Designing Proteins from Scratch

Open Science Grid
In the first part of 2007 the Open Science Grid (OSG) consortium established and operated the first generation of a
shared national cyberinfrastructure bringing together advanced grid technologies to provide end-to-end distributed
capabilities to a broad range of compute intensive application. The 0.6.0 OSG software stack released early this year
offers the community additional capabilities integrated into the Virtual Data Toolkit. These capabilities were used to
deliver opportunistic computing to the DZero Tevatron Experiment at Fermilab, demonstrated their power in the
data challenges for the CERN LHC experiments, are being tested at scale by the LIGO gravitational wave and
STAR nuclear physics experiments, and provide a basis for the use of OSG by non-physics communities. Training
and outreach to campus organizations, together with targetted engagement activities, are bringing additional users
and communities to use the emerging cyberinfrastructure.
D0 Reprocessing on Opportunistically Available Resources
During the first half of 2007 DZero reprocessed their complete dataset. Over 50% of the events were processed
using opportunistically available resources on the OSG (see Figure 1). This was an important demonstration of the
ability of the OSG Consortium stakeholders to contribute resources to the common infrastructure while still
maintaining control for their own use. DZero was able to use more than twelve sites on the OSG including the LHC
Tier-1s in the US (BNL and Fermilab) and
university Tier-2 centers, LIGO and other
university sites.
On OSG, DZero sustained execution of over
1000 simultaneous jobs, and overall moved
over 70 Terabytes of data. "This is the first
major production of real high energy physics
data (as opposed to simulations) ever run on
OSG resources," said Brad Abbott of the
University of Oklahoma, head of the DZero
Computing group. Reprocessing was completed
in June. Towards the end of the production run
the throughput on OSG was more than 5
million events per daytwo to three times
more than originally planned. In addition to the
reprocessing effort, OSG provided 300,000
CPU hours to DZero for one of the most precise
Figure 1: D0 Event Processing on Different Grids
measurements to date of the top quark mass,
and to achieve this result in time for the spring
physics conferences.
LHC Data Challenges: Simulated Data Distribution and Analysis
As part of the preparations for data acquired from the accelerator at CERN, the ATLAS and CMS experiments
organize “data challenges” which test the performance and functionality of their global data distribution and analysis
systems. The latest round of activities covered the managed distribution and placement of data around the world,
including moving data between storage resources at CERN to more than 10 Tier-1 sites for each experiment
worldwide. Movement of data between the Tier-1s and the OSG University Tier-2 sites was also part of these
exercises (see Figure 2). The sustained
performance is as important, and more
difficult to achieve in many cases, as the peak
throughput delivered. Each experiment uses
the Globus GridFTP protocols to distribute
the data, the Enabling Grids for EsciencE
(EGEE) gLITE File Transfer Service (FTS)
to manage contention for and policies within
the network pipes, and an experiment specific
data placement service (known as DQ2 for
ATLAS and PHEDEX for CMS) to
orchestrate the data catalogs, namespaces and
End-to-end analysis and production job
Figure 2: CMS Data Transfer
scheduling and throughput are another
important aspect of the exercises, which
Open Science Grid
July 2007
included support from OSG. Both experiments achieved throughputs of more than 10K jobs a day, with success
rates of more than 80%.. For data taking next year all these rates must increase by factors of 2-5. The tests are
continuing and the sites and middleware are being scaled to meet the deliverables.
Virtual Data Toolkit Extensions
Number of major components
The OSG Virtual Data Toolkit (VDT) provides the underlying packaging and distribution of the OSG software
stack. The distribution was initially built and supported by the Trillium projects – GriPhyN, iVDGL and PPDG.
VDT continues to be the packaging and distribution vehicle for Condor, Globus, myproxy, and common
components of the OSG and EGEE software. VDT packaged components are also used by EGEE, the LIGO Data
Grid, the Australian Partnership for Advanced Computing and the UK national grid, and the underlying middleware
versions and testing infrastructure are shared between OSG and TeraGrid. The VDT distribution (See Figure 3) is
available as either a set of pacman caches or RPMs, with specific distributions available for making processing
farms or storage resources accessible from a Grid infrastructure.
In the first nine months of the OSG project the VDT
Both added and
has been further extended to include: OSG
removed software
accounting probes, collectors and a central
More dev releases
repository for accounting information, contributed
VDT 1.3.9
VDT 1.3.6
by Fermilab; The EGEE CEMON information
For OSG 0.4
For OSG 0.2
manager which converts information from the
VDT 1.1.8
VDT 1.3.0
Adopted by LCG
MDS2 LDIF format to Condor ClassADS; Virtual
VDT 1.6.1
25 VDT 1.0
For OSG 0.6.0
Organization (VO) management registration
Globus 2.0b
20 Condor-G 6.3.1
software developed for the World Wide LHC
VDT 1.1.11
Computing Grid (WLCG) and used by most physics
collaborations; An additional implementation of
storage software, interfaced through the Storage
Resource Management (SRM) interface. The
dCache software, provided by a collaboration
between the DESY laboratory in Hamburg, and
VDT 1.1.x
VDT 1.2.x
VDT 1.3.x
VDT 1.4.0
VDT 1.5.x
VDT 1.6.x
Fermilab, is also in use by the WLCG and High
Energy Physics experiments in the US. VDT
Figure 3: Timeline of VDT Releases
releases are tested on the OSG Integration Grid
before being put in production. VDT is an effective
vehicle for the rapid managed dissemination of security patches to the component middleware. Patches and updates
are provided to the installation administrators for security and bug fixes.
