Closed slamander closed 4 years ago
Update: I reinstalled Julia and now Omniscape
passes Pkg.test
, however run_omniscape
still returns the same error (see error 1 above). Just to confirm, the files I used are here.
Hi @slamander sorry for my late reply here. For some reason I missed the notification when you posted the original issue! Tests are passing for me as well in Julia 1.5.0 -- glad you got that working.
I will get a chance to look into this issue more thoroughly tomorrow, but right off the bat, I am seeing [a38d70fc] Omniscape v0.1.4
in the error output above. It looks like you are using Omniscape v0.1.4 (not v0.4.0) and Circuitscape v5.7.0, and those two versions are not compatible. Usually the reason for an old version of Omniscape being used is due to Julia not being at the latest version.
Can you share with me the following info?
Pkg.status("Omniscape")
run both from R and from the Julia terminal directlyThanks!
Hey @vlandau, no worries, I'm sure my incessant issue posting is driving you mad. Now that I've updated Julia and Omniscape, I believe you solved it! Here's what you asked for:
Can you share with me the following info?
- what version of Julia are you using (also verify that this is the version linked to R)
Julia:
julia> VERSION
v"1.5.1"
R:
R> julia_command('VERSION')
v"1.5.1"
- The output of Pkg.status("Omniscape") run both from R and from the Julia terminal directly
Julia:
julia> Pkg.status("Omniscape")
Status `C:\Users\jbaecher\.julia\environments\v1.5\Project.toml`
[a38d70fc] Omniscape v0.4.0
R:
R> julia_installed_package("Omniscape")
[1] "0.4.0"
I no longer get the errors mentioned above, instead a more common OutOfMemoryError()
error. Curious, are there any resources you can point me toward that give 'best practice' recommendations for setting block_size
, radius
, buffer
, and/or any other Omniscape parameters, given the job?
Again, I can't thank you enough for being such a great resource.
Best,
-Alex.
No worries at all! The out of memory error means that your machine doesn't have the memory resources needed to run given the problem size. This isn't significantly affected by block_size
, radius
, or buffer
, unless you have an very large radius (>>1000 pixels). In my experience out of memory errors have been due to very large resistance grids. How many pixels is your resistance grid?
One way to reduce memory consumption is to use fewer parallel processes. More parallel processes -> larger memory requirements. You could start by running in with parallelize = false
in your .ini to see if that helps.
I'm going to close this issue for now since the memory issue is a hardware problem and not an Omniscape issue per se, but feel free to continue to comment. Chatting on gitter might make sense for this since it's more about general usage, but either works for me!
Great, thanks @vlandau. This is very helpful information, and I appreciate you turning me to the gitter forum! Omniscape is an awesome tool!
-Alex.
Hi CS and OS community,
I'm attempting to run OS (v 0.4.0) through R (v 4.0.1), however it always returns the same error (see Error 1). So, I then ran a
Pkg.test
in Julia, which returned a testing error (see Error 2). I then installed a dev version, which passed the package test, but when I attempt to run it on my own data (through R or Julia), it throws Error 1 again. I have almost 300 focal raster grids I would like to analyze, but I've uploaded a single example grid & .ini here.BTW--because I have no idea what I'm doing, I created my .ini file to be proportional to
block_size
,radius
, andbuffer
parameters values set inhttps://github.com/Circuitscape/Omniscape.jl/blob/main/test/input/config4.ini
.Error 1
Error 2
Thanks a ton,
Alex.