Julia is not working for loading large data in docker container [Bus error]

Question

I have a Julia program which loads 8 GB of data. It is working fine in my local machine.

But when I try it in docker container it is not loading data and giving bus error. It is working fine with small data like 20 MB in docker container.

Dockerfile

FROM ubuntu:16.04

WORKDIR /julia

RUN apt-get -y update

RUN apt-get -y install unzip

RUN apt-get -y install cmake

RUN apt-get -y install clang

RUN apt-get -y install wget

RUN cd /tmp/

RUN wget "https://julialang.s3.amazonaws.com/bin/linux/x64/0.5/julia-0.5.0-linux-x86_64.tar.gz"

RUN tar -xzvf julia-0.5.0-linux-x86_64.tar.gz

RUN mv julia-3c9d75391c/ ~/julia

ENV PATH="/root/julia/bin:${PATH}"

RUN julia --eval 'Pkg.add("JSON")'

RUN julia --eval 'Pkg.add("HttpServer")'

RUN julia --eval 'Pkg.add("URIParser")'

RUN julia --eval 'Pkg.clone("https://github.com/deep-compute/AdaGram.jl.git")'

RUN julia --eval 'Pkg.build("AdaGram")'

CMD ["julia", "/tmp/adagram_server.jl", "80", "/julia/full.embed"]

docker-compose.yml

version: "3.1"
services:
    julia:
        image: ramidavalapati/julia:v-1
        volumes:
            - /home/ram/adagram_data/40MBfull.embed:/julia/full.embed
        ports:
            - 8080:80
        command: ["sleep", "1h"]

Next I am doing

sudo docker-compose up
sudo docker exec -it $(sudo docker-compose ps -q julia) bash
root@3748d5958f77:/julia# julia
julia> using AdaGram
julia> AdaGram.load_model("/julia/full.embed")

Error

signal (7): Bus error
while loading no file, in expression starting on line 0
macro expansion at ./cartesian.jl:62 [inlined]
macro expansion at ./multidimensional.jl:429 [inlined]
_unsafe_batchsetindex! at ./multidimensional.jl:421
_setindex! at ./multidimensional.jl:370 [inlined]
setindex! at ./abstractarray.jl:832 [inlined]
#9 at /root/.julia/v0.5/AdaGram/src/AdaGram.jl:64
#600 at ./multi.jl:1030
run_work_thunk at ./multi.jl:1001
run_work_thunk at ./multi.jl:1010 [inlined]
#597 at ./event.jl:68
unknown function (ip: 0x7fe1822db16f)
jl_call_method_internal at /home/centos/buildbot/slave/package_tarball64/build/src/julia_internal.h:189 [inlined]
jl_apply_generic at /home/centos/buildbot/slave/package_tarball64/build/src/gf.c:1942
jl_apply at /home/centos/buildbot/slave/package_tarball64/build/src/julia.h:1392 [inlined]
start_task at /home/centos/buildbot/slave/package_tarball64/build/src/task.c:253
unknown function (ip: 0xffffffffffffffff)
Allocations: 9661042 (Pool: 9659980; Big: 1062); GC: 16
Bus error (core dumped)

Docker version

Client:
 Version:      17.09.0-ce
 API version:  1.32
 Go version:   go1.8.3
 Git commit:   afdb6d4
 Built:        Tue Sep 26 22:42:18 2017
 OS/Arch:      linux/amd64

Server:
 Version:      17.09.0-ce
 API version:  1.32 (minimum version 1.12)
 Go version:   go1.8.3
 Git commit:   afdb6d4
 Built:        Tue Sep 26 22:40:56 2017
 OS/Arch:      linux/amd64
 Experimental: false

