Shifter: Containers in HPC Environments

Shifter: Containers in HPC environments
HPC Advisory Council Switzerland
Miguel Gila, CSCS
March 21, 2016

What is Docker and how does it work?
§ “Docker containers wrap up a piece of software in a complete filesystem that
contains everything it needs to run: code, runtime, system tools, system libraries
– anything you can install on a server. This guarantees that it will always run the
same, regardless of the environment it is running in.” [*]
Shifter: Containers in HPC environments 3
Virtual Machines Containers
[*] https://www.docker.com/what-docker
[*]
[*]

What is Docker and how does it work?
§ A Docker image is a file that contains a filesystem within it. It can be a full
filesystem (i.e. CentOS) or partial (i.e. python3.4-slim). Images are stored either
on a public registry (Docker hub) or private
§ Docker leverages the namespaces feature of the kernel to isolate processes
§ On its simplest form, Docker basically
1. Pulls an image to the local system
2. Creates a chrooted environment with the image (=container)
3. Runs our application in the container (’isolated’ from the host thanks to kernel namespaces)
§ However, it can also do other things:
§ Isolate network by creating NAT or bridge devices
§ Can use a nice GUI

Docker in HPC environments
§ Docker is a nice tool, but it’s not built for HPC environments, because:
§ Does not integrate well with workload managers
§ Does not isolate users on shared filesystems
§ Requires running a daemon on all nodes
§ Not designed to run on diskless clients
§ Network is, by default, ‘NATed’
§ Building Docker is done within a Docker container. It can be done outside, but is a complex
task (Go language, seriously??)
§ But after all, a sysadmin can make anything to work on a cluster, right?
§ We can create (and hopefully maintain) monstrous wrappers to run Docker containers…

What is Shifter and how does it work?
§ Shifter is a container-based solution thought from the ground up for HPC
environments
§ It leverages the current Docker environment and can use Docker images to
create containers
§ Shifter basically
1. Pulls an image to a shared location (/scratch)
2. Creates a loop device with the image (=container)
3. Creates a chrooted environment on the loop device
4. Runs our application in chrooted environment
§ Designed to work on HPC clusters and, particularly, on Cray systems
§ It is possible to choose which filesystems to expose to the containers

External nodeCompute node
Architecture of Shifter
§ Shifter consists on two parts
§ udiRoot is responsible for creating the loop devices, doing chroot and cleaning up after the
binary execution is done. Workload manager plugins are available. Written in C
§ imageGateway is responsible for fetching a Docker image, converting it to a squashfs file and
transfer it to a shared location on a filesystem. It also keeps track of the images and tells
udiRoot which are available. Written in Python
scratch
udiRoot imageGateway
query
restful API
db
Docker
Hub
Or private
registry

Workflow
1. User creates an image on his/her computer and pushes it to Docker Hub
Docker
image
1 2
$ docker build .
Uploading context 10240 bytes
Step 1 : FROM busybox
Pulling repository busybox
---> e9aa60c60128MB/2.284 MB (100%) endpoint: https://cdn-registry-
1.docker.io/v1/
Step 2 : RUN ls -lh /
---> Running in 9c9e81692ae9
total 24
drwxr-xr-x 2 root root 4.0K Mar 12 2013 bin
drwxr-xr-x 5 root root 4.0K Oct 19 00:19 dev
drwxr-xr-x 2 root root 4.0K Oct 19 00:19 etc
drwxr-xr-x 2 root root 4.0K Nov 15 23:34 lib
lrwxrwxrwx 1 root root 3 Mar 12 2013 lib64 -> lib
dr-xr-xr-x 116 root root 0 Nov 15 23:34 proc
lrwxrwxrwx 1 root root 3 Mar 12 2013 sbin -> bin
dr-xr-xr-x 13 root root 0 Nov 15 23:34 sys
drwxr-xr-x 2 root root 4.0K Mar 12 2013 tmp
drwxr-xr-x 2 root root 4.0K Nov 15 23:34 usr
---> b35f4035db3f
Step 3 : CMD echo Hello world
---> Running in 02071fceb21b
---> f52f38b7823e
Successfully built f52f38b7823e
Removing intermediate container 9c9e81692ae9
Removing intermediate container 02071fceb21b
docker build docker push
$ docker push miguelgila/wlcg_wn:20161212
Docker
Hub
Or private
registry

Workflow
2. User tells imageGateway to pull his image and make it available
$ ssh santis01
$ module load shifter
$ shifterimg pull docker:ubuntu:14.04
$ sleep 300 # :-)
$ shifterimg images
santis docker READY 2934337e50 2015-12-10T09:03:38 python:2.7-slim
santis docker READY a4f04f71be 2015-12-10T09:47:17 python:3.5-slim
santis docker READY b0197931ac 2015-12-10T09:53:54 python:3.2-slim
santis docker READY 0bb6b50d84 2015-12-10T10:34:24 python:3.3-slim
santis docker READY cd86406b32 2015-12-10T10:36:55 python:3.5.1
santis docker READY 48bc52cc28 2015-12-10T10:47:35 python:3.4.3
santis docker READY 0b92f1735f 2015-12-10T11:17:26 python:3.4-slim
santis docker READY 3fba104814 2015-12-10T11:31:23 centos:6.7
santis docker READY 12c9d795d8 2015-12-10T11:37:35 centos:6.6
santis docker READY 3e0c71ada2 2015-12-10T15:19:24 ubuntu:15.10
santis docker READY e751d10964 2015-12-10T13:38:05 miguelgila/wlcg_wn:20151125v2
santis docker READY d55e68e6cc 2015-12-10T15:52:09 ubuntu:14.04
shifterimg pull
/scratch/
santis
imageGateway
1
2
3 4
Docker
image
Shifter
image
Shifter
image
Docker
Hub
Or private
registry

