So I have a 2TB hard drive with 2 collections in 1 mongoDB.
Collection 1 is about 500gb and completely essential
Collection 2 is about 1500gb and needs to be deleted.
I was running a process that accidentally filled up the entire HDD, leaving 0% space. There is literally nothing on the machine apart from a Linux Distro and this mongoDB.
I would like to delete Collection 2.
In order to do this, I would normally just go into mongo and type db.collection.drop()
However, mongoDB is not currently running. In order to start it, I'm using:
[bobby#myPC bin]# ./mongod --dbpath /home/mongo &
However, since there is no space on the HDD, it returns:
[bobby#myPC bin]# Thu Feb 14 17:47:10 [initandlisten] MongoDB starting : pid=1264 port=27017 dbpath=/home/mongo 64-bit host=localhost.localdomain
Thu Feb 14 17:47:10 [initandlisten] db version v2.2.3, pdfile version 4.5
Thu Feb 14 17:47:10 [initandlisten] git version: f570771a5d8a3846eb7586eaffcf4c2f4a96bf08
Thu Feb 14 17:47:10 [initandlisten] build info: Linux ip-10-2-29-40 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_49
Thu Feb 14 17:47:10 [initandlisten] options: { dbpath: "/home/mongo" }
Thu Feb 14 17:47:10 [initandlisten] journal dir=/home/mongo/journal
Thu Feb 14 17:47:10 [initandlisten] recover : no journal files present, no recovery needed
Thu Feb 14 17:47:10 [initandlisten]
Thu Feb 14 17:47:10 [initandlisten] ERROR: Insufficient free space for journal files
Thu Feb 14 17:47:10 [initandlisten] Please make at least 3379MB available in /home/mongo/journal or use --smallfiles
Thu Feb 14 17:47:10 [initandlisten]
Thu Feb 14 17:47:10 [initandlisten] exception in initAndListen: 15926 Insufficient free space for journals, terminating
Thu Feb 14 17:47:10 dbexit:
Thu Feb 14 17:47:10 [initandlisten] shutdown: going to close listening sockets...
Thu Feb 14 17:47:10 [initandlisten] shutdown: going to flush diaglog...
Thu Feb 14 17:47:10 [initandlisten] shutdown: going to close sockets...
Thu Feb 14 17:47:10 [initandlisten] shutdown: waiting for fs preallocator...
Thu Feb 14 17:47:10 [initandlisten] shutdown: lock for final commit...
Thu Feb 14 17:47:10 [initandlisten] shutdown: final commit...
Thu Feb 14 17:47:10 [initandlisten] shutdown: closing all files...
Thu Feb 14 17:47:10 [initandlisten] closeAllFiles() finished
Thu Feb 14 17:47:10 [initandlisten] journalCleanup...
Thu Feb 14 17:47:10 [initandlisten] removeJournalFiles
Thu Feb 14 17:47:10 [initandlisten] shutdown: removing fs lock...
Thu Feb 14 17:47:10 dbexit: really exiting now
I can't remove this collection cause there's no space. And there's no space because I can't remove this collection.
How can I fix this? Is there some way of identifying which mongoDB files in /home/mongo I can take out?
Based on the error message, its complaining about not having enough space for the journal. Its not ideal in a production environment to run with out journaling, but you could try starting with out it while you fix the issue.
./mongod --nojournal --dbpath /home/mongo &
edit: to answer your question though, mongo creates and allocates files per database, not collection. So you wouldn't be able to target a specific file to remove a collection.
