SDM-Center Quarterly Report

April-June 2005

**[Introduction]{.underline}**

Scientific exploration and discovery typically takes place in two
phases: data collection/generation and data analysis. In the data
collection/generation phase large volumes of data are generated by
simulation programs running on supercomputers or collected from
experiments' instruments. This requires efficient parallel data systems
that can keep up with the volumes of data generated. In the data
analysis phase, it is necessary to have efficient indexes and effective
analysis tools to find and focus on the information that can be
extracted from the data, and the knowledge learned from that
information. This requires sophisticated workflow tools, as well as
efficient dataflow capabilities to move large volumes of data between
the analysis components.

We have organized the SDM center's activities based on a three-layer
framework, where the components of each layer can use components in the
layers below it. The three layers of the framework starting from the
bottom are:

-   Storage Efficient Access (SEA) techniques,

-   Data Mining and Analysis (DMA) components

-   Scientific Process Automation (SPA) tools

The SEA layer is immediately on top of hardware, operating systems, file
systems, and mass storage systems. The SEA layer provides parallel disk
access technology (PVFS, ROMIO, MPI-IO), parallel structured data access
(parallel NetCDF), and a Storage Resource Manager (SRM) -- a software
layer to manage multi-file requests from the mass storage system
(currently HPSS). On top of the SEA layer exists the DMA layer,
consisting of indexing (bitmap index), feature selection and
identification, and parallel statistical analysis components
(parallel-R, based on R package), as well as a parallel visualization
component (parallel VTK). This layer also provides an integration
framework (ASPECT) that allows the analysis components to interact. The
SPA layer which is on top of the DMA layer provides the ability to
compose workflows from the components in the DMA layer as well as
user-provided simulation and analysis components. The scientific
workflow engine, called Kepler, was developed by enhancing an event
modeling tool (called Ptolemy) to support capabilities needed in
scientific applications. These include the ability to wrap any
components as Web services, and invoke computational components in a
prescribed fashion. It also provides the capability to launch user's
components wrapped with CCA (Common Component Architecture) interfaces ,
and to initiate and monitor data transfer components.

# This report consists of the following sections, organized according to the three layers, as follows:

-   Storage Efficient Access (SEA) techniques,

    -   Parallel I/O on Clusters

    -   Application Interfaces to I/O

    -   SRM/MPI-IO Parallel File System Caching and Migration Service

    -   LN/MPI-IO: MPI-IO Interface to Logistical Networks (LNs)

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-   Data Mining and Analysis (DMA) components

    -   ASPECT: Adaptable Simulation Product Exploration and Control
        Tool

    -   Feature Selection in Scientific Applications

    -   High-dimensional indexing techniques

    -   Integrated Data Management and Analysis Facility

-   Scientific Process Automation (SPA) tools

    -   Mediated Query Environment

    -   Outreach and User Interaction

    -   Incorporation of Agent / Workflow Technology

    -   SCIRun/Kepler integration

The reports by each of the three areas follow.

**[1. Storage Efficient Access (SEA)]{.underline}**

***Participants:*** Bill Gropp, Rob Ross, Rajeev Thakur, Rob Latham, and
Jonghyun Lee (ANL), Alok Choudhary, Wei-keng Liao, Jianwei Li, and Avery
Ching (NWU), Arie Shoshani and Ekow Otoo (LBNL)

The goal of this project is to provide significant improvements in the
parallel I/O subsystems used on today\'s machines while ensuring that
the capabilities available now will continue to be available as systems
increase in scale and technologies improve. A two-fold approach of
immediate payoff improvements and medium-term infrastructure development
is employed.

Our two keystone components are the PVFS2 parallel file system and the
ROMIO MPI-IO implementation. These tools together address the
scalability requirements of upcoming parallel machines and are designed
to leverage the technology improvements in areas such as
high-performance networking. These are both widely deployed and freely
available, making them ideal tools for use in today's systems. Our work
in application I/O interfaces, embodied by our Parallel NetCDF
interface, also promises to provide short-term benefits to a number of
climate and fusion applications.

At the same time we continue to push for support of common,
high-performance interfaces to additional storage technologies. Our work
combining the Storage Resource Manager (SRM) with MPI-IO, in conjunction
with PVFS2, will provide a single solution for the problems of
high-performance parallel storage access, integration of file system
with tertiary storage, and remote data access. Finally, our work
creating a MPI-IO interface for access to logistical networks will
provide another option for remote data access.

