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I've got Django app with mongoengine, which executes some aggregation-queries often enough.

The main problem is that mongod takes all the RAM and then crashes, so no LRU working, mongod just trying to get more and more memory.

My mongodb version is 3.2 and default engine is MMAPv1. As docs says, for caching MMAPv1 needs dataSize+indexSize amount of RAM. In my case that's about 370Mb (~290 for dataSize and ~80 for indexSize).

Here is my db.stats():

{
    "db" : "random_db",
    "collections" : 14,
    "objects" : 155613,
    "avgObjSize" : 1859.8720672437394,
    "dataSize" : 289420272,
    "storageSize" : 338821120,
    "numExtents" : 32,
    "indexes" : 22,
    "indexSize" : 82512192,
    "fileSize" : 1006632960,
    "nsSizeMB" : 16,
    "extentFreeList" : {
        "num" : 25,
        "totalSize" : 258314240
    },
    "dataFileVersion" : {
        "major" : 4,
        "minor" : 22
    },
    "ok" : 1
}

Actually I've got 1GB RAM and made swap-file for another 1GB. When my app executes first aggregation query (taking only 50 documents from collection), mongod RAM usage increasing to ~300Mb (when I start service it's about 50-100Mb), and till ~70 such queries been executed - all of my memory+swap ends and mongod crashes.

I've created all the indexes, that needs for aggregation's '$match', if needed, I can add some of them here.

So why ~4000 documents in cache taking more than 2GB of RAM, if my entire database takes only 370Mb and there is only 150k documents in db? I know I'm doing something wrong, the question is very simple, but still I can't find explanation at docs.

BTW, here is my db.serverStatus.mem:

{
    "bits" : 64,
    "resident" : 112,//this value growth when queries executed
    "virtual" : 2523,
    "supported" : true,
    "mapped" : 1136,
    "mappedWithJournal" : 2272
}

So, I guess, my mongod can't take more than 2523Mb for entire db in cache?

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The problem is that you make several wrong assumptions. Below you will find some corrections

MongoDB is not optimized for small resources

MongoDB was specifically designed to take a lot of data (recording clickstreams were the first application, iirc). As far as I can read, you have your django app on the same server as MongoDB. The problem here is that a lot of users for your django app would translate in a lot of queries/aggregations/write operations done on the MongoDB side. So django and MongoDB would have a race for resources especially during high load times. Since django is the first in the stack, it will almost always "win", for example requesting RAM which MongoDB now can not request. So it might well happen that MongoDB refuses something because of the lack of resources, the request is cancelled and your system appears to do nothing while really the two parts of your application did their best to answer the request, but failed to do so for the lack of resources.

To be honest: Running MongoDB on an 1GB instance alone would imho be not reasonable. Let alone with a django application. Imho, with this setup, you should at the very least have 4GB of RAM, and it might work until you put real load on it. For comparison: I usually suggest between 32 and 128GB of RAM per node (depending on the data, indices and a few other factors) for machines using SSDs as storage technology. Mind you, that is for MongoDB only – at an according scale of data, of course.

"Working set" does not (only) mean cache

Disclaimer: brutally simplified and terminology might be off

MMAPv1 uses memory mapped files. All the details put aside, this means that a file is treated as an addressable range of memory. So if MongoDB wants to read a certain doc, it uses a memory address and a range it wants to read. That memory address might either be already in RAM or it has to be read from disk. Or, and here is the misconception, from the OSes filesystem cache, which – you guessed it – resides in RAM, though just a different part. (Iirc, what happens in this situation is that the address a pointer refers to is changed). So, not only would MongoDB have the working set in RAM, but it would be the direct cause of quite some part of the filesystem cache. So, we have another part of MongoDB requiring even more RAM than the working set only.

The working set is not the only thing consuming memory

  1. Actually, the way journaling works, it doubles the RAM required by MongoDB.
  2. Each connection (and remember each driver basically opens a connection pool) gets 1MB of RAM allocated.
  3. Operations need some memory. Lets take aggregations as an example. They are capped to 100MB memory consumption – that alone would be 10% of your RAM, 5% of your allocatable memory.

However since you use MMAPv1: Do NOT turn off journaling! It is vital for crash recovery in MMAPv1.

Conclusion

Your machine is vastly underprovisioned in terms of RAM. Even if you have a tight budget, I can not stress the need of putting more RAM into that machine enough. I'd at least put 4GB into that machine (physical, that is, not swap) and see how it goes.

Be aware though, that with this setup, you'll always have django and MongoDB compete for resources the most when you need it the least: when your application has comparatively many concurrent users.

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