Related
I tried to recover from a sudden shutdown of Mongo, but I'm experiencing some problems. Here is the log file:
***** SERVER RESTARTED *****
Thu Apr 25 01:09:17 [initandlisten] MongoDB starting : pid=19996 port=27017 dbpath=/var/lib/mongodb 64-bit host=Vault
Thu Apr 25 01:09:17 [initandlisten] db version v2.2.3, pdfile version 4.5
Thu Apr 25 01:09:17 [initandlisten] git version: f570771a5d8a3846eb7586eaffcf4c2f4a96bf08
Thu Apr 25 01:09:17 [initandlisten] build info: Linux ip-10-2-29-40 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_49
Thu Apr 25 01:09:17 [initandlisten] options: { config: "/etc/mongodb.conf", dbpath: "/var/lib/mongodb", logappend: "true", logpath: "/var/log/mongodb/mongodb.log", nohttpinterface: "true" }
Thu Apr 25 01:09:17 [initandlisten] journal dir=/var/lib/mongodb/journal
Thu Apr 25 01:09:17 [initandlisten] recover begin
Thu Apr 25 01:09:17 [initandlisten] recover lsn: 3778163987
Thu Apr 25 01:09:17 [initandlisten] recover /var/lib/mongodb/journal/j._0
Thu Apr 25 01:09:17 [initandlisten] dbexception during recovery: 13537 journal file header invalid. This could indicate corruption in a journal file, or perhaps a crash where sectors in file header were in flight written out of order at time of crash (unlikely but possible).
Thu Apr 25 01:09:17 [initandlisten] exception in initAndListen: 13537 journal file header invalid. This could indicate corruption in a journal file, or perhaps a crash where sectors in file header were in flight written out of order at time of crash (unlikely but possible)., terminating
Thu Apr 25 01:09:17 dbexit:
Thu Apr 25 01:09:17 [initandlisten] shutdown: going to close listening sockets...
Thu Apr 25 01:09:17 [initandlisten] shutdown: going to flush diaglog...
Thu Apr 25 01:09:17 [initandlisten] shutdown: going to close sockets...
Thu Apr 25 01:09:17 [initandlisten] shutdown: waiting for fs preallocator...
Thu Apr 25 01:09:17 [initandlisten] shutdown: lock for final commit...
Thu Apr 25 01:09:17 [initandlisten] shutdown: final commit...
Thu Apr 25 01:09:17 [initandlisten] shutdown: closing all files...
Thu Apr 25 01:09:17 [initandlisten] closeAllFiles() finished
Thu Apr 25 01:09:17 [initandlisten] shutdown: removing fs lock...
Thu Apr 25 01:09:17 dbexit: really exiting now
Based on your log file, you are using MongoDB version v2.2.3. This version is not officially supported by MongoDB, so I'd recommend you plan to upgrade to a newer version. The latest stable version, MongoDB 4.0.9.
As per the log message, the journal file j._0 in /var/lib/mongodb/journal/ folder is corrupted.
Try, removing the j._0 file and do the recovery process.
Disclaimer: you may lose some data that present in the journal file.
I installed mongo on ubuntu using the instructions on the following page:
https://docs.mongodb.org/manual/tutorial/install-mongodb-on-os-x/
deploy#stockgame-with-login:~$ mongod --dbpath ~/data/db
Sun Jan 10 15:16:22.090 [initandlisten] MongoDB starting : pid=28452 port=27017 dbpath=/home/deploy/data/db 64-bit host=stockgame-with-login
Sun Jan 10 15:16:22.091 [initandlisten] db version v2.4.14
Sun Jan 10 15:16:22.092 [initandlisten] git version: 05bebf9ab15511a71bfbded684bb226014c0a553
Sun Jan 10 15:16:22.092 [initandlisten] build info: Linux ip-10-154-253-119 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_49
Sun Jan 10 15:16:22.092 [initandlisten] allocator: tcmalloc
Sun Jan 10 15:16:22.093 [initandlisten] options: { dbpath: "/home/deploy/data/db" }
Sun Jan 10 15:16:22.098 [initandlisten] journal dir=/home/deploy/data/db/journal
Sun Jan 10 15:16:22.099 [initandlisten] recover : no journal files present, no recovery needed
Sun Jan 10 15:16:22.209 [initandlisten] ****
Sun Jan 10 15:16:22.210 [initandlisten] ****
Sun Jan 10 15:16:22.210 [initandlisten] need to upgrade database local with pdfile version 4.22, new version: 4.5
Sun Jan 10 15:16:22.210 [initandlisten] Not upgrading, exiting
Sun Jan 10 15:16:22.210 [initandlisten] run --upgrade to upgrade dbs, then start again
Sun Jan 10 15:16:22.210 [initandlisten] ****
Sun Jan 10 15:16:22.210 dbexit:
Sun Jan 10 15:16:22.211 [initandlisten] shutdown: going to close listening sockets...
