ZioLib: A parallel I/O library

Technical Report · Fri Aug 01 04:00:00 EDT 2003

DOI:https://doi.org/10.2172/819966· OSTI ID:819966

Yang, Woo-Sun ^[1]; Ding, Chris

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1. LBNL Library

In a distributed memory parallel environment, many applications rely on a serial I/O strategy, where the global array is gathered on a single MPI process and then written out to a file. I/O performance with this approach is largely limited by single process I/O bandwidth. Even when parallel I/O is used, satisfactory parallel scaling is not always observed. It is because in many applications fields are not necessarily in a most favorable parallel decomposition for I/O. The best I/O rates are obtained when a field is decomposed with respect to the array's last dimension (referred to here as Z). Another situation often encountered in many applications is that a field in CPU resident memory is in one index order but must be stored in a disk file in another order. Changing index orders can complicate a parallel I/O implementation and slow down I/O. ZioLib facilitates an efficient parallel I/O for arrays in such situations. In case of a write, ZioLib remaps a distributed field into a Z-decomposition on a subset of processes (which will be called the I/O staging processes) and from there writes to a disk file in parallel. In this Z-decomposition, the data layout of the remapped array on the staging processes memory is the same as on disk, thus only block data transfer occurs during parallel I/O, achieving maximum efficiency. In case of a read the steps are reversed to build the required distributed arrays on the computational processes.

• Research Organization: Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (US)
• Sponsoring Organization: USDOE Director. Office of Science. Biological and Environmental Research (US)
• DOE Contract Number: AC03-76SF00098
• OSTI ID: 819966
• Report Number(s): LBNL--53521
• Country of Publication: United States
• Language: English

Related Subjects

99 GENERAL AND MISCELLANEOUS
DIMENSIONS
EFFICIENCY
IMPLEMENTATION
PERFORMANCE