Docker vs Singularity vs Shifter vs UGE Container Edition

Docker vs Singularity vs Shifter vs UGE Container Edition

Here is a comparison of HPCS Singularity vs NeRSC Shifter. They both bring the benefits of container to the HPC world. As such, both provide very similar features. The subtleties are in their implementation approach. MPI maybe the place with the biggest difference.
Please comment on the blogger comment section to improve the doc. Much thanks!
(For large screen avoiding the mangling by blogger, view the working version of this file in github.)

Oveview of VM vs Docker vs Singularity

container vs vm stack diagram from GMK keynote slide deck
Source: Greg Kurtzer keynote at HPC Advisory Council 2017 @ Stanford

Tabular comparison

Docker Singularity Shifter UGE Container Ed.
Docker Singularity Shifter UGE Container Ed.
Main problem being addressed DevOps, microservices. Enterprise applications Application portability (single image file, contain all dependencies)
Reproducibility, run cross platform, provide support for legacy OS and apps.
Utilize the large number of docker apps. Provides a way to run them in HPC after a conversion process. It also strip out all the requirements of root so that they are runnable as user process.
Running dockers containers in HPC, with UGE managing the docker daemon process (?)
Interaction w/ Docker Singularity work completely independent of Docker.
It does have ability to import docker images, convert them to singularity images, or run docker container directly
Shifter primary workflow is to pull and convert docker image into shifter image.
Image Gateway connects to Docker Hub using its build-in functions, docker does not need to be installed.
User group of primary focus Developers/DevOps Scientific Application Users UGE users
Use Case Focus microservices. Do one small thing alone but does it well. Often daemon listening on TCP port 24/7 Images that target a single application or workflow (often with very complicated stacks), software that has difficult dependencies (e.g. old or different library versions)
Examplifying Use Scenario A trio of container to host a blogging site:
One docker container running httpd listen to a mapped TCP port 80
A second container running a MySql DB
Finally a WordPress container running on top taking user requests
  • A large-ish container with all dependencies build-in, but targetting only a very specific application (eg a custom python program needed a specific version of Anaconda and set of python libraries)
  • A "gigantic" image containing the whole OS of a dying computer, running a mission critical legacy app
  • Potentially docker-like, with many small containers, and string them together via command chain (not sure if there are ways to configure dependencies/versions in definition file)
A validated image containing high energy particle physics workflow.
Portability Docker Hub
Single image file. Container purpose build for singularity. Can import docker images. Working to accept docker file or Rocket definition syntax as Singularity definition.
Singularity Hub host a repository of images and definition files
Image Gateway pulls from Docker Hub, automatically convert to shifter image.
Version 1.15-1 2.2
Documentation is decent, with many community articles popping up as well.
16.08.3 (pre-release)
Documentation is work needing progress :).
Host OS Req Linux kernel 3.10+, eg:
Debian 8.0
Ubuntu 12.04
SUSE Linux Enterprise 12
Cray Linux Environment
Linux with kernel 2.6.25+, eg
Newer version of Linux that supports Docker/cgroup.
Run different OS Yes.
docker pull centos/ubuntu/etc
Yes. Utilize commands like debootstrap and febootstrap to bootstrap a new image Yes
Guiding principle Make container as transparent as possible to user. Run as much as possible as normal user process, change environment only enough to provide portability of the application Leverage Docker as it is well established. Extract Docker image into squash-FS, run in chroot env
Scheduler Docker Swarm Agnostic, run singularity as a job. Works well with Slurm, UGE, etc. Can work as stand alone container environment. For scalability, scheduler integration currently exist for SLURM, via SPANK plugin. (Should work with other scheduler) qsub -l to request docker boolean resource. UGE will be able to assign different priorities to diff containers
Resource Orchaestration SwarmKit provided by Docker Scheduler's job to spin multiple instances on multiple nodes Yes.
salloc -N4 ...
srun ...
Namespace isolation paradigm By Default, share little.
Process, Network, user space are isolated by default, but can be shared via cli arg
PID 1 is not init, but the process started by docker.
User inside container cannot see hosts' processes.
Network typically NAT'ed
HPC workflow doesn't benefit much from process isolation, thus by default share most everything, so process running inside container is largely the same as running on actual host. But process namespace isolation can easily be enabled.