Sun Jan 10 15:16:22.211 [initandlisten] shutdown: going to flush diaglog...
Sun Jan 10 15:16:22.211 [initandlisten] shutdown: going to close sockets...
Sun Jan 10 15:16:22.211 [initandlisten] shutdown: waiting for fs preallocator...
Sun Jan 10 15:16:22.211 [initandlisten] shutdown: lock for final commit...
Sun Jan 10 15:16:22.211 [initandlisten] shutdown: final commit...
Sun Jan 10 15:16:22.211 [initandlisten] shutdown: closing all files...
Sun Jan 10 15:16:22.213 [initandlisten] closeAllFiles() finished
Sun Jan 10 15:16:22.213 [initandlisten] journalCleanup...
Sun Jan 10 15:16:22.213 [initandlisten] removeJournalFiles
Sun Jan 10 15:16:22.214 [initandlisten] shutdown: removing fs lock...
Sun Jan 10 15:16:22.215 dbexit: really exiting now
deploy#stockgame-with-login:~$
You need to run
mongod --dbpath ~/data/db --upgrade
The current database you are pointing appears to be from an older version of Mongo and it's format is deprecated.
Beware that this --upgrade argument will most likely not be backwards compatible, and older Mongo versions will not be able to read it. If that's not acceptable, you will need to open the database with an older version of Mongo such as 2.6.
I am getting the below error when enabling text search in mongodb. Any Suggestion.
I have mongo.config filw which contains :
##store data here
dbpath=C:\mongodb\data
##all output go here
logpath=C:\mongodb\log\mongo.log
##log read and write operations
diaglog=3
Error is :
C:\mongodb-win32-x86_64-2.4.6\bin>mongod --setParameter textSearchEnabled=true
Tue Jan 14 16:52:51.336 [initandlisten] MongoDB starting : pid=976 port=27017 dbpath=\data\db\ 64-bit host=dellvostro3
Tue Jan 14 16:52:51.337 [initandlisten] db version v2.4.6
Tue Jan 14 16:52:51.337 [initandlisten] git version: b9925db5eac369d77a3a5f5d98a145eaaacd9673
Tue Jan 14 16:52:51.337 [initandlisten] build info: windows sys.getwindowsversion(major=6, minor=1, build=7601, platform=2, service_pack='Service Pack
1') BOOST_LIB_VERSION=1_49
Tue Jan 14 16:52:51.337 [initandlisten] allocator: system
Tue Jan 14 16:52:51.337 [initandlisten] options: { setParameter: [ "textSearchEnabled=true" ] }
Tue Jan 14 16:52:51.337 [initandlisten] exception in initAndListen: 10296
*********************************************************************
ERROR: dbpath (\data\db\) does not exist.
Create this directory or give existing directory in --dbpath.
See http://dochub.mongodb.org/core/startingandstoppingmongo
*********************************************************************
, terminating
Tue Jan 14 16:52:51.338 dbexit:
Tue Jan 14 16:52:51.338 [initandlisten] shutdown: going to close listening sockets...
Tue Jan 14 16:52:51.338 [initandlisten] shutdown: going to flush diaglog...
Tue Jan 14 16:52:51.338 [initandlisten] shutdown: going to close sockets...
Tue Jan 14 16:52:51.338 [initandlisten] shutdown: waiting for fs preallocator...
Tue Jan 14 16:52:51.338 [initandlisten] shutdown: lock for final commit...
Tue Jan 14 16:52:51.338 [initandlisten] shutdown: final commit...
