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@@ -1,64 +0,0 @@
|
||||
name: CI
|
||||
on:
|
||||
push:
|
||||
branches:
|
||||
- main
|
||||
tags: ['*']
|
||||
pull_request:
|
||||
concurrency:
|
||||
# Skip intermediate builds: always.
|
||||
# Cancel intermediate builds: only if it is a pull request build.
|
||||
group: ${{ github.workflow }}-${{ github.ref }}
|
||||
cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
|
||||
jobs:
|
||||
test:
|
||||
name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
|
||||
runs-on: ${{ matrix.os }}
|
||||
strategy:
|
||||
fail-fast: false
|
||||
matrix:
|
||||
version:
|
||||
- '1.9'
|
||||
os:
|
||||
- ubuntu-latest
|
||||
arch:
|
||||
- x64
|
||||
steps:
|
||||
- uses: actions/checkout@v3
|
||||
- uses: julia-actions/setup-julia@v1
|
||||
with:
|
||||
version: ${{ matrix.version }}
|
||||
arch: ${{ matrix.arch }}
|
||||
- uses: julia-actions/cache@v1
|
||||
- uses: julia-actions/julia-buildpkg@v1
|
||||
- uses: julia-actions/julia-runtest@v1
|
||||
docs:
|
||||
name: Documentation
|
||||
runs-on: ubuntu-latest
|
||||
permissions:
|
||||
contents: write
|
||||
statuses: write
|
||||
steps:
|
||||
- uses: actions/checkout@v3
|
||||
- uses: julia-actions/setup-julia@v1
|
||||
with:
|
||||
version: '1'
|
||||
- name: Set up Python
|
||||
uses: actions/setup-python@v4.7.0
|
||||
with:
|
||||
python-version: '3.9'
|
||||
- name: Install nbconvert
|
||||
run: |
|
||||
python -m pip install jupyter nbconvert
|
||||
- name: Configure doc environment
|
||||
run: |
|
||||
julia --project=docs/ -e '
|
||||
using Pkg
|
||||
Pkg.develop(PackageSpec(path=pwd()))
|
||||
Pkg.instantiate()'
|
||||
- uses: julia-actions/julia-buildpkg@v1
|
||||
- uses: julia-actions/julia-docdeploy@v1
|
||||
env:
|
||||
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
|
||||
|
||||
|
||||
@@ -1,8 +0,0 @@
|
||||
*.swp
|
||||
Manifest.toml
|
||||
.ipynb_checkpoints/
|
||||
.vscode/
|
||||
docs/src/notebooks/
|
||||
docs/src/notebook-html/
|
||||
*.code-workspace
|
||||
*.DS_Store
|
||||
-395
@@ -1,395 +0,0 @@
|
||||
Attribution 4.0 International
|
||||
|
||||
=======================================================================
|
||||
|
||||
Creative Commons Corporation ("Creative Commons") is not a law firm and
|
||||
does not provide legal services or legal advice. Distribution of
|
||||
Creative Commons public licenses does not create a lawyer-client or
|
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other relationship. Creative Commons makes its licenses and related
|
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information available on an "as-is" basis. Creative Commons gives no
|
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warranties regarding its licenses, any material licensed under their
|
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terms and conditions, or any related information. Creative Commons
|
||||
disclaims all liability for damages resulting from their use to the
|
||||
fullest extent possible.
|
||||
|
||||
Using Creative Commons Public Licenses
|
||||
|
||||
Creative Commons public licenses provide a standard set of terms and
|
||||
conditions that creators and other rights holders may use to share
|
||||
original works of authorship and other material subject to copyright
|
||||
and certain other rights specified in the public license below. The
|
||||
following considerations are for informational purposes only, are not
|
||||
exhaustive, and do not form part of our licenses.
|
||||
|
||||
Considerations for licensors: Our public licenses are
|
||||
intended for use by those authorized to give the public
|
||||
permission to use material in ways otherwise restricted by
|
||||
copyright and certain other rights. Our licenses are
|
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irrevocable. Licensors should read and understand the terms
|
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and conditions of the license they choose before applying it.
