Recovering a WiredTiger collection from a corrupt MongoDB installation

Reference: http://www.alexbevi.com/blog/2016/02/10/recovering-a-wiredtiger-collection-from-a-corrupt-mongodb-installation/

Recently at work, we experienced a series of events that could have proven to be catastrophic for one of our datasets. We have a daily process that does daily cleanup, but relies on the presence of control data that is ETL’d in from another process.

The secondary process failed, and as a result, everything was “cleaned” … aka, we purged an entire dataset.

This data happens to be on a 5 node replicaset (primary-secondary-secondary-arbiter-hidden), and the hidden node died over the holidays and I waited too long to recover it, so it was unable to ever catch up to the primary (always stuck in a RECOVERING state).

My incredible foresight (… laziness … ) resulted in us having a backup of the data ready to be extracted from the out of sync hidden node. All we had to do was start up mongod … right?

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18

2016-01-29T21:06:05.180-0500 I CONTROL ***** SERVER RESTARTED ***** 2016-01-29T21:06:05.241-0500 I CONTROL [initandlisten] MongoDB starting : pid=1745 port=27021 dbpath=/data 64-bit host=xxx 2016-01-29T21:06:05.241-0500 I CONTROL [initandlisten] db version v3.0.8 2016-01-29T21:06:05.241-0500 I CONTROL [initandlisten] git version: 83d8cc25e00e42856924d84e220fbe4a839e605d 2016-01-29T21:06:05.241-0500 I CONTROL [initandlisten] build info: Linux build3.ny.cbi.10gen.cc 2.6.32-431.3.1.el6.x86_64 #1 SMP Fri Jan 3 21:39:27 UTC 2014 x86_64 BOOST_LIB_VERSION=1_49 2016-01-29T21:06:05.241-0500 I CONTROL [initandlisten] allocator: tcmalloc ... 2016-01-29T21:06:05.315-0500 W - [initandlisten] Detected unclean shutdown - /data/mongod.lock is not empty. 2016-01-29T21:06:05.315-0500 W STORAGE [initandlisten] Recovering data from the last clean checkpoint. 2016-01-29T21:06:05.324-0500 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=13G,session_max=20000,eviction=(threads_max=4),statistics=(fast),log=(enabled=true,archive=true ,path=journal,compressor=snappy),file_manager=(close_idle_time=100000),checkpoint=(wait=60,log_size=2GB),statistics_log=(wait=0), 2016-01-29T21:06:05.725-0500 E STORAGE [initandlisten] WiredTiger (0) [1454119565:724960][1745:0x7f2ac9534bc0], file:WiredTiger.wt, cursor.next: read checksum error for 4096B block at offset 6 799360: block header checksum of 1769173605 doesn't match expected checksum of 4176084783 2016-01-29T21:06:05.725-0500 E STORAGE [initandlisten] WiredTiger (0) [1454119565:725067][1745:0x7f2ac9534bc0], file:WiredTiger.wt, cursor.next: WiredTiger.wt: encountered an illegal file form at or internal value 2016-01-29T21:06:05.725-0500 E STORAGE [initandlisten] WiredTiger (-31804) [1454119565:725088][1745:0x7f2ac9534bc0], file:WiredTiger.wt, cursor.next: the process must exit and restart: WT_PANI C: WiredTiger library panic 2016-01-29T21:06:05.725-0500 I - [initandlisten] Fatal Assertion 28558

Aw crap. I could not for the life of me get the node back up and running. Since this was a replica-set member, I thought maybe if I just copied the failing file from the (working) primary it would just work. Apparently that’s not the way MongoDB or WiredTiger works :P. Back to the drawing board.

I could see that my data directory contained a bunch of collection-*.wt and index-*.wt files, so I assumed these were the WiredTiger collection and index files. These are binary files so grep-ing didn’t help me identify the collection I needed.

I wanted to next see if I could just copy the collection’s backing file directly to a new (working) MongoDB installation, so I started up a new mongod, created a new collection with a document in it, then copied over any collection-*.wt file to see what would happen.

Guess what … didn’t work.

