TGQR 2010Q4 Report.pdf - Teragridforum.org

• Joel Ledford of the California Academy of Sciences and UC Berkeley,
and RAxML jobs were run on Trestles for
• Joel Guenther of UC Berkeley.
The parallel version of the MAFFT multiple sequence alignment code was installed on Abe,
Dash, and Trestles. Parallelization is via Pthreads and gives a parallel efficiency that is fairly
high at 8 threads, but much lower above that.
Benchmark runs on 8 cores gave best run times that were
1.89x slower on Abe than Dash and
1.05x slower on Trestles than Dash.
The times vary appreciably from run to run because the parallel search algorithm uses random
numbers in a way that is not reproducible. Thus the number of iterations and even the final
alignment vary from run to run, though the resulting alignments seem to be of similar quality.
In light of the preceding results, it is planned to make CIPRES gateway runs of MAFFT on
Trestles. Currently such runs are made with a serial version of MAFFT on Triton, a non-
TeraGrid computer at SDSC.
PI: Demeler (U. Texas Health Science Center, Biochemistry and Molecular Structure and
Function) High-Resolution Modeling of Hydrodynamics Experiments. Continuing through 03/11.
ASTA support is provided by Suresh Marru, Raminder Singh (IU), Roberto Gomez (PSC), and
Phil Cheeseman (Purdue). The ASTA team consists of staff from both the Science Gateway area
and the Advanced User Support area since the PI’s project requires advanced support for
gateways as well as MPI optimization. Further description of activities is provided in the Science
Gateways section.
PI: Quinn (Boston University, Solar Terrestrial Research). Center for Integrated Space Weather
Modeling. Continuing through 12/10. The ASTA staff for this project are Justin Whitt, Glenn
Brook (NICS), and Carlos Rosales-Fernandez (TACC). The ASTA completed in 12/10. Glenn
Brook and Justin White have continued to advise the group via bi-weekly teleconferences. They
began examining the performance characteristics of their latest skeletal communications model
and verified the gains realized by the message buffering previously suggested by Glenn Brook.
They also examined the effects of different MPI rank orderings and the use of the MPI memory
copy optimization on the current model and saw no significant improvements. They completed
weak and strong scaling studies of the new communications model; as well as, compared the
performance on multiple architectures and determined the new communications model to be
bound by both latency and contention for network resources. This led them to suggest an
alternate communications stencil requiring less messages that were larger in size to be sent.
Work by the Quinn team continues toward this end.
PI: Kimber (University of Pittsburgh, Thermal Systems). Computational Modeling of Thermal
Striping in Nuclear Reactors. Completed 12/10. Anirban Jana from PSC is the ASTA staff for
this project. On the turbulence modeling and thermal striping of jets, the realizable k-epsilon
model was found to be a good candidate turbulence model for the jets, for isothermal conditions.
FLUENT simulations with this model provided close agreement with experimentally measured
axial velocity decay. Currently non-isothermal jet validations are being pursued.
On LBM, several critical physics related to boiling, namely liquid-vapor equilibrium, surface
tension of a vapor bubble, establishment of an exponential density gradient in a fluid due to
gravity, establishment of a horizontal interface between liquid and and vapor under gravity were
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