|
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Licensors should also secure all rights necessary before
|
||||
applying our licenses so that the public can reuse the
|
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material as expected. Licensors should clearly mark any
|
||||
material not subject to the license. This includes other CC-
|
||||
licensed material, or material used under an exception or
|
||||
limitation to copyright. More considerations for licensors:
|
||||
wiki.creativecommons.org/Considerations_for_licensors
|
||||
|
||||
Considerations for the public: By using one of our public
|
||||
licenses, a licensor grants the public permission to use the
|
||||
licensed material under specified terms and conditions. If
|
||||
the licensor's permission is not necessary for any reason--for
|
||||
example, because of any applicable exception or limitation to
|
||||
copyright--then that use is not regulated by the license. Our
|
||||
licenses grant only permissions under copyright and certain
|
||||
other rights that a licensor has authority to grant. Use of
|
||||
the licensed material may still be restricted for other
|
||||
reasons, including because others have copyright or other
|
||||
rights in the material. A licensor may make special requests,
|
||||
such as asking that all changes be marked or described.
|
||||
Although not required by our licenses, you are encouraged to
|
||||
respect those requests where reasonable. More considerations
|
||||
for the public:
|
||||
wiki.creativecommons.org/Considerations_for_licensees
|
||||
|
||||
=======================================================================
|
||||
|
||||
Creative Commons Attribution 4.0 International Public License
|
||||
|
||||
By exercising the Licensed Rights (defined below), You accept and agree
|
||||
to be bound by the terms and conditions of this Creative Commons
|
||||
Attribution 4.0 International Public License ("Public License"). To the
|
||||
extent this Public License may be interpreted as a contract, You are
|
||||
granted the Licensed Rights in consideration of Your acceptance of
|
||||
these terms and conditions, and the Licensor grants You such rights in
|
||||
consideration of benefits the Licensor receives from making the
|
||||
Licensed Material available under these terms and conditions.
|
||||
|
||||
|
||||
Section 1 -- Definitions.
|
||||
|
||||
a. Adapted Material means material subject to Copyright and Similar
|
||||
Rights that is derived from or based upon the Licensed Material
|
||||
and in which the Licensed Material is translated, altered,
|
||||
arranged, transformed, or otherwise modified in a manner requiring
|
||||
permission under the Copyright and Similar Rights held by the
|
||||
Licensor. For purposes of this Public License, where the Licensed
|
||||
Material is a musical work, performance, or sound recording,
|
||||
Adapted Material is always produced where the Licensed Material is
|
||||
synched in timed relation with a moving image.
|
||||
|
||||
b. Adapter's License means the license You apply to Your Copyright
|
||||
and Similar Rights in Your contributions to Adapted Material in
|
||||
accordance with the terms and conditions of this Public License.
|
||||
|
||||
c. Copyright and Similar Rights means copyright and/or similar rights
|
||||
closely related to copyright including, without limitation,
|
||||
performance, broadcast, sound recording, and Sui Generis Database
|
||||
Rights, without regard to how the rights are labeled or
|
||||
categorized. For purposes of this Public License, the rights
|
||||
specified in Section 2(b)(1)-(2) are not Copyright and Similar
|
||||
Rights.
|
||||
|
||||
d. Effective Technological Measures means those measures that, in the
|
||||
absence of proper authority, may not be circumvented under laws
|
||||
fulfilling obligations under Article 11 of the WIPO Copyright
|
||||
Treaty adopted on December 20, 1996, and/or similar international
|
||||
agreements.
|
||||
|
||||
e. Exceptions and Limitations means fair use, fair dealing, and/or
|
||||
any other exception or limitation to Copyright and Similar Rights
|
||||
that applies to Your use of the Licensed Material.
|
||||
|
||||
f. Licensed Material means the artistic or literary work, database,
|
||||
or other material to which the Licensor applied this Public
|
||||
License.
|
||||
|
||||
g. Licensed Rights means the rights granted to You subject to the
|
||||
terms and conditions of this Public License, which are limited to
|
||||
all Copyright and Similar Rights that apply to Your use of the
|
||||
Licensed Material and that the Licensor has authority to license.
|
||||
|
||||
h. Licensor means the individual(s) or entity(ies) granting rights
|
||||
under this Public License.
|
||||
|
||||
i. Share means to provide material to the public by any means or
|
||||
process that requires permission under the Licensed Rights, such
|
||||
as reproduction, public display, public performance, distribution,
|
||||
dissemination, communication, or importation, and to make material
|
||||
available to the public including in ways that members of the
|
||||
public may access the material from a place and at a time
|
||||
individually chosen by them.
