The issue
We have a strange issue on our mongodb setup. Sometimes we get peaks of high connections and high queues and the mongodb process stops responding if we let the queues and connections increase. We need to restart the instance using sigkill with htop.
It seems that there is a system limit / mongodb configuration blocking mongodb from operating, because hardware resources are ok. Versions of this issue happening on stand alone and then replica set on production servers. Details ahead.
About the software environment
This is a stand alone mongodb instance (not sharded nor replica sets), it's operating on a dedicated machine, and it's queried by other machines. I'm using mongodb-linux-x86_64-2.6.12 under Debian 7.7.
The machines querying mongo are using Django==1.7.4, Mongoengine=0.10.1 with pymongo==2.8, nginx 1.6.2 and gunicorn 19.1.1.
On the Django settings.py file I'm connecting to the database using the following lines:
from mongoengine import connect
connect(
MONGO_DB,
username = MONGO_USER,
password = MONGO_PWD,
host = MONGO_HOST,
port = MONGO_PORT
)
MMS Stats
As you can see in the following img from the MMS service we have peaks on connections and queques:
When this happens, our mongodb process completely freezes. We must use SIGKILL to restart mongodb, which is really bad.
In the image there are 3 freeze events.
As the img shows, when this happens, we have a peak on Non-Mapped Virtual Memory too.
Also we spotted an increase on the Btree chart around the 2nd and 3rd freeze.
We have checked the logs, but there is no suspicious query, also the Opcounters don't skyrocket, it seems that there are no more queries than usual.
Here is another screenshot on the same bug but on another day/time:
On all the cases, the lock on the DB is not significantly increasing, it has a peak but not reaching even 4%:
OpCounter drops to zero, it seems that every op goes to the mongodb queque, so the database creates new connections to try to execute new requests, all of them going to the queue as well.
Machine Resources
Regarding hardware, the machine is a Google Cloud Compute instance with 4 Intel Xeon Cores, 16 Gb ram, 100 GB SSD disk.
No noticeable high network/io/CPU/ram issues detected, no peaks on resources, even when the mongod process is frozen.
MySQL on another machine also gets affected
Also we detect that at the same time of this mongod peak on queques and connections, we also get a spike on mysql connections, which is running on another machine. When I kill the mongodb process, all the mysql connections are released too (without doing a mysql restart).
ulimit
We set up system limits as recommended on this MongoDB article, to see if that was the cause of the issue but it seems that this did not fix the problem.
The spike on connections continue. It seems that every request the application has goes to queue when this issue begins.
$ ulimit -a
core file size (blocks, -c) unlimited
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 60240
max locked memory (kbytes, -l) 64
max memory size (kbytes, -m) unlimited
open files (-n) 409600
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 60240
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited
db.currentOp
I just added a shell scripts that runs every 1 second with the following:
var ops = db.currentOp().inprog
if (ops !== undefined && ops.length > 0){
ops.forEach(function(op){
if(op.secs_running > 0) printjson(op);
})
}
The log does not report any operation that is taking more than 1 second to execute. I was thinking about a process taking long time on something but it seems that is not the case.
MongoDB threads
Similar to connections, I'm monitoring threads of the mongod -f process, here is what happens, similar to connections:
[Wed May 18 19:02:01 UTC 2016] MONGOD PROCESSES 1 THREADS 94
[Wed May 18 19:03:01 UTC 2016] MONGOD PROCESSES 1 THREADS 94
# starts
[Wed May 18 19:04:01 UTC 2016] MONGOD PROCESSES 1 THREADS 96
[Wed May 18 19:05:01 UTC 2016] MONGOD PROCESSES 1 THREADS 118
[Wed May 18 19:09:01 UTC 2016] MONGOD PROCESSES 1 THREADS 196
[Wed May 18 19:10:01 UTC 2016] MONGOD PROCESSES 1 THREADS 211
# sigkill to mongodb
[Wed May 18 19:11:01 UTC 2016] MONGOD PROCESSES 3 THREADS 6
[Wed May 18 19:12:01 UTC 2016] MONGOD PROCESSES 1 THREADS 43
[Wed May 18 19:13:01 UTC 2016] MONGOD PROCESSES 1 THREADS 48
MongoDB Logs
Regarding the mongodb.log, here is the full mongodb log around the problem.