Tue Jan 14 16:52:51.338 [initandlisten] shutdown: closing all files...
Tue Jan 14 16:52:51.338 [initandlisten] closeAllFiles() finished
Tue Jan 14 16:52:51.338 dbexit: really exiting now
You provide wrong path to your data
ERROR: dbpath (\data\db\) does not exist.
\data\db\ is default mongo data path, you need to create this directory or get provide another path when running mongod
When you run
mongod --setParameter textSearchEnabled=true
MongoDB will take \data\db\ as the dbpath. Which is not there in your machine and hence you get the error.
I see you have a config file containing the dbpath etc, but you haven't specified the config file while starting mongod.
mongod --config mongo.config --setParameter textSearchEnabled=true
See using config file here.
Also you could move the textSearchEnabled=true to your config file.
##store data here
dbpath=C:\mongodb\data
##all output go here
logpath=C:\mongodb\log\mongo.log
##log read and write operations
diaglog=3
setParameter=textSearchEnabled=true
Now you can start mongod by just using
mongod --config mongo.config
I just did a manual installation of mongoDB like the documentation says and when I run ./mongocommand this is what I get.
./mongo
MongoDB shell version: 2.4.8
connecting to: test
It doesn't say anymore and doesn't connect to testdatabase.
Anyone know how can I solve this problem?
Thank's in advance
EDIT: I uninstall all and re-install using Brew. Now this is what I get when I run mongod
all output going to: /usr/local/var/log/mongodb/mongo.log
And this when i run mongo
MongoDB shell version: 2.4.8
connecting to: test
Wed Jan 8 13:35:04.634 Error: couldn't connect to server 127.0.0.1:27017 at src/mongo/shell/mongo.js:145
exception: connect failed
And this is what /usr/local/var/log/mongodb/mongo.logshows
***** SERVER RESTARTED *****
Wed Jan 8 13:34:11.749 [initandlisten] MongoDB starting : pid=745 port=27017 dbpath=/usr/local/var/mongodb 64-bit host=MacBook-Pro-de-Kemical.local
Wed Jan 8 13:34:11.749 [initandlisten]
Wed Jan 8 13:34:11.749 [initandlisten] ** WARNING: soft rlimits too low. Number of files is 256, should be at least 1000
Wed Jan 8 13:34:11.749 [initandlisten] db version v2.4.8
Wed Jan 8 13:34:11.749 [initandlisten] git version: nogitversion
Wed Jan 8 13:34:11.749 [initandlisten] build info: Darwin minimountain.local 12.5.0 Darwin Kernel Version 12.5.0: Sun Sep 29 13:33:47 PDT 2013; root:xnu-2050.48.12~1/RELEASE_X86_64 x86_64 BOOST_LIB_VERSION=1_49
Wed Jan 8 13:34:11.749 [initandlisten] allocator: tcmalloc
Wed Jan 8 13:34:11.749 [initandlisten] options: { bind_ip: "127.0.0.1", config: "/usr/local/etc/mongod.conf", dbpath: "/usr/local/var/mongodb", logappend: "true", logpath: "/usr/local/var/log/mongodb/mongo.log" }
Wed Jan 8 13:34:11.750 [initandlisten] exception in initAndListen: 10310 Unable to lock file: /usr/local/var/mongodb/mongod.lock. Is a mongod instance already running?, terminating
Wed Jan 8 13:34:11.750 dbexit:
Wed Jan 8 13:34:11.750 [initandlisten] shutdown: going to close listening sockets...
Wed Jan 8 13:34:11.750 [initandlisten] shutdown: going to flush diaglog...
Wed Jan 8 13:34:11.750 [initandlisten] shutdown: going to close sockets...
Wed Jan 8 13:34:11.750 [initandlisten] shutdown: waiting for fs preallocator...
Wed Jan 8 13:34:11.750 [initandlisten] shutdown: lock for final commit...
Wed Jan 8 13:34:11.750 [initandlisten] shutdown: final commit...
