Performance study

[Christian Chilan]

Hi,

We are trying to reproduce the results of your comparison between HDF5 and 
parallel netCDF on an IBM ps690 (AIX 5.3, GPFS). We downloaded and 
installed parallel netCDF from http://www.mcs.anl.gov/parallel-netcdf/, and 
flash benchmark from 
http://flash.uchicago.edu/~jbgallag/io_bench/flash_io_bench.tar.gz.

After making some modifications to the makefile and to the flash source 
code (such as changing netcdf.h for pnetcdf.h and nc_ prefixes for ncmpi_) 
, we have the benchmark running. For now, we are executing flash using 1 
through 4 processors.

We noted that there are some problems. For example, after dumping the 
checkpoint files, we noticed that the file generated with HDF5 contains 
non-zero values and its size (7MB through 36 MB approx.) depends on the 
number of processors, but the file generated with parallel netCDF contains 
mostly zero values and its very small size (1844 bytes) is the same for 
different numbers of processors. In addition, the speedup resulting from 
going from 1 to 2 processors is about 10 for both HDF5 and netCDF.

We'd appreciate that you let us know what tuning and modifications were 
done in your comparison study.

Thanks,

Christian Chilan
National Center for Supercomputing Applications
University of Illinois at Urbana-Champaign