|
||||
|
||||
j. Sui Generis Database Rights means rights other than copyright
|
||||
resulting from Directive 96/9/EC of the European Parliament and of
|
||||
the Council of 11 March 1996 on the legal protection of databases,
|
||||
as amended and/or succeeded, as well as other essentially
|
||||
equivalent rights anywhere in the world.
|
||||
|
||||
k. You means the individual or entity exercising the Licensed Rights
|
||||
under this Public License. Your has a corresponding meaning.
|
||||
|
||||
|
||||
Section 2 -- Scope.
|
||||
|
||||
a. License grant.
|
||||
|
||||
1. Subject to the terms and conditions of this Public License,
|
||||
the Licensor hereby grants You a worldwide, royalty-free,
|
||||
non-sublicensable, non-exclusive, irrevocable license to
|
||||
exercise the Licensed Rights in the Licensed Material to:
|
||||
|
||||
a. reproduce and Share the Licensed Material, in whole or
|
||||
in part; and
|
||||
|
||||
b. produce, reproduce, and Share Adapted Material.
|
||||
|
||||
2. Exceptions and Limitations. For the avoidance of doubt, where
|
||||
Exceptions and Limitations apply to Your use, this Public
|
||||
License does not apply, and You do not need to comply with
|
||||
its terms and conditions.
|
||||
|
||||
3. Term. The term of this Public License is specified in Section
|
||||
6(a).
|
||||
|
||||
4. Media and formats; technical modifications allowed. The
|
||||
Licensor authorizes You to exercise the Licensed Rights in
|
||||
all media and formats whether now known or hereafter created,
|
||||
and to make technical modifications necessary to do so. The
|
||||
Licensor waives and/or agrees not to assert any right or
|
||||
authority to forbid You from making technical modifications
|
||||
necessary to exercise the Licensed Rights, including
|
||||
technical modifications necessary to circumvent Effective
|
||||
Technological Measures. For purposes of this Public License,
|
||||
simply making modifications authorized by this Section 2(a)
|
||||
(4) never produces Adapted Material.
|
||||
|
||||
5. Downstream recipients.
|
||||
|
||||
a. Offer from the Licensor -- Licensed Material. Every
|
||||
recipient of the Licensed Material automatically
|
||||
receives an offer from the Licensor to exercise the
|
||||
Licensed Rights under the terms and conditions of this
|
||||
Public License.
|
||||
|
||||
b. No downstream restrictions. You may not offer or impose
|
||||
any additional or different terms or conditions on, or
|
||||
apply any Effective Technological Measures to, the
|
||||
Licensed Material if doing so restricts exercise of the
|
||||
Licensed Rights by any recipient of the Licensed
|
||||
Material.
|
||||
|
||||
6. No endorsement. Nothing in this Public License constitutes or
|
||||
may be construed as permission to assert or imply that You
|
||||
are, or that Your use of the Licensed Material is, connected
|
||||
with, or sponsored, endorsed, or granted official status by,
|
||||
the Licensor or others designated to receive attribution as
|
||||
provided in Section 3(a)(1)(A)(i).
|
||||
|
||||
b. Other rights.
|
||||
|
||||
1. Moral rights, such as the right of integrity, are not
|
||||
licensed under this Public License, nor are publicity,
|
||||
privacy, and/or other similar personality rights; however, to
|
||||
the extent possible, the Licensor waives and/or agrees not to
|
||||
assert any such rights held by the Licensor to the limited
|
||||
extent necessary to allow You to exercise the Licensed
|
||||
Rights, but not otherwise.
|
||||
|
||||
2. Patent and trademark rights are not licensed under this
|
||||
Public License.
|
||||
|
||||
3. To the extent possible, the Licensor waives any right to
|
||||
collect royalties from You for the exercise of the Licensed
|
||||
Rights, whether directly or through a collecting society
|
||||
under any voluntary or waivable statutory or compulsory
|
||||
licensing scheme. In all other cases the Licensor expressly
|
||||
reserves any right to collect such royalties.
|
||||
|
||||
|
||||
Section 3 -- License Conditions.
|
||||
|
||||
Your exercise of the Licensed Rights is expressly made subject to the
|
||||
following conditions.
|
||||
|
||||
a. Attribution.
