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Getting started

Introduction

The programming of this course will be done using the Julia programming language. Thus, we start by explaining how to get up and running with Julia. After learning this page, you will be able to:

  • Use the Julia REPL;
  • Run serial and parallel code;
  • Install and manage Julia packages.

Why Julia?

Courses related with high-performance computing (HPC) often use languages such as C, C++, or Fortran. We use Julia instead to make the course accessible to a wider set of students, including the ones that have no experience with C/C++ or Fortran, but are willing to learn parallel programming. Julia is a relatively new programming language specifically designed for scientific computing. It combines a high-level syntax close to interpreted languages like Python with the performance of compiled languages like C, C++, or Fortran. Thus, Julia will allow us to write efficient parallel algorithms with a syntax that is convenient in a teaching setting. In addition, Julia provides easy access to different programming models to write distributed algorithms, which will be useful to learn and experiment with them.

Tip

You can run the code in this link to learn how Julia compares to other languages (C and Python) in terms of performance.

Installing Julia

This is a tutorial-like page. Follow these steps before you continue reading the document.

The Julia REPL

Starting Julia

There are several ways of opening Julia depending on your operating system and your IDE, but it is usually as simple as launching the Julia app. With VSCode, open a folder (File > Open Folder). Then, press Ctrl+Shift+P to open the command bar, and execute Julia: Start REPL. If this does not work, make sure you have the Julia extension for VSCode installed. Independently of the method you use, opening Julia results in a window with some text ending with:

julia>

You have just opened the Julia read-evaluate-print loop, or simply the Julia REPL. Congrats! You will spend most of time using the REPL, when working in Julia. The REPL is a console waiting for user input. Just as in other consoles, the string of text right before the input area (julia> in the case) is called the command prompt or simply the prompt.

Basic usage

The usage of the REPL is as follows:

  • You write some input
  • press enter
  • you get the output

For instance, try this

julia> 1 + 1

A "Hello world" example looks like this in Julia

julia> println("Hello, world!")

Try to run it in the REPL.

Help mode

Curious about what function println does? Enter into help mode to look into the documentation. This is done by typing a question mark (?) into the inut field:

julia> ?

After typing ?, the command prompt changes to help?>. It means we are in help mode. Now, we can type a function name to see its documentation.

help?> println

Package and shell modes

The REPL comes with two more modes, namely package and shell modes. To enter package mode type

julia> ]

Package mode is used to install and manage packages. We are going to discuss the package mode in greater detail later. To return back to normal mode press the backspace key several times.

To enter shell mode type semicolon (;)

julia> ;

The prompt should have changed to shell> indicating that we are in shell mode. Now you can type commands that you would normally do on your system command line. For instance,

shell> ls

will display the contents of the current folder in Mac or Linux. Using shell mode in Windows is not straightforward, and thus not recommended for beginners.

Running Julia code

Running more complex code

Real-world Julia programs are not typed in the REPL in practice. They are written in one or more files and included in the REPL. To try this, create a new file called hello.jl, write the code of the "Hello world" example above, and save it. If you are using VSCode, you can create the file using File > New File > Julia File. Once the file is saved with the name hello.jl, execute it as follows

julia> include("hello.jl")

\warn{ Make sure that the file "hello.jl" is located in the current working directory of your Julia session. You can query the current directory with function pwd(). You can change to another directory with function cd() if needed. Also, make sure that the file extension is .jl.}

The recommended way of running Julia code is using the REPL as we did. But it is also possible to run code directly from the system command line. To this end, open a terminal and call Julia followed buy the path to the file containing the code you want to execute.

$ julia hello.jl

Previous line assumes that you have Julia properly installed in the system and that is usable from the terminal. In UNIX systems (Linux and Mac), the Julia binary needs to be in one of the directories listed in the PATH environment variable. To check that Julia is properly installed, you can use

$ julia --version

If this runs without error and you see a version number, you are good to go!

Note

In this tutorial, when a code snipped starts with $, it should be run in the terminal. Otherwise, the code is to be run in the Julia REPL.

