WorkflowPlot Shiny Loading Error - VM

[tonygardella]

To Reproduce Steps to reproduce the behavior:

1. Open Web GUI with pecan VM running by going to http://localhost:6480/ in local browser
2. Click on 'Output Visualization'
3. Click on "WorkflowPlot"
4. See error when loading.

[tonygardella]

Thanks to @robkooper, looked at log files by:

sudo -s
echo "preserve_logs true;" >> /etc/shiny-server/shiny-server.conf
service shiny-server restart

Run App then look at log `/var/log/shiny-server"

Found that it wasn't finding '"workflow-id". Took a shot in the dark and disabled all add-ons in my browser and the app loads fine now! Loading one year for Sipnet run took about 10 min but it works now.

[tonygardella]

Closing issue now because it loads fine.

[mdietze]

As with #2053, not sure I agree that we can consider this fixed if turning off browser add-ons is a general requirement and, at a minimum, if there's not an informative error message suggesting that the user try that if the app isn't loading

[serbinsh]

I just hit this error in the workflow plot when "loading external data"

2018-08-27 08:39:39 INFO   [read.output] :
   GPP NPP TotalResp AutoResp HeteroResp SoilResp NEE AbvGrndWood
   leaf_carbon_content TotLivBiom TotSoilCarb Qle Transp SoilMoist
   SoilMoistFrac SWE litter_carbon_content LAI fine_root_carbon_content
   coarse_root_carbon_content GWBI AGB Mean: 78900000 1.59e-08 4.67e-09
   3.76e-08 1.13e-08 2.63e-08 2.78e-08 2.16e-08 4.88 0.292 12.4 26 29.6
   2.03e-05 35.4 0.295 17.7 0.28 1.47 2.16 5.12 NaN 5.17 Median: 78900000 0
   -2.59e-09 3.39e-08 7.59e-09 2.74e-08 2.83e-08 2.69e-08 3.13 0.277 10.2
   28.3 18.2 0 23.1 0.193 0 0.28 1.39 1.66 5.09 NA 3.41
Warning: attributes are not identical across measure variables;
they will be dropped
`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
2018-08-27 08:55:57 WARN   [PEcAn.DB::query.format.vars] :
   Units not convertible for airT with units of degrees C .  Please make
   sure the varible has units that can be converted to K
Warning in postgresqlExecStatement(conn, statement, ...) :
  RS-DBI driver warning: (unrecognized PostgreSQL field type geometry (id:77969) in column 17)
udunits system database read
Warning: Error in if: missing value where TRUE/FALSE needed
  119: fcn
  118: PEcAn.benchmark::load_data
  117: eventReactiveHandler
   73: load.model.data
   72: observeEventHandler
    1: runApp
2018-08-27 08:55:57 WARN   [PEcAn.DB::query.format.vars] :
   Units not convertible for airT with units of degrees C .  Please make
   sure the varible has units that can be converted to K

and this crashed Shiny.

[serbinsh]

I just tried another data file and got a similar error

Warning: attributes are not identical across measure variables;
they will be dropped
2018-08-27 08:59:26 WARN   [PEcAn.DB::query.format.vars] :
   Units not convertible for precipitation_flux with units of Kg/m2/s .
   Please make sure the varible has units that can be converted to kg m-2
   s-1
Warning in postgresqlExecStatement(conn, statement, ...) :
  RS-DBI driver warning: (unrecognized PostgreSQL field type geometry (id:77969) in column 17)
udunits system database read
Warning: Error in vobjtovarid4: Variable not found
  123: stop
  122: vobjtovarid4
  121: FUN
  120: lapply
  119: fcn
  118: PEcAn.benchmark::load_data
  117: eventReactiveHandler
   73: load.model.data
   72: observeEventHandler
    1: runApp
2018-08-27 08:59:26 WARN   [PEcAn.DB::query.format.vars] :
   Units not convertible for precipitation_flux with units of Kg/m2/s .
   Please make sure the varible has units that can be converted to kg m-2
   s-1

[serbinsh]

And get this if I load multiple model outputs at once:

2018-08-27 09:00:30 INFO   [read.output] :
   GPP NPP TotalResp AutoResp HeteroResp SoilResp NEE AbvGrndWood
   leaf_carbon_content TotLivBiom TotSoilCarb Qle Transp SoilMoist
   SoilMoistFrac SWE litter_carbon_content LAI fine_root_carbon_content
   coarse_root_carbon_content GWBI AGB Mean: 78900000 1.59e-08 4.67e-09
   3.76e-08 1.13e-08 2.63e-08 2.78e-08 2.16e-08 4.88 0.292 12.4 26 29.6
   2.03e-05 35.4 0.295 17.7 0.28 1.47 2.16 5.12 NaN 5.17 Median: 78900000 0
   -2.59e-09 3.39e-08 7.59e-09 2.74e-08 2.83e-08 2.69e-08 3.13 0.277 10.2
   28.3 18.2 0 23.1 0.193 0 0.28 1.39 1.66 5.09 NA 3.41
Warning: attributes are not identical across measure variables;
they will be dropped
Warning: Error in :: NA/NaN argument
  122: read.output
  121: load_data_single_run
  120: .f
  119: map2
  118: map2_df
  117: eventReactiveHandler
   73: load.model
   72: observeEventHandler
    1: runApp

Execution halted

i.e. "multiple run IDs"

[serbinsh]

Getting random "execution halted" errors

Read 105 items
2018-09-07 14:32:13 INFO   [PEcAn.settings::read.settings] :
   Loading inpufile=
   /data/Model_Output/pecan.output/PEcAn_2000001045/pecan.CONFIGS.xml
2018-09-07 14:32:13 INFO   [read.output] :
   No start or end year provided; reading output for all years
2018-09-07 14:32:13 INFO   [read.output] :
   Reading output for Years: 2006 - 2007 in directory:
   /data/Model_Output/pecan.output/PEcAn_2000001045/out/2000078754
   including files 2006.nc 2007.nc
2018-09-07 14:32:14 INFO   [read.output] :
   time_bounds GPP NPP TotalResp AutoResp HeteroResp SoilResp NEE
   AbvGrndWood leaf_carbon_content TotLivBiom TotSoilCarb Qle Transp
   SoilMoist SoilMoistFrac SWE litter_carbon_content LAI
   fine_root_carbon_content coarse_root_carbon_content GWBI AGB Mean:
   31500000 182 3.38e-08 -3.09e-08 1.5e-07 6.47e-08 8.49e-08 9.21e-08
   1.16e-07 16.9 0.0605 23 13.7 58.2 0.000538 85 0.709 0.0581 0.28 106
   0.596 5.46 NaN 16.9 Median: 31500000 182 0 -1.22e-08 1.15e-07 2.83e-08
   6.56e-08 7.17e-08 7.78e-08 16.9 0 22.4 14 26.9 0 97.9 0.815 0 0.28 106
   0.0383 5.44 NA 16.9
2018-09-07 14:32:14 WARN   [read.output] :
   Variable time_bounds has 2 dimensions, it cannot be loaded and will be
   omitted.
Warning: attributes are not identical across measure variables;
they will be dropped
`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'

Execution halted

no other error? works for a few plots then this happens

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