DockerCon EU 2015: Finding a Theory of the Universe with Docker and Volunteer Computers

Finding a Theory of the Universe with Docker and Volunteer Computers

Marius MilleaLagrange Postdoctoral FellowInstitut Lagrange de Paris

About Me

• I'm a cosmologist• ...but I've always been really into

computers• I work on analyzing data from a

satellite called Planck• I'm the main developer at

Cosmology@Home

Thanks to...

Ben Wandelt Rom Walton Cam Boehmer

Original creator of Cosmology@Home

A BOINC developer Introduced me to Docker

...and many others

• Cosmology@Home is a volunteer-based computer cluster

Active computers: (as of July 2015)

• Our aim is to better understand our universe

(in particular the mass of the neutrino particle)

ServerVolunteersPossible universes

Outline

• Measuring the mass of the neutrino particle with Planck

• Cosmology@Home and how Docker has helped

• Future Docker use at Cosmology@Home and in the field of physics in general

Why the science?• Show you a definite

example of the type of calculations we do

• Give you a sense of their ever-changing nature

“For the discovery of neutrino oscillations, which shows that neutrinos have mass”

So what is the mass?

neutrinos

Created in nuclear power plants

Created in the sun

Created by the big bang

nasa.gov

wikipedia.org

Known particles

● Neutrinos interact very weakly● Makes measuring their mass difficult

Neutrinos emitted from the sun, as seen through the earth Super-Kamiokande

Source Detector

DetectorSourceBacklight

The History of the Universe (backwards)

The History of the Universe (forwards)

The Planck satellite

Cold (-270.3999˚C) Hot (-270.4001˚C)

Cold (-270.3999˚C) Hot (-270.4001˚C)

DetectorSourceBacklight

Summary thus far

• We measure the distortion of the CMB due to neutrinos released from the big bang to infer the mass of the neutrino particle

• Our volunteer computers simulate different hypothetical universes with different neutrino masses to tell us how much distortion we would expect, then we compare to data

Outline

• Measuring the mass of the neutrino particle with Planck

• Cosmology@Home and how Docker has helped

• Future Docker use at Cosmology@Home and in the field of physics in general

From the user's POV

z

http://www.cosmologyathome.org

https://boinc.berkeley.edu

From our POV

Regular apps

• Compile executable for each platform• Either statically link or include all necessary libraries• Link against the BOINC libraries and manage user

requests for suspend/checkpoint/resume, etc…• BOINC takes care of sending it each host, running it, etc...

Cosmology@Home computers

VM apps

• Just create one VM image, works on all platforms• BOINC handles suspend/checkpoint/resume• Still some downsides

– Its clunky to create a VM image– New app version, user has to redownload whole thing?

Cosmology@Home internet connections

Docker apps

+Debian base image (~40Mb compressed)+our app (~3Mb compressed)

BOINC

BOINC Virtualbox wrapper

“boinc2docker” ISO

Docker container

handles pause/resumegenerally “BOINC things...”

lightly modified to interact with BOINC

Persistence

Logging

Startup script

boot2docker ISO modifications

#!/bin/sh/etc/init.d/docker stoptar cf /root/scratch/boinc2docker_persistence.tar /var/lib/docker/*/etc/init.d/docker start

#!/bin/shdocker inspect $IMAGE || { docker pull $IMAGE && save_docker.sh; }docker run --rm -v /root/shared:/root/shared $IMAGE

via Virtualbox guest-logging, logs are uploaded to our DB

What running jobs now looks like• Create the Docker image which runs my

calculation and push to Docker hub

docker build -t cosmohome/mytheory .docker push cosmohome/mytheory

...

FROM debian:wheezy

RUN apt-get update && \ apt-get -y install libgfortran3 libgomp1 && \ rm -rf /var/lib/apt/lists/*

COPY ["camb", "HighLExtrapTemplate_lenspotentialCls.dat", "/root/"]

What running jobs now looks like

• Submit workunit on Cosmology@Home server pointing to my image

./create_work --app boinc2docker \ boinc_app \ params

e.g. neutrino mass = X...

A short script like you saw before which does adocker run cosmohome/mytheory

End result• Its easy!• I can spend my time being a physicist,

not a programmer

Previously

Planck

Outline

• Measuring the mass of the neutrino particle with Planck

• Cosmology@Home and how Docker has helped

• Future Docker use at Cosmology@Home and in the field of physics in general

Docker and volunteer computing

“BOINC is the #5 super-computer in the world. What if

it ran Docker?”

42

Docker and volunteer computing

Cosmology@Home:• “Higher fidelity” simulations of the universe

Generally:• An “IPython Parallel”-like interface to BOINC• “Service to scientists”• Swarm, Tutum..?

• From the top: the most computer savvy physicists know of and may use Docker

• From the grassroots: more work needed– Good news: physicists develop, ship, and

modify code– Docker and MPI (e.g. see “Shifter” at NERSC)

Docker and scientific computing

Summary

• Cosmology@Home, a cluster of volunteer computers, now runs Docker

• Docker allows us to spend our time being physicists

• If anyone is looking for open source projects to contribute to, we welcome helpers, find me or our github.com/marius311/cosmohome

Thank you!Marius [email protected]