It just happens on log line 361. There the connections start to go up, and no more queries get executed. Also I cant call the mongo shell, it says:
[Wed Feb 10 15:46:01 UTC 2016] 2016-02-10T15:48:31.940+0000 DBClientCursor::init call() failed
2016-02-10T15:48:31.941+0000 Error: DBClientBase::findN: transport error: 127.0.0.1:27000 ns: admin.$cmd query: { whatsmyuri: 1 } at src/mongo/shell/mongo.js:148
Log extract
2016-02-10T15:41:39.930+0000 [initandlisten] connection accepted from 10.240.0.3:56611 #3665 (79 connections now open)
2016-02-10T15:41:39.930+0000 [conn3665] command admin.$cmd command: getnonce { getnonce: 1 } keyUpdates:0 numYields:0 reslen:65 0ms
2016-02-10T15:41:39.930+0000 [conn3665] command admin.$cmd command: ping { ping: 1 } keyUpdates:0 numYields:0 reslen:37 0ms
2016-02-10T15:41:39.992+0000 [conn3529] command db.$cmd command: count { count: "notification", fields: null, query: { read: false, recipient: 310 } } planSummary: IXSCAN { recipient: 1 } keyUpdates:0 numYields:0 locks(micros) r:215 reslen:48 0ms
2016-02-10T15:41:40.038+0000 [conn2303] query db.column query: { _id: ObjectId('56b395dfbe66324cbee550b8'), client_id: 20 } planSummary: IXSCAN { _id: 1 } ntoreturn:2 ntoskip:0 nscanned:1 nscannedObjects:1 keyUpdates:0 numYields:0 locks(micros) r:116 nreturned:1 reslen:470 0ms
2016-02-10T15:41:40.044+0000 [conn1871] update db.column query: { _id: ObjectId('56b395dfbe66324cbee550b8') } update: { $set: { last_request: new Date(1455118900040) } } nscanned:1 nscannedObjects:1 nMatched:1 nModified:1 fastmod:1 keyUpdates:0 numYields:0 locks(micros) w:126 0ms
2016-02-10T15:41:40.044+0000 [conn1871] command db.$cmd command: update { update: "column", writeConcern: { w: 1 }, updates: [ { q: { _id: ObjectId('56b395dfbe66324cbee550b8') }, u: { $set: { last_request: new Date(1455118900040) } }, multi: false, upsert: true } ] } keyUpdates:0 numYields:0 reslen:55 0ms
2016-02-10T15:41:40.048+0000 [conn1875] query db.user query: { sn: "mobile", client_id: 20, uid: "56990023700" } planSummary: IXSCAN { client_id: 1, uid: 1, sn: 1 } ntoreturn:2 ntoskip:0 nscanned:1 nscannedObjects:1 keyUpdates:0 numYields:0 locks(micros) r:197 nreturned:1 reslen:303 0ms
2016-02-10T15:41:40.056+0000 [conn2303] Winning plan had zero results. Not caching. ns: db.case query: { sn: "mobile", client_id: 20, created: { $gt: new Date(1454295600000), $lt: new Date(1456800900000) }, deleted: false, establishment_users: { $all: [ ObjectId('5637640afefa2654b5d863e3') ] }, is_closed: true, updated_time: { $gt: new Date(1455045840000) } } sort: { updated_time: 1 } projection: {} skip: 0 limit: 15 winner score: 1.0003 winner summary: IXSCAN { client_id: 1, is_closed: 1, deleted: 1, updated_time: 1 }