Tip

Avoid calling Julia code from the terminal, use the Julia REPL instead! Each time you call Julia from the terminal, you start a fresh Julia session and Julia will need to compile your code from scratch. This can be time consuming for large projects. In contrast, if you execute code in the REPL, Julia will compile code incrementally, which is much faster. Running code in a cluster (like in DAS-5 for the Julia assignment) is among the few situations you need to run Julia code from the terminal.

Running parallel code

Since we are in a parallel computing course, let's run a parallel "hello world" example in Julia. Open a Julia REPL and write

julia> using Distributed
+Getting started · XM_40017
Edit on GitHub
Getting started
Introduction
The programming of this course will be done using the Julia programming language. Thus, we start by explaining how to get up and running with Julia. After learning this page, you will be able to:
  • Use the Julia REPL;
  • Run serial and parallel code;
  • Install and manage Julia packages.
Why Julia?
Courses related with high-performance computing (HPC) often use languages such as C, C++, or Fortran. We use Julia instead to make the course accessible to a wider set of students, including the ones that have no experience with  C/C++ or Fortran, but are willing to learn parallel programming. Julia is a relatively new programming language specifically designed for scientific computing. It combines a high-level syntax close to interpreted languages like Python with the performance of compiled languages like C, C++, or Fortran. Thus, Julia will allow us to write efficient parallel algorithms with a syntax that is convenient in a teaching setting. In addition, Julia provides easy access to different programming models to write distributed algorithms, which will be useful to learn and experiment with them.
Tip
You can run the code in this link to learn how Julia compares to other languages (C and Python) in terms of performance.
Installing Julia
This is a tutorial-like page. Follow these steps before you continue reading the document.
The Julia REPL
Starting Julia
There are several ways of opening Julia depending on your operating system and your IDE, but it is usually as simple as launching the Julia app. With VSCode, open a folder (File > Open Folder). Then,  press Ctrl+Shift+P to open the command bar, and execute Julia: Start REPL. If this does not work, make sure you have the Julia extension for VSCode installed. Independently of the method you use, opening Julia results in a window with some text ending with:
julia>
You have just opened the Julia read-evaluate-print loop, or simply the Julia REPL. Congrats! You will spend most of time using the REPL, when working in Julia. The REPL is a console waiting for user input. Just as in other consoles, the string of text right before the input area (julia> in the case) is called the command prompt or simply the prompt.
Basic usage
The usage of the REPL is as follows:
  • You write some input
  • press enter
  • you get the output
For instance, try this
julia> 1 + 1
A "Hello world" example looks like this in Julia
julia> println("Hello, world!")
Try to run it in the REPL.
Help mode
Curious about what function println does? Enter into help mode to look into the documentation. This is done by typing a question mark (?) into the inut field:
julia> ?
After typing ?, the command prompt changes to help?>. It means we are in help mode. Now, we can type a function name to see its documentation.
help?> println
Package and shell modes
The REPL comes with two more modes, namely package and shell modes. To enter package mode type
julia> ]
Package mode is used to install and manage packages. We are going to discuss the package mode in greater detail later. To return back to normal mode press the backspace key several times.
To enter shell mode type semicolon (;)
julia> ;
The prompt should have changed to shell> indicating that we are in shell mode. Now you can type commands that you would normally do on your system command line. For instance,
shell> ls
will display the contents of the current folder in Mac or Linux. Using shell mode in Windows is not straightforward, and thus not recommended for beginners.
Running Julia code
Running more complex code
Real-world Julia programs are not typed in the REPL in practice. They are written in one or more files and included in the REPL. To try this, create a new file called hello.jl, write the code of the "Hello world" example above, and save it. If you are using VSCode, you can create the file using File > New File > Julia File. Once the file is saved with the name hello.jl, execute it as follows
julia> include("hello.jl")
\warn{ Make sure that the file "hello.jl" is located in the current working directory of your Julia session. You can query the current directory with function pwd(). You can change to another directory with function cd() if needed.  Also, make sure that the file extension is .jl.}
The recommended way of running Julia code is using the REPL as we did. But it is also possible to run code directly from the system command line. To this end, open a terminal and call Julia followed buy the path to the file containing the code you want to execute.
$ julia hello.jl
Previous line assumes that you have Julia properly installed in the system and that is usable from the terminal. In UNIX systems (Linux and Mac), the Julia binary needs to be in one of the directories listed in the PATH environment variable. To check that Julia is properly installed, you can use
$ julia --version
If this runs without error and you see a version number, you are good to go!
Note
In this tutorial, when a code snipped starts with $, it should be run in the terminal. Otherwise, the code is to be run in the Julia REPL.
Tip
Avoid calling Julia code from the terminal, use the Julia REPL instead! Each time you call Julia from the terminal, you start a fresh Julia session and Julia will need to compile your code from scratch. This can be time consuming for large projects. In contrast, if you execute code in the REPL, Julia will compile code incrementally, which is much faster. Running code in a cluster (like in DAS-5 for the Julia assignment) is among the few situations you need to run Julia code from the terminal.
Running parallel code
Since we are in a parallel computing course, let's run a parallel "hello world" example in Julia. Open a Julia REPL and write
julia> using Distributed
 julia> @everywhere println("Hello, world! I am proc $(myid()) from $(nprocs())")
Here, we are using the Distributed package, which is part of the Julia standard library that provides distributed memory parallel support. The code prints the process id and the number of processes in the current Julia session.
You will provably only see output from 1 proces. We need to add more processes to run the example in parallel. This is done with the addprocs function.
julia> addprocs(3)
We have added 3 new processes, plus the old one, we have 4 processes. Run the code again.
julia> @everywhere println("Hello, world! I am proc $(myid()) from $(nprocs())")
Now, you should see output from 4 processes.
It is possible to specify the number of processes when starting Julia from the terminal with the -p argument (useful, e.g., when running in a cluster).  If you launch Julia from the terminal as
$ julia -p 3
and then run
julia> @everywhere println("Hello, world! I am proc $(myid()) from $(nprocs())")
You should get output from 4 processes as before.
Installing packages
One of the most useful features of Julia is its package manager. It allows one to install Julia packages in a straightforward and platform independent way. To illustrate this, let us consider the following parallel "Hello world" example. This example uses the message passing interface (MPI). We will learn more about MPI later in the course.
Copy the following block of code into a new file named "hello_mpi.jl"
# file hello_mpi.jl
 using MPI
 MPI.Init()
@@ -14,4 +14,4 @@ julia> DataFrame(a=[1,2],b=[3,4])
You should get an error or a
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"

