I was attempting to reduce the size of my indexes on a mongo collection and ran db.collection.reIndex().
After about 90 minutes, I began to think it had somehow gotten locked up and tried to cancel. Now (about 2 hours after cancelling) the collection appears to be locked to all write commands. All my other collections are allowing writes. Is there any way to unlock it?
The period of time that it takes to perform this operation is going is dependent on a few things, namely:
The size of the collection.
The number of indexes in that collection.
This is a blocking operation.
Simply put, a small database (less than 500MB) should only take a few minutes to reindex whereas a larger database (5-10GB or more) could take much longer ... with increasing length as the database size increases.
While it is best to let the procedure finish, if you absolutely needed to stop it, then restarting the process would be the way to do it. Also, send in a support ticket to: support#mongohq.com (including the name of the database) and the team can help more there.
Related
I am designing a search that will be fed around 50 to 200 GB of text data per day (similar to logs) and it only needs to retain that data for week or two. This data will be piped at a constant rate (5,000/per second for example), non-stop, 24 hours a day. After a week or two, the document should drop out of the index never to be heard from again.
The index should be searchable with free-form text across only 1 field (pretty small in size, around 512 characters max). At most, the schema could have 2 attributes that could be categorized.
The system needs to be indexed in near real-time as data is fed to it. A delay of 15 to 30 seconds is acceptable.
We prefer to stream data into the indexer/service with a constant stream of pipe data.
Lastly, a single stand-alone solution is prefer over any type of distribution setup (this will be part of a package to deploy and setup on local machines for testers).
I'm looking closely at Sphinx search engine with RT updates via the API as it checks off most of these. But, I am not seeing an easy way to expire documents after a certain length of time.
I am aware that I could track the IDs and a timestamp and issue a batch DELETE through the Sphinx API. But, that creates an issue of tracking large amounts of IDs in a separate datastore that will need the same kind of 5,000/per second inserts and deleting them when done.
I also have a concern around Sphinx Fragmentation of mass-inserting, and mass-deleting in the middle of inserting.
We would really prefer the search engine/indexer to handle the expiration itself.
I think I can perform a WHERE timestamp < UNIXTIMESTAMP-OF-TWO-WEEEKS-AGO as the where clause in the Sphinx API in order to gather the Document IDs to delete. The problem with that is if the system does not stay ontop of the deletes, the total number of documents/search results will be in the 10s of millions, maybe even billions in count after a two week timeframe if it has to gather a few days worth of document ids to delete. That's not a feasible query.
You can actually run
DELETE FROM rt WHERE timestamp < UNIXTIMESTAMP-OF-TWO-WEEEKS-AGO
As a query to delete the old documents, which is much simpler :)
You will also need to call OPTIMIZE INDEX from time to time.
Both these will have to be called on some sort of 'cron' schedule, as they wont be run automatically.
You might be better not using Sphinxes DELETE function at all. When writing RT indexes, as soon as the RAM chunk is full its writen out as a disk chunk. So you end up with a number of disk chunks on the disk. The oldest documents will be in the oldest chunk, sequentially.
So to clear out the oldest documents, you could just dispose of the oldest chunks. (on a rolling basis)
The problem is sphinx does not include a function to delete individual chunks.
Will need to shutdown searchd, delete the chunk(s), manipulate the header files and then restart Sphinx. Not an easy process.
But in the more general sense, not sure if sphinx will be able to keep up with a continuous stream of 5,000/documents per second (even ignoreing delete for a moment) - Sphinx is generally designed for write-infrequently, read-frequently. It builds a (for the most part) monolithic inverted index. This is great for querying, but is very hard to keep updated. Its not great for incremental updates.
My postgres was running really slow lately, an aggregation for a month it usually ended up taking more than 1 minute (to be more exact the last one took 7 mins and 23 secs).
Last friday i recreated the servers (master and replica) and reimported the database.
First thing I noticed is that from 133gb now the database is 42gb (the actual data is around 12gb, i guess the rest are the indexes).
Everything was fast as hell for a day, after that the indexing finished (26gb on indexes) and now I'm back to square 1.
A count on ~5 million rows takes 3 mins 42 secs.
Made the autovacuum more aggressive and it looks like it's doing it's job now but the DB is still slow.
I am using the db for an API so it's constantly growing. Atm i have 2 tables one that has around 5 mil rows and the other 28 mil.
