Frequently
Asked Questions
What is PRAGMA?
PRAGMA
has been founded as an open organization in which Pacific Rim institutions
will collaborate more formally to develop grid-enabled applications
and will deploy the needed infrastructure throughout the Pacific
Region to allow data, computing, and other resource sharing. Based
on current collaborations, PRAGMA will enhance these collaborations
and connections among individual investigators by promoting visiting
scholars' and engineers' programs, building new collaborations,
formalizing resource-sharing agreements, and continuing trans-Pacific
network deployment. PRAGMA provides an opportunity for member institutions
to work together to address applications and infrastructure research
of common interest. PRAGMA is supported by SDSC, NSF, and participating
institutions.
Why start PRAGMA
at all?
We wish to also exploit
the talent in other parts of the world to build this infrastructure.
Whereas many isolated approaches were used to build other software
(e.g. clusters), it will take a global effort to make the global
infrastructure usable.
We also wish to building
upon existing effort, which are for the most part national, and
expand the Grid internationally.
Sharing with Pacific
Rim, we have not tapped into (avoid parallel development).
Give shared geography
and history, we need to build these ties to create ties to avoid
duplication and accelerate progress.
Why start PRAGMA now?
As indicated, the
community is now ready to consider a global Grid. This was not
the case even two years ago. However, as has been seen by groups
such as the Global Grid Forum, the APGrid, the EU-DataGrid,
and the UK eScience, the world is focused on the grid. The United
States just funded the TeraGrid, with the expectation of it
coming on line in 2003. Now is the time to begin to anticipate
its use by the users, and to begin developing applications for
the Grid.
Why is University of
California San Diego an appropriate institution to launch this initiative?
The University of
California San Diego (UCSD) has a number of unique features
to help lead this initiative. First, UCSD is the home of the
San Diego Supercomputer Center (SDSC), which is the leading
edge site for the National Partnership for Advanced Computational
Infrastructure (NPACI). NPACI is the investment by the National
Science Foundation (NSF) to provide high-end computing for the
broad academic research community. In addition, SDSC on behalf
of NPACI, is one of four initial sites of the TeraGrid, NSF’s
further investment in developing a grid.
UCSD is also the
home of the California Institute of Telecommunications and Information
Technology, which is looking at technologies that will expand
the Grid to the wireless world.
UCSD has a broad
set of collaborations with individuals in the Asia Pacific Region,
which we will capitalize on.
UCSD is itself an
institution that is on the Pacific Rim.
This particular
proposal has the strong support of the following offices within
the University of California: The Office of the Associate Vice
Chancellor of Research, The San Diego Supercomputer Center and
the California Institute of Telecommunications and Information
Technology, and the Center for Research for Biological Structures.
What are possible applications
to drive this effort?
We will focus on
a handful of applications of interest to a broader set of participants.
Specific applications will be determined at the first meeting;
we would anticipate that at each meeting the host site would
bring additional applications based on local expertise. The
applications below are in the realm of biology and biomedical
sciences, which is a strength UCSD application scientists and
their international collaborators bring to PRAGMA. This list
is illustrative of the types of applications that would push
the grid technologies and advance PRAGMA’s interest. The
chosen applications will also stress different aspects of the
grid environment: in computing from on-demand computing, to
computing at pre-determined times to create incorporate new
information, to applications that need incredible amounts of
compute cycles for long periods of time; in remote control of
instruments; in access to federated databases. We will also
choose applications that have natural collaborators across the
Pacific Rim.
Telescience,
as mentioned above, allows for sharing of resources on the grid,
in this case high voltage electron microscopes. For telescience
to be useful on a daily bases, several technological challenges
will need to be overcome: scheduling and tuning the network,
moving and storing data at rates fast enough to be meaningful
to the researcher who is attempting to obtain the best image
at the microscope, scheduling and allocation of compute resources
on demand, and manipulating images with software that will allow
for viewing with collaborators geographically distributed.
In the case of telescience,
there has been a great deal of activity via a series of Federal
funding by NSF and NIH. In addition, there has been international
activity between the National Center for Microscopy and Image
Research (http://www-ncmir.ucsd.edu/)
and colleagues at the Research Center for Ultra-High Voltage
Electron Microscopy at the University of Osaka (http://www.uhvem.osaka-u.ac.jp/official/news.html).
There is also interest in expanding this collaboration to other
countries along the Pacific Rim, and PRAGMA is the ideal vehicle
to make this happen. Closely associated with this application
is the computing on demand needed to construct, real-time, tomographic
images from the specimens in the microscope. This will entail
using grid software to obtain computing resources on the grid.
This activity has been supported by many agencies and projects,
notably the National Biomedical Computation Resource (NIH) and
the National Partnership for Advanced Computational Infrastructure
(NSF).
Another example
would be in the arena of digitally enabled genomic medicine.
This area is driven by the vast amounts of genomic information
being produced via high through-put devices and accelerators
on the one hand, and the ability to wirelessly access and manipulate
these data with the ultimate goal of personalized medicine.
Here the challenges will be to use federated data resources
via the grid. Aspects of this problem appear in the various
genetic, DNA sequence, or three-dimensional macromolecular structure
databases. One particular resource that has interactions with
Japan is the Protein Data Bank (PDB/Bourne). In the case of
PDB and other data resources, regular updates of new entries
will be made that will add new information (e.g. new structure
data) and will demand access to compute resources to create
additional updates (e.g. determining how new structure are related
to existing families of structure).
A final example
is from the broader area of computational simulation
to gain insight into, say, biological process from the molecular
to cellular level. Here, aspects of a neuroscience simulator,
MCell, is one where there is a great deal of existing interaction
between neuroscientist and grid scientists, and builds upon
activity underway, both in the National Partnership for Advanced
Computational Infrastructure and the Virtual Instruments for
the Grid (both projects supported by NSF). Related activities
will link critical input data with other simulation techniques
as a finer biological resolution. These will demand other aspects
of the grid, and will build upon and expand existing collaborations
between the US and Japan.
We will also consider
areas outside of the biological and biomedical ones mentioned
above. Some examples that would push the PRAGMA development
agenda, and have natural international collaborations include
areas of earthquake dynamics, astronomy, climate and environment,
and earthquake engineering. With applications such as these
we expect PRAGMA to help bridge that gulf on the technology
issues, and address issues of scheduling and co-allocation of
resources by institutions, networks and countries.
What is the planned relationship
of PRAGMA to other entities?
PRAGMA will maintain
an open and collaborative stance with respect to all groups
and institutions seeking to advance the worldwide grid and its
uses. For example, the Global Grid Forum (GGF) is the organization
through which all recommendations for standardization of grid
infrastructure should be made. GGF is similar in spirit to the
Internet Engineering Task Force (IETF) in that it addresses
grid infrastructure standards. PRAGMA should be seen as one
of several important groups that provide input this infrastructure
standardization. A large number of PRAGMA members directly participate
in the GGF and/or the APGrid. Furthermore, PRAGMA will closely
interact with APGrid (in fact, several key APGrid organizers
and participants are part of PRAGMA also), whose key focus is
on the development of Grid standards and environments in the
Asia Pacific Region. APGrid is essentially the region-specific
activity of the global grid forum.
|