Compute node
Workflow
2. User tells imageGateway to pull his image and make it available
3. User runs SBATCH and prepends shifter to his/her executable
#!/bin/bash –l
#SBATCH --job-name="shifter_osversion”
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --time=00:30:00
#SBATCH --exclusive
#SBATCH --output=/users/miguelgi/jobs/out/shifter_hostname.stdout.log.%j
#SBATCH --error=/users/miguelgi/jobs/out/shifter_hostname.stdout.log.%j
#SBATCH --image=docker:miguelgila/wlcg_wn:20151218
#SBATCH --imagevolume=/users/miguelgi:/users/miguelgi
#SBATCH --imagevolume=/apps:/apps
#SBATCH --imagevolume=/scratch/santis:/scratch/santis
module load slurm
module load shifter/15.12.0
srun shifter --volume=/scratch/santis:/scratch/santis --volume=/users:/users cat
/etc/redhat-release
sbatch
/scratch/
santis
SRUN/SPANK
1
3
udiRoot
Loop device
/dev/loopY
Shifter
image
Create loop dev
shifter binary
Run bin in loop dev
/users
2

Full OS containers
§ Cray compute nodes run CLE (a version of SLES 11)
§ With Shifter it is possible to run applications built for specific OS:
[miguelgi@santis01]-[11:34:45]-[~/examples]:-($ salloc -t 00:15:00 -N1 --image=docker:centos:6.7
salloc: Granted job allocation 16313
salloc: Waiting for resource configuration
salloc: Nodes nid00012 are ready for job
[miguelgi@santis01]-[11:34:50]-[~/examples]:-)$ srun shifter cat /etc/redhat-release
CentOS release 6.7 (Final)
[miguelgi@santis01]-[11:35:03]-[~/examples]:-)$ srun shifter yum --version |head -4
3.2.29
Installed: rpm-4.8.0-47.el6.x86_64 at 2015-08-19 18:25
Built : CentOS BuildSystem <http://bugs.centos.org> at 2015-07-24 11:28
Committed: Lubos Kardos <lkardos@redhat.com> at 2015-06-15
CentOS 6 – non-interactive session
[miguelgi@santis01]-[10:52:40]-[~/examples]:-)$ salloc -t 00:15:00 -N1 --image=docker:debian:7.9
[miguelgi@santis01]-[10:58:29]-[~/examples]:-($ srun --pty shifter /bin/bash
[miguelgi@nid00012]-[10:58:31]-[~/examples]:-)$ cat /etc/debian_version
7.9
[miguelgi@nid00012]-[10:58:33]-[~/examples]:-)$ uname –a
Linux nid00012 3.0.101-0.46.1_1.0502.8871-cray_ari_c #1 SMP Tue Aug 25 21:41:26 UTC 2015 x86_64 GNU/Linux
[miguelgi@nid00012]-[10:59:46]-[~/examples]:-)$ apt-get --version |head -n1
apt 0.9.7.9 for amd64 compiled on Oct 17 2014 09:15:56
Debian 7.9 – interactive session

Application containers: Python/Ruby
[miguelgi@santis01]-[09:57:23]-[~]:-)$ salloc -t 01:00:00 -n1 --image=docker:python:3.5.1
[miguelgi@santis01]-[10:00:51]-[~]:-)$ srun --pty shifter /bin/bash
[miguelgi@nid00012]-[09:01:04]-[~]:-)$ python –V
Python 3.5.1
[miguelgi@nid00012]-[09:01:08]-[~]:-)$ which python
/usr/local/bin/python
Python 3.5.1 – interactive session
[miguelgi@santis01]-[10:16:35]-[~]:-)$ salloc -t 01:00:00 -n1 --image=docker:python:3.2-slim
[miguelgi@santis01]-[10:19:34]-[~/tmp]:-)$ srun shifter ./myscript.py
3.2.6
Python 3.2 – non-interactive session
$ cat myscript.py
#! /usr/bin/env python
import platformprint(platform.python_version())
myscript.py
[miguelgi@santis01]-[09:57:23]-[~]:-)$ salloc -t 01:00:00 -n1 --image=docker:ruby:2.1.8
[miguelgi@santis01]-[10:22:14]-[~]:-)$ srun --pty shifter /bin/bash
miguelgi@nid00012]-[09:22:28]-[~]:-)$ ruby –v
ruby 2.1.8p440 (2015-12-16 revision 53160) [x86_64-linux
Ruby 2.1.8 – interactive session
[miguelgi@santis01]-[10:22:05]-[~]:-)$ salloc -t 01:00:00 -n1 --image=docker:ruby:2.1.8
[miguelgi@santis01]-[10:22:08]-[~/tmp]:-)$ srun shifter ./myscript.rb
2.1.8
Ruby 2.1.8 – non-interactive session
$ cat myscript.rb
#!/usr/bin/env ruby
puts RUBY_VERSION
myscript.rb
§ Can run application specific containers:

