My system crashed, and I saw the following error when I tried to repair my MongoDB database. I'm going to try to keep a copy of the corrupted database around for a while in case you need it.

Note that the database in question wasn't vital; I had used it months ago for benchmarking GridFS. And I have no idea why mongod thinks it needs to upgrade anything—I haven't touched my MongoDB installation in the last several reboots, and I've been running it continuously.

$ mongod --version
db version v1.6.0, pdfile version 4.5
Tue Oct 26 16:01:55 git version: nogitversion

$ mongod --repair
Tue Oct 26 15:27:48 MongoDB starting : pid=729 port=27017 dbpath=/data/db/ 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

Tue Oct 26 15:27:48 db version v1.6.0, pdfile version 4.5
Tue Oct 26 15:27:48 git version: nogitversion
Tue Oct 26 15:27:48 sys info: Darwin whitestar.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 BOOST_LIB_VERSION=1_43
Tue Oct 26 15:27:48 [initandlisten] ****
Tue Oct 26 15:27:48 [initandlisten] ****
Tue Oct 26 15:27:48 [initandlisten] need to upgrade database benchmark-gridfs with pdfile version 4.5, new version: 4.5
Tue Oct 26 15:27:48 [initandlisten] starting upgrade
Tue Oct 26 15:27:48 [initandlisten] benchmark-gridfs repairDatabase benchmark-gridfs
Tue Oct 26 15:27:49 [initandlisten] benchmark-gridfs.system.namespaces Assertion failure magic == 0x41424344 db/pdfile.h 239
0x77651 0x870ec 0x292e89 0x282a7d 0x285562 0x2a035c 0x15c6c7 0x29dad7 0x2a4614 0x2a988b 0x2ab963 0x2ac668 0x145f08 0x25b284 0x2673da 0x267ffa 0xbc4a4 0x9e8f9 0x22b45d 0x22d5ae
0 mongod 0x00077651 _ZN5mongo12sayDbContextEPKc + 193
1 mongod 0x000870ec _ZN5mongo8assertedEPKcS1_j + 300
2 mongod 0x00292e89 _ZN5mongo11DataFileMgr9getExtentERKNS_7DiskLocE + 137
3 mongod 0x00282a7d _ZN5mongo11DataFileMgr7findAllEPKcRKNS_7DiskLocE + 61
4 mongod 0x00285562 _ZN5mongo13findTableScanEPKcRKNS_7BSONObjERKNS_7DiskLocE + 146
5 mongod 0x002a035c _ZNK5mongo9QueryPlan9newCursorERKNS_7DiskLocEi + 1228
6 mongod 0x0015c6c7 _ZN5mongo11UserQueryOp5_initEv + 407
7 mongod 0x0029dad7 _ZN5mongo12QueryPlanSet6Runner6initOpERNS_7QueryOpE + 311
8 mongod 0x002a4614 _ZN5mongo12QueryPlanSet6Runner3runEv + 788
9 mongod 0x002a988b _ZN5mongo12QueryPlanSet5runOpERNS_7QueryOpE + 635
10 mongod 0x002ab963 _ZN5mongo16MultiPlanScanner9runOpOnceERNS_7QueryOpE + 99
11 mongod 0x002ac668 _ZN5mongo16MultiPlanScanner5runOpERNS_7QueryOpE + 40
12 mongod 0x00145f08 ZN5mongo8runQueryERNS_7MessageERNS_12QueryMessageERNS_5CurOpES1 + 3480
13 mongod 0x0025b284 _ZN5mongo10flushOpLogERSt18basic_stringstreamIcSt11char_traitsIcESaIcEE + 836
14 mongod 0x002673da _ZN5mongo16assembleResponseERNS_7MessageERNS_10DbResponseERKNS_8SockAddrE + 5962
15 mongod 0x00267ffa _ZN5mongo14DBDirectClient4callERNS_7MessageES2_b + 122
16 mongod 0x000bc4a4 _ZN5mongo14DBClientCursor4initEv + 244
17 mongod 0x0009e8f9 _ZN5mongo12DBClientBase5queryERKSsNS_5QueryEiiPKNS_7BSONObjEii + 601
18 mongod 0x0022b45d _ZN5mongo6Cloner2goEPKcRSsRKSsbbbb + 797
19 mongod 0x0022d5ae _ZN5mongo9cloneFromEPKcRSsRKSsbbbb + 78
Tue Oct 26 15:27:49 [initandlisten] assertion 0 assertion db/pdfile.h:239 ns:benchmark-gridfs.system.namespaces query:{}
Tue Oct 26 15:27:49 [initandlisten] query benchmark-gridfs.system.namespaces exception 183ms
Tue Oct 26 15:27:49 [initandlisten] Assertion: 10290:bad system.namespaces object

0x863ff 0x22b85b 0x22d5ae 0x27defa 0x3a109f 0x3a48bc 0x3a8211 0x3a8afa 0x3aa609 0x1b36
0 mongod 0x000863ff _ZN5mongo11msgassertedEiPKc + 367
1 mongod 0x0022b85b _ZN5mongo6Cloner2goEPKcRSsRKSsbbbb + 1819
2 mongod 0x0022d5ae _ZN5mongo9cloneFromEPKcRSsRKSsbbbb + 78
3 mongod 0x0027defa _ZN5mongo14repairDatabaseESsRSsbb + 1562
4 mongod 0x003a109f _ZN5mongo11doDBUpgradeERKSsSsPNS_14DataFileHeaderE + 111
5 mongod 0x003a48bc _ZN5mongo15repairDatabasesEv + 1036
6 mongod 0x003a8211 _ZN5mongo14_initAndListenEiPKc + 1089
7 mongod 0x003a8afa _ZN5mongo13initAndListenEiPKc + 42
8 mongod 0x003aa609 main + 4633
9 mongod 0x00001b36 start + 54
Tue Oct 26 15:27:49 [initandlisten] exception in initAndListen std::exception: bad system.namespaces object

, terminating
Tue Oct 26 15:27:49 dbexit:

Tue Oct 26 15:27:49 [initandlisten] shutdown: going to close listening sockets...
Tue Oct 26 15:27:49 [initandlisten] shutdown: going to flush oplog...
Tue Oct 26 15:27:49 [initandlisten] shutdown: going to close sockets...
Tue Oct 26 15:27:49 [initandlisten] shutdown: waiting for fs preallocator...
Tue Oct 26 15:27:49 [initandlisten] shutdown: closing all files...
Tue Oct 26 15:27:49 closeAllFiles() finished

Tue Oct 26 15:27:49 [initandlisten] shutdown: removing fs lock...
Tue Oct 26 15:27:49 dbexit: really exiting now