TGQR 2010Q2 Report.pdf - Teragridforum.org

• Subversion source management has resulted in better collaboration
• ASTA work has allowed runtime parameters control grid size and process count as well
as other IO-related settings
• SPRNG random number library was added
• A project wiki space was created for the project on NCSA wiki: wiki.ncsa.uiuc.edu and
the wiki is being used to develop a code developer/user guide. This is very beneficial as
there are always new students who need to get up to speed with the (rapidly changing)
software
• It is anticipated that the wiki will help with documentation and legacy support once the
active development stage of the project collaboration has completed
• 3D transpose routines were integrated with the existing code
Darren’s main focus was to design a new HDF5 date format and optimize I/O routines. The new
HDF5 code, developed at NCSA for the PI’s DNS data has these basic properties:
• A lightweight c library (dubbed “h5dns”) with Fortran interface routines. The library is
designed to be used both as a writer (from the dns code) and a reader (from dns code and
visualization codes)
• The c library only requires HDF5 (usually with MPI –“PHDF5”)
• All hdf I/O routines will be optimized for parallel I/O when they are compiled with MPI
• Files are intended to be “self-describing” with attributes and metadata datasets
• The file format will be used for both 2D and 3D Rectilinear Grid data consisting of both
scalar and 3d vector variables
• Information about the per MPI-process layout of the data is preserved as supplementary
metadata to the main datasets. The datasets themselves are single array spanning the
global computational grid.
Initial testing of basic I/O functionality and unit testing of the library are happening currently. It
is expected that runs will be done in early to mid August to get new visualization dump via the
HDF5 routines and it will allow to explore the data in both VisIt and with David Bock’s
visualization tools.
Following many tasks remain to be completed:
• Fully integrate HDF5 routines with the main code
• Test new data format for correctness
• Create reader routine for VisIt
• Integrate Isotropic turbulence code into new executable
• Update code to perform 2d domain decomposition
• Optimize I/O patterns both by system and by taking special measure when running at
very large scale
PI: Buehler (MIT, Mechanics and Materials). Multiscale Analysis of Size Dependence of
Deformation and Fracture of Hierarchy Protein Materials. Continuing through 12/10. The
project is lead by Ross Walker (SDSC). The PI used the executables, build by Walker
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