Load and run Julia¶

Info

At the Swedish HPC centers we call the applications available via the module system modules:

Objectives

Learn to load Julia
Get started with the Julia command line
Learn to run Julia scripts

Instructor note

Lecture and demo 15 min
Exercise 15 min
Total time 30 min

Julia can be started after a Julia module is loaded. The module activates paths to a specific version of the julia interpreter and its libraries and packages.

Short cheat sheet

See which modules exists: module spider or ml spider.
Find module versions for a particular software: module spider <software>
Modules depending only on what is currently loaded: module avail or ml av
See which modules are currently loaded: module list or ml
Load a module: module load <module>/<version> or ml <module>/<version>
Unload a module: module unload <module>/<version> or ml -<module>/<version>
Unload all modules except the ‘sticky’ modules: module purge or ml purge

Warning

Note that the module systems at UPPMAX and HPC2N are slightly different. All modules at UPPMAX, for instance, not directly related to bio-informatics are shown by ml avail.

Modules at many other centres are only available when one has loaded all prerequisites, for instance the compilers (GNU, Intel, etc.).

Check for Julia versions¶

Principle¶

For some clusters

module avail julia

Example output

From Tetralith:

$ module avail julia
---------------------------------- /software/sse2/tetralith_el9/modules -----------------------------------
   julia/recommendation          (D)    julia/1.6.1-nsc1-bdist    julia/1.9.4-bdist
   julia/1.1.0-nsc1-gcc-2018a-eb        julia/1.7.2-nsc1-bdist    julia/1.10.2-bdist
   julia/1.4.1                          julia/1.8.5-nsc1-bdist


 Where:
  D:  Default Module

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

Or, at clusters that hides the modules until relevant dependencies are loaded (HPC2N & PDC)

module spider julia

Example output

From Dardel:

$ module spider julia
-------------------------------------------------------------------------------------------------------
  julia:
-------------------------------------------------------------------------------------------------------
    Description:
      Julia is a high-level general-purpose dynamic 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 to be fast, also usable for client and server web use,
      low-level systems programming or as a specification language (wikipedia.org). Julia provides
      ease and expressiveness for high-level numerical computing, in the same way as languages such as
      R, MATLAB, and Python, but also supports general programming. To achieve this, Julia builds upon
      the lineage of mathematical programming languages, but also borrows much from popular dynamic
      languages, including Lisp, Perl, Python, Lua, and Ruby (julialang.org).

     Versions:
        julia/1.8.2-cpeGNU-22.06
        julia/1.9.3-cpeGNU-22.06
        julia/1.9.3-cpeGNU-23.03
        julia/1.10.2-cpeGNU-23.03
        julia/1.10.2-cpeGNU-23.12
     Other possible modules matches:
        Julia  libuv-julia

-------------------------------------------------------------------------------------------------------
  To find other possible module matches execute:

      $ module -r spider '.*julia.*'

-------------------------------------------------------------------------------------------------------
  For detailed information about a specific "julia" package (including how to load the modules) use the module's full name.
  Note that names that have a trailing (E) are extensions provided by other modules.
  For example:

     $ module spider julia/1.10.2-cpeGNU-23.12
-------------------------------------------------------------------------------------------------------

Load a Julia module¶

For reproducibility, we recommend ALWAYS loading a specific module for the Julia version instead of using the default one.

Principle¶

Use the output of existing module above!
Load the module!

At some clusters:

module load julia/1.8.5

or at cluster that includes “architecture” or “build name” in module name:

ml julia/1.10.2-bdist

Some clusters will require other modules to be loaded (Kebnekaise and Dardel)

First check how to load (see Check for Julia versions above)

$ module spider julia/1.10.2-cpeGNU-23.12

...
You will need to load all module(s) on any one of the lines below before the "julia/1.10.2-cpeGNU-23.12" module is available to load.

PDC/23.12

Load PDC/23.12 first and then the julia module

ml PDC/23.12 julia/1.10.2-cpeGNU-23.12

Run¶

Run Julia as a session¶

After loading the appropriate modules for Julia, you will have access to the read-eval-print-loop (REPL) command line by typing julia:

julia

In julia REPL

Example

This is what loading the Julia REPL looks like on Pelle:

[username@pelle1 ~]$ ml
No modules loaded
[username@pelle1 ~]$ ml Julia/1.10.9
[username@pelle1 ~]$ ml

Currently Loaded Modules:
  1) Julia/1.10.9-LTS-linux-x86_64



[username@pelle1 ~]$ julia
           _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.10.9 (2025-03-10)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia>

Modes: Julian mode¶

Julia has different modes, the one we arrive at is the so-called Julian mode, where one can execute commands.
The description for accessing these modes will be given in the following paragraphs.
Once you are done with your work in any of the modes, you can return to the Julian mode by pressing the backspace key.

