Packages on JupyterNotebook Supercloud

New to Julia
1

Hi.

I have some troubles installing packages on Jupyter Notebook supercloud.

Packages like Flux, Plots work with :

import Pkg; Pkg.add("Flux")

However, packages from git clones fail to clone.

Examples are DiffEqFlux, OrdinaryDiffEq, DifferentialEquations.

Sample output error is as follows


Resolving package versions...
   Cloning [0c46a032-eb83-5123-abaf-570d42b7fbaa] DifferentialEquations from https://github.com/JuliaDiffEq/DifferentialEquations.jl.git
failed to clone from https://github.com/JuliaDiffEq/DifferentialEquations.jl.git, error: GitError(Code:ERROR, Class:Net, curl error: 
)

Stacktrace:
 [1] pkgerror(::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/Types.jl:120
 [2] #clone#3(::String, ::Base.Iterators.Pairs{Symbol,Any,Tuple{Symbol,Symbol},NamedTuple{(:isbare, :credentials),Tuple{Bool,LibGit2.CachedCredentials}}}, ::Function, ::String, ::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/GitTools.jl:111
 [3] (::getfield(Pkg.Operations, Symbol("##18#20")){Base.UUID,String,Base.SHA1,Array{String,1}})(::LibGit2.CachedCredentials) at ./none:0
 [4] shred!(::getfield(Pkg.Operations, Symbol("##18#20")){Base.UUID,String,Base.SHA1,Array{String,1}}, ::LibGit2.CachedCredentials) at ./secretbuffer.jl:184

I tried Pkg.update() but it doesn’t seem to fix the problem as it gives me the following error.

 Cloning git-repo `https://github.com/Accla/D4M.jl`
failed to clone from https://github.com/Accla/D4M.jl, error: GitError(Code:ERROR, Class:Net, curl error: 
)

Stacktrace:
 [1] pkgerror(::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.1/Pkg/src/Types.jl:120

Any help will be greatly appreciated! Thanks.

2

Hello and welcome. I don’t have access to the MIT Supercloud, but perhaps the package help will help with using your home directory? Good luck!

From: https://supercloud.mit.edu/software-and-package-management#modules

Installing Software/Packages in your Home Directory

Many packages and software can be installed in user space, meaning they are
installed just for the user installing the package or software. Often the flag
to do this is "--user". The way to do this for Julia, Python, and R packages
is described below, for other tools refer to its documentation to find out how
to do this. Julia Packages

Since Julia is a new evolving language, there are different ways to install
packages depending on the version. For Julia version 0.6 you load the
beta-julia-0.6 module, Julia 1.0 is the julia-1.0 module, and Julia 1.1 is the
julia-latest module. We recommend you use the latest Julia version on our
system, if possible. Julia-1.1

Adding new packages in Julia 1.1 doesn't require doing anything special. On
the login node, load the julia-latest module and start Julia. You can enter
package mode by pressing the "]" key and entering add packagename, where
packagename is the name of your package. Or you can load Pkg and run
Pkg.add("packagename").

The easiest way to check if a package already exists is to try to load it by
running using packagename. The Pkg.status() command will only show packages
that you have added to your home environment. If you would like a list of the
packages we have installed, the following lines should do the trick:

    using Pkg; Pkg.activate(DEPOT_PATH[2]*"/environments/v1.1");
    installed_pkgs = Pkg.installed();
    Pkg.activate(DEPOT_PATH[1]*"/environments/v1.1"); installed_pkgs

Julia-1.0

Julia's package manager changed drastically with the new Julia 1.0 release.
Future releases should support having both a system package directory and a
user package directory, but for now if there is a package you need that we
don't already have installed, you will have to create your own package
directory.

To see what packages you have installed in the default environment, start
Julia, load Pkg, and run Pkg.status() (in lieu of loading Pkg, you can press
the "]" key to enter package mode and type "st").

If you decide you need to create your own package directory, you set the
JULIA_DEPOT_PATH environment variable. At the command line:

    export JULIA_DEPOT_PATH=/home/gridsan/USERNAME/.julia echo
    $JULIA_DEPOT_PATH

When you start Julia you will be able to add packages to this new path (you
can use Pkg.add("packageName"), or type "]" and enter the command "add
packageName").