issues. Is there another manual way to backup my file of collections ?
I tried to copy paste them in a new folder but they don't appear in mongo. I just want to save as many collections as possible. I don't have a good backup to use
At the time of backup firebird database (gbak -g -ig) I have the following error:
gbak: writing data for table ORDERS
gbak: ERROR:message length error (encountered 532, expected 528)
gbak: ERROR:gds_$receive failed
gbak:Exiting before completion due to errors
When I'm using gfix with different parameters (-v -full, -mend, -ignore), I have the message:
Summary of validation errors
Number of index page errors : 540
In firebird.log file I see the lines:
PC (Server) Thu Sep 20 08:37:01 2018
Database: E:\...GDB
Index 2 is corrupt on page 134706 level 1. File: ..\..\..\src\jrd\validation.cpp, line: 1699
in table COMPONENTS (197)
However, the database works OK without problems.
Please help me to fix the error and make a backup.
(I need the backup to migrate to on 64bit server).
I'm having an issue with mongodb 2.6.5 and grails 2.4.4 that I can't resolve. For the sake of isolating the problem I created a simple 2.4.4 grails app, installed the grails mongodb plugin (compile ":mongodb:3.0.2"), commented out the hibernate dependencies, added my mongodb datasource, and set up a simple domain class (com.nerds.Nerd). When I generate-all and then start the app and navigate to the NerdController CRUD page I get the following error every time:
MongoTimeoutException occurred when processing request: [GET] /MONGO/nerd/index
Timed out while waiting to connect after 10000 ms. Stacktrace follows:
com.mongodb.MongoTimeoutException: Timed out while waiting to connect after 10000 ms
I can access mongo via http using http://localhost:28017/
I have also tested manually adding data and querying from mongo. This all works fine.
In the debug log prior to the timeout it looks like GORM aquired a mongo session and then tried rolling back a transaction.
DatastoreTransactionManager:128 - Found thread-bound Session [org.grails.datastore.mapping.mongo.MongoSession#e47ee6] for Datastore transaction
DatastoreTransactionManager:128 - Creating new transaction with name [null]: PROPAGATION_REQUIRED,ISOLATION_DEFAULT,readOnly
DatastoreTransactionManager:128 - Initiating transaction rollback
DatastoreTransactionManager:128 - Rolling back Datastore transaction on Session [org.grails.datastore.mapping.mongo.MongoSession#e47ee6]
DatastoreTransactionManager:128 - Resuming suspended transaction after completion of inner transaction
Any insight would be helpful. Thanks
edit: The mongo datasource is pretty simple. I'm using the correct port.
From the mongo log:
014-11-18T13:10:13.388-0900 [initandlisten] MongoDB starting : pid=17275 port=27017 dbpath=/var/lib/mongodb 32-bit host=enterprise
from DataSource.groovy
grails { mongo { host = 'localhost' port = 27017 databaseName = 'mydb' } }
I'm fairly certain the issue was on the mongod side. I stopped the mongo daemon, put it into high verbose debug mode (using mongod -vvvv command), and when I tried to replicate the issue while watching the console output, the issue did not happen. I'm not entirely sure what the exact cause of the timeout was, but its not happening now. Thanks for the responses.
My mongo shell is starting without any error
>use mydb is also working properly (here db name is mydb)
but when i am giving show collections command, it is showing following error.
>show collections
Wed Oct 15 17:38:30 uncaught exception: error: {
"$err" : "file /var/lib/mongodb/mydb.6 open/create failed in createPrivateMap (look in log for more information)",
"code" : 13636
}
Here is the error log
17:38:22 [initandlisten] connection accepted from 127.0.0.1:53178 #1
17:38:30 [conn1] ERROR: mmap private failed with out of memory. You are using a 32-bit build and probably need to upgrade to 64
17:38:30 [conn1] Assertion: 13636:file /var/lib/mongodb/mydb.6 open/create failed in createPrivateMap (look in log for more information)
17:38:30 [conn1] assertion 13636 file /var/lib/mongodb/mydb.6 open/create failed in createPrivateMap (look in log for more information) ns:mydb.system.namespaces query:{}
17:39:01 [clientcursormon] mem (MB) res:2 virt:90 mapped:0
Based on one solution given for another stackoverflow question ,couldn't connect to server 127.0.0.1 shell/mongo.js , i tried same step in my case and problem was solved for time being, but the main issue is whenever i shutdown my machine and restart again i get the same error and i have to repeat same steps (as given in above link) to make mongo shell working and it ultimately lead to data loss within collections. Can anyone suggest what could be the reason , is there some problem with my mongodb installation? Please let me know if anyone had similar issue and successfully resolved it . Thanks
I think there's two possible sources of the problem:
your computer doesn't have enough RAM available
as the log message says, you are using a 32-bit build of MongoDB and should use a 64-bit build, because you have two much data to memory map with 32-bit (> about 2.5 GB)
I'm trying to dump a database from another server (this works fine), then restore it on a new server (this does not work fine).
I first run:
mongodump --host -d
This creates a folder dump/db which contains all of the bson documents.
Then in the dump folder, I'm running:
mongorestore -d dbname db
This works and iterates through the files, but I get this error on dbname.system.users
Wed May 23 02:08:05 { key: { _id: 1 }, ns: "dbname.system.users", name: "_id_" }
Error creating index dbname.system.usersassertion: 13111 field not found, expected type 16
Any ideas how to resolve this?
If it realy different versions, use --noIndexRestore option. And create all index after that.
Any chance the source and destination are different versions?
In any case, to get around this, restore the collections individually using the -c flag to the target DB and then build the indexes afterward. The system collection is the one used for indexes, so it is fairly easy to recreate - try it last once everything else has been restore, and if it still fails you can always just recreate the relevant indexes.
The issue could also caused by this bug in older versions of Mongo (In my case it was 2.0.8):
https://jira.mongodb.org/browse/SERVER-7181
Basically, you get 13111 field not found, expected type 16 error when it should actually be prompting you to enter your authentication details.
And example of how I fixed it:
root#precise64:/# mongorestore /backups/demand/ondemand.05-24-2013T114223/
connected to: 127.0.0.1
[REDACTED]
Fri May 24 11:48:15 going into namespace [test.system.indexes]
Fri May 24 11:48:15 { key: { _id: 1 }, ns: "test.system.users", name: "_id_" }
Error creating index test.system.usersassertion: 13111 field not found, expected type 16
# Error when not giving username and password
root#precise64:/# mongorestore -u fakeuser -p fakepassword /backups/demand/ondemand.05-24-2013T114223/
connected to: 127.0.0.1
[REDACTED]
Fri May 24 11:57:11 /backups/demand/ondemand.05-24-2013T114223/test/system.users.bson
Fri May 24 11:57:11 going into namespace [test.system.users]
1 objects found
# Works fine when giving username and password! :)
Hope that helps anyone who's issue doesn't get fixed by the previous 2 replies!
This can also happen if you are trying to mongorestore into MongoDB 2.6+ and the dump you are trying to restore contains a system.users table in any database other than admin. In MongoDB 2.2 and 2.4 the system.userscollections could occur in any database. The auth schema migration associated with MongoDB 2.6 moved all users into the system.users table in the admin database, but left behind the system.users tables in the other databases (MongoDB 2.6 just ignores these). This seems to cause this assertion when importing into MongoDB 2.6.