Docker info

Containers: 24
 Running: 0
 Paused: 0
 Stopped: 24
Images: 24
Server Version: 17.09.0-ce
Storage Driver: overlay2
 Backing Filesystem: extfs
 Supports d_type: true
 Native Overlay Diff: true
Logging Driver: json-file
Cgroup Driver: cgroupfs
Plugins:
 Volume: local
 Network: bridge host macvlan null overlay
 Log: awslogs fluentd gcplogs gelf journald json-file logentries splunk syslog
Swarm: active
 NodeID: jlkmigmtyjhz6yvi3zuvkobu7
 Is Manager: true
 ClusterID: rqt03ulgvvnym235m1qm8vd17
 Managers: 4
 Nodes: 15
 Orchestration:
  Task History Retention Limit: 5
 Raft:
  Snapshot Interval: 10000
  Number of Old Snapshots to Retain: 0
  Heartbeat Tick: 1
  Election Tick: 3
 Dispatcher:
  Heartbeat Period: 5 seconds
 CA Configuration:
  Expiry Duration: 3 months
  Force Rotate: 0
 Autolock Managers: false
 Root Rotation In Progress: false
 Node Address: X.X.X.X
  Manager Addresses:
   X.X.X.X:2377
   X.X.X.X:2377
   X.X.X.X:2377
   X.X.X.X:2377
 Runtimes: runc
 Default Runtime: runc
 Init Binary: docker-init
 containerd version: 06b9cb35161009dcb7123345749fef02f7cea8e0
 runc version: 3f2f8b84a77f73d38244dd690525642a72156c64
 init version: 949e6fa
 Security Options:
  apparmor
  seccomp
   Profile: default
 Kernel Version: 4.10.0-35-generic
 Operating System: Ubuntu 16.04.3 LTS
 OSType: linux
 Architecture: x86_64
 CPUs: 12
 Total Memory: 251.8GiB
 Name: ram
 ID: 3OGG:275C:Q3IW:O4HX:DPLP:DPI3:5TIT:AG5J:EDMK:7NK3:L4UZ:BTQH
 Docker Root Dir: /var/lib/docker
 Debug Mode (client): false
 Debug Mode (server): false
 Username: ramidavalapati
 Registry: https://index.docker.io/v1/
 Experimental: false
 Insecure Registries:
  127.0.0.0/8
 Live Restore Enabled: false

 WARNING: No swap limit support

Thanks in advance for any kind of help

link to 40MBfull.embed file

What is your Docker version? Post docker info and docker version A docker image is limited by default to 10 GB (or 100, not sure). Post also your Dockerfile — user2915097
– user2915097, Commented Oct 31, 2017 at 8:29
Very unlikely this is a julia issue. Loading 8GB data (depending on how you do it) may well use more than 8GB RAM (you can check how much it uses on your local machine). AFAIK there is no default limit on docker containers themselves, but often they are run on VMs that do have a memory limit. (Basically we'll probably need a few more details about your setup!) — Alexander Morley
– Alexander Morley, Commented Oct 31, 2017 at 9:12
I have edited and posted some more details. Please let me know if need more details. — Ram Idavalapati
– Ram Idavalapati, Commented Nov 2, 2017 at 11:17

Ram Idavalapati · Accepted Answer · 2018-07-07 07:34:49Z

The problem is, there is no sufficient shared memory in docker container(default is 64 MB).

The problem was solved by giving the option --shm-size while running docker image.

Run : sudo docker run --shm-size 1G sample:latest

docker-compose file

version: "3.1"
services:
    julia:
        image: ramidavalapati/julia:v-1
        shm_size: 1g
        volumes:
            - /home/ram/adagram_data/40MBfull.embed:/julia/full.embed
        ports:
            - 8080:80
        command: ["sleep", "1h"]

If we want to work in swarm mode, we need to refer shared memory in volume section.

version: "3.3"
services:
    julia:
        image: ramidavalapati/julia:v-1
        volumes:
            - /home/ram/adagram_data/40MBfull.embed:/julia/full.embed
            - /dev/shm:/dev/shm
        ports:
            - 8080:80
        command: ["sleep", "1h"]

Here container uses shared memory of the host in which it is running.

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Julia is not working for loading large data in docker container [Bus error]

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