|
||||
|
||||
1. If You Share the Licensed Material (including in modified
|
||||
form), You must:
|
||||
|
||||
a. retain the following if it is supplied by the Licensor
|
||||
with the Licensed Material:
|
||||
|
||||
i. identification of the creator(s) of the Licensed
|
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Material and any others designated to receive
|
||||
attribution, in any reasonable manner requested by
|
||||
the Licensor (including by pseudonym if
|
||||
designated);
|
||||
|
||||
ii. a copyright notice;
|
||||
|
||||
iii. a notice that refers to this Public License;
|
||||
|
||||
iv. a notice that refers to the disclaimer of
|
||||
warranties;
|
||||
|
||||
v. a URI or hyperlink to the Licensed Material to the
|
||||
extent reasonably practicable;
|
||||
|
||||
b. indicate if You modified the Licensed Material and
|
||||
retain an indication of any previous modifications; and
|
||||
|
||||
c. indicate the Licensed Material is licensed under this
|
||||
Public License, and include the text of, or the URI or
|
||||
hyperlink to, this Public License.
|
||||
|
||||
2. You may satisfy the conditions in Section 3(a)(1) in any
|
||||
reasonable manner based on the medium, means, and context in
|
||||
which You Share the Licensed Material. For example, it may be
|
||||
reasonable to satisfy the conditions by providing a URI or
|
||||
hyperlink to a resource that includes the required
|
||||
information.
|
||||
|
||||
3. If requested by the Licensor, You must remove any of the
|
||||
information required by Section 3(a)(1)(A) to the extent
|
||||
reasonably practicable.
|
||||
|
||||
4. If You Share Adapted Material You produce, the Adapter's
|
||||
License You apply must not prevent recipients of the Adapted
|
||||
Material from complying with this Public License.
|
||||
|
||||
|
||||
Section 4 -- Sui Generis Database Rights.
|
||||
|
||||
Where the Licensed Rights include Sui Generis Database Rights that
|
||||
apply to Your use of the Licensed Material:
|
||||
|
||||
a. for the avoidance of doubt, Section 2(a)(1) grants You the right
|
||||
to extract, reuse, reproduce, and Share all or a substantial
|
||||
portion of the contents of the database;
|
||||
|
||||
b. if You include all or a substantial portion of the database
|
||||
contents in a database in which You have Sui Generis Database
|
||||
Rights, then the database in which You have Sui Generis Database
|
||||
Rights (but not its individual contents) is Adapted Material; and
|
||||
|
||||
c. You must comply with the conditions in Section 3(a) if You Share
|
||||
all or a substantial portion of the contents of the database.
|
||||
|
||||
For the avoidance of doubt, this Section 4 supplements and does not
|
||||
replace Your obligations under this Public License where the Licensed
|
||||
Rights include other Copyright and Similar Rights.
|
||||
|
||||
|
||||
Section 5 -- Disclaimer of Warranties and Limitation of Liability.
|
||||
|
||||
a. UNLESS OTHERWISE SEPARATELY UNDERTAKEN BY THE LICENSOR, TO THE
|
||||
EXTENT POSSIBLE, THE LICENSOR OFFERS THE LICENSED MATERIAL AS-IS
|
||||
AND AS-AVAILABLE, AND MAKES NO REPRESENTATIONS OR WARRANTIES OF
|
||||
ANY KIND CONCERNING THE LICENSED MATERIAL, WHETHER EXPRESS,
|
||||
IMPLIED, STATUTORY, OR OTHER. THIS INCLUDES, WITHOUT LIMITATION,
|
||||
WARRANTIES OF TITLE, MERCHANTABILITY, FITNESS FOR A PARTICULAR
|
||||
PURPOSE, NON-INFRINGEMENT, ABSENCE OF LATENT OR OTHER DEFECTS,
|
||||
ACCURACY, OR THE PRESENCE OR ABSENCE OF ERRORS, WHETHER OR NOT
|
||||
KNOWN OR DISCOVERABLE. WHERE DISCLAIMERS OF WARRANTIES ARE NOT
|
||||
ALLOWED IN FULL OR IN PART, THIS DISCLAIMER MAY NOT APPLY TO YOU.