Identify the WiredTiger collection’s backing file

Since we had access to a working node, plus the collection hadn’t been dropped (just purged), I thought maybe the files on each node would be the same. I logged into the primary via the shell to get some info from my collection.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34

db.getCollection('borkedCollection').stats() { "ns" : "production.borkedCollection", "count" : 0, "size" : 0, "storageSize" : 1138688, "capped" : false, "wiredTiger" : { "metadata" : { "formatVersion" : 1 }, "creationString" : "allocation_size=4KB,app_metadata=(formatVersion=1),block_allocation=best,block_compressor=snappy,cache_resident=0,checkpoint=(WiredTigerCheckpoint.5149=(addr=\"01808080808080c0b081e40ebe4855808080e3113fc0e401417fc0\",order=5149,time=1454966060,size=21078016,write_gen=119495)),checkpoint_lsn=(224134,44112768),checksum=on,collator=,columns=,dictionary=0,format=btree,huffman_key=,huffman_value=,id=178668,internal_item_max=0,internal_key_max=0,internal_key_truncate=,internal_page_max=4KB,key_format=q,key_gap=10,leaf_item_max=0,leaf_key_max=0,leaf_page_max=32KB,leaf_value_max=1MB,memory_page_max=10m,os_cache_dirty_max=0,os_cache_max=0,prefix_compression=0,prefix_compression_min=4,split_deepen_min_child=0,split_deepen_per_child=0,split_pct=90,value_format=u,version=(major=1,minor=1)", "type" : "file", "uri" : "statistics:table:collection-7895--1435676552983097781", "LSM" : { //... }, "block-manager" : { //... }, "btree" : { // ... }, // ... }, "nindexes" : 4, "totalIndexSize" : 1437696, "indexSizes" : { "_id_" : 212992, // ... }, "ok" : 1 }

That "uri" : "statistics:table:collection-7895--1435676552983097781"entry looked promising.

I started hunting for a way to extract the data from this file without having to “mount” the file in another MongoDB installation, as I assumed this was not possible. I stumbled across a command line utility for WiredTiger that happened to have a ‘salvage’ command.

Salvaging the WiredTiger collection

In order to use the wt utility, you have to build it from source. Being comfortable in Linux, this was not daunting ;)

wget http://source.wiredtiger.com/releases/wiredtiger-2.7.0.tar.bz2
tar xvf wiredtiger-2.7.0.tar.bz2
cd wiredtiger-2.7.0
sudo apt-get install libsnappy-dev build-essential
./configure --enable-snappy
make

NOTE adding support for Google’s snappy compressor when building WiredTiger will save you some errors that I initially encountered when trying to salvage the data.

Now that I had a wt utility, I wanted to test it out on the collection file. It turns out that you need additional supporting files before you can do this. Once I’d copied over the necessary files, my working directory (called mongo-bak) looked like this:

-rw-r--r-- 1 root      root      4738772992 Feb  9 14:06 collection-2657--1723320556100349955.wt
-rw-r--r-- 1 root      root         1155072 Feb  9 14:05 _mdb_catalog.wt
-rw-r--r-- 1 root      root        26935296 Feb  9 14:05 sizeStorer.wt
-rw-r--r-- 1 root      root              95 Feb  9 14:05 storage.bson
-rw-r--r-- 1 root      root              46 Feb  9 14:04 WiredTiger
-rw-r--r-- 1 root      root             495 Feb  9 14:04 WiredTiger.basecfg
-rw-r--r-- 1 root      root              21 Feb  9 14:04 WiredTiger.lock
-rw-r--r-- 1 root      root             916 Feb  9 14:04 WiredTiger.turtle
-rw-r--r-- 1 root      root        10436608 Feb  9 14:04 WiredTiger.wt

Now, from the directory where we compiled WiredTiger, we started salvaging the collection:

./wt -v -h ../mongo-bak -C "extensions=[./ext/compressors/snappy/.libs/libwiredtiger_snappy.so]" -R salvage collection-2657--1723320556100349955.wt

You know it’s working if you see output along the lines of:

WT_SESSION.salvage 639400

which I believe is just counting up the number of documents recovered. Once the operation has completed, it will have overwritten the source *.wt collection file with whatever it could salvage.

