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First Quarter FY 2003 Report Ð The National Fusion Collaboratory

Edited by D.P. Schissel1

1General Atomics (schissel@fusion.gat.com)

Overview

The focus this quarter was supporting scientific data analysis facilitated by the Collaboratory Project for presentation at the 19th IAEA Fusion Energy Conference and the 44th Annual Meeting of the Division of Plasma Physics (American Physical Society: APS/DPP). Additionally, work this quarter focused on refining and giving presentations and demonstrations by the Collaboratory Project at the SC02 and APS/DPP 2002 meetings.

General accomplishments include:

á             TRANSP on the FusionGrid was used for scientific data analysis presented at both the IAEA and APS/DPP meetings.

á             SCIRun combined with MDSplus data storage of NIMROD data was used for scientific analysis that was presented at the APS/DPP meeting.

á             Major demonstrations and presentations on Collaboratory Project work were given at the APS/DPP meeting and the SC02 meeting including an oral presentation at the DOE SciDAC booth.

á             A meeting of the User Oversight Committee was held in conjunction with the APS/DPP meeting and favorable comments were given by the committee in response to the first yearÕs work of the Collaboratory Project.

á             The FusionGrid was demonstrated to Kevin Cook (House Appropriations Committee Staff).

General

The Collaboratory Project supported scientific data analysis presented at both the 19th IAEA Fusion Energy Conference and the 44th Annual Meeting of the Division of Plasma Physics. TRANSP on the FusionGrid was used to perform scientific data analysis that was presented at the APS/DPP meeting in an invited oral presentation by Masanori Murakami (abstract FI1.002). SCIRun along with MDSplus data storage was used to perform scientific visualization that was presented at the APS/DPP meeting in an invited oral presentation by Dylan Brennan (abstract FI1.006).

 

The Collaboratory Project had a largeÐscale presence, including demonstrations and presentations, at the 2002 APS/DPP meeting. These computer science demonstrations were a first for the APS/DPP meeting and presented an excellent opportunity to vividly illustrate the fundamental concepts of the Collaboratory Project to the U.S. magnetic fusion community. Photographs from the APS/DPP meeting are available on the projectÕs website. Given the uniqueness of these demonstrations, the entire computer science infrastructure had to be created by the Collabortory team at the headquarters hotel in Orlando. More information on the CollaboratoryÕs work at the APS/DPP meeting is available on the projectÕs website. In anticipation of having a similar presence at next years APS/DPP meeting and in an effort to reduce the large amount of work necessary to create such an infrastructure, initial discussions were held in Orlando with the organizers of the 2003 APS/DPP meeting.

 

Figure 1 Collaboratory demonstrations at the APS/DPP meeting in Orlando: a) hall entrance, b) TRANSP computing, c) tiled movie playback, d) AG on tiled display with shared SCIRun, e) Desktop access to AG with shared SCIRun, f) SCIRun.

 

 

A meeting of the User Oversight Committee was held in conjunction with the APS/DPP meeting in Orlando. The committee responded favorably to the work accomplished during the projectÕs first year. The main recommendation for work in the second year was to move beyond demonstrations at meetings to training and documentation for scientists so that they may begin to utilize these tools in their daily research.

The Collaboratory project was well represented at the SC02 meeting in Baltimore with demonstrations in the ANL and LBNL booths. These demonstrations included remote computing, reservation based QoS for between pulse data analysis, and share visualization combined with AG technology. A paper summarizing work on enforcement was presented at the 3rd International Workshop on Grid Computing that was held in conjunction with SC02. From the SC02 show floor, TRANSP running on the FusionGrid was demonstrated to Kevin Cook (House Appropriations Committee Staff) who was visiting PPPL. This demonstration included AG node connections between SC02 and PPPL, the TRANSP server at PPPL, the DIIIÐD MDSplus server, and code control from SC02.