Interoperability and Federation
Campus Grids
OSG includes within its scope the support and gateways between campus and the OSG infrastructures:
 FermiGrid: The Fermilab Campus Grid provides a uniform interface to OSG and dispatches jobs to available
resources on site. A shared data area allows sharing of data across the local sites.
 Grid Laboratory Of Wisconsin (GLOW): Work continues to enable applications to be automatically “elevated”
to OSGchallenging because the security infrastructures are different on the two facilities, and to allow
GLOW users to use their existing local kerberos identities. The "football problem" from LeHigh University, is
the first such application to be thus "elevated".
OSG collaborates with Educause, Internet2 and TeraGrid to sponsor day-long workshops local to university
CampusesCyberInfrastructure (CI) Days. These workshops bring expertise to the Campus to foster research and
teaching faculty, IT facility, and CIO discussions .The first such workshop, held at the University of California
Davis in March, had an extremely positive response. At least four more CI days will happen in the fall at the
University of New Mexico, Elizabeth College, the University of Arkansas and in collaboration with Clemson
OSG interoperates with the EGEE in support of the LHC and other physics VOs. This is now working well based on
the correct configuration of the information service. OSG sites must also report the results of site functional tests to
the WLCG in support of the LHC infrastructure. WLCG and OSG have worked together on common definitions for
the output of such tests, and these are being promulgated to the wider community. The foundation of federation is
translation of published information to a format that other grids can use. OSG contributors continue to participate in
this activity as part of the Open Grid Forum GLUE work.
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July 2007
Engagement of Non-Physics Communities
The OSG Engagement activity’s mission is to work closely with new communities over periods of several months to
help them use the production infrastructure and transition to be full contributing members of the OSG.
In the nine months since the start of the OSG project engagement activities have succeeded in:
 Production running opportunistically using more than a hundred thousand CPU hours of the Rosetta application
from the Kuhlman Laboratory in North Carolina across more than thirteen OSG sites. Experience shows that
once a site has been “commissioned” it is fairly stable against errors unless, and until, a scheduled maintenance
occurs, and once jobs are submitted they run quickly across the grid (See Figure 4).
 Production runs of the Weather Research and
Forecast (WRF) application using more than
one hundred and fifty thousand CPUhours on
the NERSC OSG site at Lawrence Berkeley
3,000 jobs
National Laboratory.
 Improvement of the performance of the
nanoWire application from the nanoHub
project on sites on the OSG and TeraGrid, such
that stable running of batches of five hundred
jobs across more than five sites is routine.
 Adaptation of the ATLAS workload
management system, PANDA, for the
Chemistry at Harvard Molecular Mechanics
(CHARMM) program for macromolecular
simulations, in this case for the study of water
Figure 4:Rosetta Jobs Submitted across the OSG
penetration in staphylococcal nuclease by Dr
A. Damjanovic at Johns Hopkins University
who has used over thirty thousand CPUHours on twelve OSG resources over the last few months.
Grid Schools and the Education Virtual Organization
The heart of the Open Science Grid education training builds on the successful annual grid schools run by the
Trillium projects. Each of the OSG grid schools is two to three days of lectures and hands on practicals. Schools
have so far been held in at the University of Illinois at Chicago and at the University of Texas Brownsville (UTB, a
Minority Serving Institution), with a third school taking place at the beginning of August at the University of
Nebraska, Lincoln (an Espcor state). The schools are focused on the graduate level student but at each session
several faculty members have signed up with their students. This has resulted in good follow up after the classes as
the teachers provide a foundation for continuing to use the material. As well as schools in the US, international
organizationsto date in Argentina, Columbia and Brazil have used the material provided (See Figure 5).
For the first time OSG has contributed to the annual
International Summer School for Grid Computing,
which is organized by the National Escience
Research Center in Edinburgh. Ten students who
have taken the short OSG course were able to spend
two weeks immersive hands on training, with close
contact with the staff, and in a group of more than
60 students worldwide. The concepts and challenges
of distributed computing are taught in tandem with
hands on exercises using today’s technologies and
systems. After attending a school participants can
register, with the OSG Virtual Organization and
access opportunistically available resources. At the
University of Texas Brownsville, for example,
students are continuing to work with LIGO on their
Figure 5: Sample of Grid School Curriculum
data analysis.
OSG is supported by the Department of Energy Office of Science SciDAC-2 program from the High Energy
Physics, Nuclear Physics and Advanced Software and Computing Research programs, and the National Science
Foundation Math and Physical Sciences, Office of CyberInfrastructure and Office of International Science and
Engineering Directorates.
Open Science Grid
July 2007