So if the master has a lot of activity and let's say that i'm expecting some performance loss, i don't expect it from the replica.
What's curios is that after a restart it's really fast for an hour or so.
Also another thing that i noticed was that on every query I do the IO is 100% while the memory and cpu are almost not used at all.
Any help would be greatly appreciated.
Update
Same database on a smaller machine works like a charm.
Same queries, same indexes.
The only difference is the traffic, not writing or updating that much.
Also i forgot to mention one thing, one of my indexes is clustered.
The live machine is a 5 core with 64gb and 3k IO.
The test machine is a 2 core with 4gb and an SSD.
Update
Found my issue.
Apparently the autovacuum can't get a lock and by the time it gets it the dead tuples increased.
Made the autovacuum more aggresive for now and deleted a bunch of unused indexes.
Still don't know how to fix the lock issue tho.
Update
Looks like something is increasing the estimated row count.
Since my last update here the row count increased by 2 mil.
I guess that by tomorrow the row count will be again around 12 mil and the count will be slow as hell again.
Could this be related to autovacuum?
Update
Well found my issue.
Looks like postgres is losing a lot of speed on a write intensive database.
Had a column that was used as a flag and updated a lot of times per day.
Everything looks really good after the flag and update was removed.
Any clue on how to fix this issue on a write intensive table?
May be the following pointers help:
Are you really sure you want to do a 5mil row Aggregation for an API? Everytime ? Can't you split the data into chunks such that only a small number of chunks actually get most of the new rows (and so the aggregation of all the previous chunks can be reused for the next Query)? Time is one such measure, serial numbers could be another, etc. If so, partitioning the data is an obvious solution you should investigate, it really has a good chance of giving you sub-second query times (assuming you store aggregations for previous chunks smartly).
A hunch about that first hour magic is that although this data fits RAM, concurrent querying pushes that data-set out and then its purely disk I/O... and in that case, CPU / RAM being idle isn't a surprise.
Finally, I think this setup is asking for a re-design where there is only so much you could do with a single SQL, and in that expecting sub-second Query times for data that is not within RAM for a 5mil data-set is probably being too optimistic!
(Nonetheless, do post your findings, if possible)
I'm doing some user analytics tracking with mongo. I'm averaging about 200 updates a second to documents (around 400k) based on a users email address. There are 3 shards split along email alphabetically. It works pretty well except for the daily user state change scripts. It bursts the requests to about 6k per second.
This causes a tail spin effect where it overloads the mongo queue and it never seems to catch up again. Scripts fail, bosses get angry, etc. They also won't allow the scripts to be throttled. Since they are update operations and not insert they are not able to be submitted in bulk. What I see for me options are.
1:) Finding a way to allocate a large queue to mongo so it can wait for low points and get the data updated
2:) Writing a custom throttling solution
3:) Finding a more efficient indexing strategy (currently just indexing the email address)
Pretty much anything is on the table.
Any help is greatly appreciated
My application needs only read access to all of its databases. One of those databases (db_1) hosts a collection coll_1 whose entire contents* need to be replaced periodically**.
My goal is to have no or very little effect on read performance for servers currently connected to the database.
Approaches I could think of with so far:
1. renameCollection
Build a temporary collection coll_tmp, then use renameCollection with dropTarget: true to move its contents over to coll_1. The downside of this approach is that as far as I can tell, renameCollection does not copy indexes, so once the collection is renamed, coll_1 would need reindexing. While I don't have a good estimate of how long this would take, I would think that query-performance will be significantly affected until reindexing is complete.
2. TTL Index
Instead of straight up replacing, use a time-to-live index to expire documents after the chosen replacement period. Insert new data every time period. This seems like a decent solution to me, except that for our specific application, old data is better than no data. In this scenario, if the cron job to repopulate the database fails for whatever reason, we could potentially be left with an empty coll_1 which is undesirable. I think this might have a negligible effect, but this solution also requires on-the-fly indexing as every document is inserted.
3. Communicate current database to read-clients
Simply use two different databases (or collections?) and inform connected clients which one is more recent. This solution would allow for finishing indexing the new coll_1_alt (and then coll_1 again) before making it available. I personally dislike the solution since it couples the read clients very closely to the database itself, and of course communication channels are always imperfect.
4. copyDatabase
Use copyDatabase to rename (designate) an alternate database db_tmp to db_1.db_tmp would also have a collection coll_1. Once reindexing is complete on db_tmp.coll_1, copyDatabase could be used to simply rename db_tmp to db_1. It seems that this would require droppping db_1 before renaming, leaving a window in which data won't be accessible.