The Project web site continued to be updated with substantial information being added regarding the APS/DPP and SC02 meetings.

Security/Remote Computing

The TRANSP code on the FusionGrid was used by scientists at DIIIÐD and PPPL for data analysis that was presented at the IAEA and APS/DPP meetings. Supporting this analysis effort required continued development and refinement work in a multitude of areas including the preTRANSP GUI, the new FusionGrid monitoring system (http://nssrv1.gat.com:8000/fgm), and the run management database. Additionally, the capability to delegate a userÕs Globus proxy credential was created to allow developers to troubleÐshoot a run on behalf of the user. This complete system was demonstrated to scientists at the APS/DPP meeting and involved an MDSplus server in San Diego, the TRANSP cluster in Princeton, and local workstations in Orlando. Details are available on the project website. After the APS/DPP meeting, TRANSP on the FusionGrid was released to the MIT scientists.

The prototype Globus JobManager with Akenti authorization was deployed to a test system at PPPL and used during the demonstrations at SC02. Based on the results of these tests, a detailed plan has been developed to integrate this functionality into the Globus Toolkit (GT2). It is anticipated that this work will be completed next quarter. An updated version of the Akenti code was released that included general clean up, removing some Java dependencies, a new C interface, and better documentation.

Work continued on the prototype of a FusionGrid reservationÐbased QoS for job execution. This system allows the user to place an upper bound on job execution time. An evaluation of capabilities was completed using the fusion science application EFIT. The goal of this work is to utilize the FusionGrid for betweenÐpulse experimental data analysis (preemptive scheduling). This prototype system was demonstrated at the SC02 meeting.

Work continued on improving the MDSplus documentation (http://www.mdsplus.org) to better support the user community. These improvements included recording software download request information allowing better tracking of the growing MDSplus community.

Visualization

Further modifications were made to SCIRun in support of NIMROD data visualization that was presented at the APS/DPP meeting. Improvements to the SCIRun Òfusion packageÓ included creating a more robust MDSplus interface and allowing for multiÐthreading and multiple data retrievals, support for structured grid 1D and 2D data types, 2D plotting module, enhanced documentation, and ease of software downloading via an RPM.

Visualization demonstrations at APS/DPP and SCO2 included tiled wall displays, AG technology, and SCIRun. This demonstrations included movie playback of large scientific visualization movies, realÐtime capture and display of live video to tiled display environments, AG running on a tiled display, personal interface to the AG (PIG), and a shared desktop on PIG and Tiled Display AG. Shared desktops and the use of AG on tiled displays utilized VNC and DMX. The response by the fusion scientific community to these demonstrations was very positive with numerous nearÐterm applications discussed.

A demonstration was given to the NSTX scientific staff on the concept of a collaborative display wall for control room use. This capability was well received and a design study is currently underway that will place a display wall in the NSTX control room. Display wall user and management tools were made Linux compatible and are available to download from the PCS website. These tools provide a GUI interface to aid users in performing command tasks and help administrators to control and manage the cluster.

Appendix A: NonÐEdited Reports from Individual Institutions

A.1      M. Papka for the ANL MCS, Futures Laboratory

Much of this quarterÕs effort was consumed with the preparation and presenting of this years results at the APS 44th Annual Meeting of the Division of Plasma Physics, November 11-15, 2002 in Orlando, Florida and The International Conference for High Performance Computing and Communications, November 16 Ð 22, 2002 in Baltimore, Maryland. The Futures Laboratory group sent a PIG and the mMural display to Orlando for 2.5 days where the following was demonstrated:

 

AG on tiled display with
shared SCIRun session.

Desktop access to the Access Grid, PIG running SCIRun shared with other AG nodes.

Tiled movie playback on
the ANL mMural.

