pnetCDF performance issues

[Russ Rew]

Hi Bill,

> 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.

A relatively straightforward fix for new files would be to force the
header to always be a good size, such as a multiple of 4MB.  When
writing a new file, all other variable offsets are computed relative to
where the first variable begins.

--Russ