**[Task 1.1: Parallel I/O on Clusters]{.underline}**

The objective of this work is to improve the state of parallel I/O
support on Linux clusters and enable the use of high performance
parallel I/O systems by application scientists. The Second Parallel
Virtual File System (PVFS2) and ROMIO MPI-IO implementations, primarily
developed at ANL, are in wide use and provide parallel I/O
functionality. This work builds on these two components by enhancing
them and building core infrastructure in order to ensure these
capabilities continue to be available as clusters continue to scale.

***Progress Report***

PVFS2 has been ported to the IBM BG/L system \[1\], and plans are now
underway for investigating fault-tolerant PVFS2 deployments in the
context of BG/L and the future BG/P systems. Our new programmer, Sam
Lang, has also started working with us and is getting up to speed on the
PVFS2 system. Version 1.1.0 of PVFS2 was released on June 6.

A collection of improvements, including PanFS (from Panasas) support,
have been integrated into ROMIO. These improvements were made available
in the latest MPICH2 release, and a stand-alone ROMIO release is
upcoming.

Finally, we are continuing to spread the word about parallel I/O
techniques through invited talks and tutorials \[1-7\]. The emphasis in
our I/O tutorials is on understanding how parallel I/O systems work,
what interfaces are available, and how these interfaces match to the
needs of applications.

## Plans for next quarter

After putting the finishing touches on the stand-alone ROMIO release we
will work towards a new PVFS2 release. Many improvements, including
extended attribute support and performance improvements for NFS exports,
are underway.

In the next quarter the emphasis will be on improving performance. We
will be examining the PVFS2 system for the purposes of enhancing
performance for HPC applications, and we will be tuning the interactions
between ROMIO and underlying file systems.

**[Task 1.2: Application Interfaces to I/O]{.underline}**

The objective of this work is to improve the observed I/O throughput for
applications using parallel I/O by enhancements to or replacements for
popular application interfaces to parallel I/O resources. This task was
added in response to a perceived need for improved performance at this
layer, in part due to our previous work with the FLASH I/O benchmark.
Because of their popularity in the scientific community we have focused
on the NetCDF and HDF5 interfaces, and in particular on a parallel
interface to NetCDF files. Recently we have seen increased interest in
the PnetCDF interface from the astrophysics scientists at NCSU (contact:
John Blondin).

***Progress Report***

A collection of improvements for PnetCDF on the NEC SX platform were
integrated in the last quarter, and some bugs specific to the Cray X1
were fixed. At this point we are ready for a 1.0 release of PnetCDF.

We are also investigating what it means to support data mining in
PnetCDF. This will likely include augmented APIs designed to allow users
to easily and efficiently perform key operations.

##  Plans for next quarter

We have begun working with John Blondin on the use of PnetCDF and PVFS2
with their applications, both on the Cray X1 (PnetCDF only) and on
clusters at NCSU (PnetCDF and PVFS2). Functionally we are in great
shape, but performance problems are showing up on the Cray machine. It
is unclear whether these are PnetCDF problems or something inherent in
the MPI-IO or file system on that machine, and additional testing will
be necessary to determine this.

J. Li continues to lead the data mining support efforts at the PnetCDF
layer. That work will lead to a prototype API for aiding data mining on
PnetCDF files.

**[Task 1.3: SRM/MPI-IO Parallel File System Caching and Migration
Service]{.underline}**

The objective of this work is to combine the parallel I/O capabilities
of MPI-IO with the remote access and mass storage management
capabilities of the Storage Resource Manager (SRM), allowing
applications to access remote and local data and to stage data on local
parallel I/O resources. Functionality is being built to allow caching of
files on a local parallel file system (such as PVFS) and migrating data
between the cache and a remote tertiary storage system in the context of
a MPI application. For example, this capability would allow for movement
of data between HPSS and PVFS.

***Progress Report***

Currently this effort, led by E. Otoo at LBNL, is focusing on completing
read functionality and tuning for performance. In the last quarter, the
test system at LBNL was moved to new PVFS2 and MPICH2 versions. Also,
the SRM/MPI-IO functions were updated to use the new SRM-1.2.8 package,
new features were added, and bugs were fixed. Finally, a draft manual
for the SRM/MPI-IO library was written.

## Plans for next quarter

Testing in the following quarter will help identify any performance
bottlenecks in the system. Following this a paper will be written and
submitted to a major conference in order to help advertise this work.