Figure A.1Ð1 Demonstrations at the 2002 APS/DPP Meeting in Orlando, Florida.


being driven by Linux based PIG Immediately after the APS conference the Futures Laboratory sent the PIG and mMural display to Baltimore for Supercomputing, where the demonstrations were repeated. In addition a corner of the ANL booth was used to do a complete Fusion Collaboratory demonstration that included all components of the collaboratory. ANL also lent a PIG node to the University of Utah which they demonstrated in their SC booth and from which they participated in the full collaboratory demo.

 

In order to prepare for the demonstration, continued work was done using VNC and DMX in order to enable shared desktops and the use of the AG on tiled displays. Also in effort to reduce the duplication of effort with Princeton CS in the area of tiled displays a research summary was produced covering the ANL efforts in the area.

A.2      K. Keahey for the ANL MCS, Distributed Systems Laboratory

In the last quarter we made contributions in the following areas:

 

  1. Work on authorization and enforcement
    1. We continued work on the authorization prototype initiated in the previous quarter; the main thrust of the work involved integration with Akenti, and deployment of the prototype at PPPL where it was used as part of the first network service provided by Fusion.
    2. Towards the end of the quarter, based on our experiences with the prototype, we developed a detailed plan to integrate this functionality into the Globus Toolkit 2 (GT2). We expect to complete this work during the next quarter.
    3. We presented a paper on our enforcement work at the Grid 2002 workshop held in conjunction with SC2002
    4. Together with our LBNL collaborators, we submitted an abstract of a paper describing how our enforcement solution was integrated with the Akenti authorization system to the CHEP03 conference. It is our hope to use that conference to share our solution with other SciDAC teams.

 

  1. Work on QoS-based application servers
    1. We continued our work on a prototype of a network services infrastructure with a reservation-based QoS interface module enabling users to run fusion applications as network services guaranteeing a certain QoS which will enable Fusion scientists to run code between pulses. Specifically, we focused on evaluation of the capabilities of our prototype in the context of the Fusion EFIT application; the results were encouraging. We also improved the user interface to this infrastructure.
    2. We wrote a paper describing the design of the application server, and our experiences with it.

 

  1. Demonstrations, outreach and conference participation
    1. We prepared and together with our collegues from GA, PPPL and LBNL, presented a demonstration of the authorization prototype at the Fusion APS conference as well as the SC02 conference. In addition, our participation in the APS conference included valuable requirement discussions with Fusion scientists.
    2. We prepared a demonstration of the work on QoS-based application servers and showed it at the SC02 conference.

 

  1. Requirement development
    1. Together with our collegues from GA, MIT, and PPPL we started the process of developing requirement documents detailing Fusion needs in the area of authorization, resource management, and application server infrastructures.

 

  1. General interaction
    1. We provided technical support, assisted with debugging and troubleshooting of Globus installation and associated technologies. This involved providing explanations and technical discussions of Globus functionality as well as providing examples, help with troubleshooting and answering questions.
    2. We also interacted with our collaborators through teleconferences, meetings, discussions, etc.

A.3      D. Schissel for the General Atomics Fusion Group

General

á             Organized and created the local infrastructure required for both the remote computing and shared visualization demonstrations at the 2002 APS/DPP meeting in Orlando Florida including network connectivity, meeting space, posters, and handouts (Peng, Schissel).

á             Completed the deployment of the FusionGrid at DIIIÐD that enabled TRANSP calculations to be done in support of papers given at the 19th IAEA Fusion Energy Conference and the 44th Annual Meeting of the Division of Plasma Physics (American Physical Society: APS/DPP) (Burruss, Flanagan, Peng).

á             Particpated in the design, creation, and presentation of the remote computing and visualization demonstrations at SC02 in the ANL and LBNL booths (Peng, Schissel).

á             Presented results from the National Fusion Collaboratory Project at the DOE SciDAC booth at SC02 (Schissel).

á             Organized and ran the User Oversight Committee Meeting held in conjunction with APS/DPP (Schissel).

