TGQR 2010Q2 Report.pdf - Teragridforum.org

Amanda Hughes, a PhD student of Dr. Van Briesen, had developed a MATLAB code that could,
on her laptop, run 330 MC simulations before running out of memory. Over the last quarter, her
original serial MATLAB code was ported to the MATLAB Star-P platform on Pople and
parallelized. As part of the porting process:
1) The original code structure was thoroughly reviewed.
2) The code was restructured so that the parallelizable parts of the code were consolidated into a
single for loop.
3) During the restructuring, additional vectorization and other code tweaks were performed to
improve the serial performance.
4) Finally the code was parallelized with Star-P by moving the contents of the parallelizable for
loop into a functions and doing a ppeval on the function.
This has now enabled simulations with up to 10000 MC runs. The scaling of computational time
with increasing # cores was found to be very satisfactory too.
Note that because the code was restructured to put everything to be parallelized into a single for
loop, it will be trivial to run this in parallel on *other parallel MATLAB platforms*. For example,
if using the Mathworks Parallel Computing Toolbox, instead of a ppeval, the for loop just needs
to be replaced by the parfor loop.
PI: Brasseur (Penn State, BioPhysics).Villous Motility as a Critical Mechanism for Efficient
Nutrient Absorption in the Small Intestine. Continuing through 03/11. Lonnie Crosby (NICS), for
computational work, and Amit Chourasia (SDSC), for visualization work, are involved in this
ASTA project. In this quarter effort focused on computational work by Lonnie. This group's code,
Intestine3D, initially produced a large amount of metadata traffic on the file system. This large
traffic volume was due to the I/O pattern employed by the application in which files are opened
and closed for each read/write operation. Twelve files were identified which could benefit from
remaining open during the course of the application's runtime. This approach was able to
decrease the application's runtime by 33%.
A full profile of application performance was performed and sent to members of the project. This
profile identified an inherent load imbalance in the application. Addressing this load imbalance
could improve performance by an estimated 10%. Additionally, the implementation of MPI-IO
parallel I/O in order to produce concatenated binary files instead of individual (one per process or
group) ANSCI files can improve application performance by about 10%. Suggestions and
instructions for implementing MPI-IO parallel-IO were sent to members of the project.
PI. Engel (U. North Carolina, Physics). Systematics of Nuclear Surgace Vibrations in Deformed
Nuclei. Continuing through 03/11. ASTA staff for this project are Meng-Shiou Wu (NICS) and
Victor Eijkhout (TACC). During the first quarter of this ASTA project focus was on gathering
detail specifications and understanding the code structure of the project. Meng-Shiou has been
working with the group in order to explore possible approaches to improve the code efficiency on
Kraken. Jointly with the PI’s group they have identified and discussed why their approach to use
ScaLapack was not working, and what are possible choices for them to conduct diagonalization
on a multi-core XT5 node. Both shared memory approach (use threaded libraries) and distributed
memory approach (use sub-communicator and re-design memory management in their code)
were discussed. Several scientific libraries that support multi-core architecture were tested
(Libsci of Cray, AMD's ACML and ATLAS), but very limited or no performance improvement
was observed. Currently work is on integration of their code with a code segment provided by
another research team that use a master-slave style programming to utilize MPI's subcommunicator
for the project.
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