**[Task 1.4: LN/MPI-IO: MPI-IO Interface to Logistical Networks
(LNs)]{.underline}**

The objective of this work is to provide a high-performance MPI-IO
interface to logistical networks, a distributed storage infrastructure
being developed at UTK. Many application groups, including astrophysics
groups at NCSU and SUNY Stony Brook, are using logistical networks as a
mechanism to move data from supercomputing centers to their local
clusters for postprocessing. This interface would enable these groups to
write data directly into the logistical network, eliminating one step in
their workflow.

***Progress Report***

Currently this effort, led by J. Lee at ANL, is in early development. J.
Lee visited the UTK group to better understand their components and is
leveraging his previous experience with ROMIO to design a component to
hook to LNs. At this point a beta version of the LN/MPI-IO support has
been implemented and tested for correctness and performance.

## Plans for next quarter

At this point our beta version is ready for use by friendly users. We
are actively pursuing collaborators for this effort. At the same time,
we are reporting our performance results to the LN group at UTK and
suggesting ways in which the LN system could be improved to better
interact with HPC applications in this direct manner.

***References***

\[1\] Robert Ross, "PVFS2 and Parallel I/O on BG/L," invited talk at
2005 BG/L Consortium System Software Workshop, Salt Lake City, UT,
February, 2005.

\[2\] Robert Latham and Robert Ross, "High-Performance I/O for
Scientific Applications," tutorial at CCGrid 2005, Cardiff, UK, May,
2005.

\[3\] Robert Ross, "The Parallel I/O Software Crisis," invited talk at
ISC 2005, Heidelberg, Germany, June, 2005.

\[4\] Robert Ross, "Achievements and Challenges for I/O in Computational
Science", invited talk at SciDAC 2005, June, 2005.

\[5\] Robert Latham, "Parallel I/O in Practice," tutorial to be
presented at Cluster 2005, Boston, MA, September, 2005.

\[6\] Robert Latham, William Loewe, Robert Ross, Rajeev Thakur,
"Practical Parallel I/O," tutorial to be presented at SC2005, Seattle,
WA, November, 2005.

\[7\] Bill Gropp, Rusty Lusk, Rob Ross, and Rajeev Thakur, "Advanced
MPI: I/O and One-Sided Communication," tutorial to be presented at
SC2005, Seattle, WA, November, 2005.

**[2. Data Mining and Analysis (DMA)]{.underline}**

### [Task 2.1: ASPECT: Adaptable Simulation Product Exploration and Control Tool (ORNL)]{.underline}

***Contact:*** Nagiza Samatova, ORNL

The following staff people have contributed to the project over this
quarter:

Guru Kora, Nagiza Samatova, and Srikanth Yoginath

## Progress report 

The purpose of this work is to provide an efficient, scalable and
extensible framework for high performance statistical analysis of
scientific data. The framework aims to enable the user to carryout
statistical computations in parallel without dealing with the
intricacies of parallel programming. The open source R package for
statistical computing and graphics is used as the base platform. The
parallel computation capabilities are added through the means of
enabling data parallelism and task parallelism. Specifically, the
development of RScaLAPACK and taskPR packages and their integration
under a single parallel R package is pursued. Below, we describe our
major accomplishments for this quarter in each of those three
directions.

[The RScaLAPACK Package:]{.underline}

This quarter we released the new version of the RscaLAPACK package. The
parallel Matrix-Multiplication feature was added; some irregularities in
the earlier release were identified and fixed; and some memory related
issues were addressed to make the new release to handle memory more
efficiently.

We worked toward the completion of our paper named "RScaLAPACK:
High-Performance Parallel Statistical Computing with R and ScaLAPACK",
the paper was accepted by the conference PDCS 2005, Las Vegas. The final
version of the paper was composed and submitted.

[The taskPR Package:]{.underline}

This quarter we assessed the capabilities of our current taskPR package
with respect to its application in diverse fields like, climate
community, proteomics etc.. Based on this analysis, we decided to
considerably modify the package design, to stabilize and make the system
more efficient, flexible, and supporting richer set of features than the
current design provides. Toward this goal, we have been testing and
documenting the constraints posed by the current system. With a better
understanding of the system needs, we have also been researching for
efficient parallel computing means for the taskPR system. The work is
still in progress, the design of the system is expected to be completed
and prototyped next quarter.

