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Re: update

>To: address@hidden
>From: Ben Foster <address@hidden>
>Subject: Re: 20000202: slow netcdf access on Cray
>Organization: HAO
>Keywords: 200002042214.PAA09139 j90 NETCDF_FFIOSPEC ffio

Hi Ben,

> Re the slow i/o on the Cray j90se's that I mentioned
> yesterday: I tried various NETCDF_FFIOSPEC settings,
> and they did speed up the i/o noticeably. With the
> default setting, it was so slow I could not wait for
> it to finish, but it would have taken many minutes.
>
> After several experiments, the best i/o wait time
> was with ffio cache:128:8. This took 33.8 secs locked
> i/o wait time. Several other settings took between
> 33.9 and 83 seconds. But this was still *many* times
> slower than reading the same file on SGI dataproc.
>
> So I decided to bite the bullet and read the whole
> thing at once, rather than in the latitude loop, 
> which is where I was reading slices. This takes more
> memory, but the locked i/o wait time was only 2.5 secs! 
> Needless to say, this is the route I will take. With
> f90 I can deallocate after I'm done processing, so 
> memory is not too big a deal. I may be reading many 
> histories in a single run, so i/o is much more important 
> than memory anyway.
>
> I guess the moral is to read with stride-1, as close as 
> possible to the way the file was originally written. 
> ffio can help, but only if stride-1 is impossible.

This is a case where the "chunked I/O" of an HDF-based netCDF could
really pay off.  It will make it possible to read data long any
chunked dimension with about equal access times, and without requiring
the memory necessary to read everything in at once.

> P.S.: We use solar geomagnetic indices (ap, kp, f10.7, 
> etc) from NGDC for some model runs. In the past, I have
> downloaded ascii files from the NGDC web site and
> written direct access unformatted fortran files for
> use in the model. Now that I'm going with netcdf, I'm
> wondering if this data is already available in netcdf
> form, or if anyone has already written code to write
> these data to netcdf files? I have sent this question
> to NGDC but have not heard back from them yet.

I don't know whether this data is available in netCDF form, but you
might check into whether DODS access is practical for this kind of
data.  If NGDC set up a DODS server for this data in its FreeForm
format, it might make it accessible with netCDF calls using the DODS
library, even if the data was stored in the NGDC "FreeForm" format.
See

  http://top.gso.uri.edu/FFND/ffnd.dods.html
or
  http://www.ngdc.noaa.gov/seg/freeform/freeform.shtml

for example.  I know NGDC has utilities for using FreeForm with HDF
data also.

--Russ

_____________________________________________________________________

Russ Rew                                         UCAR Unidata Program
address@hidden                     http://www.unidata.ucar.edu