2016-02-10T15:41:40.057+0000 [conn2303] query db.case query: { $query: { sn: "mobile", client_id: 20, created: { $gt: new Date(1454295600000), $lt: new Date(1456800900000) }, deleted: false, establishment_users: { $all: [ ObjectId('5637640afefa2654b5d863e3') ] }, is_closed: true, updated_time: { $gt: new Date(1455045840000) } }, $orderby: { updated_time: 1 } } planSummary: IXSCAN { client_id: 1, is_closed: 1, deleted: 1, updated_time: 1 } ntoreturn:15 ntoskip:0 nscanned:26 nscannedObjects:26 keyUpdates:0 numYields:0 locks(micros) r:5092 nreturned:0 reslen:20 5ms
2016-02-10T15:41:40.060+0000 [conn300] command db.$cmd command: count { count: "notification", fields: null, query: { read: false, recipient: 309 } } planSummary: IXSCAN { recipient: 1 } keyUpdates:0 numYields:0 locks(micros) r:63 reslen:48 0ms
2016-02-10T15:41:40.547+0000 [conn3529] query db.case query: { $query: { answered: true, sn: "email", client_id: 1, establishment_users: { $all: [ ObjectId('5669b930fefa2626db389c0e') ] }, deleted: false, is_closed: { $ne: true } }, $orderby: { updated_time: -1 } } planSummary: IXSCAN { client_id: 1, establishment_users: 1, updated_time: 1 } ntoskip:0 nscanned:103 nscannedObjects:103 keyUpdates:0 numYields:0 locks(micros) r:9410 nreturned:0 reslen:20 9ms
2016-02-10T15:41:40.557+0000 [conn3529] Winning plan had zero results. Not caching. ns: db.case query: { answered: true, sn: "email", client_id: 1, establishment_users: { $all: [ ObjectId('5669b930fefa2626db389c0e') ] }, deleted: false, is_closed: { $ne: true } } sort: { updated_time: -1 } projection: {} skip: 0 limit: 15 winner score: 1.0003 winner summary: IXSCAN { client_id: 1, establishment_users: 1, updated_time: 1 }
2016-02-10T15:41:40.558+0000 [conn3529] query db.case query: { $query: { answered: true, sn: "email", client_id: 1, establishment_users: { $all: [ ObjectId('5669b930fefa2626db389c0e') ] }, deleted: false, is_closed: { $ne: true } }, $orderby: { updated_time: -1 } } planSummary: IXSCAN { client_id: 1, establishment_users: 1, updated_time: 1 } ntoreturn:15 ntoskip:0 nscanned:103 nscannedObjects:103 keyUpdates:0 numYields:0 locks(micros) r:7572 nreturned:0 reslen:20 7ms
2016-02-10T15:41:40.569+0000 [conn3028] command db.$cmd command: count { count: "notification", fields: null, query: { read: false, recipient: 145 } } planSummary: IXSCAN { recipient: 1 } keyUpdates:0 numYields:0 locks(micros) r:237 reslen:48 0ms
2016-02-10T15:41:40.774+0000 [conn3053] command db.$cmd command: count { count: "notification", fields: null, query: { read: false, recipient: 143 } } planSummary: IXSCAN { recipient: 1 } keyUpdates:0 numYields:0 locks(micros) r:372 reslen:48 0ms
2016-02-10T15:41:41.056+0000 [conn22] command admin.$cmd command: ping { ping: 1 } keyUpdates:0 numYields:0 reslen:37 0ms
#########################
HERE THE PROBLEM STARTS
#########################
2016-02-10T15:41:41.175+0000 [initandlisten] connection accepted from 127.0.0.1:43268 #3667 (80 connections now open)
2016-02-10T15:41:41.212+0000 [initandlisten] connection accepted from 10.240.0.6:46021 #3668 (81 connections now open)
