Julia and Packages

By default, Julia Programming Language is available via module.

Load & list available modules

module use /applis/PSMN/debian11/E5/modules/all
module avail

Load the version of Julia you want to work with

module load Julia/1.9.4-linux-x86_64

If you want to work with another particular version of Julia (See below section JILL), you will have to install it in your $HOME or team storage (see Where to store files?).

For the rest of this documentation, replace mylogin by your login as provided by PSMN.

Project Management with Julia

You can manage packages within a project environment (similar to a python venv)

Create a directory where you want to store your project

mylogin@c8220node1:~/$ mkdir -p ~/julia/julia194 && cd ~/julia/julia194

Enter Project Manager

Type ] key:

mylogin@c8220node1:~/julia/julia194$ julia
mylogin@c8220node1:~/julia/julia194$ ]

Activate a new project

(@v1.9) pkg> activate tutorial
    Activating new project at `~/julia/julia194/tutorial`
(tutorial) pkg> status
    Status `~/julia/julia194/tutorial/Project.toml` (empty project)

Install a package inside Julia project environment

For example, Roots:

(tutorial) pkg> add Roots

You can now use Roots in your project environment

(tutorial) pkg> status
    Status `~/julia/julia194/tutorial/Project.toml`
[f2b01f46] Roots v2.1.5

Verify the dependencies of your project

mylogin@x5570comp1:~/julia/julia194/tutorial$ ls
Manifest.toml  Project.toml
mylogin@x5570comp1:~/julia/julia194/tutorial$ less Project.toml

Exit (deactivate) a project environment

(tutorial) pkg> activate
Activating project at `~/.julia/environments/v1.9`

(@v1.9) pkg>

Exit package manager

Type backspace key.

Exit Julia

julia> exit()

Alternative Project Management with Julia

This method will create a project folder and source folder.

Enter Project Manager

Type ] key:

mylogin@c8220node1:~/julia/julia194$ julia
mylogin@c8220node1:~/julia/julia194$ ]

Generate new project

(@v1.9) pkg> generate tutorial2
Generating  project tutorial2:
    tutorial2/Project.toml
    tutorial2/src/tutorial2.jl

mylogin@c8220node1: ls ~/julia/julia194/tutorial2
Project.toml  src

Exit package manager

Type backspace key.

Exit Julia

julia> exit()

Two files were created:

~/julia/julia194/tutorial2/Project.toml specifies the dependencies.

~/julia/julia194/tutorial2/src/tutorial2.jl is a placeholder for your code.

Activate Existing Project

mylogin@c8220node1:~$ cd ~/julia/julia194/tutorial2
mylogin@c8220node1:~/julia/julia194/tutorial2$ julia --project=.

Add Packages to project

julia> ]
(tutorial2) pkg> add Roots
(tutorial2) pkg> status
Project tutorial2 v0.1.0
Status `~/julia/julia194/tutorial2/Project.toml`
[f2b01f46] Roots v2.1.5

You can now use the package Roots in your project environment.

Multiple Versions of Julia with JILL

The most simple way to manage and work with multiple versions of Julia in your $HOME is to install the python package, JILL.

Install JILL

mylogin@c8220node1:~$ python3.9 -m pip install jill
mylogin@c8220node1:~$ export PATH="/home/mylogin/.local/bin:$PATH"

If you wish to make JILL permanently available in your environment, add the export line (export PATH="/home/mylogin/.local/bin:$PATH") to the end of your ~/.bashrc file.

Install latest version of Julia with Jill

mylogin@c8220node1:~$ jill list
mylogin@c8220node1:~$ jill install

Launch Julia

mylogin@c8220node1:~$ julia
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.10.4 (2024-06-04)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia>

Install specific Julia version with JILL

mylogin@c8220node1:~$ jill install 1.6.2
mylogin@c8220node1:~$ jill list
Found 4 julia(s) in /home/mylogin/.local/bin:
julia           -->     1.10.4
julia-1         -->     1.10.4
julia-1.6       -->     1.6.2
julia-1.10      -->     1.10.4

Launch specific Julia version with JILL

mylogin@c8220node1:~$ julia-1.6
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.6.2 (2021-07-14)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia>

Julia on GPU

To run a Julia program on GPU, you must launch your job on a GPU machine (See Partition E5-GPU). As an example, we will run a test on r730gpu01 (which is a login node). However, this is only a test.. Once you are prepared to launch your job, you should write a script and submit it through the queuing system (See Submitting a job).

Load Julia and CUDA modules

PSMN has NVidia GPUs therefore you must load the CUDA API. (NOTE: CUDA version may vary for your software!)

mylogin@r730gpu01: module use /applis/PSMN/debian11/E5/modules/all
module load Julia/1.9.4-linux-x86_64
module load CUDA/11.4.1

Call Julia and run command

This is an example using the package Oceananigans.

mylogin@r730gpu01:~$ julia
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.10.4 (2024-06-04)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia> using Oceananigans
grid = RectilinearGrid(GPU(), size=(128, 128), x=(0, 2π), y=(0, 2π), topology=(Periodic, Periodic, Flat))
model = NonhydrostaticModel(; grid, advection=WENO())
ϵ  (x, y) = 2rand() - 1
set!(model, u=ϵ, v=ϵ)
simulation = Simulation(model; Δt=0.01, stop_time=4)
run!(simulation)