Load Error with getfieldspecs

[francispoulin]

I tried to run the barotropic QG example and unfortunately got an error in the first importing step.

Is this a known problem? I'm using julia 1.5.2, in case that helps.

https://fourierflows.github.io/GeophysicalFlowsDocumentation/dev/generated/barotropicqg_betadecay/

julia> import GeophysicalFlows.BarotropicQG
[ Info: Precompiling GeophysicalFlows [44ee3b1c-bc02-53fa-8355-8e347616e15e]
ERROR: LoadError: LoadError: UndefVarError: getfieldspecs not defined
Stacktrace:
 [1] include(::Function, ::Module, ::String) at ./Base.jl:380
 [2] include at ./Base.jl:368 [inlined]
 [3] include(::String) at /home/fpoulin/.julia/packages/GeophysicalFlows/mZXo8/src/GeophysicalFlows.jl:1
 [4] top-level scope at /home/fpoulin/.julia/packages/GeophysicalFlows/mZXo8/src/GeophysicalFlows.jl:13
 [5] include(::Function, ::Module, ::String) at ./Base.jl:380
 [6] include(::Module, ::String) at ./Base.jl:368
 [7] top-level scope at none:2
 [8] eval at ./boot.jl:331 [inlined]
 [9] eval(::Expr) at ./client.jl:467
 [10] top-level scope at ./none:3
in expression starting at /home/fpoulin/.julia/packages/GeophysicalFlows/mZXo8/src/barotropicqg.jl:27
in expression starting at /home/fpoulin/.julia/packages/GeophysicalFlows/mZXo8/src/GeophysicalFlows.jl:13
ERROR: Failed to precompile GeophysicalFlows [44ee3b1c-bc02-53fa-8355-8e347616e15e] to /home/fpoulin/.julia/compiled/v1.5/GeophysicalFlows/xFqhg_lrx0p.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1305
 [3] _require(::Base.PkgId) at ./loading.jl:1030
 [4] require(::Base.PkgId) at ./loading.jl:928
 [5] require(::Module, ::Symbol) at ./loading.jl:923

[glwagner]

This is example is broken for me too, although the error I get is different than @francispoulin:

~/Projects/GeophysicalFlows.jl/examples$ julia --project
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.5.2 (2020-09-23)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia> include("barotropicqg_betadecay.jl")
ERROR: LoadError: MethodError: no method matching Problem(::CPU; nx=128, Lx=6.283185307179586, β=10.0, μ=0.0, dt=0.05, stepper="FilteredRK4")
Closest candidates are:
  Problem(; nx, Lx, ny, Ly, dt, f0, β, eta, ν, nν, μ, stepper, calcFU, calcFq, stochastic, T, dev) at /Users/gregorywagner/.julia/packages/GeophysicalFlows/i9qG7/src/barotropicqg.jl:34
Stacktrace:
 [1] top-level scope at /Users/gregorywagner/Projects/GeophysicalFlows.jl/examples/barotropicqg_betadecay.jl:45
 [2] include(::String) at ./client.jl:457
 [3] top-level scope at REPL[1]:1
in expression starting at /Users/gregorywagner/Projects/GeophysicalFlows.jl/examples/barotropicqg_betadecay.jl:45

julia> 

[glwagner]

It's a bit perplexing, because presumably the example is run to generate the documentation. I'm not sure what's happening.

[glwagner]

@francispoulin your error may arise because you are trying to run the example with a different version of GeophysicalFlows than what you've cloned from github.

Try navigating to examples/ and typing

julia --project

and then

julia> include("barotropicqg_betadecay.jl")

[glwagner]

Oh my. The Manifest.toml in the examples is extremely outdated.

Ok, it's on users to keep this updated.

[glwagner]

@francispoulin I think the issue is unfortunately partly due to the fact that we don't provide a Manifest.toml which means that your environment can drift even when you're on the master branch of the git repo.

Let me know if these steps solve it for you:

1. Navigate to the root directory, eg /GeophysicalFlows.jl/.
2. Type git checkout master; git pull.
3. Open julia with the project's environment: julia --project.
4. Within julia, update the Manifest.toml file by typing julia> using Pkg; Pkg.update().
5. Now try running the example by typing julia> include("examples/barotropicqg_betadecay.jl").