Copy the contents of previous code block into a file called Project.toml and place it in an empty folder named newproject. It is important that the file is named Project.toml. You can create a new folder from the REPL with

julia> mkdir("newproject")

To install all the packages registered in this file you need to activate the folder containing your Project.toml file

(@v1.8) pkg> activate newproject

and then instantiating it

(newproject) pkg> instantiate

The instantiate command will download and install all listed packages and their dependencies in just one click.

Getting help in package mode

You can get help about a particular package operator by writing help in front of it

(@v1.8) pkg> help activate

You can get an overview of all package commands by typing help alone

(@v1.8) pkg> help

Package operations in Julia code

In some situations it is required to use package commands in Julia code, e.g., to automatize installation and deployment of Julia applications. This can be done using the Pkg package. For instance

julia> using Pkg
-julia> Pkg.status()

is equivalent to call status in package mode.

(@v1.8) pkg> status

Conclusion

We have learned the basics of how to work with Julia. If you want to further dig into the topics we have covered here, you can take a look and the following links

+julia> Pkg.status()

is equivalent to call status in package mode.

(@v1.8) pkg> status

Conclusion

We have learned the basics of how to work with Julia. If you want to further dig into the topics we have covered here, you can take a look and the following links

diff --git a/dev/index.html b/dev/index.html index 704f6ad..064d43e 100644 --- a/dev/index.html +++ b/dev/index.html @@ -1,5 +1,5 @@ -Home · XM_40017
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Programming Large-Scale Parallel Systems (XM_40017)

Welcome to the interactive lecture notes of the Programming Large-Scale Parallel Systems course at VU Amsterdam!