Default share Process Namespace, username space (user inside container can kill process on host)
While inside a singularity shell, ps -ef shows all process of host, or those of other containers. container user can kill PID of process on host.
User does not change ID inside container, cannot become root from inside the process.
Network is transparent to the process.
/home mount is made available in container, -B will add additional bind mounts easily.
Resource restriction via cgroup? docker run -c ... -m ... --cpuset ... Not touched by Singularity. Scheduler/Resource Manager to control what is available to Singularity Let SLURM manage cgroup restrictions cgroups_params in qconf -mconf
MPI MP-what? :-)
Singularity has build-in support for MPI (OpenMPI, MPICH, IntelMPI).
Once app is build with MPI libraries, execute mpirun as normal, replacing the usual binary with the single file singularity app.
While the app is running inside the singularity container, Process Management Interface (PMI/PMIx) calls will pass thru the singularity launcher onto ORTED. This is what MPI is designed to do, no hacks, so works well.
Shifter relies on MPICH Application Binary Interface (ABI).
Apps that use vanilla MPI that is compatibile with MPICH would work. Site-specific MPI libraries need to be copied to the container at run time. LD_LIBRARY_PATH need to include for example /opt/udiImage/...
MPI eg mpirun singularity exec centos_ompi.img /usr/bin/mpi_ring
  • The mpirun command is executed on the host.
  • The mpi_ring command is from inside the container.
  • PMIx in OpenMPI perform a version handshake, and everything will work so long as the host's version is equal or newer than the one inside the container.
  • MPI host list come from the host, the container don't need to worry about host discovery.
  • See the singularity mpi diagram below for MPI call flow details.
IB Likely ok for IPoIB. Probably no support for RDS. Native access
GPU Your app should run head-less, why you trying to access video card? :-) Native access, native speed. See NIH's page for setup In progress. Reportedly getting near native performance
Network access Utilize Network Namespace. NAT is default Transparent. Access network like any user process would. Transparent?
Host's device access /dev, /sys and /proc are bind mounted to container by default. /dev, /sys and /proc of host show up inside container
Host's file system access docker run -v hostpath:containerpath will bind mount to make host's FS accessible to container. container can be modified and saved. root access possible. Singularity app run as a user process, therefore it has access to all of host's fs and devices that any user process have access to, including specially optimized FS like Lustre and GPFS. Singularity performs a bind mount between host's mount to the inside of the container.
-B /opt:/mnt will bind mount host's /opt to container's /mnt
Container writable if started with -w.
Root access possible if singularity is run by root
Start shifter with volume mapping, done using loop dev.
User has access to all typical mounts from host.
Allows mounting a localized loop mounted file system on each node to act as a local cache, especially useful in diskless cluster.
qsub -xdv to map host's FS to container
Data persistence in image
  • Container is writable at run time, but need to issue docker commit from outside the container for changes to persist.
  • No host FS mounted/mapped by default.
  • By default container's FS is mounted Read-only; the bind mounts to the host drive is always writable
  • Can use -w flag of singularity to start container in read/write mode.
Deployment Single package install.
Daemon service with root priviledge
Use in batch processing environment left as an exercise to the reader
root to install singularity, sexec-setuid need setuid root to work correctly.
Single .rpm/.deb per host.
No scheduler modification needed.
Shifter need to be installed in all hpc nodes
Docker NOT needed in hpc
Need an ImageGateway
Upgrade to new version of UGE
Head and compute nodes need to be newer version of Linux that supports Docker (eg RHEL 7).
Container activation Docker daemon running on each host loopback mount on singularity image file to utilize container. No daemon process. No docker daemon on CN. srun ... loopback mount May employ a set of nodes with running docker daemon, such nodes are flagged as providing a boolean resource for job to make request against. (?)
Container build-up
  1. Docker spec file.
  2. Interactive build container, then use docker commit.
  3. Pull existing image from repository such as docker hub, docker store, private repository.
  1. Create singularity .def file. Package dependencies are automatically analyzed and incorporated into the image
  2. Interactive expand on existing image by leveraging (sudo) singularity shell -w.
  3. Import/convert a docker image into a singularity image singularity import.