2016-02-10T15:41:41.213+0000 [conn3668] command db.$cmd command: getnonce { getnonce: 1 } keyUpdates:0 numYields:0 reslen:65 0ms
2016-02-10T15:41:41.213+0000 [conn3668] authenticate db: db { authenticate: 1, user: "xxx", nonce: "xxx", key: "xxx" }
2016-02-10T15:41:41.213+0000 [conn3668] command db.$cmd command: authenticate { authenticate: 1, user: "xxx", nonce: "xxx", key: "xxx" } keyUpdates:0 numYields:0 reslen:82 0ms
2016-02-10T15:41:41.348+0000 [initandlisten] connection accepted from 10.240.0.6:46024 #3669 (82 connections now open)
2016-02-10T15:41:41.349+0000 [conn3669] command db.$cmd command: getnonce { getnonce: 1 } keyUpdates:0 numYields:0 reslen:65 0ms
2016-02-10T15:41:41.349+0000 [conn3669] authenticate db: db { authenticate: 1, user: "xxx", nonce: "xxx", key: "xxx" }
2016-02-10T15:41:41.349+0000 [conn3669] command db.$cmd command: authenticate { authenticate: 1, user: "xxx", nonce: "xxx", key: "xxx" } keyUpdates:0 numYields:0 reslen:82 0ms
2016-02-10T15:41:43.620+0000 [initandlisten] connection accepted from 10.240.0.6:46055 #3670 (83 connections now open)
2016-02-10T15:41:43.621+0000 [conn3670] command db.$cmd command: getnonce { getnonce: 1 } keyUpdates:0 numYields:0 reslen:65 0ms
2016-02-10T15:41:43.621+0000 [conn3670] authenticate db: db { authenticate: 1, user: "xxx", nonce: "xxx", key: "xxx" }
2016-02-10T15:41:43.621+0000 [conn3670] command db.$cmd command: authenticate { authenticate: 1, user: "xxx", nonce: "xxx", key: "xxx" } keyUpdates:0 numYields:0 reslen:82 0ms
2016-02-10T15:41:43.655+0000 [initandlisten] connection accepted from 10.240.0.6:46058 #3671 (84 connections now open)
2016-02-10T15:41:43.656+0000 [conn3671] command db.$cmd command: getnonce { getnonce: 1 } keyUpdates:0 numYields:0 reslen:65 0ms
2016-02-10T15:41:43.656+0000 [conn3671] authenticate db: db { authenticate: 1, user: "xxx", nonce: "xxx", key: "xxx" }
2016-02-10T15:41:43.656+0000 [conn3671] command db.$cmd command: authenticate { authenticate: 1, user: "xxx", nonce: "xxx", key: "xxx" } keyUpdates:0 numYields:0 reslen:82 0ms
2016-02-10T15:41:44.045+0000 [initandlisten] connection accepted from 10.240.0.6:46071 #3672 (85 connections now open)
2016-02-10T15:41:44.045+0000 [conn3672] command db.$cmd command: getnonce { getnonce: 1 } keyUpdates:0 numYields:0 reslen:65 0ms
2016-02-10T15:41:44.046+0000 [conn3672] authenticate db: db { authenticate: 1, user: "xxx", nonce: "xxx", key: "xxx" }
2016-02-10T15:41:44.046+0000 [conn3672] command db.$cmd command: authenticate { authenticate: 1, user: "xxx", nonce: "xxx", key: "xxx" } keyUpdates:0 numYields:0 reslen:82 0ms
2016-02-10T15:41:44.083+0000 [initandlisten] connection accepted from 10.240.0.6:46073 #3673 (86 connections now open)
2016-02-10T15:41:44.084+0000 [conn3673] command db.$cmd command: getnonce { getnonce: 1 } keyUpdates:0 numYields:0 reslen:65 0ms
2016-02-10T15:41:44.084+0000 [conn3673] authenticate db: db { authenticate: 1, user: "xxx", nonce: "xxx", key: "xxx" }