The only issue is that you still can’t load this into MongoDB yet.

Importing the WiredTiger collection via dump/load into MongoDB

In order to get the data into MongoDB, first we need to generate a dump file from the WiredTiger collection file. This is done using the wt utility:

./wt -v -h ../data -C "extensions=[./ext/compressors/snappy/.libs/libwiredtiger_snappy.so]" -R dump -f ../collection.dump collection-2657--1723320556100349955

This operation produces no output, so you’ll just have to sit tight and wait a while. You can always watch ls -l in another console if you want to make sure it’s working ;)

Once completed, you’ll have a collection.dump file, but this still can’t be loaded directly into MongoDB. You can however, using the wt utility one more time, load the dump back into a WiredTiger collection.

First, let’s startup a new mongod instance that we can try this out on.

mongod --dbpath tmp-mongo --storageEngine wiredTiger --nojournal

Next, let’s connect to this instance via the mongo shell and create a new collection:

use Recovery
db.borkedCollection.insert({test: 1})
db.borkedCollection.remove({})
db.borkedCollection.stats()

I’ve created a new db called Recovery, and inserted/removed a document so the collection’s backing file would be generated. You can use the stats() method to get the collection name, but since we’re only using one collection, it’s easy enough to find just using ls.

Now we’re going to take the backing file name of the collection we just created and use that to load our WiredTiger dump file:

./wt -v -h ../data -C "extensions=[./ext/compressors/snappy/.libs/libwiredtiger_snappy.so]" -R load -f ../collection.dump -r collection-2-880383588247732034

Note that we drop the .wt extension from the collection file above. Also, the -h flag needs to point to the directory where our mongod has it’s dbPath. Finally, mongod should not be running.

This operation also provides a progress indicator showing how much data has been loaded:

table:collection-4--4286091263744514813: 1386220

Once completed, we can start mongod back up, shell in and have a look:

1 2 3 4 5 6 7 8 9 10 11 12 13

$ mongo MongoDB shell version: 3.2.1 connecting to: test Mongo-Hacker 0.0.9 laptop(mongod-3.2.1) test> show dbs Recovery → 0.087GB local → 0.000GB laptop(mongod-3.2.1) test> use Recovery switched to db Recovery laptop(mongod-3.2.1) Recovery> show collections borkedCollection → 0.000MB / 88.801MB laptop(mongod-3.2.1) Recovery> db.borkedCollection.count() 0

WTF? The size looks right, but there are no documents???

1 2 3 4 5 6 7 8 9 10 11 12

laptop(mongod-3.2.1) Recovery> db.borkedCollection.find({}, {_id: 1}) { "_id": ObjectId("55e07f3b2e967329c888ac74") } { "_id": ObjectId("55e07f3b2e967329c888ac76") } ... { "_id": ObjectId("55e07f402e967329c888ac85") } Fetched 20 record(s) in 29ms -- More[true]

Well that’s promising, but the collection still hasn’t been properly restored yet.

Restoring the MongoDB collection to a usable state

This final part is pretty straightforward, as we’re just going to do a mongodump, followed by a mongorestore.

NOTE The mongodump will fail if you’re using a version of MongoDB < 3.2, as 3.2 is built against WiredTiger 2.7. I initially tested this using MongoDB 3.0.9 and the dump operation just returned 0 results.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37

