Re: [netcdf-java] ToolsUI, opendap, CF Discrete Geometries - BUG on Windows/OS X

• To: Aleksander Vines <aleksander.vines@xxxxxxxx>
• Subject: Re: [netcdf-java] ToolsUI, opendap, CF Discrete Geometries - BUG on Windows/OS X
• From: Christian Ward-Garrison <cwardgar@xxxxxxxx>
• Date: Tue, 1 Nov 2016 02:58:14 -0600

Hi Aleksander,

Sorry for the delay in getting back to you. At its root, this is a
performance problem in our PointFeature stack that ToolsUI is obscuring.
I've summarized the issue on GitHub [1]. Do you mind that I'm using your
dataset as an example? If so, I'll take it down.

Thanks for the report!
-Christian

[1] https://github.com/Unidata/thredds/issues/671

On Tue, Oct 18, 2016 at 6:02 AM, Aleksander Vines <aleksander.vines@xxxxxxxx
> wrote:

> Hi list,
>
> I believe there to be a bug in ToolsUI. I'm getting this when reading a
> profile written as contiguous ragged array representation of profiles
> through opendap (ref http://cfconventions.org/cf-conventions/v1.6.0/cf-
> conventions.html#_contiguous_ragged_array_representation_of_profiles ).
> There might be a problem with more than this specific structure, but this
> is the only one I've tested. For me it seems related to port bindings when
> creating all these thousands of requests that are used to read the stream .
> I'm also not sure if the problem lies within toolsUI, netcdf-java or if
> it's really an underlying issue.
>
> If I download the netcdf file, and open it directly in toolsui
> (featuretypes->pointfeature with default "ANY_POINT), 7 profiles are
> displayed and all seems fine. The same is the case if I use the opendap on
> Linux.
>
> However, if I open the dataset through opendap on windows or OS X,
> initially the featureType=Profile and 
> name=PsuedoStructure(profile)/Contif(rowSize)
> is correctly detected. Then, when selecting this feature, after a short
> while of loading, only some of the profiles are displayed. If I run ToolsUI
> through a terminal, I see that I get a lot of exceptions and stacktraces,
> mostly "SocketException: Permission denied: connect", sometimes also with a
> variable name and port(?) number, sometimes with bind exceptions. Also a
> few "WARNING: Profile empty" messages.
>
> On Linux I tested with openjdk-8-jdk and on OS X/Windows Java SE 8 jdk.
>
> The dataset i've tested with is this one: http://thredds.nersc.no/
> thredds/arcticData/fram-strait.html?dataset=NERSC_ARC_PHYS_OBS_XBT_2012_v1
>
> Attached is the std out for execution of this on a Windows machine.
>
> Thanks,
> ------------------------------
>
> [image: NERSC logo] *Aleksander Vines*
>
> Programmer
>
> IT | Scientific Data Management
>
> Nansen Environmental and Remote Sensing Center
>
> (+47) 465 05 891 | aleksander.vines@xxxxxxxx
>
>
>
> ------------------------------
>
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• References:
  • [netcdf-java] ToolsUI, opendap, CF Discrete Geometries - BUG on Windows/OS X
    • From: Aleksander Vines