2016-02-10T15:41:44.084+0000 [conn3673] command db.$cmd command: authenticate { authenticate: 1, user: "xxx", nonce: "xxx", key: "xxx" } keyUpdates:0 numYields:0 reslen:82 0ms
2016-02-10T15:41:44.182+0000 [initandlisten] connection accepted from 10.240.0.6:46076 #3674 (87 connections now open)
Collection Information
Currently our database contains 163 collections. The important ones are messages, column and cases, this are the ones that get heavy inserts, updates and queries on. The rest if for analytics and are many collections of about 100 records each:
{
"ns" : "db.message",
"count" : 2.96615e+06,
"size" : 3906258304.0000000000000000,
"avgObjSize" : 1316,
"storageSize" : 9305935856.0000000000000000,
"numExtents" : 25,
"nindexes" : 21,
"lastExtentSize" : 2.14643e+09,
"paddingFactor" : 1.0530000000000086,
"systemFlags" : 0,
"userFlags" : 1,
"totalIndexSize" : 7952525392.0000000000000000,
"indexSizes" : {
"_id_" : 1.63953e+08,
"client_id_1_sn_1_mid_1" : 3.16975e+08,
"client_id_1_created_1" : 1.89086e+08,
"client_id_1_recipients_1_created_1" : 4.3861e+08,
"client_id_1_author_1_created_1" : 2.29713e+08,
"client_id_1_kind_1_created_1" : 2.37088e+08,
"client_id_1_answered_1_created_1" : 1.90934e+08,
"client_id_1_is_mention_1_created_1" : 1.8674e+08,
"client_id_1_has_custom_data_1_created_1" : 1.9566e+08,
"client_id_1_assigned_1_created_1" : 1.86838e+08,
"client_id_1_published_1_created_1" : 1.94352e+08,
"client_id_1_sn_1_created_1" : 2.3681e+08,
"client_id_1_thread_root_1" : 1.88089e+08,
"client_id_1_case_id_1" : 1.89266e+08,
"client_id_1_sender_id_1" : 1.5182e+08,
"client_id_1_recipient_id_1" : 1.49711e+08,
"client_id_1_mid_1_sn_1" : 3.17662e+08,
"text_text_created_1" : 3320641520.0000000000000000,
"client_id_1_sn_1_kind_1_recipient_id_1_created_1" : 3.15226e+08,
"client_id_1_sn_1_thread_root_1_created_1" : 3.06526e+08,
"client_id_1_case_id_1_created_1" : 2.46825e+08
},
"ok" : 1.0000000000000000
}
{
"ns" : "db.case",
"count" : 497661,
"size" : 5.33111e+08,
"avgObjSize" : 1071,
"storageSize" : 6.29637e+08,
"numExtents" : 16,
"nindexes" : 34,
"lastExtentSize" : 1.68743e+08,
"paddingFactor" : 1.0000000000000000,
"systemFlags" : 0,
"userFlags" : 1,
"totalIndexSize" : 8.46012e+08,
"indexSizes" : {
"_id_" : 2.30073e+07,
"client_id_1" : 1.99985e+07,
"is_closed, deleted_1" : 1.31061e+07,
"is_closed_1" : 1.36948e+07,
"sn_1" : 2.1274e+07,
"deleted_1" : 1.39728e+07,
"created_1" : 1.97777e+07,
"current_assignment_1" : 4.20819e+07,
"assigned_1" : 1.33678e+07,
"commented_1" : 1.36049e+07,
"has_custom_data_1" : 1.42426e+07,
"sentiment_start_1" : 1.36049e+07,
"sentiment_finish_1" : 1.37275e+07,
"updated_time_1" : 2.02192e+07,
"identifier_1" : 1.73822e+07,
"important_1" : 1.38256e+07,
"answered_1" : 1.41772e+07,
"client_id_1_is_closed_1_deleted_1_updated_time_1" : 2.90248e+07,
"client_id_1_is_closed_1_updated_time_1" : 2.86569e+07,
"client_id_1_sn_1_updated_time_1" : 3.58436e+07,
