Hi Don, yes, it's indeed a very useful feature ...thanks for helping to make it
possible!
I can further add that even closing the Python notebook that originally
accessed the GEMPAK file will not cause the file handles listed in lsof to
close. Only a restart of THREDDS will accomplish that.
So yes, Sean, if you can check into this hopefully a solution can be
forthcoming.
Cheers,
Kevin
_____________________________________________
Kevin Tyle, M.S.; Manager of Departmental Computing
NSF XSEDE Campus Champion
Dept. of Atmospheric & Environmental Sciences
University at Albany
Earth Science 228, 1400 Washington Avenue
Albany, NY 12222
Email: ktyle@xxxxxxxxxx
Phone: 518-442-4578
_____________________________________________
-----Original Message-----
From: thredds <thredds-bounces@xxxxxxxxxxxxxxxx> On Behalf Of Don Murray via
thredds
Sent: Wednesday, May 6, 2020 3:55 PM
To: thredds@xxxxxxxxxxxxxxxx
Subject: Re: [thredds] THREDDS/NCSS/Open Files
Hi Kevin-
Since I wrote the GEMPAK IOSP over 10 years ago, my guess is that it might be
missing some dataset close method. The netCDF-java IOSP API changed in that
time, so it might just be a matter of adding some close methods to the IOSP
classes. Sean would know more. Glad to know that you still find that useful.
Don
On 5/6/20 1:10 PM, Tyle, Kevin R wrote:
> Hi,
>
> Our THREDDS server (http://thredds.atmos.albany.edu:8080/thredds , still
> running 4.6.13 at this time) serves both a current-week and longer term
> archive of GEMPAK-formatted METAR files as Feature Collections. Very
> nicely, THREDDS invokes netcdf-java to handle the conversion of GEMPAK
> to NetCDF. The archive is accessed especially frequently at this time of
> the year, when my co-instructor and I have the students do a case study
> of their choice and use MetPy and Siphon to access, subset, and display
> surface maps and meteograms for their event of interest.
>
> Typically, I soon run into issues where the THREDDS server fails with
> 500 server errors when an arbitrary GEMPAK surface file gets accessed
> via NCSS. I have traced this to our NCSS and Random Access caches having
> max values set too low.
>
> I see messages in the content/thredds/logs/cache.log file that look like
> this:
>
> [2020-05-06T00:25:01.089+0000] FileCache NetcdfFileCache cleanup
> couldnt remove enough to keep under the maximum= 150 due to locked
> files; currently at = 905
>
> [2020-05-06T00:25:44.105+0000] FileCache RandomAccessFile cleanup
> couldnt remove enough to keep under the maximum= 500 due to locked
> files; currently at = 905
>
> No prob, I have upped these limits now. But those "locked files"
> references made me do some poking around on the machine which is running
> THREDDS. I notice that when I run the *lsof* command and grep for one of
> the GEMPAK files that has been accessed, I see a really large # of matches.
>
> For example, just now I picked one particular file, ran my Jupyter
> notebook on it that queries and returns the subsetted data via Siphon,
> and then ran *lsof *and grepped specifically for that one file.
>
> Not surprisingly, it was listed in the *lsof* output. But surprisingly,
> *lsof *had it listed 89 times! Why might that be the case?
>
> Multiply this by a dozen or so students and co-instructors, and 1-4
> individual GEMPAK files per case, and now I'm seeing why I consistently
> run into issues, particularly with these types of datasets. Once the
> notebook instance is closed, the open files disappear from *lsof*, but
> often times students (and even I) forget to close and halt their Jupyter
> notebooks.
>
> Curiously, when I look into my content/thredds/cache/ncss directory, I
> don't see anything.
>
> So my two questions are:
>
> 1. Why does *lsof* return such a large number of duplicate references
> for a single file that's being accessed via NCSS?
> 2. Why do I not see files appear in the *cache* directory, even when
> there are clearly instances when the cache scouring script detects them?
>
> Thanks,
>
> Kevin
>
> _____________________________________________
>
> Kevin Tyle, M.S.; Manager of Departmental Computing
>
> NSF XSEDE Campus Champion
>
> Dept. of Atmospheric & Environmental Sciences
>
> University at Albany
>
> Earth Science 228, 1400 Washington Avenue
>
> Albany, NY 12222
>
> Email: ktyle@xxxxxxxxxx <mailto:ktyle@xxxxxxxxxx>
>
> Phone: 518-442-4578
>
> _____________________________________________
>
>
> _______________________________________________
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--
Don Murray
NOAA/PSL and CU-CIRES
303-497-3596
https://www.psl.noaa.gov/people/don.murray/
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