Multi-node containers
§ It is possible to run the same container across multiple nodes:
§ Working on getting MPI across nodes to function
§ Working on getting GPUs to be accessible to containers with good results so far (native
performance!)
lucasbe@santis01 ~/shifter-gpu> sbatch ./nvidia-docker/samples/cuda-stream/benchmark.sbatch
Submitted batch job 496
lucasbe@santis01 /scratch/santis/lucasbe/jobs> cat shifter-gpu.out.log
Launching GPU stream benchmark on nid00012 ...
STREAM Benchmark implementation in CUDA
Array size (double precision) = 1073.74 MB
using 192 threads per block, 699051 blocks
Function Rate (GB/s) Avg time(s) Min time(s) Max time(s)
Copy: 184.3169 0.01167758 0.01165104 0.01170397
Scale: 183.1849 0.01175387 0.01172304 0.01178598
Add: 180.3075 0.01790012 0.01786518 0.01792288
Triad: 180.1056 0.01790700 0.01788521 0.01794291
GPU
#! /usr/bin/env python
import platform
import socket
print(platform.python_version())
print(socket.gethostname())
hostname.py
[miguelgi@santis01]-[10:39:43]-[~/examples]:-)$ salloc -t 00:15:00 -N2 -w nid00013,nid00014 --image=docker:python:3.2-slim
salloc: Nodes nid000[13-14] are ready for job
[miguelgi@santis01]-[10:41:21]-[~/examples]:-)$ srun shifter ./hostname.py
3.2.6
nid00013
3.2.6
nid00014
Python 3.2 – non-interactive session

Practical use case: WLCG Swiss Tier-2
§ CSCS operates the cluster Phoenix on behalf of CHIPP, the Swiss Institute of
Particle Physics
§ Phoenix runs Tier-2 jobs for ATLAS, CMS and LHCb, 3 experiments of the LHC
at CERN and part of WLCG (Worldwide LHC Computing Grid)
§ WLCG jobs need and expect RHEL-compatible OS. All software is precompiled
and exposed in a cvmfs[*] filesystem
§ But Cray XC compute nodes run CLE, a modified version of SLES 11 SP3
§ So, how do we get these jobs to run on a Cray?
Shifter: Containers in HPC environments 16 [*] https://cernvm.cern.ch/portal/filesystem

Practical use case: WLCG Swiss Tier-2
§ Using Shifter, we are able to run unmodified ATLAS,
CMS and LHCb production jobs on a Cray XC40 TDS
§ Jobs see standard CentOS 6 containers
§ Nodes are shared: multiple single-core and multi-core
jobs, from different experiments, can run on the same
compute node
§ Job efficiency is comparable in both systems
JOBID USER ACCOUNT NAME NODELIST ST REASON START_TIME END_TIME TIME_LEFT NODES CPU
82471 atlasprd atlas a53eb5f8_34f0_ nid00043 R None 15:03:33 Thu 15:03 1-23:54:18 1 8
82476 cms04 cms gridjob nid00043 R None 15:08:39 Tomorr 03:08 11:59:24 1 2
82451 lhcbplt lhcb gridjob nid00043 R None 15:00:10 Tomorr 03:00 11:50:55 1 2

§ Can isolate network by creating NAT or
bridge devices. What about IB?
§ Users can write as root on exposed RW
filesystems
§ Needs a local daemon running
§ Isn’t SLURM-friendly
§ Can run on multiple nodes with own tool
(Swarm)
§ Can use GPUs?
§ MPI?
§ Can run images on private registry
§ It shows all /dev, /sys and /proc to the
container environment. Easy
§ Users can write as their $USER on any
exposed RW filesystem
§ Does not need a local daemon on CN
§ Is SLURM-friendly (SPANK plugin)
§ Can run on multiple nodes with WLM
integration
§ Can use GPUs. Working on it!
§ MPI on its way!
§ Can run images on private registry
Docker vs. Shifter
Docker

Conclusion
§ Shifter works very well on our HPC environment
§ It’s being constantly developed and new features are appearing on a weekly
basis
§ It’s open source and developed by the HPC community
§ It needs some additional work to cover basic HPC use cases (MPI)
§ Interacting with some parts of Shifter is not very user-friendly:
§ The process of pulling images is easy, but has no visual feedback
§ At times, error messages are difficult to understand
§ No ACLs yet

Reference links
§ NERSC info: http://www.nersc.gov/research-and-development/user-defined-images/
§ The code: https://github.com/NERSC/shifter

Shifter: Containers in HPC Environments

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