"client_id_1_deleted_1_updated_time_1" : 2.8477e+07,
"client_id_1_updated_time_1" : 2.79619e+07,
"client_id_1_current_assignment_1_updated_time_1" : 5.6071e+07,
"client_id_1_assigned_1_updated_time_1" : 2.87713e+07,
"client_id_1_commented_1_updated_time_1" : 2.86896e+07,
"client_id_1_has_custom_data_1_updated_time_1" : 2.88286e+07,
"client_id_1_sentiment_start_1_updated_time_1" : 2.87223e+07,
"client_id_1_sentiment_finish_1_updated_time_1" : 2.88776e+07,
"client_id_1_identifier_1_updated_time_1" : 3.48216e+07,
"client_id_1_important_1_updated_time_1" : 2.88776e+07,
"client_id_1_answered_1_updated_time_1" : 2.85669e+07,
"client_id_1_establishment_users_1_updated_time_1" : 3.93838e+07,
"client_id_1_identifier_1" : 1.86413e+07,
"client_id_1_sn_1_users_1_updated_time_1" : 4.47309e+07
},
"ok" : 1.0000000000000000
}
{
"ns" : "db.column",
"count" : 438,
"size" : 218672,
"avgObjSize" : 499,
"storageSize" : 696320,
"numExtents" : 4,
"nindexes" : 2,
"lastExtentSize" : 524288,
"paddingFactor" : 1.0000000000000000,
"systemFlags" : 0,
"userFlags" : 1,
"totalIndexSize" : 65408,
"indexSizes" : {
"_id_" : 32704,
"client_id_1_owner_1" : 32704
},
"ok" : 1.0000000000000000
}
Mongostat
Here is some of the lines we have running mongostat during normal operation:
insert query update delete getmore command flushes mapped vsize res faults locked db idx miss % qr|qw ar|aw netIn netOut conn time
*0 34 2 *0 0 10|0 0 32.6g 65.5g 1.18g 0 db:0.1% 0 0|0 0|0 4k 39k 87 20:44:44
2 31 13 *0 0 7|0 0 32.6g 65.5g 1.17g 3 db:0.8% 0 0|0 0|0 9k 36k 87 20:44:45
1 18 2 *0 0 5|0 0 32.6g 65.5g 1.12g 0 db:0.4% 0 0|0 0|0 3k 18k 87 20:44:46
5 200 57 *0 0 43|0 0 32.6g 65.5g 1.13g 12 db:2.3% 0 0|0 0|0 46k 225k 86 20:44:47
1 78 23 *0 0 5|0 0 32.6g 65.5g 1.01g 1 db:1.6% 0 0|0 0|0 18k 313k 86 20:44:48
*0 10 1 *0 0 5|0 0 32.6g 65.5g 1004m 0 db:0.2% 0 0|0 1|0 1k 8k 86 20:44:49
3 48 23 *0 0 11|0 0 32.6g 65.5g 1.05g 4 db:1.1% 0 0|0 0|0 16k 48k 86 20:44:50
2 38 13 *0 0 8|0 0 32.6g 65.5g 1.01g 8 db:0.9% 0 0|0 0|0 10k 76k 86 20:44:51
3 28 16 *0 0 9|0 0 32.6g 65.5g 1.01g 7 db:1.1% 0 0|0 1|0 11k 62k 86 20:44:52
*0 9 4 *0 0 8|0 0 32.6g 65.5g 1022m 1 db:0.4% 0 0|0 0|0 3k 6k 87 20:44:53
insert query update delete getmore command flushes mapped vsize res faults locked db idx miss % qr|qw ar|aw netIn netOut conn time
3 107 34 *0 0 6|0 0 32.6g 65.5g 1.02g 1 db:1.1% 0 0|0 0|0 23k 107k 87 20:44:54
4 65 37 *0 0 8|0 0 32.6g 65.5g 2.69g 57 db:6.2% 0 0|0 0|0 24k 126k 87 20:44:55
9 84 45 *0 0 8|0 0 32.6g 65.5g 2.63g 17 db:5.3% 0 0|0 1|0 32k 109k 87 20:44:56
4 84 47 *0 0 44|0 0 32.6g 65.5g 1.89g 10 db:5.9% 0 0|0 1|0 30k 146k 86 20:44:57
3 73 32 *0 0 9|0 0 32.6g 65.5g 2.58g 12 db:4.7% 0 0|0 0|0 20k 112k 86 20:44:58
2 165 48 *0 0 7|0 0 32.6g 65.5g 2.62g 7 db:1.3% 0 0|0 0|0 34k 147k 86 20:44:59
3 61 26 *0 0 12|0 0 32.6g 65.5g 2.2g 6 db:4.7% 0 0|0 1|0 19k 73k 86 20:45:00
3 252 64 *0 0 12|0 0 32.6g 65.5g 1.87g 85 db:3.2% 0 0|0 0|0 52k 328k 86 20:45:01
