Re: [netcdfgroup] read performance slow compared to netCDF on other systems

• To: Charlie Zender <zender@xxxxxxx>
• Subject: Re: [netcdfgroup] read performance slow compared to netCDF on other systems
• From: Liam Forbes <loforbes@xxxxxxxxxx>
• Date: Mon, 14 Nov 2016 10:20:53 -0900

On Sun, Nov 13, 2016 at 10:35 AM, Charlie Zender <zender@xxxxxxx> wrote:

> Does the system blocksize differ on the new and old systems?
> To find out, use "stat <any file>".
> If the blocksizes differ, then "ncks in.nc out.nc"
> reads/writes different numbers of times.
> To adjust this behavior, read how NCO uses the system blocksize
> to determine the chunksize of datasets:
> http://nco.sf.net/nco.html#blocksize
> You can override the defaults with different chunking policies,
> as described in the manual, and examine the chunksizes with
> ncks --cdl --hdn -m in.nc.
>

Charlie,

That makes sense to me, especially since I'm using different versions of
the packages in my comparisons.

Based on the stat output from each system, it looks like the blocksizes are
the same. In the lustre filesystem I'm getting 2097152 for the IO block,
the same file size, and the same number of blocks. In /dev/shm, I'm getting
4096 for the IO block, the same file size, and the same number of blocks.

When I try to examine the chunksizes thought, I get the ncks help message.
I think --hdn is not a valid option with either of the NCO versions I'm
using. What is that option meant to be?

I've been reading the chunking section in the NCO 4.6.2-beta03 user guide
reference you provided. Based on that, I'm thinking there is significant
enough differences between the older versions of NCO (4.1.0), NetCDF
(4.2.0), and HDF5 (1.8.8) on our Cray and the versions I'm installing on
our new cluster (4.6.1, 4.4.1, 1.8.17) that comparing performance between
them is not apples to apples.

-- 
Regards,
-liam

-There are uncountably more irrational fears than rational ones. -P. Dolan
Liam Forbes  loforbes@xxxxxxxxxx  ph: 907-450-8618 fax: 907-450-8601
UAF Research Computing Systems Senior HPC Engineer  LPIC1, CISSP

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  • Re: [netcdfgroup] read performance slow compared to netCDF on other systems
    • From: Charlie Zender