á             An abstract was submitted to the GlobusWorld conference titled ÒNational Fusion Collaboratory: Building the FusionGrid.Ó

á             Gheni Abla has joined General Atomics and will be working halfÐtime on the DIIIÐD Project and halfÐtime on the National Fusion Collaboratory Project.

á             The project web site (http://www.fusiongrid.org) was maintained including updates for the APS/DPP and SC2002 meetings.

Security/Remote

á             Based on feedback from the DIIIÐD National Team, the GUI PreTRANSP, used for preparation of inputs and securely invoking the Grid enabled version of TRANSP was further modified for use by the scientific team (Burruss).

á             The FusionGrid monitoring system (http://nssrv1.gat.com:8000/fgm) was modified based on feedback from the DIIIÐD National Team and was used exclusively to monitor DIIIÐD TRANSP runs (Flanagan).

á             This implementation of the FusionGrid was used to support scientific analysis presented at the 19th IAEA Fusion Energy Conference and the 44th Annual Meeting of the Division of Plasma Physics (Burruss).

á             Supported prototype QoS work by Keahey for a preemptive scheduling that was demonstrated at the SC02 meeting (Peng).

á             Demonstrated TRANSP running on the FusionGrid at the APS/DPP meeting (Burruss, Flanagan, Schissel) and at the SC02 meeting (Peng, Schissel).

Visualization

á             Minor updates and improvements to SCIRun combined with general support resulted in successful visualization of NIMROD data in support of scientific results presented at the APS/DPP meeting (Peng).

á             Further decreases in the time required to write NIMROD data from NERSC to the GA MDSplus server were accomplished this quarter (Flanagan, Kruger). Presently, there is approximately 111 GB of NIMROD data stored in MDSplus.

á             Demonstrated SCIRun visualization, shared visualization, and AG with shared visualization on a Tiled Wall at the APS/DPP meeting and at the SC02 meeting (Peng, Schissel).

A.4      M. Thompson for the Lawrence Berkeley National Laboratory

The prototype Globus JobManager with Akenti authorization was deployed to a test system at PPPL and used during the demonstrations at SC02. More users were given X.509 and Akenti authorization certificates in order to use the secured system. In most cases, access was granted using the simplest possible policy, e.g. the user could unconditionally run the TRANSP scripts and a few other test programs.

In the course of transferring the JobManager code from ANL to PPPL it became obvious that a simplified version of the implemenation was needed. A new design was done and the API specified. The new version will provide the same ability to control access based on the RSL parameters such as the executable to run, the ability to control jobs started by other users, the time of day, the amount of requested CPU time allowed for runs, etc. The evaluation of the RLS run time parameters will be removed from the JobManager code and put in a separate authorization plug-in module. A generalized API has been specified between the JobManager and the Authorization plug-in. Work will begin in the next quarter to implement this design..

An updated version of the Akenti code was released. The new release cleans up some code, removes some dependencies on Java and better documents how to use the various interfaces to Akenti. A new, easier to use C interface was added to facilitate the use of Akenti by the new JobManager API.

A.5      T. Fredian for the MIT Plasma Fusion Science Center

Work continues on improving web based (http://www.mdsplus.org/) documentation for MDSplus. Enhancements to the software download procedures have been made which now record download request information in a relational database.

The TRANSP job submission procedures at the PSFC have been  modified to use the secure globus enabled procedures for submitting code runs at PPPL. This mechanism will be thoroughly tested in the next few months. TRANSP users are MIT are obtaining DOE grid certificates to authenticate themselves to the PPPL TRANSP compute servers.

A.6      D. McCune for the Princeton Plasma Physics Laboratory

This report covers the period of Oct. 1, 2002 through Dec. 31, 2002 Ð 1st quarter of the 2003 fiscal year (report compiled by D. McCune with contributions from E. Feibush and L. Randerson).

PPPL made leading contributions to the SciDAC Fusion Collaboratory in this quarter.