[The Generic Parallel Agent:]{.underline}

Considering some of the advanced requirements of application scientists,
we are in the process of expanding existing parallel R system to add new
functionalities. Some of the proposed features include an open-ended
Parallel Agent that will support interfacing the 3^rd^ party MPI or
OpenMP codes, added with transparent data handling mechanisms, efficient
memory management, and more. The design document was produced and we
started the prototyping phase.

## Plans for next quarter

-   Completing the TaskPR design, for a better task-parallel system that
    would incorporate radical changes in the scheduling mechanism, to
    support various task-parallel features.

-   Third release of RScaLAPACK that would allow the package to work
    with both LAM-MPI and MPICH2 distributions of MPI. Efficient
    data-distribution and result collection mechanism using *Pthreads*
    will be incorporated in the package.

-   Prototyping the Generic Parallel Agent.

### [Task 2.2: Feature Selection in Scientific Applications (LLNL)]{.underline}

#  

# *Contact:* Chandrika Kamath, LLNL

## Progress report

In preparation for the licensing of our software to General Atomics, we
have been working with the LLNL Industrial partnerships program to
complete the required paperwork. On the software side, we redesigned the
dimension reduction library to provide a more consistent interface. In
the process, we developed a suite of test codes and fixed various bugs
which were found during testing. In addition, we checked the
documentation to ensure it was complete and consistent. We have also
obtained a computer account at GAT to port the software over.

We continued our work on the classification of Poincare plots. A C++
version of our piecewise polynomial approach is working, along with test
code, and examples illustrating its use from C, Fortran, and C++. In
addition, summer student Abraham Bagherjeiran has been implementing the
KAM approach for the classification. Neil Pomphrey had pointed us to
this approach as a possible alternative. Our early experiences have
shown that the thresholds used in the classification in KAM are not
appropriate for our simulation data. However, the features extracted in
the KAM approach can be used in a classifier to obtain better results.
We are currently making all our codes more user friendly by adding error
handling and improved feedback on errors. We also obtained additional
data for testing our codes.

We have continued our interactions with scientists at PPPL on the
Poincare plot analysis. In addition to the classification of the orbits,
they also want specific features extracted for certain orbits (islands
and separatrices). We have been seeking clarifications on these
features.

## Plans for Next Quarter

We will complete the implementation and testing of the first version of
various methods for the classification of the Poincare plots and make it
available to PPPL. We will also work on extracting the specific features
of interest for islands and separatices.

## Outreach

We plan to complete the paperwork for licensing our software for
dimension reduction and anomaly detection in streaming data to General
Atomics. This software was developed with partial funding from SciDAC.

We will continue our outreach efforts by publicizing our results and
drawing attention to the other activities of the SDM center when
interacting with new and existing customers.

### [Task 2.3: High-dimensional indexing techniques (LBNL)]{.underline}

#  

# Contact: John Wu, LBNL

Contributors: Kurt Stockinger

## Progress report

-   Added two new features to Grid Collector: enabled query of
    set-valued attributes and enabled tracking of progress of clients.
    The first feature is used to handle attributes like trigger setup.
    This attribute is frequently used to select STAR events that are
    produced from a particular trigger, a hardware device that started
    the recording an event. In STAR, as many as 32 hardware triggers can
    be used in any run of the experiment. In the data, they are simply
    recorded as triggerSetup\[0\] to triggerSetup\[31\] without any
    particular order. Previously, to select all events produced by
    trigger A, the user would have to state it as "triggerSetup\[0\] = A
    \|\| triggerSetup\[1\] = A \|\| triggerSetup\[2\] = A ...." This is
    tedious for the user to specify and inefficient for Grid Collector
    to process. The new feature allows the user to specify the same
    condition as "Any(triggerSetup) = A," which is much more compact. We
    also implemented an efficient indexing strategy to process this type
    of conditions. The second new feature enables the Grid Collector
    coordinator to better track the progress the clients and allows a
    client to take over the work originally assigned to a different
    client in case the original client failed to make any progress. This
    should improve the resilience of the Grid Collector.

-   Presented our work on Grid Collector as the International
    Supercomputer Conference 2005 at Heidelberg, Germany. Grid Collector
    received an award in the category of Data Management on the Grid.

-   Built a ROOT loadable library to make FastBit indexing schemes
    available to ROOT users. This preliminary version mainly support
    selective access to entries stored in ROOT files through the
    function Draw available from a number of ROOT classes. This is the
    first step of our integration work with ROOT system.

-   Presented our work on DEX at SSDBM 2005.

