UndefVarError: libsgtsnepi not defined

[AlexanderJCS]

Hi there,

I was following the Graph embedding guide in the documentation and there is an issue with SGtSNEpi.jl.

I ran this code after downloading the sample data in that the documentation references:

using DataDeps, MatrixMarket

L = vec( MatrixMarket.mmread( datadep"optdigits/optdigits_10NN/optdigits_10NN_label.mtx" ) );
L = Int.( L );

using SGtSNEpi, Random

# reproducible results
Random.seed!(0);
Y0 = 0.01 * randn( size(A,1), 2 );

Y = sgtsnepi(A; Y0 = Y0);

The program ran successfully up to line 12, where this error occurs:

ERROR: UndefVarError: libsgtsnepi not defined
Stacktrace:
 [1] _sgtsnepi_c(P::SparseArrays.SparseMatrixCSC{Float64, Int64}, d::Int64, max_iter::Int64, early_exag::Int64, λ::Int64; Y0::Matrix{Float64}, np::Int64, h::Float64, bb::Float64, eta::Float64, run_exact::Bool, fftw_single::Bool, alpha::Int64, profile::Bool, drop_leaf::Bool, list_grid_size::Vector{Int64}, par_scheme_grid_thres::Int64)
   @ SGtSNEpi C:\Users\d8amo\.julia\packages\SGtSNEpi\4wQHp\src\sgtsne.jl:250
 [2] sgtsnepi(A::SparseArrays.SparseMatrixCSC{Float64, Int64}; d::Int64, λ::Int64, max_iter::Int64, early_exag::Int64, Y0::Matrix{Float64}, profile::Bool, np::Int64, version::SGtSNEpi.SGTSNEPI_VERSION, h::Float64, u::Int64, k::Int64, eta::Float64, alpha::Int64, fftw_single::Bool, exact::Bool, drop_leaf::Bool, list_grid_size::Vector{Int64}, bound_box::Float64, par_scheme_grid_thres::Int64)
   @ SGtSNEpi .\array.jl:0
 [3] top-level scope
   @ c:\Users\path\to\my\file\SGtSNEpi_test.jl:12

Following the stack trace, the error occurs on line 250 of sgtsne.jl. Do you know how to fix this? Thanks.

[fcdimitr]

Hello and thank you for reporting this issue!

Are you using Windows? Currently, this package only works on Linux and macOS, due to cilk not supporting Windows natively.

I will leave this issue open in order to update the documentation/manual to make this clear.

[AlexanderJCS]

Thank you for your reply. I am on Windows. Is there an alternative library that you know of that allows visualizing 3D graphs on Windows, or a way to get this library to work on Windows?

[fcdimitr]

You could try running Julia via WSL2.

[varnerlab]

Hmmm. I'm on a Mac M1 2021, running Ventura 13.2.1 (22D68), and I have the same error as above.

running the sample visualization code from Graphs.jl:
using GLMakie, SGtSNEpi, SNAPDatasets

GLMakie.activate!()

g = loadsnap(:as_caida)
y = sgtsnepi(g);
show_embedding(y;
A = adjacency_matrix(g), # show edges on embedding
mrk_size = 1, # control node sizes
lwd_in = 0.01, lwd_out = 0.001, # control edge widths
edge_alpha = 0.03 )

It runs until the y = sgtsnepi(g) line.

[fcdimitr]

Hello, @varnerlab, and thank you for the feedback! Are you running Julia natively on your M1 or through Rosetta2?

We have not tested it natively on Mac M1 yet; we need to check whether cilk is compatible with M1.

[varnerlab]

Hi @fcdimitr, I'm running natively on the M1.

I ran the same code on a 2013 trashcan mac pro (macOS 12.6.3, Julia 1.8.5, Xeon), and it ran fine. So I'm guessing it's the M1 native issue.

[fcdimitr]

Hello @AlexanderJCS and @varnerlab,

This issue is temporarily closed by adding a warning on the front page.

We plan to add support for M1 Macs (natively) and Windows; I will re-open the issue when we have a pull request for you to try.

Thank you!