pnetCDF performance issues

[William Gropp]

Hi,

We've been running various benchmarks, including IOR (I know - there  
are lots of problems with this benchmark) and found that pnetCDF tends  
to perform poorly on several of the systems we're using.  We tracked  
it down to the header  on the netCDF file - if this header is written  
and isn't a good size (like 4MB), performance can become very poor.   
This may be an artifact of the MPI-IO implementation (which includes  
ones that use ROMIO), but it impacts uses of pnetCDF.  Have you seen  
this problem?  What is the best way to fix this (e.g., can/should  
pnetCDF expect unaligned writes to be poor in MPI-IO, and work to  
force aligned writes?).  Note that HDF-5 appears to work around this  
problem; in any event, in our tests, we didn't see a serious  
performance impact.

Bill

William Gropp
Deputy Director for Research
Institute for Advanced Computing Applications and Technologies
Paul and Cynthia Saylor Professor of Computer Science
University of Illinois Urbana-Champaign