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Julia

Julia is a dynamically-typed programming language that was originally designed to address the needs of high-performance numerical analysis and computational science, without the typical need of separate compilation.

Julia is available as a module on Apocrita.

Usage

To run the default installed version of Julia, simply load the Julia module:

module load julia

then run Julia with a script file:

julia example.jl

Example jobs

Serial jobs

Here is an example job running on 1 core with 1GB RAM:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load julia
julia example.jl

Here is an example job running on 4 cores with 4GB RAM:

Core Usage

The modules for Julia will automatically set the JULIA_NUM_THREADS environment variable to match ${NSLOTS} (number of cores requested by the job script) when loaded.

If for some reason you manually add a --threads argument, please set it to the value of ${NSLOTS} to avoid overloading the compute nodes.

https://docs.julialang.org/en/v1/manual/multi-threading/

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 4
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load julia
julia example.jl

Julia package management

The standard package manager for Julia 1.0 and newer is Pkg. To interface with Pkg, start the Julia application and press the ] key. To return to the original prompt, either press backspace when the input line is empty or press Ctrl+c.

Adding packages

Packages can be added with the add command followed by the name of the package. It is also possible to add multiple packages in one command.

(v1.10) pkg> add Example
 Installing known registries into `~/.julia`
    Updating registry at `~/.julia/registries/General.toml`
   Resolving package versions...
   Installed Example ─ v0.5.5
    Updating `~/.julia/environments/v1.10/Project.toml`
  [7876af07] + Example v0.5.5
    Updating `~/.julia/environments/v1.10/Manifest.toml`
  [7876af07] + Example v0.5.5
Precompiling project...
  1 dependency successfully precompiled in 1 seconds

Removing packages

Packages can be removed using the rm command. If the package has not been loaded in the current project, the removal command will fail with a warning message.

(@v1.10) pkg> rm Example
    Updating `~/.julia/environments/v1.10/Project.toml`
  [7876af07] - Example v0.5.5
    Updating `~/.julia/environments/v1.10/Manifest.toml`
  [7876af07] - Example v0.5.5
        Info We haven't cleaned this depot up for a bit, running Pkg.gc()...
      Active manifest files: 1 found
      Active artifact files: 0 found
      Active scratchspaces: 0 found
     Deleted no artifacts, repos, packages or scratchspaces

Listing installed packages

To list the installed packages, run st (short for status).

(v1.0) pkg> st
    Status `~/.julia/environments/v1.10/Project.toml`
  [7876af07] Example v0.5.5

Testing packages

The tests for a package can be run using the test command:

(v1.10) pkg> test Example
   Testing Example
    Status `/tmp/456364.1.test.q/tmpgFlC6Y/Manifest.toml`
  [7876af07] Example v0.5.1
  [2a0f44e3] Base64  [`@stdlib/Base64`]
  [8ba89e20] Distributed  [`@stdlib/Distributed`]
  [b77e0a4c] InteractiveUtils  [`@stdlib/InteractiveUtils`]
  [8f399da3] Libdl  [`@stdlib/Libdl`]
  [37e2e46d] LinearAlgebra  [`@stdlib/LinearAlgebra`]
  [56ddb016] Logging  [`@stdlib/Logging`]
  [d6f4376e] Markdown  [`@stdlib/Markdown`]
  [9a3f8284] Random  [`@stdlib/Random`]
  [9e88b42a] Serialization  [`@stdlib/Serialization`]
  [6462fe0b] Sockets  [`@stdlib/Sockets`]
  [8dfed614] Test  [`@stdlib/Test`]
   Testing Example tests passed

References