Omniscape fails on specific row / column: "median of empty array is undefined" #122
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Sorry for the delay in getting back to you on this. Is this still giving you problems? It does make sense that the timing of the error being thrown is random since the order of the moving window solves is randomized for more accurate ETA estimates in the progress bar. If possible, would you mind sharing your input files (and the associate ini file)? I'll try to take a look in the coming couple of weeks. |
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@vlandau, and my apologies for taking even longer to get back. Yes, this is still giving me issues, across several different input files. Here's the input data and ini file: https://drive.google.com/drive/folders/1kC4FVzw2HjlXVbLLot4a6LU0EPu-E-7s?usp=sharing. |
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By the way, here's the problem cells from two failed runs. The value of all of these cells are NA. |
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Hi guys, I'm having the exact same error launching a Europe-wide Omniscape scan. The error appeared after adding a conditional layer in the .ini file. I've already checked that the conditional layer has the same size and resolution as the resistance layer. I tried to change some parameters (radius and block size) but the error keeps appearing. Omniscape failed on the moving window centered on row 3323 column 2228 Stacktrace: |
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My best guess is at the column/row of one of your inputs, the resulting slice/chunks of the array is just empty (all NaN values). Would you be able to clip out a section (square, with side lengths equal to 2×radius + 1) of each of your input rasters centered on the failing row/column and share it with me? |
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Hi @vlandau and thanks for replying, you're probably right. I share the clipped input rasters with your options. However, if this is the problem, I don't know why using only the resistance raster doesn't cause problems, while this error only occurs when using a second layer as a condition.
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Hi there! I'm a PhD student and I'm building a tool to help developers automatically track down where NaNs come from in computations, and I'd like to try it out on the problem you're having here to see if I can help. Would someone mind showing me how to fire it all off to reproduce the problems that you're having here? I think I have the |
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Hi @ashton314! If you already have .ini and .tiff file, I think you just need to donwload Omniscape on Julia and then run the .ini file. You can get information on this page https://docs.circuitscape.org/Omniscape.jl/stable/usage/#Running-Omniscape |
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@vlandau I also thought there could be NaNs on the failing pixels, but after investigating the failures I found no NaNs. Does it make sense that identical jobs fail at different locations/durations? Sometimes the job will near completion (>90%), but others will fail early--all failing on different pixels. Unlike @Daviser95, some jobs will fail whether or not I have conditional criteria (it's not very predictable). Here's an output from the last job I ran without conditional criteria: |
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It does make sense that it would occur at different times because the order in which the windows are solved is random (this helps the ETA on the progress bar to be more accurate). I assume in your case there are multiple moving window locations that will cause failure, but which one you run into first is random due to the random solve order. |
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I regularly get the same issue as @slamander and @Daviser95. Omniscape will fail on specific row / columns. These are not No Data or Nan pixels however. I have clipped out a small area centered on these pixels and run OS on the subset and it finishes successfully. What are the potential reasons for this type of error? |
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@geomenke this is a different error than the empty array error mentioned above (but I see now one of the stack traces had an AssertionError too), coming directly from Circuitscape, but fortunately, we just made a patch release to Circuitscape that may fix that issue. Would you update to Circuitscape 5.13.2 (you'll need Julia 1.9) and try again? |
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@vlandau I am already at Julia 1.9.2 so what is the best way to update to Circuitscape 5.13.2? Do I upgrade Omniscape? Can that be done via the command line? |
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Oh great! To update, in a Julia terminal, enter the package interface by typing the |
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It did not specifically list Circuitscape as being updated, just things like updating registry etc. |
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In the same package prompt/interface you should be able to run |
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I see that I have an outdated and restricted by compatibility contraints version of Omniscape and that Circuitscape did not update after running update. Running update Omniscape did not update Omniscape. Do I need to run |
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You shouldn't need to do that. There are some solutions in this thread that might work for you: https://discourse.julialang.org/t/how-to-force-an-update/73071/12 |
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I updated to Circuitscape v5.13.2 and Omniscape v0.6.1, but it failed again with a similar stacktrace as before: Any recommendations? |
Cross-posting from gitter: there have two mentions of Omniscape failing on a specific row / column.
In my case, I receive this error:
ERROR: ArgumentError: median of an empty array is undefined, Float64[]. The run will fail at different stages--sometimes quite far into a run, other times immediately--but always at the same row-column combination. I've tried to diagnose the error by changing the raster inputs or adjusting model parameters (e.g., solver, block size, r_cutoff [for source = resistance], and running conditional and non-conditional criteria).Here's my error print-out. Let me know if additional information is needed.
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