Wed Jan 8 13:34:11.750 [initandlisten] shutdown: closing all files...
Wed Jan 8 13:34:11.750 [initandlisten] closeAllFiles() finished
Wed Jan 8 13:34:11.750 dbexit: really exiting now
First of all, have you actually started the "mongod" server process?
If you have, you need to find out what is happening and one way to do this is with the "strace" tool. Running it like follows creates a log file in /tmp/strace.log and that should tell you system level wise what's going on:
strace -o /tmp/strace.log ./mongo
I was running MongoDB on Amazon AWS, until one day it ran out of space. Then, the database is completely inaccessible,and I tried to shutdown the database. Having restarted the server and installed larger disk, the MongoDB can't be started.
I tried to repair the database, and the error is shown like below:
Wed Aug 15 10:08:04 [initandlisten] MongoDB starting : pid=1447 port=27017 dbpath=/var/lib/mongodb/ 32-bit
** NOTE: when using MongoDB 32 bit, you are limited to about 2 gigabytes of data
** see http://blog.mongodb.org/post/137788967/32-bit-limitations
** with --dur, the limit is lower
Wed Aug 15 10:08:04 [initandlisten] db version v1.8.3, pdfile version 4.5
Wed Aug 15 10:08:04 [initandlisten] git version: c206d77e94bc3b65c76681df5a6b605f68a2de05
Wed Aug 15 10:08:04 [initandlisten] build sys info: Linux domU-12-31-39-01-70-B4 2.6.21.7-2.fc8xen #1 SMP Fri Feb 15 12:39:36 EST 2008 i686 BOOST_LIB_VERSION=1_37
Wed Aug 15 10:08:04 [initandlisten] **
Wed Aug 15 10:08:04 [initandlisten] **
Wed Aug 15 10:08:04 [initandlisten] need to upgrade database md with pdfile version 559903.1345021735, new version: 4.5
Wed Aug 15 10:08:04 [initandlisten] starting upgrade
Wed Aug 15 10:08:04 [initandlisten] md repairDatabase md
Wed Aug 15 10:08:04 [initandlisten] md.system.namespaces Assertion failure isOk() db/pdfile.h 259
0x817c27b 0x819121e 0x83cf525 0x83d6bec 0x83f5420 0x82a4fb7 0x83f8680 0x83fcece 0x8401358 0x8401e29 0x8402abd 0x828f755 0x83b3d67 0x83b931c 0x83bb3df 0x81ce25f 0x81ae714 0x8380f31 0x83831ba 0x83d4faf
mongod(_ZN5mongo12sayDbContextEPKc+0xcb) [0x817c27b]
mongod(_ZN5mongo8assertedEPKcS1_j+0x12e) [0x819121e]
mongod(_ZN5mongo11DataFileMgr7findAllEPKcRKNS_7DiskLocE+0x7a5) [0x83cf525]
mongod(_ZN5mongo13findTableScanEPKcRKNS_7BSONObjERKNS_7DiskLocE+0x13c) [0x83d6bec]
mongod(_ZNK5mongo9QueryPlan9newCursorERKNS_7DiskLocEi+0x830) [0x83f5420]
mongod(_ZN5mongo11UserQueryOp5_initEv+0x437) [0x82a4fb7]
mongod(_ZN5mongo12QueryPlanSet6Runner6initOpERNS_7QueryOpE+0x110) [0x83f8680]
mongod(_ZN5mongo12QueryPlanSet6Runner3runEv+0x2ee) [0x83fcece]
mongod(_ZN5mongo12QueryPlanSet5runOpERNS_7QueryOpE+0x2e8) [0x8401358]
mongod(_ZN5mongo16MultiPlanScanner9runOpOnceERNS_7QueryOpE+0x59) [0x8401e29]
mongod(_ZN5mongo16MultiPlanScanner5runOpERNS_7QueryOpE+0x2d) [0x8402abd]
