Motivation

Array variables comprise the bulk of the data in a netCDF dataset, and for accesses to large regions of single array variables, PnetCDF attains very high performance. However, the current PnetCDF interface only allows access to one array variable per call. If an application instead accesses a large number of small-sized array variables, this interface limitation can cause significant performance degradation, because high end network and storage systems deliver much higher performance with larger request sizes. Moreover, the record variables data is stored interleaved by record, and the contiguity information is lost, so the existing MPI-IO collective I/O optimization can not help.

We provided a new mechanism for PnetCDF to combine multiple I/O operations for better I/O performance. This mechanism can be used in a new function that takes arguments for reading/writing multiple array variables, allowing application programmers to explicitly access multiple array variables in a single call. It can also be used in the implementation of asynchronous I/O functions, so that the combination is carried out implicitly, without changes to the application. Our performance results demonstrate significant improvement using well-known application benchmarks.

Usage

There are two ways to use this feature:

Explicit Method: New routines (e.g. ncmpi_mput_vara_all) take a list of variables to access

Implicit Method Several variable accesses can be "scheduled" with the nonblocking routines. Then, when the application waits for completion of those accesses, the library will service them all in a single call.

The function calls for the explicit method look like this:

int ncmpi_put_mvara_all(int ncid, int nvars, int varid[],
                   MPI_Offset *start[], MPI_Offset *count[],
                   void **buf, MPI_Offset *bufcount,
                   MPI_Datatype *datatype);

int ncmpi_get_mvara_all(int ncid, int nvars, int varid[],
                   MPI_Offset *start[], MPI_Offset *count[],
                   void **buf, MPI_Offset *bufcount,
                   MPI_Datatype *datatype);

References

You can see examples of this new API in action in the test/mcoll_perf directory: https://trac.mcs.anl.gov/projects/parallel-netcdf/browser/trunk/test/mcoll_perf

We wrote a paper describing the API, the implementation, and some results: Kui Gao, Wei-keng Liao, Alok Choudhary, Robert Ross, and Robert Latham. "Combining I/O Operations for Multiple Array Variables in Parallel NetCDF". In the Proceedings of the Workshop on Interfaces and Architectures for Scientific Data Storage, held in conjunction with the the IEEE Cluster Conference, New Orleans, Louisiana, September 2009.