This sequence of steps worked for me.

[navidcy]

I'll streamline the process!
Thanks @francispoulin for pointing this out.

[navidcy]

@glwagner, did you follow what the examples Readme suggests?

Perhaps we should update that also + add some basic instructions in the Docs.

[francispoulin]

Thanks for all the feedback.

First, I did go to examples and try julia --project and then the inclue but that gave the same error.

Second, I verified I was on master and pulled. No changes. The updating worked fine and including command does work without any error. And the annimation works great! Unfortunately, I can't view ti using vlc but mplayer works fine in ubuntu.

Also, when I try the first commands in the script, which failed before, they work fine now.

Do I gather that the problem was that my package was not update date? If I was supposed to udpate something, sorry for not trying that before.

I will keep this open in case you two feel like something needs to be modified. But if you like I'm happy to close it.

[francispoulin]

Maybe I should have said that the following command, which didn't work before, does work now.

import GeophysicalFlows.BarotropicQG

[navidcy]

Could you print the output of

using Pkg; Pkg.status()

[francispoulin]

Sure thing:

julia> using Pkg; Pkg.status()
Status `~/.julia/environments/v1.5/Project.toml`
  [7a1cc6ca] FFTW v1.2.4
  [2aec4490] FourierFlows v0.6.3
  [44ee3b1c] GeophysicalFlows v0.8.0
  [da04e1cc] MPI v0.15.1
  [91a5bcdd] Plots v1.7.3
  [37e2e46d] LinearAlgebra
  [de0858da] Printf
  [9a3f8284] Random

[navidcy]

The problem was the the BarotropicQG module was importing an old, now deprecated, function from FourierFlows.jl package (named getfieldspecs). I've removed this import but have forgotten to make a new patch release of GeophysicalFlows.jl package. So when you did

] add GeophysicalFlows

you installed the latest released version of GeophysicalFlows and it wasn't working. When you followed @glwagner steps you installed the version on master...

[navidcy]

An "easy" fix for now is to do

add GeophysicalFlows#master

until I make a new release. Sorry for that :)

[francispoulin]

Ah, I guess adding what you suggest above is a good fix for now.

When I know it's been fixed I will add the regular version without #master.

[francispoulin]

I tried removing the old package and then adding the master version and both have an Error.

(GeophysicalFlows) pkg> remove GeophysicalFlows
ERROR: The following package names could not be resolved:
 * GeophysicalFlows (not found in project or manifest)


(GeophysicalFlows) pkg> add GeophysicalFlows#master
   Updating git-repo `https://github.com/FourierFlows/GeophysicalFlows.jl.git`
ERROR: package `GeophysicalFlows [44ee3b1c]` has same name or UUID as the active project

[navidcy]

Seems you have activated the repo's project now. I guess you started julia with julia --project from the your GeophysicalFlows.jl local repo folde. Notice that

(GeophysicalFlows) pkg>

So in that case, the GeophysicalFlows will be the version in the local repo you cloned.

Boy... it's not as easy as I would have thought for people to run the examples :(

[navidcy]

(Perhaps, some of the confusions that I may have created about "activated project" can be alleviated via julia's docs...)

[francispoulin]

Thanks for the link @navidcy . That was helpful.

I'm used to using virtual environments in python, and I guess I created one without realizing it. Good to know.

I left Julia, re-entered and saw that I was in the (@v1.5) so I guess I am in a "normal" environment now, not virtual.

I then managed to rm GeophysicalFlows, even though I might not have had to, and then added GeophysicalFlows#master, as suggested. That worked.

Then, I coudl import GeophysicalFlows.BarotropicQG, without a problem

That was a bit of a steap learning curve but I am glad to have learned it and hope not to make that mistake again. But will certainly make others.

[navidcy]

I'll try to add some more clarifications in the docs and I may ping you to give me your opinion whether they are clearer :)

[francispoulin]

I am happy to help and please ask. I am a novice now so a good target audience.

[navidcy]

v0.8.1 was released and that should have dealt with this issue; I'm closing it in favour of #132