What

This page contains part of the course material of the Programming Large-Scale Parallel Systems course at VU Amsterdam. In this page, we provide several lecture notes in jupyter notebook format, which will help you to learn how to design, analyze, and program parallel algorithms on multi-node computing systems. Further information about the course is found in the study guide (click here) and our Canvas page (for registered students).

Note

This page contains only part of the course material. The rest is available on Canvas. In particular, the lecture notes in this public webpage do not fully cover all topics in the final exam.

How to use this page

You have two main ways of running the notebooks:

  • Download the notebooks and run them locally on your computer (recommended)
  • Run the notebooks on the cloud via mybinder.org (high startup time).

You also have the static version of the notebooks displayed in this webpage for quick reference. At each notebook page you will find a green box with links to download the notebook or to open in on mybinder.

How to run the notebooks locally

To run a notebook locally follow these steps:

  • Install Julia (if not done already). More information in Getting started.
  • Download the notebook.
  • Launch Julia. More information in Getting started.
  • Execute these commands in the Julia command line:
julia> using Pkg
+Home · XM_40017
Edit on GitHub
Programming Large-Scale Parallel Systems (XM_40017)
Welcome to the interactive lecture notes of the Programming Large-Scale Parallel Systems course at VU Amsterdam!
What
This page contains part of the course material of the Programming Large-Scale Parallel Systems course at VU Amsterdam. We provide several lecture notes in jupyter notebook format, which will help you to learn how to design, analyze, and program parallel algorithms on multi-node computing systems. Further information about the course is found in the study guide (click here) and our Canvas page (for registered students). 
Note
This page contains only part of the course material. The rest is available on Canvas. In particular, the lecture notes in this public webpage do not fully cover all topics in the final exam.
How to use this page
You have two main ways of running the notebooks:
  • Download the notebooks and run them locally on your computer (recommended)
  • Run the notebooks on the cloud via mybinder.org (high startup time).
You also have the static version of the notebooks displayed in this webpage for quick reference. At each notebook page you will find a green box with links to download the notebook or to open in on mybinder.
How to run the notebooks locally
To run a notebook locally follow these steps:
  • Install Julia (if not done already). More information in Getting started.
  • Download the notebook.
  • Launch Julia. More information in Getting started.
  • Execute these commands in the Julia command line:
julia> using Pkg
 julia> Pkg.add("IJulia")
 julia> using IJulia
-julia> notebook()
  • These commands will open a jupyter in your web browser. Navigate in jupyter to the notebook file you have downloaded and open it.
Authorship
This material was created by Francesc Verdugo with the help of Gelieza Kötterheinrich. Part of the notebooks are based on the course slides by Henri Bal.
License
All material in this page that is original to this course may be used under a CC BY 4.0 license.
Acknowledgment
This page was created with the support of the Faculty of Science of Vrije Universiteit Amsterdam in the framework of the project "Interactive lecture notes and exercises for the Programming Large-Scale Parallel Systems course" funded by the "Innovation budget BETA 2023 Studievoorschotmiddelen (SVM) towards Activated Blended Learning".

+julia> notebook()
  • These commands will open a jupyter in your web browser. Navigate in jupyter to the notebook file you have downloaded and open it.

Authors

This material is created by Francesc Verdugo with the help of Gelieza Kötterheinrich. Part of the notebooks are based on the course slides by Henri Bal.

License

All material in this page that is original to this course may be used under a CC BY 4.0 license.

Acknowledgment

This page was created with the support of the Faculty of Science of Vrije Universiteit Amsterdam in the framework of the project "Interactive lecture notes and exercises for the Programming Large-Scale Parallel Systems course" funded by the "Innovation budget BETA 2023 Studievoorschotmiddelen (SVM) towards Activated Blended Learning".

