Re: [netcdfgroup] abysmal performance

That sounds like it, ncdump on 1 file shows "time = UNLIMITED ; // (8 currently)" it's kind of unexpected that these 8 values not be in a contiguous array! Oh well. Thanks for clarifying. This is simulation output, so our options may be limited. I will be sure to mention this to the scientists. Hopefully they can write them as a fixed dimension.

On 06/02/2016 01:24 PM, Bowman, Kenneth P wrote:
Hi Burlen,

If time is your unlimited (record) dimension, then the time values are scattered through the 433 MB file. That is true for any variables that have a time dimension. To read the time variable, the netCDF library has to jump through the file and collect the values.

The longitude variable is contiguous in memory and can be read quickly.

If you know the number of time steps in the file before you write the file, you can change the unlimited time dimension to a fixed dimension. Then something dimensioned by (only) time will be contiguous in memory.

Or you can rewrite the files with fixed dimensions. That read performance penalty is one of the tradeoffs of having the flexibility of an unlimited dimension.

Good luck!


Date: Thu, 2 Jun 2016 12:41:53 -0700
From: Burlen Loring <bloring@xxxxxxx <mailto:bloring@xxxxxxx>>
To: Tom Fogal <tfogal@xxxxxxxxxxxx <mailto:tfogal@xxxxxxxxxxxx>>, netcdfgroup@xxxxxxxxxxxxxxxx <mailto:netcdfgroup@xxxxxxxxxxxxxxxx>
Subject: Re: [netcdfgroup] abysmal performance
Message-ID: <961631fd-2aad-d348-ce1d-8a70a9e67287@xxxxxxx <mailto:961631fd-2aad-d348-ce1d-8a70a9e67287@xxxxxxx>>
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Hi Tom,

That's not an option, and it has it's own issues. for example if file
size exceeds the size of a tape drive we can't archive it. Beside it
doesn't seem like a lustre metadata issue, open is relatively fast, like
0.096 sec. and wouldn't explain why reading the time dimension with only
8 values takes on the order of 1 sec while reading the lon dimension
with 1152 values takes on the order of 1e-4 sec. ?


Dr. Kenneth P. Bowman                      1014A Eller Building
David Bullock Harris Professor of Geosciences            979-862-4060
Department of Atmospheric Sciences                       979-862-4466 fax
Texas A&M University
3150 TAMU
College Station, TX   77843-3150