mongod(_ZN5mongo8runQueryERNS_7MessageERNS_12QueryMessageERNS_5CurOpES1_+0x1575) [0x828f755]
mongod() [0x83b3d67]
mongod(_ZN5mongo16assembleResponseERNS_7MessageERNS_10DbResponseERKNS_8SockAddrE+0x70c) [0x83b931c]
mongod(_ZN5mongo14DBDirectClient4callERNS_7MessageES2_bPSs+0x7f) [0x83bb3df]
mongod(_ZN5mongo14DBClientCursor4initEv+0x15f) [0x81ce25f]
mongod(_ZN5mongo12DBClientBase5queryERKSsNS_5QueryEiiPKNS_7BSONObjEii+0x2a4) [0x81ae714]
mongod(_ZN5mongo6Cloner2goEPKcRSsRKSsbbbb+0x451) [0x8380f31]
mongod(_ZN5mongo9cloneFromEPKcRSsRKSsbbbb+0x5a) [0x83831ba]
mongod(_ZN5mongo14repairDatabaseESsRSsbb+0x38f) [0x83d4faf]
Wed Aug 15 10:08:04 [initandlisten] assertion 0 assertion db/pdfile.h:259 ns:md.system.namespaces query:{}
Wed Aug 15 10:08:04 [initandlisten] Assertion: 10290:bad system.namespaces object { $err: "assertion db/pdfile.h:259" }
0x819045e 0x8381181 0x83831ba 0x83d4faf 0x852a30c 0x852b217 0x852e733 0x852f59c 0x85366bb 0xb74a4ce7 0x810b551
mongod(_ZN5mongo11msgassertedEiPKc+0x15e) [0x819045e]
mongod(_ZN5mongo6Cloner2goEPKcRSsRKSsbbbb+0x6a1) [0x8381181]
mongod(_ZN5mongo9cloneFromEPKcRSsRKSsbbbb+0x5a) [0x83831ba]
mongod(_ZN5mongo14repairDatabaseESsRSsbb+0x38f) [0x83d4faf]
mongod(_ZN5mongo11doDBUpgradeERKSsSsPNS_14DataFileHeaderE+0x6c) [0x852a30c]
mongod() [0x852b217]
mongod(_ZN5mongo14_initAndListenEiPKc+0x4b3) [0x852e733]
mongod(ZN5mongo13initAndListenEiPKc+0x2c) [0x852f59c]
mongod(main+0x6bdb) [0x85366bb]
/lib/libc.so.6(_libc_start_main+0xe7) [0xb74a4ce7]
mongod() [0x810b551]
Wed Aug 15 10:08:04 [initandlisten] exception in initAndListen std::exception: bad system.namespaces object { $err: "assertion db/pdfile.h:259" }, terminating
Wed Aug 15 10:08:04 dbexit:
Wed Aug 15 10:08:04 [initandlisten] shutdown: going to close listening sockets...
Wed Aug 15 10:08:04 [initandlisten] shutdown: going to flush diaglog...
Wed Aug 15 10:08:04 [initandlisten] shutdown: going to close sockets...
Wed Aug 15 10:08:04 [initandlisten] shutdown: waiting for fs preallocator...
Wed Aug 15 10:08:04 [initandlisten] shutdown: closing all files...
Wed Aug 15 10:08:04 closeAllFiles() finished
Wed Aug 15 10:08:04 [initandlisten] shutdown: removing fs lock...
Wed Aug 15 10:08:04 dbexit: really exiting now
I have all *.number and *.ns file completely. But it seems the ns file is corrupted. Any way I could repair the database?
Thanks
If repair doesn't work then you are unfortunately out of luck.
I'm presuming that you didn't have journaling enabled or any back-ups. I would strongly encourage you to run with journaling enabled and follow one of the back-up strategies outlined here. The LVM snapshot is easy to implement, fairly quick and reliable.
You are better to run MongoDB on a 64-bit system also. 32-bit limits you to 2gb of data. You say that you "ran out of space"?