$ mongodump 2016-02-10T22:04:00.580-0500 writing Recovery.borkedCollection to 2016-02-10T22:04:03.579-0500 Recovery.borkedCollection 268219 2016-02-10T22:04:06.579-0500 Recovery.borkedCollection 340655 2016-02-10T22:04:09.579-0500 Recovery.borkedCollection 496787 2016-02-10T22:04:12.579-0500 Recovery.borkedCollection 670894 2016-02-10T22:04:15.579-0500 Recovery.borkedCollection 778539 2016-02-10T22:04:18.579-0500 Recovery.borkedCollection 848525 2016-02-10T22:04:21.579-0500 Recovery.borkedCollection 991277 2016-02-10T22:04:24.579-0500 Recovery.borkedCollection 1147718 2016-02-10T22:04:27.579-0500 Recovery.borkedCollection 1187600 2016-02-10T22:04:30.579-0500 Recovery.borkedCollection 1353665 2016-02-10T22:04:33.579-0500 Recovery.borkedCollection 1376255 2016-02-10T22:04:33.681-0500 Recovery.borkedCollection 1386220 2016-02-10T22:04:33.682-0500 done dumping Recovery.borkedCollection (1386220 documents) $ mongorestore --drop 2016-02-10T22:05:51.959-0500 using default 'dump' directory 2016-02-10T22:05:51.960-0500 building a list of dbs and collections to restore from dump dir 2016-02-10T22:05:52.307-0500 reading metadata for Recovery.borkedCollection from dump/Recovery/borkedCollection.metadata.json 2016-02-10T22:05:52.330-0500 restoring Recovery.borkedCollection from dump/Recovery/borkedCollection.bson 2016-02-10T22:05:54.962-0500 [#.......................] Recovery.borkedCollection 32.8 MB/569.8 MB (5.8%) 2016-02-10T22:05:57.962-0500 [###.....................] Recovery.borkedCollection 80.5 MB/569.8 MB (14.1%) 2016-02-10T22:06:00.962-0500 [#####...................] Recovery.borkedCollection 131.5 MB/569.8 MB (23.1%) 2016-02-10T22:06:03.962-0500 [#######.................] Recovery.borkedCollection 178.5 MB/569.8 MB (31.3%) 2016-02-10T22:06:06.962-0500 [#########...............] Recovery.borkedCollection 230.1 MB/569.8 MB (40.4%) 2016-02-10T22:06:09.962-0500 [###########.............] Recovery.borkedCollection 271.6 MB/569.8 MB (47.7%) 2016-02-10T22:06:12.962-0500 [#############...........] Recovery.borkedCollection 320.6 MB/569.8 MB (56.3%) 2016-02-10T22:06:15.962-0500 [###############.........] Recovery.borkedCollection 366.3 MB/569.8 MB (64.3%) 2016-02-10T22:06:18.962-0500 [#################.......] Recovery.borkedCollection 414.9 MB/569.8 MB (72.8%) 2016-02-10T22:06:21.962-0500 [###################.....] Recovery.borkedCollection 464.8 MB/569.8 MB (81.6%) 2016-02-10T22:06:24.962-0500 [#####################...] Recovery.borkedCollection 504.0 MB/569.8 MB (88.4%) 2016-02-10T22:06:27.962-0500 [#######################.] Recovery.borkedCollection 554.5 MB/569.8 MB (97.3%) 2016-02-10T22:06:29.082-0500 [########################] Recovery.borkedCollection 569.8 MB/569.8 MB (100.0%) 2016-02-10T22:06:29.082-0500 restoring indexes for collection Recovery.borkedCollection from metadata 2016-02-10T22:06:29.104-0500 finished restoring Recovery.borkedCollection (1386220 documents) 2016-02-10T22:06:29.104-0500 done

Now that we’ve dumped and reloaded the collection yet again, we can shell back in and validate that our recovery attempt has succeeded:

1 2 3 4 5 6 7 8 9 10 11 12 13

$ mongo MongoDB shell version: 3.2.1 connecting to: test Mongo-Hacker 0.0.9 laptop(mongod-3.2.1) test> show dbs Recovery → 0.099GB local → 0.000GB laptop(mongod-3.2.1) test> use Recovery switched to db Recovery laptop(mongod-3.2.1) Recovery> show collections borkedCollection → 569.845MB / 88.594MB laptop(mongod-3.2.1) Recovery> db.borkedCollection.count() 1386220

BOOYA! Everything is back and properly accessible.

The mongorestore could actually have been done to the primary node in order to recover the data for production purposes. Once that’s done, just recreate the necessary indexes and you’re back in business.