Ideally (and naively), I'd just set db_1 to be something akin to a symlink, switching to the most current database as needed.
Anyone has good suggestions on how to achieve the desired effect?
*There are about 10 million documents in coll_1.
** The current plan is to replace the collection once every 24 hours. The replacement interval might get as low as once every 30 minutes, but not lower.
The problem that you point out in option 4 you will also have with option 1. dropTarget will also mean that the collection is not available.
Another alternative could be to just have both the old and the new data in the same collection, and use a "version ID" that you then still have to communicate to your clients to do a query on. That at least stops you from having to do reindexing like you pointed out for option 1.
I think your best bet is actually option 3, and it's the most equivalent to changing a symlink, except it is on the client side.
I'm using MongoDB with approximately 4 million documents and around 5-6GB database size. The machine has 10GB of RAM, and free only reports around 3.7GB in use. The database is used for a video game related ladder (rankings) website, separated by region.
It's a fairly write heavy operation, but still gets a significant number of reads as well. We use an updater which queries an outside source every hour or two. This updater then processes the records and updates documents on the database. The updater only processes one region at a time (see previous paragraph), so approximately 33% of the database is updated.
When the updater runs, and for the duration that it runs, the average flush time spikes up to around 35-40 seconds, and we experience general slowdowns with other queries. The updater is RAN on a SEPARATE MACHINE and only queries MongoDB at the end, when all the data has been retrieved and processed from the third party.
Some people have suggested slowing down the number of updates, or only updating players who have changed, but the problem comes down to rankings. Since we support ties between players, we need to pre-calculate the ranks - so if only a few users have actually changed ranks, we still need to update the rest of the users ranks accordingly. At least, that was the case with MySQL - I'm not sure if there is a good solution with MongoDB for ranking ~800K->1.2 million documents while supporting ties.
My question is: how can we improve the flush and slowdown we're experiencing? Why is it spiking so high? Would disabling journaling (to take some load off the i/o) help, as data loss isn't something I'm worried about as the database is updated frequently regardless?
Server status: http://pastebin.com/w1ETfPWs
You are using the wrong tool for the job. MongoDB isn't designed for ranking large ladders in real time, at least not quickly.
Use something like Redis, Redis have something called a "Sorted List" designed just for this job, with it you can have 100 millions entries and still fetch the 5000000th to 5001000th at sub millisecond speed.
From the official site (Redis - Sorted sets):
Sorted sets
With sorted sets you can add, remove, or update elements in a very fast way (in a time proportional to the logarithm of the number of elements). Since elements are taken in order and not ordered afterwards, you can also get ranges by score or by rank (position) in a very fast way. Accessing the middle of a sorted set is also very fast, so you can use Sorted Sets as a smart list of non repeating elements where you can quickly access everything you need: elements in order, fast existence test, fast access to elements in the middle!
In short with sorted sets you can do a lot of tasks with great performance that are really hard to model in other kind of databases.
With Sorted Sets you can:
Take a leader board in a massive online game, where every time a new score is submitted you update it using ZADD. You can easily take the top users using ZRANGE, you can also, given an user name, return its rank in the listing using ZRANK. Using ZRANK and ZRANGE together you can show users with a score similar to a given user. All very quickly.
Sorted Sets are often used in order to index data that is stored inside Redis. For instance if you have many hashes representing users, you can use a sorted set with elements having the age of the user as the score and the ID of the user as the value. So using ZRANGEBYSCORE it will be trivial and fast to retrieve all the users with a given interval of ages.
Sorted Sets are probably the most advanced Redis data types, so take some time to check the full list of Sorted Set commands to discover what you can do with Redis!
Without seeing any disk statistics, I am of the opinion that you are saturating your disks.
This can be checked with iostat -xmt 2, and checking the %util column.
Please don't disable journalling - you will only cause more issues later down the line when your machine crashes.
Separating collections will have no effect. Separating databases may, but if you're IO bound, this will do nothing to help you.
Options
If I am correct, and your disks are saturated, adding more disks in a RAID 10 configuration will vastly help performance and durability - more so if you separate the journal off to an SSD.
Assuming that this machine is a single server, you can setup a replicaset and send your read queries there. This should help you a fair bit, but not as much as the disks.