Shell mode¶

While being on the Julian mode you can enter the shell mode by typing ;:

   julia>;
   shell>pwd
   /current-folder-path

this will allow you to use Linux commands. Notice that the availability of these commands depend on the OS, for instance, on Windows it will depend on the terminal that you have installed and if it is visible to the Julia installation.

Package manage mode ...................

Another mode available in Julia is the package manager mode, it can be accessed by typing ] in the Julian mode:

.. code-block:: julia-repl

julia>] (v1.8) pkg>

this will make your interaction with the package manager Pkg easier, for instance, instead of typing the complete name of Pkg commands such as Pkg.status() in the Julian mode, you can just type status in the package mode.

Help mode .........

The last mode is the help mode, you can enter this mode from the Julian one by typing ?, then you may type some string from which you need more information:

.. code-block:: julia

julia>?

help?> ans search: ans transpose transcode contains expanduser instances MathConstants readlines LinearIndices leading_ones leading_zeros

ans

A variable referring to the last computed value, automatically set at the interactive prompt.

Exiting .......

Exit with

.. code-block:: julia-repl

julia>

or

.. code-block:: julia-repl

julia> exit()

.. admonition:: The Julian modes summary

- enter the *shell mode* by typing ``;``
- go back to *Julian* mode by ``<backspace>``
- access the *package manager* mode by typing ``]`` in the *Julian* mode
- use the *help mode* by typing ``?`` in the *Julian mode*

.. seealso::

More detailed information about the modes in Julia can be found <https://docs.julialang.org/en/v1/stdlib/REPL/>_.

Run a Julia script

¶

You can run a Julia script on the Linux shell as follows:

.. code-block:: console

$ julia example.jl

where the script is a text file could contain these lines:

.. code-block:: bash

println(“hello world”)

Exercises¶

.. challenge:: 1a. Find out which versions are on your cluster from documentation

Find/search for that documentation!

.. solution:: Solution :class: dropdown

  - `UPPMAX <http://docs.uppmax.uu.se/software/julia/>`_
  - `HPC2N <https://www.hpc2n.umu.se/resources/software/julia>`_
  - `LUNARC <The user demand on Julia has been low, so there is currently no site-specific documentation.>`_
  - `NSC <https://www.nsc.liu.se/software/installed/tetralith/julia/>`_
  - `PDC <https://support.pdc.kth.se/doc/applications/>`_

.. challenge:: 1b. Find out which versions are on your cluster from command line

Use the spider or avail module commands

.. solution:: Solution :class: dropdown

  .. tabs::

     .. tab:: UPPMAX

       Check all available Julia versions with:

        .. code-block:: console

            $ module avail julia


     .. tab:: HPC2N

        Check all available version Julia versions with:

        .. code-block:: console

           $ module spider julia

        Notice that the output if you are working on the Intel (*kebnekaise.hpc2n.umu.se*) or AMD
        (*kebnekaise-amd.hpc2n.umu.se*) login nodes is different. In the former, you will see more
        installed versions of Julia as this hardware is older.

        To see how to load a specific version of Julia, including the prerequisites, do

        .. code-block:: console

           $ module spider Julia/<version>

        Example for Julia 1.8.5

        .. code-block:: console

           $ module spider Julia/1.8.5-linux-x86_64

     .. tab:: LUNARC

        Check all available version Julia versions with:

        .. code-block:: console

           $ module spider Julia

        To see how to load a specific version of Julia, including the prerequisites, do

        .. code-block:: console

           $ module spider Julia/<version>

        Example for Julia 1.8.5

        .. code-block:: console

           $ module spider Julia/1.8.5-linux-x86_64

     .. tab:: Tetralith

        Check all available version Julia versions with:

        .. code-block:: console

           $ module avail Julia

        Example for Julia 1.8.5

        .. code-block:: console

           $ module spider julia/1.8.5-nsc1-bdist

     .. tab:: Dardel

        Check all available version Julia versions with:

