NOTICE: This version of the NSF Unidata web site (archive.unidata.ucar.edu) is no longer being updated.
Current content can be found at unidata.ucar.edu.
To learn about what's going on, see About the Archive Site.
NOTICE: This version of the NSF Unidata web site (archive.unidata.ucar.edu) is no longer being updated.
Current content can be found at unidata.ucar.edu.
To learn about what's going on, see About the Archive Site.
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 > > _____________________________________________ > > > _______________________________________________ > NOTE: All exchanges posted to Unidata maintained email lists are > recorded in the Unidata inquiry tracking system and made publicly > available through the web. Users who post to any of the lists we > maintain are reminded to remove any personal information that they > do not want to be made public. > > > thredds mailing list > thredds@xxxxxxxxxxxxxxxx > For list information or to unsubscribe, visit: > https://www.unidata.ucar.edu/mailing_lists/ > -- Don Murray NOAA/PSL and CU-CIRES 303-497-3596 https://www.psl.noaa.gov/people/don.murray/ _______________________________________________ NOTE: All exchanges posted to Unidata maintained email lists are recorded in the Unidata inquiry tracking system and made publicly available through the web. Users who post to any of the lists we maintain are reminded to remove any personal information that they do not want to be made public. thredds mailing list thredds@xxxxxxxxxxxxxxxx For list information or to unsubscribe, visit: https://www.unidata.ucar.edu/mailing_lists/
thredds archives: