diff --git a/dev/LEQ/index.html b/dev/LEQ/index.html index 35404ce..b53e63b 100644 --- a/dev/LEQ/index.html +++ b/dev/LEQ/index.html @@ -14,4 +14,4 @@ var myIframe = document.getElementById("notebook"); iFrameResize({log:true}, myIframe); }); - + diff --git a/dev/asp/index.html b/dev/asp/index.html index 9bfeac6..b4917d8 100644 --- a/dev/asp/index.html +++ b/dev/asp/index.html @@ -14,4 +14,4 @@ var myIframe = document.getElementById("notebook"); iFrameResize({log:true}, myIframe); }); - + diff --git a/dev/getting_started_with_julia/index.html b/dev/getting_started_with_julia/index.html index 662f5e9..8bb8191 100644 --- a/dev/getting_started_with_julia/index.html +++ b/dev/getting_started_with_julia/index.html @@ -6,7 +6,7 @@ MPI.Init() comm = MPI.COMM_WORLD rank = MPI.Comm_rank(comm) nranks = MPI.Comm_size(comm) -println("Hello world, I am rank $rank of $nranks")

As you can see from this example, one can access MPI from Julia in a clean way, without type annotations and other complexities of C/C++ code.

Now, run the file from the REPL

julia> include("hello_mpi.jl")

It probably didn't work, right? Read the error message and note that the MPI package needs to be installed to run this code.

To install a package, we need to enter package mode. Remember that we entered into help mode by typing ?. Package mode is activated by typing ] : 

julia> ]

At this point, the prompt should have changed to (@v1.8) pkg> indicating that we are in package mode. The text between the parentheses indicates which is the active project, i.e., where packages are going to be installed. In this case, we are working with the global project associated with our Julia installation (which is Julia 1.8 in this example, but it can be another version in your case).

To install the MPI package, type

(@v1.8) pkg> add MPI

Congrats, you have installed MPI!

Note

Many Julia package names end with .jl. This is just a way of signaling that a package is written in Julia. When using such packages, the .jl needs to be omitted. In this case, we have isntalled the MPI.jl package even though we have only typed MPI in the REPL.

Note

The package you have installed it is the Julia interface to MPI, called MPI.jl. Note that it is not a MPI library by itself. It is just a thin wrapper between MPI and Julia. To use this interface, you need an actual MPI library installed in your system such as OpenMPI or MPICH. Julia downloads and installs a MPI library for you, but it is also possible to use a MPI library already available in your system. This is useful, e.g., when running on HPC clusters. See the documentation of MPI.jl for further details.

To check that the package was installed properly, exit package mode by pressing the backspace key several times, and run it again

julia> include("hello_mpi.jl")

Now, it should work, but you probably get output from a single MPI rank only.

Running MPI code

To run MPI applications in parallel, you need a launcher like mpiexec. MPI codes written in Julia are not an exception to this rule. From the system terminal, you can run

$ mpiexec -np 4 julia hello_mpi.jl

But it will probably not work since the version of mpiexec needs to match with the MPI version we are using from Julia. You can find the path to the mpiexec binary you need to use with these commands

julia> using MPI
+println("Hello world, I am rank $rank of $nranks")

As you can see from this example, one can access MPI from Julia in a clean way, without type annotations and other complexities of C/C++ code.

Now, run the file from the REPL

julia> include("hello_mpi.jl")

It probably didn't work, right? Read the error message and note that the MPI package needs to be installed to run this code.

To install a package, we need to enter package mode. Remember that we entered into help mode by typing ?. Package mode is activated by typing ] : 

julia> ]

At this point, the prompt should have changed to (@v1.8) pkg> indicating that we are in package mode. The text between the parentheses indicates which is the active project, i.e., where packages are going to be installed. In this case, we are working with the global project associated with our Julia installation (which is Julia 1.8 in this example, but it can be another version in your case).

To install the MPI package, type

(@v1.8) pkg> add MPI

Congrats, you have installed MPI!

Note

Many Julia package names end with .jl. This is just a way of signaling that a package is written in Julia. When using such packages, the .jl needs to be omitted. In this case, we have isntalled the MPI.jl package even though we have only typed MPI in the REPL.

Note

The package you have installed it is the Julia interface to MPI, called MPI.jl. Note that it is not a MPI library by itself. It is just a thin wrapper between MPI and Julia. To use this interface, you need an actual MPI library installed in your system such as OpenMPI or MPICH. Julia downloads and installs a MPI library for you, but it is also possible to use a MPI library already available in your system. This is useful, e.g., when running on HPC clusters. See the documentation of MPI.jl for further details.

To check that the package was installed properly, exit package mode by pressing the backspace key several times, and run it again

julia> include("hello_mpi.jl")

Now, it should work, but you probably get output from a single MPI rank only.

Running MPI code

To run MPI applications in parallel, you need a launcher like mpiexec. MPI codes written in Julia are not an exception to this rule. From the system terminal, you can run

$ mpiexec -np 4 julia hello_mpi.jl

But it will probably not work since the version of mpiexec needs to match with the MPI version we are using from Julia. You can find the path to the mpiexec binary you need to use with these commands

julia> using MPI
 julia> MPI.mpiexec_path

and then try again

$ /path/to/my/mpiexec -np 4 julia hello_mpi.jl

with your particular path.

However, this is not very convenient. Don't worry if you could not make it work! A more elegant way to run MPI code is from the Julia REPL directly, by using these commands:

julia> using MPI
 julia> mpiexec(cmd->run(`$cmd -np 4 julia hello_mpi.jl`))

Now, you should see output from 4 ranks.

Package manager

Installing packages locally

We have installed the MPI package globally and it will be available in all Julia sessions. However, in some situations, we want to work with different versions of the same package or to install packages in an isolated way to avoid potential conflicts with other packages. This can be done by using local projects.

A project is simply a folder in the hard disk. To use a particular folder as your project, you need to activate it. This is done by entering package mode and using the activate command followed by the path to the folder you want to activate.

(@v1.8) pkg> activate .

The previous command will activate the current working directory. Note that the dot . is indeed the path to the current folder.

The prompt has changed to (lessons) pkg> indicating that we are in the project within the lessons folder. The particular folder name can be different in your case.

Tip

You can activate a project directly when opening Julia from the terminal using the --project flag. The command $ julia --project=. will open Julia and activate a project in the current directory. You can also achieve the same effect by setting the environment variable JULIA_PROJECT with the path of the folder you want to activate.

Note

The active project folder and the current working directory are two independent concepts! For instance, (@v1.8) pkg> activate folderB and then julia> cd("folderA"), will activate the project in folderB and change the current working directory to folderA.

At this point all package-related operations will be local to the new project. For instance, install the DataFrames package.

(lessons) pkg> add DataFrames

Use the package to check that it is installed

julia> using DataFrames
 julia> DataFrame(a=[1,2],b=[3,4])

Now, we can return to the global project to check that DataFrames has not been installed there. To return to the global environment, use activate without a folder name.

(lessons) pkg> activate

The prompt is again (@v1.8) pkg>

Now, try to use DataFrames.

julia> using DataFrames
@@ -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 calling 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 at the following links:

+julia> Pkg.status()

is equivalent to calling 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 at the following links:

diff --git a/dev/index.html b/dev/index.html index 383c5fc..9ec7c6e 100644 --- a/dev/index.html +++ b/dev/index.html @@ -2,4 +2,4 @@ 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

Material will be added incrementally to the website as the course advances.

Warning

This page will eventually contain only a part of the course material. The rest will be available on Canvas. In particular, the material in this public webpage does not fully cover all topics in the final exam.

How to use this page

You have two main ways of studying the notebooks:

  • Download the notebooks and run them locally on your computer (recommended). At each notebook page you will find a green box with links to download the notebook.
  • You also have the static version of the notebooks displayed in this webpage for quick reference.

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.

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 on 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()

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 on 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 index f693cc4..d130247 100644 --- a/dev/jacobi_2D/index.html +++ b/dev/jacobi_2D/index.html @@ -14,4 +14,4 @@ var myIframe = document.getElementById("notebook"); iFrameResize({log:true}, myIframe); }); - + diff --git a/dev/jacobi_method/index.html b/dev/jacobi_method/index.html index cf54caa..0802d67 100644 --- a/dev/jacobi_method/index.html +++ b/dev/jacobi_method/index.html @@ -14,4 +14,4 @@ var myIframe = document.getElementById("notebook"); iFrameResize({log:true}, myIframe); }); - + diff --git a/dev/julia_async/index.html b/dev/julia_async/index.html index 2e7966e..314cef9 100644 --- a/dev/julia_async/index.html +++ b/dev/julia_async/index.html @@ -14,4 +14,4 @@ var myIframe = document.getElementById("notebook"); iFrameResize({log:true}, myIframe); }); - + diff --git a/dev/julia_basics/index.html b/dev/julia_basics/index.html index 16f85c8..777ca51 100644 --- a/dev/julia_basics/index.html +++ b/dev/julia_basics/index.html @@ -14,4 +14,4 @@ var myIframe = document.getElementById("notebook"); iFrameResize({log:true}, myIframe); }); - + diff --git a/dev/julia_distributed/index.html b/dev/julia_distributed/index.html index 0026bda..14057c6 100644 --- a/dev/julia_distributed/index.html +++ b/dev/julia_distributed/index.html @@ -14,4 +14,4 @@ var myIframe = document.getElementById("notebook"); iFrameResize({log:true}, myIframe); }); - + diff --git a/dev/julia_intro/index.html b/dev/julia_intro/index.html index b49de05..31f6073 100644 --- a/dev/julia_intro/index.html +++ b/dev/julia_intro/index.html @@ -14,4 +14,4 @@ var myIframe = document.getElementById("notebook"); iFrameResize({log:true}, myIframe); }); - + diff --git a/dev/julia_jacobi/index.html b/dev/julia_jacobi/index.html index 1096324..22e1816 100644 --- a/dev/julia_jacobi/index.html +++ b/dev/julia_jacobi/index.html @@ -14,4 +14,4 @@ var myIframe = document.getElementById("notebook"); iFrameResize({log:true}, myIframe); }); - + diff --git a/dev/julia_tutorial/index.html b/dev/julia_tutorial/index.html index a27dc81..4e986e3 100644 --- a/dev/julia_tutorial/index.html +++ b/dev/julia_tutorial/index.html @@ -14,4 +14,4 @@ var myIframe = document.getElementById("notebook"); iFrameResize({log:true}, myIframe); }); - + diff --git a/dev/matrix_matrix/index.html b/dev/matrix_matrix/index.html index 7521635..20c65e2 100644 --- a/dev/matrix_matrix/index.html +++ b/dev/matrix_matrix/index.html @@ -14,4 +14,4 @@ var myIframe = document.getElementById("notebook"); iFrameResize({log:true}, myIframe); }); - + diff --git a/dev/mpi_tutorial/index.html b/dev/mpi_tutorial/index.html index c759d16..2ba2ade 100644 --- a/dev/mpi_tutorial/index.html +++ b/dev/mpi_tutorial/index.html @@ -14,4 +14,4 @@ var myIframe = document.getElementById("notebook"); iFrameResize({log:true}, myIframe); }); - + diff --git a/dev/notebook-hello/index.html b/dev/notebook-hello/index.html index 8324af6..021260c 100644 --- a/dev/notebook-hello/index.html +++ b/dev/notebook-hello/index.html @@ -14,4 +14,4 @@ var myIframe = document.getElementById("notebook"); iFrameResize({log:true}, myIframe); }); - + diff --git a/dev/search/index.html b/dev/search/index.html index 1e2e1c5..d174b64 100644 --- a/dev/search/index.html +++ b/dev/search/index.html @@ -1,2 +1,2 @@ -Search · XM_40017

Loading search...

    +Search · XM_40017

    Loading search...

      diff --git a/dev/solutions/index.html b/dev/solutions/index.html index 3d4f299..82c8eb6 100644 --- a/dev/solutions/index.html +++ b/dev/solutions/index.html @@ -14,4 +14,4 @@ var myIframe = document.getElementById("notebook"); iFrameResize({log:true}, myIframe); }); - + diff --git a/dev/tsp/index.html b/dev/tsp/index.html index bfc739a..87de08b 100644 --- a/dev/tsp/index.html +++ b/dev/tsp/index.html @@ -14,4 +14,4 @@ var myIframe = document.getElementById("notebook"); iFrameResize({log:true}, myIframe); }); - +