        .. code-block:: console

           $ module spider Julia

        To see how to load a specific version of Julia, including the prerequisites, do

        .. code-block:: console

           $ module spider Julia/<version>

        Example for Julia 1.8.5

        .. code-block:: console

           $ module spider Julia/1.8.5-linux-x86_64

.. admonition:: Output at UPPMAX as of Oct 2024 :class: dropdown

   .. code-block::  console

      $ module avail julia
      ----------------------------- /sw/mf/rackham/compilers -----------------------------
         julia/1.0.5_LTS    julia/1.6.1        julia/1.7.2        julia/1.9.3 (D)
         julia/1.1.1        julia/1.6.3        julia/1.8.5 (L)
         julia/1.4.2        julia/1.6.7_LTS    julia/1.9.1

       Where:
        D:  Default Module

      Use "module spider" to find all possible modules and extensions.
      Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

.. admonition:: Output at HPC2N as of Oct 2024 :class: dropdown

    .. code-block:: console

       $ module spider julia  # Assuming you are working on the Intel login nodes
       ------------------------------------------------------------------------------------------------
         Julia:
       ------------------------------------------------------------------------------------------------
         Description:
           Julia is a high-level, high-performance dynamic programming language for numerical
           computing

         Versions:
            Julia/1.5.3-linux-x86_64
            Julia/1.7.1-linux-x86_64
            Julia/1.8.5-linux-x86_64
            Julia/1.9.3-linux-x86_64
       ------------------------------------------------------------------------------------------------
         For detailed information about a specific "Julia" package (including how to load the modules) use the module's full name.
         Note that names that have a trailing (E) are extensions provided by other modules.
         For example:

            $ module spider Julia/1.8.5-linux-x86_64
       ------------------------------------------------------------------------------------------------

.. admonition:: Output at LUNARC as of Oct 2024 :class: dropdown

    .. code-block:: console

       $ module spider julia
       -----------------------------------------------------------------------------------------------------
         Julia:
       -----------------------------------------------------------------------------------------------------
           Description:
             Julia is a high-level, high-performance dynamic programming language for numerical computing

            Versions:
               Julia/1.8.5-linux-x86_64
               Julia/1.9.0-linux-x86_64
               Julia/1.9.2-linux-x86_64
               Julia/1.9.3-linux-x86_64
               Julia/1.10.4-linux-x86_64

.. admonition:: Output at NSC as of Mar 2025 :class: dropdown

    .. code-block:: console

       $ module avail julia

       ---------------------------------- /software/sse2/tetralith_el9/modules -----------------------------------
          julia/recommendation          (D)    julia/1.6.1-nsc1-bdist    julia/1.9.4-bdist
          julia/1.1.0-nsc1-gcc-2018a-eb        julia/1.7.2-nsc1-bdist    julia/1.10.2-bdist
          julia/1.4.1                          julia/1.8.5-nsc1-bdist

.. admonition:: Output at PDC as of Mar 2025 :class: dropdown

    .. code-block:: console

       $ module spider julia
       -------------------------------------------------------------------------------------------------------
         julia:
       -------------------------------------------------------------------------------------------------------
           Description:
             Julia is a high-level general-purpose dynamic 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 to be fast, also usable for client and server web use,
             low-level systems programming or as a specification language (wikipedia.org). Julia provides
             ease and expressiveness for high-level numerical computing, in the same way as languages such as
             R, MATLAB, and Python, but also supports general programming. To achieve this, Julia builds upon
             the lineage of mathematical programming languages, but also borrows much from popular dynamic
             languages, including Lisp, Perl, Python, Lua, and Ruby (julialang.org).

            Versions:
               julia/1.8.2-cpeGNU-22.06
               julia/1.9.3-cpeGNU-22.06
               julia/1.9.3-cpeGNU-23.03
               julia/1.10.2-cpeGNU-23.03
               julia/1.10.2-cpeGNU-23.12
            Other possible modules matches:
               Julia  libuv-julia

       -------------------------------------------------------------------------------------------------------
         To find other possible module matches execute:

             $ module -r spider '.*julia.*'

       -------------------------------------------------------------------------------------------------------
         For detailed information about a specific "julia" package (including how to load the modules) use the module's full name.

.. challenge:: 1c. Which method to trust?

.. solution:: Solution :class: dropdown

  Looking for modules in a session on the cluster is closer to the truth

.. challenge:: 2. Try to start julia without having loaded julia module

If you have a julia module loaded already, you may unload it with the unload command.
- Tip: Type: unload julia and press <tab> until the full module name is shown, then press <enter>. (If the Julia module starts with an uppercase, use that instead!)