*0 189 40 *0 0 6|0 0 32.6g 65.5g 1.65g 0 db:1.6% 0 0|0 0|0 33k 145k 87 20:45:02
1 18 10 *0 0 5|0 0 32.6g 65.5g 1.55g 3 db:0.9% 0 0|0 0|0 6k 15k 87 20:45:03
insert query update delete getmore command flushes mapped vsize res faults locked db idx miss % qr|qw ar|aw netIn netOut conn time
1 50 11 *0 0 6|0 0 32.6g 65.5g 1.57g 6 db:0.8% 0 0|0 0|0 9k 63k 87 20:45:04
2 49 16 *0 0 6|0 0 32.6g 65.5g 1.56g 1 db:1.1% 0 0|0 0|0 12k 50k 87 20:45:05
1 35 11 *0 0 7|0 0 32.6g 65.5g 1.58g 1 db:0.9% 0 0|0 0|0 8k 41k 87 20:45:06
*0 18 2 *0 0 42|0 0 32.6g 65.5g 1.55g 0 db:0.4% 0 0|0 0|0 5k 19k 86 20:45:07
6 75 40 *0 0 11|0 0 32.6g 65.5g 1.56g 10 db:1.9% 0 0|0 0|0 27k 89k 86 20:45:08
6 60 35 *0 0 7|0 0 32.6g 65.5g 1.89g 5 db:1.5% 0 0|0 1|0 23k 101k 86 20:45:09
2 17 14 *0 0 7|0 0 32.6g 65.5g 1.9g 0 db:1.3% 0 0|0 1|0 8k 29k 86 20:45:10
2 35 7 *0 0 4|0 0 32.6g 65.5g 1.77g 1 db:1.3% 0 0|0 0|0 7k 60k 86 20:45:12
4 50 28 *0 0 10|0 0 32.6g 65.5g 1.75g 10 db:2.0% 0 0|0 0|0 19k 79k 87 20:45:13
*0 3 1 *0 0 5|0 0 32.6g 65.5g 1.63g 0 .:0.7% 0 0|0 0|0 1k 4k 87 20:45:14
insert query update delete getmore command flushes mapped vsize res faults locked db idx miss % qr|qw ar|aw netIn netOut conn time
5 77 35 *0 0 8|0 0 32.6g 65.5g 1.7g 13 db:3.0% 0 0|0 0|0 23k 124k 88 20:45:15
3 35 18 *0 0 7|0 0 32.6g 65.5g 1.7g 5 db:0.8% 0 0|0 0|0 12k 43k 87 20:45:16
1 18 5 *0 0 11|0 0 32.6g 65.5g 1.63g 2 db:0.9% 0 0|0 0|0 5k 35k 87 20:45:17
3 33 21 *0 0 5|0 0 32.6g 65.5g 1.64g 3 db:0.8% 0 0|0 0|0 13k 32k 87 20:45:18
*0 25 4 *0 0 42|0 0 32.6g 65.5g 1.64g 0 db:0.3% 0 0|0 0|0 5k 34k 86 20:45:19
1 25 5 *0 0 5|0 0 32.6g 65.5g 1.65g 3 db:0.2% 0 0|0 0|0 5k 24k 86 20:45:20
12 88 65 *0 0 7|0 0 32.6g 65.5g 1.7g 25 db:4.2% 0 0|0 0|0 42k 121k 86 20:45:21
2 53 17 *0 0 4|0 0 32.6g 65.5g 1.65g 2 db:1.5% 0 0|0 0|0 12k 82k 86 20:45:22
1 9 6 *0 0 7|0 0 32.6g 65.5g 1.64g 1 db:1.0% 0 0|0 0|0 4k 13k 86 20:45:23
*0 6 2 *0 0 7|0 0 32.6g 65.5g 1.63g 0 db:0.1% 0 0|0 0|0 1k 5k 87 20:45:24
Replica Set: Updated on May 15th 2016
We migrated our stand alone instance to a replica set. 2 secondaries serving the reads and 1 primary doing the writes. All the machines on the replica set area snapshots of the original machine. What happened with this new configuration is that the issue changed and it's harder to detect.
It happens less frequently but instead of sky rocketing connections and queues, the whole replica set stops reading/writing, with no high connections, no queues no expensive operations at all. All request to the DB just time out. To fix the issue a SIGKILL to the mongodb process must be sent to all 3 machines.
Best Answer
The issue was that our gunicorn config had sync workers. At some point the workers were entering into a deadlock but still making new connections for new requests, causing mysql and mongodb to freeze.
We updated gunicorn from 19.1.1 to 19.6.0 and switched to async greenlets workers. Also added
multi_accept on;to nginx config file.