-   Our work on DEX has also been accepted by IEEE VIS 2005, a highly
    regarded visualization conference. From the visualization's point of
    view, DEX provides a new query-driven paradigm for visual data
    analysis. The feature of support multi-variant data selection
    supported by DEX is a highly useful feature that is not well
    supported in the existing visualization frameworks.

-   Presented a poster about our work on FastBit and its applications in
    Grid Collector and DEX.

## Plans for next quarter

-   Explore alternative options for Grid Collector\'s inter-process
    communication. The STAR software team is concerned about the
    maintenance of ORBacus which is currently used by Grid Collector but
    is no longer supported by the original developers.

-   Continue to work with visualization experts to improve the rendering
    capability of DEX.

-   Continue to work with ROOT developers to provide better integration
    between FastBit and ROOT. Licensing issues may complicate the work.

-   Participate in a High-Performance Analysis Challenge (organized by
    Supercomputing 2005).

**[Task 2.4: Integrated Data Management and Analysis Facility
(IDMAF)]{.underline}**

**Contributors:** Jeffrey Vetter, Philip Roth, Richard Barrett (ORNL),
Micah Beck (UTK/ORNL)

## Progress report

Our focus over the past quarter is to improve the end-to-end data
management of scientific applications. In particular, we have been
focusing on mapping the application data generated by a parallel
filesystem to a geographically-distributed network of application users.

One of the strengths of parallel file systems is that they hide the
layout of data across multiple storage elements from the application.
This allows the application code to be independent of both the data
layout and the storage configuration. However, when data is moved to a
collaborating system (either in the LAN or WAN) that system may not be
able to benefit from the parallel data layout - the logical view of the
file becomes sequential.

We are pursuing a new approach that uses a file descriptor at the
application level which makes parallelism and other aspects of file
layout explicit. A file would be explicitly implemented as a set of
subfiles plus metadata (the file descriptor), specifying how those
subfiles are combined to create a single logical file. This would be a
generalization of the exNode data structure that is used in Logistical
Networking, but it could be used in more private environments, and could
incorporate a variety of storage resources (not just Internet Backplane
Protocol depots). This is quite different from PVFS, which is a file
system that interfaces with the kernel.

In this approach, the layout of subfiles may reflect the configuration
of the processor and pattern of access by the application. Thus, the
file layout may have to change between the stages of a computational
workflow. While this work is performed on demand by parallel file
systems, an application-layer scheme may need to implement such
operations in advance in order not to burden the executing processor.
This integration of file layout management into scientific workflow is
part of the work that is necessary in order to extend storage
parallelism beyond the domain of a shared file system.

In this regard, we have been working on optimizing large long-distance
file transfers using IBP to buffer data at a point in the middle. We
have been able to show increases in bandwidth for transfers in excess of
200GB when buffered in the middle as opposed to being sent directly from
end to end with no buffering. The increase is a result of the decreased
latency on each hop of the transfer.

Specific accomplishments this quarter include:

-   We have been generating a large (multi-gigabyte) matrix A and a
    vector b from a large parallel computer at ORNL and storing it to an
    IBP depot in Houston. From there it is read in to another large
    parallel computer running at NERSC, where the equation Ax=b is
    solved for x. Storing at the depot speeds up the transcontinental
    transfer, but also acts as a buffer if the batch queue at NERSC does
    not start the job to consume A immediately. The transfer framework
    has been implemented, and the computational component will be
    completed this summer.

-   We have begun discussions with a number of application groups
    regarding their current use of storage and I/O in large simulation
    codes, and their plans for data intensive workflows in the coming 6
    months to a year. Attendance at the SciDAC 2005 PI meeting was an
    opportunity for us to reach these individuals through informal talks
    and also through the presentation of a poster. Many researchers are
    already using or are interested in learning more about Logistical
    Networking.

-   We have continued collaborations with Jonghyun Lee of ANL who has
    implemented an ADIO on top of Logistical Networking, thus creating
    compatible ROMIO, parallel netCDF, and HDF5 layers. Future
    discussions with the group at ANL, including a planned meeting
    during Rob Ross\' upcoming visit to ORNL, may lead to tighter
    integration between their file system work (PVFS, ROMIO) and the
    traditionally wide-area work on Logistical Networking.

-   We also measured the I/O costs for the VH1 application on Phoenix
    and Seaborg as well as for the IOR synthetic benchmark code, which
    enabled us to understand the importance of I/O efficiency in our
    most important applications.

