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NOTICE: This version of the NSF Unidata web site (archive.unidata.ucar.edu) is no longer being updated.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, 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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