  4. Share pre-build singularity image file (single sparse file, very compressible). Singularity Hub (coming soon? already exist?)
  1. Import/convert docker container into shifter container
  2. Abilities to run image in other format (eg ext4), but not sure how such container image is provisioned.
Security User running docker commands need to be in special docker group to gain elevated system access
No change in security paradigm.
User run singularity image/app without special privileges.
Option to start only root-owned container image.
root to install shifter binary.
Need special integration into scheduler (or only in cray cuz they are special?).
User run shifter image/app without special privileges.
Root escalation container starts with priviledged access To obtain root in singularity container, it must have been started as root
ie, root can be had via sudo singularity shell centos7.img
Container started as normal user cannot use su or sudo to become root; singularity utilize kernel's NO_NEW_PRIV flag (Kernel 3.5 and above).
ie, /bin/su (and /bin/sudo), will have setuid flag, but it is blocked from the inside by singularity
  • container inherit the env of user invoking the singularity cmd
  • /home, /var/tmp, /tmp, /root are bind mount from host and fully writable
  • / is read-only mount and container is typically inmutable (unless started with -w flag)
User management ? Yes. Container has sanitized passwd, group files
Sample User Commands sudo docker pull httpd:latest
docker images -a
sudo docker run -p 8000:80 httpd
sudo singularity create ubuntu.img
sudo singularity bootstrap ubuntu.img ubuntu.def
singularity exec ubuntu.img bash
# the %runscript section of the container will autoamtically be invoked
module load shifter
shiftering pull docker:python:3.5 # pull docker image
shifterimg images # list images
shifter --image=python:3.5 python # execute a container app
module load slurm
sbatch --image=docker:python:3.5 shifter python # run as job
Unix pipes output of container captured by pipe. eg:
docker run centos:6 ls /etc | wc
However, docker won't take standard input, at least not for 1.5-1. The follwing does not work as one might expect:
echo 'cat("Hello world\n")' | docker run r-base:latest R --no-save
can daisy chain singularity apps like regular unix commands. eg
echo "echo hello world" | singularity exec centos7.img bash
Shifter will capture standard input as well inside an sbatch script:
echo 'cat("Hello world\n")' | shifter R --no-save
Performance Docker container startup time is much faster than traditional VM, as it does not need to emaulate hardware and is essentially just starting a new process. Container startup time a bit faster than docker, as it does away with much of the namespace settings.
On Lustre backed system, where metadata lookup span different server than data block lookup, single file container image significantly improve performance by reducing multitude of meta data lookup with the MDS.
On Lustre backed system, where metadata lookup span different server than data block lookup, single file container image significantly improve performance by reducing multitude of meta data lookup with the MDS.
Misc Singularity app can run outside HPC, without any job scheduler. It can serve as a container for app portability outside the HPC world, and since a single file encompass the whole container, this maybe advantageous for sharing, portability and archive.
Singularity recommends compiling all apps into the Singularity container, spec files would need to be written. I hear they are looking to adopt Docker and/or RKT specfile to minimize this burden.
Docker files can be imported or even run directly. Given docker operate on a different paradigm, the hit-and-miss outcome of such conversion is understandable.
In future development, maybe NeRSC's shifter could run singularity app as well.
Shifter container/app can run as stand alone outside HPC scheduler. This is certainly useful for testing and development. However, if one isn't trying to utilize container in HPC, maybe there is not much point in converting docker images to shifter images.
Shifter works by pulling the large number of existing containers. Docker isn't needed inside the HPC, some gateway location can be used for Shifter to pull docker images and store converted image in a location accessible cluster-wide, eg /scratch. See shifter workflow below for more details.
Feel High :) Building a singularity 2.2 image feels a lot like building a VM using kickstart file.
Adopters Like wildfire by internet companies UC Berkeley, Stanford, TACC, SDSC, GSI, HPC-UGent, Perdue, UFL, NIH, etc.
Seems like the non-cray community is gravitating toward Singularity.
Seems like the big physics number crunchers are gravitating toward shifter, cuz they use Cray or IBM Blue Gene?
Product integration and support nextflow Qluster, nextflow, Bright Cluster Manager, Ontropos, Open Cloud/Intel Cluster Orchestrator (in discussion). Cray

Shifter Workflow

As per CSCS/ETH slide share, based on Shifter 15.12.0.

Singularity Workflow

As per Greg Kurtzer keynote at HPC Advisory Council 2017 @ Stanford, based on Singularity 2.2.

singularity workflow diagram from GMK keynote

Workflow with Singularity Hub

MPI in Singularity

singularity mpi diagram

Example Commands in Docker

# get a container with anaconda python and jupyter notebook 

docker run -i -t -p 8888:8888 continuumio/anaconda /bin/bash -c "/opt/conda/bin/conda install jupyter -y --quiet && mkdir /opt/notebooks && /opt/conda/bin/jupyter notebook --notebook-dir=/opt/notebooks --ip='*' --port=8888 --no-browser"

Example Commands in Singularity

sudo  singularity create --size 2048 /opt/singularity_repo/ubuntu16.img
# Create an image file to host the content of the container.  
# Think of it like creating the virtual hard drive for a VM.
# The image created should be a sparse file (ie with holes),
# However, while ext4/ubuntu seems to result in compact file
# RHEL6/ext3 img take up their final file size.

sudo -E singularity bootstrap /opt/singularity_repo/ubuntu16.img /opt/src/singularity/examples/ubuntu.def
# "kickstart" build the container
# If behind a proxy, sudo -E will preserve http_proxy env var 

singularity shell ubuntu.def
singularity exec  ubuntu.img bash  # slight diff than shell, PS1 not changed, .bash_profile sourced here
singularity exec  centos.img  rpm -qa
# Note that uname and uptime will always report info of the host, not the container.

singularity  exec  -w  centos.img  zsh     # -w for writable container, FS ACL still applies
                                           # centos.img needs to be writable by the user
sudo singularity shell -w centos.img       # root can edit all contents inside container

# best to build up container using kickstart mentality.  
# ie, to add more packages to image, vi /opt/src/singularity/exampless/ubuntu.def   
# re-run bootstrap command again.  
# bootstap on existing image will build on top of it, not overwritting it/restarting from scratch
# singularity .def file is kinda like kickstart file
# unix commands can be run, but if there is any error, the bootstrap process ends.

# pipe and redirect works as input and output for singularity container executions: 

echo "echo hello world" | singularity exec centos7.img bash
singularity exec centos7.img echo 'echo hello world' | singularity exec centos7.img bash
singularity exec centos7.img rpm -qa | singularity exec centos7.img wc -l

singularity exec centos7.img python < ./

Example Singularity container definition file

# Copyright (c) 2015-2016, Gregory M. Kurtzer. All rights reserved.
# "Singularity" Copyright (c) 2016, The Regents of the University of California,
# through Lawrence Berkeley National Laboratory (subject to receipt of any
# required approvals from the U.S. Dept. of Energy).  All rights reserved.

BootStrap: yum
OSVersion: 7
Include: yum

# If you want the updates (available at the bootstrap date) to be installed
# inside the container during the bootstrap instead of the General Availability
# point release (7.x) then uncomment the following line

    echo "This is what happens when you run the container..."

    echo "Hello from inside the container"
    yum -y install vim-minimal

    # adding a number of rather useful packages
    yum -y install bash
    yum -y install zsh
    yum -y install environment-modules
    yum -y install which
    yum -y install less
    yum -y install sudo         # binary has setuid flag, but it is not honored inside singularity
    yum -y install wget
    yum -y install coreutils    # provide yes
    yum -y install bzip2        # anaconda extract
    yum -y install tar          # anaconda extract
    # bootstrap will terminate on first error, so be careful!
    test -d /etc/singularity || mkdir /etc/singularity
    touch                          /etc/singularity/singularity_bootstart.log
    echo '*** env ***'          >> /etc/singularity/singularity_bootstart.log
    env                         >> /etc/singularity/singularity_bootstart.log

    # install anaconda python by download and execution of installer script 
    # the test condition is so that subsequent singularity bootstrap to expand the image don't re-install anaconda
    cd /opt
    [[ -f ]] || wget
    [[ -d /opt/anaconda3 ]] || bash -p /opt/anaconda3 -b     # -b = batch mode, accept license w/o user input

Ubuntu snipplet.
I found that --force-yes is needed
debootstrap rpm is needed in a CentOS machine for this bootstrap to work
    echo "Hello from inside the container"
    sed -i 's/$/ universe/' /etc/apt/sources.list
    # when building from ubuntu, should avoid using --force-yes in apt-get
    # but when building from RHEL, had to use --force-yes for it to work (at least in RHEL6)
    apt-get -y --force-yes install vim
    apt-get -y --force-yes install ncurses-term

Additional singularity .def examples

Readings for Containers in HPC

Readings for Singularity

Readings for Shifter

Readings for UGE

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