.. solution:: Solution :class: dropdown

  .. code-block:: console

     $ julia

.. challenge:: 3. Load and start julia from the command line

.. solution:: Solution :class: dropdown

  .. tabs::

     .. tab:: UPPMAX

        Go back and check which Julia modules were available. To load version 1.8.5, do:

        .. code-block:: console

          $ module load julia/1.8.5

        Note: Lowercase ``j``.

        For short, you can also use:

        .. code-block:: console

           $ ml julia/1.8.5

     .. tab:: HPC2N

        .. code-block:: console

           $ module load Julia/1.8.5-linux-x86_64

        Note: Uppercase ``J``.

        For short, you can also use:

        .. code-block:: console

           $ ml Julia/1.8.5-linux-x86_64

     .. tab:: LUNARC

        .. code-block:: console

           $ module load Julia/1.8.5-linux-x86_64

        Note: Uppercase ``J``.

        For short, you can also use:

        .. code-block:: console

           $ ml Julia/1.8.5-linux-x86_64

     .. tab:: NSC

        .. code-block:: console

           $ module load julia/1.10.2-bdist

        Note: lowercase ``j``.

        For short, you can also use:

        .. code-block:: console

           $ ml julia/1.10.2-bdist

     .. tab:: PDC

        .. code-block:: console

           $ module load PDC/23.12 julia/1.10.2-cpeGNU-23.12

        Note: lowercase ``j``.

        For short, you can also use:

        .. code-block:: console

           $ ml PDC/23.12 julia/1.10.2-cpeGNU-23.12

.. challenge:: 4. Getting familiar with Julia REPL

- It is important that you know how to navigate on the Julia command line. Here is where you work live with data and test aout things and you may install packages.
- This exercise will help you to become more familiar with the REPL. Do the following steps:

   * Start a Julia session. In the ``Julian`` mode, compute the sum the numbers
     5 and 6
   * Change to the ``shell`` mode and display the current directory
   * Now, go to the ``package`` mode and list the currently installed packages
   * Finally, display help information of the function ``println`` in ``help`` mode.

.. solution:: Solution :class: dropdown

   .. code-block:: julia

        $ julia
        julia> 5 + 6
        julia>;
        shell> pwd
        julia>]
        pkg> status
        julia>?
        help?> println

.. challenge:: 5. Load another module and run a script

- Load the latest version and run
- Run the following serial script (``serial-sum.jl``) which accepts two integer arguments as input:

        .. code-block:: julia

            x = parse( Int32, ARGS[1] )
            y = parse( Int32, ARGS[2] )
            summ = x + y
            println("The sum of the two numbers is ", summ)

.. solution:: Solution for HPC2N :class: dropdown

  .. code-block:: console

        $ ml purge  > /dev/null 2>&1       # recommended purge
        $ ml Julia/1.8.5-linux-x86_64      # Julia module

        $ julia serial-sum.jl Arg1 Arg2    # run the serial script

.. solution:: Solution for UPPMAX :class: dropdown

  This batch script is for UPPMAX. Adding the numbers 2 and 3. (FIX)

  .. code-block:: console

        $ ml julia/1.8.5                   # Julia module

        julia serial-sum.jl Arg1 Arg2      # run the serial script

.. solution:: Solution for LUNARC :class: dropdown

  This batch script is for UPPMAX. Adding the numbers 2 and 3. (FIX)

  .. code-block:: console

        $ ml Julia/1.8.5-linux-x86_64           # Julia module

        julia serial-sum.jl Arg1 Arg2      # run the serial script

.. solution:: Solution for NSC :class: dropdown

  This batch script is for UPPMAX. Adding the numbers 2 and 3. (FIX)

  .. code-block:: console

        $ ml julia/1.10.2-bdist           # Julia module

        julia serial-sum.jl Arg1 Arg2      # run the serial script

.. solution:: Solution for PDC :class: dropdown

  This batch script is for UPPMAX. Adding the numbers 2 and 3. (FIX)

  .. code-block:: console

        $ ml PDC/23.12 julia/1.10.2-cpeGNU-23.12           # Julia module

        julia serial-sum.jl Arg1 Arg2      # run the serial script

.. challenge:: 6. Check your understanding

Check your understanding and answer in the shared document
Can you start Julia without loading a Julia module?
- Yes?
- No?
Which character to use to toggle
- to the package mode?
- back to the Julia mode?
- to the help mode?
- to the shell mode?

.. keypoints::

Before you can run Julia scripts or work in a Julia shell, first load a Julia module with module load <julia module>
Start a Julia shell session with julia
It offers several modes that can make your workflow easier, i.e.
- Julian
- shell
- package manager
- help
Run scripts with julia <script.jl>