{"action":"created","issue":{"url":"https://api.github.com/repos/PecanProject/pecan/issues/910","repository_url":"https://api.github.com/repos/PecanProject/pecan","labels_url":"https://api.github.com/repos/PecanProject/pecan/issues/910/labels{/name}","comments_url":"https://api.github.com/repos/PecanProject/pecan/issues/910/comments","events_url":"https://api.github.com/repos/PecanProject/pecan/issues/910/events","html_url":"https://github.com/PecanProject/pecan/issues/910","id":165233330,"number":910,"title":"Fluxnet 2015 errors","user":{"login":"tonygardella","id":8570691,"avatar_url":"https://avatars.githubusercontent.com/u/8570691?v=3","gravatar_id":"","url":"https://api.github.com/users/tonygardella","html_url":"https://github.com/tonygardella","followers_url":"https://api.github.com/users/tonygardella/followers","following_url":"https://api.github.com/users/tonygardella/following{/other_user}","gists_url":"https://api.github.com/users/tonygardella/gists{/gist_id}","starred_url":"https://api.github.com/users/tonygardella/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tonygardella/subscriptions","organizations_url":"https://api.github.com/users/tonygardella/orgs","repos_url":"https://api.github.com/users/tonygardella/repos","events_url":"https://api.github.com/users/tonygardella/events{/privacy}","received_events_url":"https://api.github.com/users/tonygardella/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-07-13T04:09:57Z","updated_at":"2016-07-13T12:22:42Z","closed_at":null,"body":"Sipnet/Fluxnet2015 at Niwot Ridge Forest/LTER NWT1 (US-NR1) failed with this error when met2model is executed from met.process:\r\n```\r\n[1] 2004\r\n[1] \"vobjtovarid4: error #F: I could not find the requsted var (or dimvar) in the file!\"\r\n[1] \"var (or dimvar) name: specific_humidity\"\r\n[1] \"file name: /home/carya/output/dbfiles/Fluxnet2015_CF_gapfill_site_0-772/FLX_US-NR1_FLUXNET2015_SUBSET_HH_1998-2014_1-2.2004.nc\"\r\nError in vobjtovarid4(nc, varid, verbose = verbose, allowdimvar = TRUE) : \r\n  Variable not found\r\nCalls: remotefunc -> <Anonymous> -> ncvar_get -> vobjtovarid4\r\nExecution halted\r\n[1] 1\r\n[1] \"RESULTS: Convert.Input\"\r\n[1] 1\r\nNULL\r\nError in result$file : $ operator is invalid for atomic vectors\r\nCalls: <Anonymous> ... convert.input -> dbfile.input.insert -> basename -> dirname\r\n> proc.time()\r\n   user  system elapsed \r\n  6.997   0.413   7.661 \r\n```\r\nIt seemed like specific humidity is missing and indeed it is. I checked the netcdf files (CF and CF gapfilled) and it wasn't there. I wasn't entirely sure if it was there in the raw csv file though because I wasn't sure about the short names of the variables in that file."},"comment":{"url":"https://api.github.com/repos/PecanProject/pecan/issues/comments/232338830","html_url":"https://github.com/PecanProject/pecan/issues/910#issuecomment-232338830","issue_url":"https://api.github.com/repos/PecanProject/pecan/issues/910","id":232338830,"user":{"login":"ankurdesai","id":3084183,"avatar_url":"https://avatars.githubusercontent.com/u/3084183?v=3","gravatar_id":"","url":"https://api.github.com/users/ankurdesai","html_url":"https://github.com/ankurdesai","followers_url":"https://api.github.com/users/ankurdesai/followers","following_url":"https://api.github.com/users/ankurdesai/following{/other_user}","gists_url":"https://api.github.com/users/ankurdesai/gists{/gist_id}","starred_url":"https://api.github.com/users/ankurdesai/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ankurdesai/subscriptions","organizations_url":"https://api.github.com/users/ankurdesai/orgs","repos_url":"https://api.github.com/users/ankurdesai/repos","events_url":"https://api.github.com/users/ankurdesai/events{/privacy}","received_events_url":"https://api.github.com/users/ankurdesai/received_events","type":"User","site_admin":false},"created_at":"2016-07-13T12:22:42Z","updated_at":"2016-07-13T12:22:42Z","body":"@tonygardella I can't replicate your US-NR1 error Fluxnet issues with any other site (US-Syv US-WCr). The latest update downloads the file, gap fills specific humidity based on VPD, and runs sipnet. I wonder if you have some corrupt files in your VM from aborted runs. Delete the CF and gap fill files from /home/carya/output/dbfiles and also from BETY dbfiles and try again. \r\n\r\nThe issue with US-Ha1 is tricker. This is because the data is hourly instead of half hourly and hence the file name as HR instead of HH. The same is probably true of US-UMB and US-PFa. Let me see if a simple fix will work.\r\n"}}
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