-   We participated in the DARPA HPCS IO workshop, organized by David
    Koester, to discuss the IO requirements of the HPCS mission
    partners. This workshop included a discussion of applications io
    requirements, computer center storage architectures, and HPCS vendor
    storage technologies.

# *Plans for Next Quarter*

-   Complete experiments for large data transfers of simulation data
    between geographically distributed sites using Logistical
    Networking.

-   Continue working with target applications teams to improve their
    strategies for data intensive workflows by using Logistical
    Networking and the Internet Backplane Plane to dynamically manage
    their simulation output. Develop a specific strategy for at least
    one team to improve their workflow.

-   Complete initial prototype of IO tracing functionality in Sequoia
    tracing toolkit. Current implementation handles MPI-IO. The final
    implementation will include partial support for Posix and Fortran
    IO.

-   Continue application IO characterization with new Sequoia toolkit.

-   Work with ANL to accelerate the ADIO development of a Logistical
    Networking layer for ROMIO, parallel netCDF, and HDF5.

# [3. Scientific Process Automation]{.underline}

The Internet is becoming the preferred method for disseminating
scientific data from a variety of disciplines. This has resulted in
information overload on the part of the scientists, who are unable to
query all of the relevant sources, even if they knew where to find them,
what they contained, how to interact with them, and how to interpret the
results. Thus instead of benefiting from this information rich
environment, scientists become experts on a small number of sources and
use those sources almost exclusively. Enabling information based
scientific advances, in domains such as functional genomics, requires
fully utilizing all available information. We are developing an
end-to-end solution using leading-edge automatic wrapper generation,
mediated query, and agent technology that will allow scientists to
interact with more information sources than currently possible.
Furthermore, by taking a workflow-based approach to this problem, we
allow them to easily adjust the dataflow between the various sources to
address their specific research needs.

# [Task 3.1: Mediated Query Environment (SDSC)]{.underline}

***Participants:*** Ilkay Altintas, Bertram Ludaescher, Reagan Moore

## Accomplishments:

-   New features, improvements, etc. to Kepler/SPA:

    -   Combined the features of the existing CommandLine and Exec
        actors into one actor. The actor, use cases, and documentation
        were checked in to the Kepler CVS.

    -   Conversion of Kepler metadata format into a docbook-style
        automated Kepler documentation. (In progress due to the metadata
        format updates in Kepler.)

    -   Application for traversing the actor list in Kepler and
        generating documentation from Kepler actors using the docbook
        transformer.

    -   Implement a generic client for SOAPLab services. (In progress).
        This is an outcome of the LINK-UP project with the myGrid
        project (UK e-Science programme) and will provide new
        SOAPLab-based bioinformatics services (among others).

    -   Implementation of JMol visualization code into Kepler.

    -   Work on adding basic visualization modules into Kepler. (Joint
        work with SDSC's VisLab. In progress.)

    -   Implementation of support for Nimrod as composite actors in
        Kepler for large-scale distributed execution. The actors can be
        searched in the Kepler tree by simply using Nimrod or Grid as a
        keyword.

-   Visit to PPPL. Goals that were decided on:

    -   Develop modules for Elvis collaboration tool in Kepler. (In
        progress, Ilkay + Pierre/NCSU)

    -   Started development of the conceptual workflow for Pellet
        Injection Simulation. (In progress, joint work with NCSU.)

-   Discussed data/process provenance and execution logging utility with
    Ayla and Oscar from Utah. Oscar and Ilkay will have a 2-day meeting
    in San Diego on July 18-19, 2005.

    -   Tried to install SciRun modules. First try was unsuccessful but
        will work on it again and test the implemented modules.

-   New Workflows and Scientific Communities and Outreach:

    -   Adoption of various actors, in particular command line, web
        service, data transformation, and browser actors in a variety of
        workflows from different communities, including in oceanography,
        phylogeny, geosciences, ecology and biology workflows.

## Publications and Presentations

-   Prepared a poster and presented: E. Frank, I. **Altintas**, J.
    Zhang, B. **Ludaescher**, D. Pennington, W. Michener, "A Scientific
    Workflow Approach to Distributed Geospatial Data Processing using
    Web Services", *17^th^ SSDBM 2005,* Santa Barbara, CA, June, 2005.

-   Joint Ptolemy/Kepler Miniconference, May 12^th^, Berkeley. Several
    presentations (including by Altintas and Ludaescher) on Kepler;
    e.g., project overview (Ludaescher), distributed Kepler workflows
    (Altintas), semantic extensions (Bowes), coupling with R (Higgins),
    the Kepler packaging and archival format (KSW), etc. .

-   Technical report, submitted for publication: W. Sudholt, I.
    **Altintas**, K. Baldridge, "Scientific Workflow Technology to
    Enable Computational Chemistry on the Grid".

-   Actor-Oriented Design of Scientific Workflows, Shawn Bowers, Bertram
    Ludaescher, Proc. Intl. Conf. on Conceptual Modeling (ER), LNCS,
    2005

## Other

-   Attended Kepler developers meeting in Santa Barbara (Altintas). Six
    month planning, including milestones and release plans for Kepler.
    SPA goals were taken into account during planning.

-   ACM SIGMOD-Record, Special Section on Scientific Workflows,
    co-edited by Bertram Ludaescher and Carole Goble (to appear
    September, 2005)

-   Attended Intl. Symposium on Grid Computing (ISGC), April 25-29,
    Taipei, Taiwan. Presentation on Kepler Scientific Workflow system
    (Ludaescher).

## Plans for coming quarter

-   Finalize: Conversion of Kepler metadata format into a docbook-style
    automated Kepler documentation.

-   Addition of \"WSDL like\" descriptions for command line actors (ACD
    file)

-   Design and implementation of the unfinished parts of the execution
    log utility. (With Oscar/Utah, in progress.)

-   Design implementation of Elvis actor and developing simple use-cases
    for it. (With Pierre/NCSU, in progress)

-   Finalize the design for the Pellet Injection Simulation Workflow
    from Scott Kalsky's group in PPPL and start implementation. (With
    NCSU, in progress.)

-   Work on the natural Web Service and Grid support in Kepler using
    specialized directors for Grid dispatching and Web Services.

-   Help testing the SciRun/Kepler interface.

# [Task 3.2: Outreach and User Interaction (LLNL)]{.underline}

***Participants:*** Terence Critchlow, Xiaowen Xin

## Progress report

-   Deployed data transfer workflow (TSI-1) at Stony Brook

-   Worked with SDSC to address deployment issues

-   Attended SciDAC PI meeting

-   Xiaowen transferred to Matt Coleman's project. She will continue to
    work on extending his workflow, and her work will remain relevant to
    SPA despite her no longer being a directly funded member of the
    team.

## Plans for next quarter

-   Fill developer position

-   Begin development of data analysis component of TSI-1 workflow.

# [Task 3.3: Incorporation of Agent / Workflow Technology (NCState)]{.underline}

***Participants:*** Mladen Vouk, Zhengang Cheng, Brent Marinello, Ruben
Lobo, Pierre Mouallem, Kera Bell

***Progress Report***

In accord with the Q1/05 plan, during the last 3 months of this
reporting period, we were working on several fronts: a) dissemination of
SDM related information and research via conferences and presentations
-- this includes work on papers, theses and reports, as well as
documentation of existing SPA codes, b) software, service and
infrastructure robustification of the SPA setup --service
fault-tolerance and fail over arrangements, development of
new/replacement services, c) in-depth analysis of the GUI aspects of the
solution, and d) further work on case-study workflows (PPPL and TSI)..
All these activities support two major goals: (i) semi-automatic
generation of data-transforms that translate into web-services and
pro-active support functions for scientific workflows, and (ii)
identification, assessment and implementation of general as well as
domain-specific workflow extensions to Ptolemy framework that enable
support of complex scientific workflow description and execution.

We released a new "TSI-NCSU" astrophysics workflow version, and initial,
draft, versions of elements of two PPPL workflows. We are also in the
process of integrating a scientific workflow methodology assessment
document based on the studies we have performed in the last few years.
We visited PPPL and participated and presented in several SDM related
meetings. Vouk, Cheng, Marinello and Moullem visited PPPL in June to
discuss workflows (SDSC and UC Davis were there as well). We are
currently Working on Integrating several PPPL workflows and components
into SDM (in coordination and cooperation with Ilkay, SDSC).

-   Ravi\'s Workflow (pellet injection simulation). We created an
    initial design(workflow) and we\'re waiting on Ravi\'s Feedback

-   Integrating Elvis into Ptolemy. Our initial approach is using the
    Command Line Actor in Ptolemy to call Elvis. Later on we will create
    an actor that wraps Elvis and make it an integral part of Ptolemy.

