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Re: T3D / T3E netcdf memory usage Steve Emmerson <address@hidden>, address@hidden

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  • Subject: Re: T3D / T3E netcdf memory usage Steve Emmerson <address@hidden>, address@hidden
  • Date: Wed, 20 Jan 1999 11:27:34 -0700
> Hi Steve,
>
>    Thanks for the binary you sent me. The good news is it works. The bad news
is
> the new version of netcdf uses lots of memory compare to the old version we
have
> here. The high consumption of memory causes the application crashed due to
run
> out of memory. Do you have any ideas why the new version uses so much memory?
>
> Thanks.
> David Wong

David:

The only significant memory allocation done directly by the
netcdf is for an i/o buffer.
For CRAY systems (using ffio), we get a default size for this from the
system using a call to fffcntl(). We use the value returned in the
st_oblksize field of struct ffc_stat_s. It could well be that this
is an absurd number. Talk it over with your Cray experts.

See libsrc/ffio.c:blksize().

The good news is that you can override the default using the "underbar
underbar" versions of the create or open function. See NF__OPEN in the
fortran man page. The 'chunksize' parameter sets the size of this allocation.
One can tune this to be the size appropriate.

It is also probable that large allocations are made on behalf of the
netcdf library by the ffio layer. I think you have control of this
via the NETCDF_FFIOSPEC environment variable. (On the T3E using the latest
NERSC modifications, this can also be controlled by an assign statement.)

Hope this helps.

-glenn

>From address@hidden  Fri Jan 22 10:37:38 1999
From: Al Bourgeois <address@hidden>
Date: Fri, 22 Jan 1999 12:37:33 -0500
Organization: Lockheed Martin
To: "Glenn P. Davis" <address@hidden>
CC: "David C. Wong" <address@hidden>, address@hidden,
        Steve Emmerson <address@hidden>,
        address@hidden
Subject: Re: T3D / T3E netcdf memory usage
References: <address@hidden> <address@hidden>

It appears that our problem is solved on both the T3D and T3E by setting
the NETCDF_FFIOSPEC variable, as you suggested below. For example, with
a little experimentation, we found that a setting of "cachea:1:50"
speeded up NCVGT (for a specific data set) by a factor of 200 on both
the T3E and T3D.

Thanks for the help.

-Al