mongodump error "Failed: error reading from db: EOF" (no entries in server log)

Question

Our mongodb.conf of version 3.06 and data files only 240 MB in size. Network is reliable at this timestamps.

# mongod.conf

# Where to store the data.

# Note: if you run mongodb as a non-root user (recommended) you may
# need to create and set permissions for this directory manually,
# e.g., if the parent directory isn't mutable by the mongodb user.
dbpath=/db/db32/mongodb/data/

# path to logfile
logpath=/db/db32/mongodb/logs/mongod.log

# add new entries to the end of the logfile
logappend=true

# Listen to local interface only. Comment out to listen on all interfaces.
#bind_ip = 127.0.0.1

# enable operation journaling
#journal = true
#smallfiles = true
nojournal = true

# Enables periodic logging of CPU utilization and I/O wait
cpu = true

# enable database authentication for users connecting from remote hosts
auth = true

# Verbose logging output.
#verbose = true

# Enable db quota management
#quota = true

# Set oplogging level where n is
#   0=off (default)
#   1=W
#   2=R
#   3=both
#   7=W+some reads
#diaglog = 0

# Ignore query hints
#nohints = true

# Turns off server-side scripting.  This will result in greatly limited
# functionality
noscripting = true

# Turns off table scans.  Any query that would do a table scan fails.
#notablescan = true

# Disable data file preallocation.
#noprealloc = true

# Specify .ns file size for new databases.
# nssize = <size>

# Replication Options

# in replicated mongo databases, specify the replica set name here
#replSet=setname
# maximum size in megabytes for replication operation log
#oplogSize=1024
# path to a key file storing authentication info for connections
# between replica set members
#keyFile=/path/to/keyfile

# Forces the mongod to validate all requests from clients
objcheck = true

# Disable HTTP status interface
nohttpinterface = true

# disable REST interface
rest = false

# database profiling 1 = only includes slow operations
profile = 1

# logs slow queries to the log
slowms = 100

# maximum number of simultaneous connections
maxConns = 25

mongodump with verbose flag. In server log no entries to this timestamp.

(...)
2016-03-09T16:51:17.378+0100    enqueued collection 'Tetzi005.xxx'
2016-03-09T16:51:17.384+0100    enqueued collection 'Tetzi005.xxxxxx'
2016-03-09T16:51:17.391+0100    enqueued collection 'Tetzi005.system.indexes'
2016-03-09T16:51:17.391+0100    finalizing intent manager with longest task first prioritizer
2016-03-09T16:51:17.391+0100    dumping with 8 job threads
2016-03-09T16:51:17.391+0100    starting dump routine with id=0
2016-03-09T16:51:17.391+0100    starting dump routine with id=4
2016-03-09T16:51:17.391+0100    starting dump routine with id=1
2016-03-09T16:51:17.391+0100    writing Tetzi005.DailyEmailUser to dbbackup/dump/Tetzi005/xxxxxxx.bson
2016-03-09T16:51:17.391+0100    starting dump routine with id=3
2016-03-09T16:51:17.391+0100    starting dump routine with id=6
2016-03-09T16:51:17.391+0100    writing Tetzi005.Prototype to dbbackup/dump/Tetzi005/xxxxxxx.bson
2016-03-09T16:51:17.392+0100    starting dump routine with id=7
2016-03-09T16:51:17.392+0100    writing Tetzi005.ProfileUser to dbbackup/dump/Tetzi005/xxxxxxx.bson
2016-03-09T16:51:17.392+0100    starting dump routine with id=2
2016-03-09T16:51:17.392+0100    writing Tetzi005.OrganizationDataSet to dbbackup/dump/Tetzi005/xxxxxxxx.bson
2016-03-09T16:51:17.392+0100    writing Tetzi005.DailyUserCount to dbbackup/dump/Tetzi005/xxxxxxxxxx.bson
2016-03-09T16:51:17.392+0100    writing Tetzi005.DailyEmailOrganization to dbbackup/dump/Tetzi005/xxxxxxxxxxxxx.bson
2016-03-09T16:51:17.392+0100    starting dump routine with id=5
2016-03-09T16:51:17.392+0100    writing Tetzi005.OrganizationStatistics to dbbackup/dump/Tetzi005/xxxxxxxxxxx.bson
2016-03-09T16:51:17.392+0100    writing Tetzi005.Organization to dbbackup/dump/Tetzi005/xxxx.bson
2016-03-09T16:51:17.398+0100        counted 112 documents in Tetzi005.xxxxxxxxxxxxx
2016-03-09T16:51:17.398+0100        counted 475 documents in Tetzi005.xxxxxxxx
2016-03-09T16:51:17.405+0100    Failed: error reading from db: EOF

No solutions when googling for Failed: error reading from db: EOF

We have this problem only with large plan. Technically the configuration doesn't differ (expect memory, disk and maxConns). All mongo Server running in Docker container. Docker runs on OpenStack VMs with RHEL7.

small          Maximum 10 concurrent connections, 1GB storage, 256MB memory   paid   
medium         Maximum 15 concurrent connections, 8GB storage, 1GB memory     paid   
large          Maximum 25 concurrent connections, 16GB storage, 4GB memory    paid   

Solution 1

The Error Failed: error reading from db: EOF is caused from running out of memory during the oplog write out.

You can use less memory as when you run mongodump add the --quiet option.

mongodump --quiet

Solution 2

The "Failed: error reading from db: EOF" is caused from running out of memory during the oplog write out.

Solution 3

For containerized setup you must remember to set storage.wiredTiger.engineConfig.cacheSizeGB.

From https://docs.mongodb.com/manual/reference/configuration-options/#storage.wiredTiger.engineConfig.cacheSizeGB :

The storage.wiredTiger.engineConfig.cacheSizeGB limits the size of the WiredTiger internal cache. The operating system will use the available free memory for filesystem cache, which allows the compressed MongoDB data files to stay in memory. In addition, the operating system will use any free RAM to buffer file system blocks and file system cache.

To accommodate the additional consumers of RAM, you may have to decrease WiredTiger internal cache size.

Comments

[iosdev33]

Sorry for the delay in responding, In the MongoDB logs it was complaining about memory. Added more memory to my virtual machine and that fixed the issue.

[Robert]

Will that reduce the memory usage of mongodump or of the mongo database itself? If it only affects mongodump then it will be of no use if mongodump uses a remote database...

[Flask]

funny stuff, its the usage of mongodump!