***Plans for next quarter***

This work is expected to continue in Q3-2005, in a) dissemination, b)
service development in the form of case-study work (new interactions),
and c) fault-tolerance, indirect flows and security. Intent is to
deliver a additions (actors) to SPA workflow libraries, workflows and
engine.

Specific end-user collaboration is with Dr. Blondin (astrophysics
workflows).and with with PPPL scientists (Klasky). We are also looking
at the security and confidentiality management of workflows.

*Personnel:*

-   Mladen Vouk (PI, Professor) - project coordination and management,
    scientific workflow research and guidance

-   Zhengang Cheng (PhD candidate) - actors, service, SPA engine
    support, semantic verification and validation, workflow composition
    -- TSI workflows

-   Brent Marinello (MS candidate) - grid services testbed, large data
    flows, automation of TSI flows and PPPL workflows

-   Ruben Lobo (PhD candidate) - software packing

-   Pierre Mouallem (MS candidate) workflow fault-tolerance and
    reliability, services, actors, packaging, automation of PPPL
    workflows

-   Kera Bell (PhD candidate) -- workflow security and confidentiality

***Relevant Publications (Q1-05)***

*[Workflow principles]{.underline}*

1.  Pierre Moulaem, M.S, 2005, NC State University \"Fault-tolerance and
    reliability in scientific workflows\", defended in Q2-05.

*[Software]{.underline}*

1.  Release of a version of Blondin workflows and documentation
    \[http://www−casc.llnl.gov/sdm/download.php\]

2.  Virtual Computing Laboratory \[http://vcl.ncsu.edu\]

3.  Development of first elements of PPPL workflows (Elvis and pe

***Professional Engagement (Vouk, Cheng)***

# Sixth Biennial Ptolemy Miniconference - Featuring the Kepler Project at Berkeley May 2005. (http://ptolemy.eecs.berkeley.edu/conferences/05/body.htm) -- attended Cheng.

-   International Conference on Information Technology Interfaces (ITT),
    2005, Member of the International Program Committee -- attended in
    June 2005 -- very interesting presentations from UK e-Science
    workflow group - Vouk

-   ACM SouthEast Conference, 2005, 2006. Member of the program
    committee - Vouk

-   High Assurance Systems Engineering Symposium, 2005, member of the
    program committee - Vouk

-   International Symposium on Software Reliability Engineering, 2005
    member of the program committee, chair of the 2006 event - Vouk

# [Task 3.4: SCIRun/Kepler integration (Utah)]{.underline}

***Participants***: Steven Parker, Ayla Khan, Oscar Barney, Thiago Ize

The University of Utah has continued to build on the SCIRun/Ptolemy
integration prototype. We now have a SCIRun connected with Kepler with a
Kepler workflow driving SCIRun. The first example is an iteration
component in Kepler that loads a series of datasets and executes them in
a SCIRun pipeline. We are currently working to commit this actor into
the Kepler repository.

This past quarter we developed a socket interface for SCIRun and
corresponding SPA actors. The benefits of this interface over the JNI
are numerous. First and foremost it is much more stable than the JNI
interface because there are no interacting threads. Also, is is almost
as fast when the SCIRun server is run on local machine. This interface
allows SCIRun to be run on a different machine than the workflow is
running on and the server has a basic ability to \"detach\" from the
workflow. We are currently working with San Diego to further test this
actor. Once we have a use case, a last few adjustments can be made and
it will be ready to go.

We have also been working on formulating ideas for logging and caching
(provenance and \"smart reruns\") in SPA and Kepler into reality. We are
currently developing a prototype of these capabilities. Our goal is to
have a standalone provenance mechanism that does not require any extra
\"wiring.\" Also we are working on integrating this with a cache manager
to facilitate \"smart reruns.\" Our goal is to have preliminary system
for \"smart reruns\" together by the end of the summer.

We continue to work on the flow of data between Kepler and SCIRun.
Currently, simple types such as strings are used to communicate data.
Large dataset exploration will require more efficient data handling.

***Accomplishments:***

-   Improved stability of Kepler/SCIRun interface by implementing a
    "remote control" facility in SCIRun. (Utah)

-   Continued design of Java to SCIRun data bridging mechanisms (Utah)

Publications/presentations:

-   Presented a poster at the Ptolemy/Kepler mini-conference.

Plans for coming quarter:

-   Incorporate actor logging and provenance into Kepler.

-   Seek out users for the SCIRun/Kepler combination