TGQR 2010Q4 Report.pdf - Teragridforum.org

of the software for an architecture, debugging the software, interaction with and training for users
regarding usage of these codes and software. This is carried out by AUS staff that have Ph.D. and
M.S. level expertise in specific domain sciences and computer science.
5.5.2.2
Projects, decided in collaboration with users, that have the potential to impact large
number of users
Under the second category of ASP efforts, AUS staff work on projects that have the potential to
benefit a large number of users (at least 10 user groups) within a specific domain science or
TeraGrid users in general, utilizing the unique expertise and experience that AUS staff hold. The
projects are identified based on impact it will have on the user community, input from users, input
from AUS staff and other TeraGrid experts. Expertise is available within the AUS staff pool,
across the RP sites, to undertake such projects that have broader impact. AUS staff from multiple
RP sites jointly collaborated on these projects. AUS staff continued to pursue five such projects.
Two of these were pursued by the AUS staff that have domain science as well as HPC expertise
in chemistry/biochemistry and materials science and are users and, in some cases, developers of
molecular dynamics and materials science codes. Large numbers of TeraGrid users use the
molecular dynamics and materials science codes on various TeraGrid machines. The third project,
investigating hybrid programming model, was pursued by AUS staff that has expertise in the area
of HPC programming paradigm. The fourth project involves investigation of PGAS languages
and comparison of performance with MPI based programming models. Initially kernels for linear
system solvers are being explored and later other kernels/codes will be added. AUS staff from
other sites can join once the project progresses. The fifth project involves developing tutorials of
profiling and tracing tools for users.
The first project involved porting, optimizing (using the best compiler options, machine specific
environment variables), benchmarking, and profiling widely used molecular dynamics (MD)
codes on various TG machines. AUS staff from PSC, SDSC, and TACC are participating in this
project. AMBER and NAMD were benchmarked on Ranger and Kraken for various input cases
and utilizing various compiler and environment options. Benchmarks were also done using all the
cores within a node, and partial number of cores within a node to see the impact on performance
and scaling. The results were presented from the AUS benchmark webpage
(https://www.teragrid.org/web/user-support/aus_projects) and feedback was received from some
users of these codes. User news was posted to inform the general users about this webpage. As
newer machines, such as the DCL machines, come into production, further benchmarking of MD
codes is ongoing on these machines.
We believe that as such detailed MD benchmark data are made available to the TeraGrid MD
users, it will greatly benefit this large community. In addition to always having the optimally
installed MD codes on various TG machines, this project will enable the MD community to (1)
gain knowledge about performance and scaling characteristics of MD codes on various machines,
(2) know about the optimal compiler and libraries to use on TG machines, (3) install their own
versions of MD codes on TeraGrid machines, and (4) justify resource requests in allocation
proposals. This will also help TRAC reviewers to cross-check users’ requests for resources in
their allocation proposals. The profiling results will be made available to the MD code developers
and enable them to tune the future released versions of the MD codes for TeraGrid machines.
Feedback regarding the usefulness of this project, was sought from about ten prominent long time
TeraGrid MD users and strong support for this project was received from the users.
The second project is similar to the MD project described above and targets codes that are used
more for materials science type simulations, such as VASP, and CPMD. AUS staff, from NCSA,
LONI, PSC and NICS, that have expertise in these codes and in the field of materials science,
carried out this second project. No further activities were needed in this quarter for this project.
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