diff --git a/dev/jacobi_2D/index.html b/dev/jacobi_2D/index.html deleted file mode 100644 index a8ec1a2..0000000 --- a/dev/jacobi_2D/index.html +++ /dev/null @@ -1,21 +0,0 @@ - -- · XM_40017
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-
Tip
-
-
    -
  • - Download this notebook and run it locally on your machine [recommended]. Click here. -
    • -
  • - You can also run this notebook in the cloud using Binder. Click here - . -
    • -
-
-
-
diff --git a/dev/jacobi_method/index.html b/dev/jacobi_method/index.html deleted file mode 100644 index f461c64..0000000 --- a/dev/jacobi_method/index.html +++ /dev/null @@ -1,21 +0,0 @@ - -Jacobi · XM_40017
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-
Tip
-
-
    -
  • - Download this notebook and run it locally on your machine [recommended]. Click here. -
    • -
  • - You can also run this notebook in the cloud using Binder. Click here - . -
    • -
-
-
-
diff --git a/dev/julia_async/index.html b/dev/julia_async/index.html deleted file mode 100644 index 16abe74..0000000 --- a/dev/julia_async/index.html +++ /dev/null @@ -1,21 +0,0 @@ - -Tasks and channels · XM_40017
Edit on GitHub
-
Tip
-
-
    -
  • - Download this notebook and run it locally on your machine [recommended]. Click here. -
    • -
  • - You can also run this notebook in the cloud using Binder. Click here - . -
    • -
-
-
-
diff --git a/dev/julia_basics/index.html b/dev/julia_basics/index.html deleted file mode 100644 index c86ebf1..0000000 --- a/dev/julia_basics/index.html +++ /dev/null @@ -1,21 +0,0 @@ - -Julia Basics · XM_40017
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diff --git a/dev/julia_distributed/index.html b/dev/julia_distributed/index.html deleted file mode 100644 index 2fc31ed..0000000 --- a/dev/julia_distributed/index.html +++ /dev/null @@ -1,21 +0,0 @@ - -Remote calls and remote channels · XM_40017
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diff --git a/dev/julia_distributed_test/index.html b/dev/julia_distributed_test/index.html deleted file mode 100644 index 11aa00c..0000000 --- a/dev/julia_distributed_test/index.html +++ /dev/null @@ -1,21 +0,0 @@ - -- · XM_40017
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diff --git a/dev/julia_intro/index.html b/dev/julia_intro/index.html deleted file mode 100644 index dec80f3..0000000 --- a/dev/julia_intro/index.html +++ /dev/null @@ -1,21 +0,0 @@ - -- · XM_40017
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diff --git a/dev/julia_jacobi/index.html b/dev/julia_jacobi/index.html deleted file mode 100644 index 839214e..0000000 --- a/dev/julia_jacobi/index.html +++ /dev/null @@ -1,21 +0,0 @@ - -- · XM_40017
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diff --git a/dev/julia_tutorial/index.html b/dev/julia_tutorial/index.html deleted file mode 100644 index 02f21f8..0000000 --- a/dev/julia_tutorial/index.html +++ /dev/null @@ -1,21 +0,0 @@ - -- · XM_40017
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diff --git a/dev/matrix_matrix/index.html b/dev/matrix_matrix/index.html deleted file mode 100644 index b7f034a..0000000 --- a/dev/matrix_matrix/index.html +++ /dev/null @@ -1,21 +0,0 @@ - -Matrix Multiplication · XM_40017
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diff --git a/dev/notebook-hello/index.html b/dev/notebook-hello/index.html deleted file mode 100644 index 6f8f40e..0000000 --- a/dev/notebook-hello/index.html +++ /dev/null @@ -1,21 +0,0 @@ - -- · XM_40017
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diff --git a/dev/notebook-output/jacobi_2D.html b/dev/notebook-html/jacobi_2D.html similarity index 100% rename from dev/notebook-output/jacobi_2D.html rename to dev/notebook-html/jacobi_2D.html diff --git a/dev/notebook-output/jacobi_method.html b/dev/notebook-html/jacobi_method.html similarity index 86% rename from dev/notebook-output/jacobi_method.html rename to dev/notebook-html/jacobi_method.html index f4d098a..2d446b2 100644 --- a/dev/notebook-output/jacobi_method.html +++ b/dev/notebook-html/jacobi_method.html @@ -7559,7 +7559,7 @@ a.anchor-link {