Presentation at useR!_2013 on July 12, 2013

1. Open Science Grid
BoscoR:
Transforming
Your
R
Desktop
into
an
R
Super
Desktop
Dan
Fraser
Open
Science
Grid
University
of
Chicago
Argonne
National
Laboratory
UseR!
2013,
Albacete,
Spain,
July
12,
2013

2. Open Science Grid
BoscoR
Team
bosco-­‐discuss@opensciencegrid.org
l Dan
Fraser
–
Team
Lead
l Open
Science
Grid,
Uchicago,
ANL
l Derek
Weitzel
–
Lead
Developer
l University
of
Nebraska,
Lincoln
l Marco
Mambelli
–
Support
/
Development
l University
of
Chicago
l Miha
Ahronovitz
–
Product
Manager
l University
of
Wisconsin
l Jaime
Frey,
Todd
Tannenbaum
–
Condor
Development
Support
l University
of
Wisconsin

3. Open Science Grid
Approaching
the
Limit
of
Desktop
Computing
l Solution
time
>>
Time
you
want
to
wait
L
l Multiple
runs
l Some
answers
require
100,000+
iterations
l Larger
datasets
l Complex
analysis
path,
…
l Perhaps
I
can
use
a
faster
computer
somewhere
on
campus?
But
…
Open Science Grid

4. Open Science Grid
Painful
Transition
For
R
Users
Condor
PBS-Remote Login
-Learn Batch CL Environment
-Setup R on Cluster
-Move Data to Cluster
-Parallelize R Script (tool)
-Use Batch Environment
-Transfer Data to Desktop
-Analyze Data
LSF/Platform
Grid Engine
Slurm
…
Available Cluster
“A long, nonlinear process”
--Margarita Rincón Hidalgo (CSIC)

5. Open Science Grid
Open
Source
BoscoR
Condor
PBS
-Install BoscoR
-Connect to Cluster
-Parallelize R Script (GridR)
-Analyze Data
LSF/
Platform
Grid
Engine
Slurm
…
Empowered User
BoscoR transforms your desktop into a “Super Desktop”

6. Open Science Grid
What
BoscoR
Does
for
You
l Transforms
your
Desktop
into
a
“Super-­‐Desktop”
l By
connecting
to
and
managing
your
server
/
cluster
l Straightforward
Path
to
Exploit
R
Parallelism
l Download
and
Install
“Bosco”
and
“GridR”
on
your
desktop
l Connect
your
cluster
(Username,
password)
with
Bosco
l Change
“apply”
to
“grid.apply”
OR
“lapply”
to
“grid.lapply”
l No
shortcuts
for
intelligence
and
thought
in
this
step
!!!
l Run
your
script
J
http://bosco.opensciencegrid.org/boscor/

7. Open Science Grid
BoscoR
Simplifies
and
Automates
l Managed
connection
to
the
Server
/
Cluster
/
Supercomputer
l Installs
&
manages
the
R
package
on
the
remote
cluster
l
May
include
specialized
CRAN
packages
l Integrates
with
an
R
parallelization
tool
l Currently
GridR
(e.g.
apply
-­‐>
grid.apply)
l There
are
other
R
parallelization
tools
l Executes
the
parallelized
R
script
on
the
cluster
l Auto
data
movement
from
desktop
and
back
to
desktop
!

8. Open Science Grid
A
Few
Details
l BoscoR
is
a
Beta
release
l Requires
a
Linux
(or
Mac)
desktop
l Mac
laptops
are
a
work
in
progress
l Cluster
access
requires
a
batch
scheduler
(PBS,
Condor,
..
l Users
must
have
an
account
(access
is
via
SSH)
l Bosco
Integration
with
GridR
only
a
starting
point
l We
welcome
other
Integrations
&
Collaborations
l Special
thank
you
to
the
GridR
development
team

9. Open Science Grid
Sample
GridR
code
in
BoscoR
l Loads
the
GridR
Library
l Initializes
GridR
with
Bosco
connection
l Creates
a
simple
function
“mult2”
l Applies
the
function
to
13,
store
result
in
x
> library("GridR")!
> grid.init(service="bosco.direct", localTmpDir="tmp")!
> mult2 <- function(s) { return (s*2) }!
> grid.apply("x", mult2, 13)!
> x!
[1] 26!

10. Open Science Grid
Summary
l Transform
your
R
desktop
into
a
“Super
Desktop”
J
l Straightforward
process
empowers
the
R
researcher
l Understanding
the
parallel
parts
of
your
R
script
is
beneficial
l Minimal
infrastructure
support
required
l Collaborate
with
us
!
l We
welcome
academic
and
commercial
collaborations
l We’re
here
to
help:
l bosco-­‐discuss@opensciencegrid.org

11. Open Science Grid
Useful
Links
l Short
summary
page:
http://bosco.opensciencegrid.org/boscor/
l Wiki
Page
https://twiki.grid.iu.edu/bin/view/CampusGrids/BoscoR
l Descriptive
Blog
Post
http://derekweitzel.blogspot.com/2013/07/the-­‐next-­‐step-­‐
for-­‐bosco-­‐boscor.html
l Contact
us:
bosco-­‐discuss@opensciencegrid.org