On the security and remote computing side of the project, the PPPL TRANSP code was deployed as a Collaboratory service, available for working scientists.  Fusion researchers at General Atomics and PPPL used the new Collaboratory-based TRANSP production system to carry out data analysis and simulation runs that contributed to papers presented at the October 2002 IAEA and November 2002 APS conferences on plasma physics.  In this work, crucial support was provided to PPPL by ANL and LBNL on the Globus, Akenti, and Grid-FTP, to enable secure job submission and file transfers, MIT on Globus-enabled MDSplus for secure data communications, and, General Atomics provided the Fusion Grid Monitor, enabling the remote monitoring of the progress of runs.  In addition, General Atomics performed the necessary remote client-side integrated testing of this systemÑa big job requiring a great deal of patience and willingness on their part to endure the teething pains of a large, complicated, newly deployed networked software system.

On the visualization front, PPPL in collaboration with the Princeton University Computer Science Department (PCS), and supported by ANL, was able to carry out two demonstrations of a collaborative Display Wall for tokamak control room users.  These demonstrations were well received by PPPL NSTX experimental physicists and by the PPPL directors, so much so that a Display Wall is now planned for the NSTX experiment, with deployment likely by the end of FY-2003 (subject to NSTX project budget constraints).  In addition, a prototype of a lightweight Java/Internet based collaborative scientific graphics and visualization system, ElVis, was deployed and used in the demonstrations.

PPPL participated in the demonstration of these new capabilities at the November 2002 APS meeting and at SC2002.

A more detailed description of Q1-FY2003 accomplishments is given in the following bulleted lists.

Security Remote Computation

Visualization and Display Walls

A.7      G. Wallace for the Princeton University Computer Science Department

á             Ported Display Wall User and Management Tools to be Linux compatible. The client was ported to Java and the Server can be compiled under Linux or Windows.

á             Released the Display Wall Tools. Can be downloaded from our website http://www.cs.princeton.edu/omnimedia/software.htm. These tools provide a GUI interface to help users perform common tasks and help administrators to control and manage the cluster. I will install these tools at PPPL soon to help their effort and get feedback from them.

á             Began work on color gamut matching algorithm for projectors. This will be especially important for mixed arrays of projectors or DLP projectors. Submitted initial results from this work in a paper to IPT 2003 (Immersive Projection Technology Symposium).

á             Worked with PPPL on the design of a prototyped display wall for their control room. Will be continuing to work with them to get this built and operational in Q1 2003.

á             Produced a 2-3 minute film about the goals of the Fusion Collaboratory.

A.8      Sanderson for the University of Utah Center for Scientific Computing and Imaging

Much of the 1st quarter was spent fine tuning and expanding SCIRun for fusion use. This work was done preparation for a presenting SCIRun tutorials during the second and third quarters. Which will allow SCIRun to be used be scientists beyond our initial test users with in the NIMROD community.

We have found that several of the tools initially developed for the fusion package have general usage to other research programs. As such, we have made efforts further generalize their usage and move them into SCIRun rather than leave them in the Fusion Package. Other efforts  included making the MDSplus interface more robust to allow for multi- threading and multiple data reads. Two new data types were developed to support structured grid data in 2D and 1D. These will be needed as part of our efforts to integrate experimental and simulation data.

We have completed our prototype of a 2D plotting module and are using it to expand SCIRun to allow for full 2D plotting.

Another project has been to fully document all of the modules and code within the Fusion Package. This documentation contains basic help information for the users and will be key part of allowing user to use the package hopefully unassisted. We have also begin documenting example networks.

SCIRun is now available as a downloadable RPM.

Other work: Error Visualization Research - Continued error research

Supported NIMROD Fusion scientists in using SCIRUN for poster and invited talks at the fall APS meeting in Orlando. This was a good test to see what items need to be expanded for for more wild spread use.

 

This report is available in PDF format for high quality printing.

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