|
||||
|
||||
b. TO THE EXTENT POSSIBLE, IN NO EVENT WILL THE LICENSOR BE LIABLE
|
||||
TO YOU ON ANY LEGAL THEORY (INCLUDING, WITHOUT LIMITATION,
|
||||
NEGLIGENCE) OR OTHERWISE FOR ANY DIRECT, SPECIAL, INDIRECT,
|
||||
INCIDENTAL, CONSEQUENTIAL, PUNITIVE, EXEMPLARY, OR OTHER LOSSES,
|
||||
COSTS, EXPENSES, OR DAMAGES ARISING OUT OF THIS PUBLIC LICENSE OR
|
||||
USE OF THE LICENSED MATERIAL, EVEN IF THE LICENSOR HAS BEEN
|
||||
ADVISED OF THE POSSIBILITY OF SUCH LOSSES, COSTS, EXPENSES, OR
|
||||
DAMAGES. WHERE A LIMITATION OF LIABILITY IS NOT ALLOWED IN FULL OR
|
||||
IN PART, THIS LIMITATION MAY NOT APPLY TO YOU.
|
||||
|
||||
c. The disclaimer of warranties and limitation of liability provided
|
||||
above shall be interpreted in a manner that, to the extent
|
||||
possible, most closely approximates an absolute disclaimer and
|
||||
waiver of all liability.
|
||||
|
||||
|
||||
Section 6 -- Term and Termination.
|
||||
|
||||
a. This Public License applies for the term of the Copyright and
|
||||
Similar Rights licensed here. However, if You fail to comply with
|
||||
this Public License, then Your rights under this Public License
|
||||
terminate automatically.
|
||||
|
||||
b. Where Your right to use the Licensed Material has terminated under
|
||||
Section 6(a), it reinstates:
|
||||
|
||||
1. automatically as of the date the violation is cured, provided
|
||||
it is cured within 30 days of Your discovery of the
|
||||
violation; or
|
||||
|
||||
2. upon express reinstatement by the Licensor.
|
||||
|
||||
For the avoidance of doubt, this Section 6(b) does not affect any
|
||||
right the Licensor may have to seek remedies for Your violations
|
||||
of this Public License.
|
||||
|
||||
c. For the avoidance of doubt, the Licensor may also offer the
|
||||
Licensed Material under separate terms or conditions or stop
|
||||
distributing the Licensed Material at any time; however, doing so
|
||||
will not terminate this Public License.
|
||||
|
||||
d. Sections 1, 5, 6, 7, and 8 survive termination of this Public
|
||||
License.
|
||||
|
||||
|
||||
Section 7 -- Other Terms and Conditions.
|
||||
|
||||
a. The Licensor shall not be bound by any additional or different
|
||||
terms or conditions communicated by You unless expressly agreed.
|
||||
|
||||
b. Any arrangements, understandings, or agreements regarding the
|
||||
Licensed Material not stated herein are separate from and
|
||||
independent of the terms and conditions of this Public License.
|
||||
|
||||
|
||||
Section 8 -- Interpretation.
|
||||
|
||||
a. For the avoidance of doubt, this Public License does not, and
|
||||
shall not be interpreted to, reduce, limit, restrict, or impose
|
||||
conditions on any use of the Licensed Material that could lawfully
|
||||
be made without permission under this Public License.
|
||||
|
||||
b. To the extent possible, if any provision of this Public License is
|
||||
deemed unenforceable, it shall be automatically reformed to the
|
||||
minimum extent necessary to make it enforceable. If the provision
|
||||
cannot be reformed, it shall be severed from this Public License
|
||||
without affecting the enforceability of the remaining terms and
|
||||
conditions.
|
||||
|
||||
c. No term or condition of this Public License will be waived and no
|
||||
failure to comply consented to unless expressly agreed to by the
|
||||
Licensor.
|
||||
|
||||
d. Nothing in this Public License constitutes or may be interpreted
|
||||
as a limitation upon, or waiver of, any privileges and immunities
|
||||
that apply to the Licensor or You, including from the legal
|
||||
processes of any jurisdiction or authority.
|
||||
|
||||
|
||||
=======================================================================
|
||||
|
||||
Creative Commons is not a party to its public
|
||||
licenses. Notwithstanding, Creative Commons may elect to apply one of
|
||||
its public licenses to material it publishes and in those instances
|
||||
will be considered the “Licensor.” The text of the Creative Commons
|
||||
public licenses is dedicated to the public domain under the CC0 Public
|
||||
Domain Dedication. Except for the limited purpose of indicating that
|
||||
material is shared under a Creative Commons public license or as
|
||||
otherwise permitted by the Creative Commons policies published at
|
||||
creativecommons.org/policies, Creative Commons does not authorize the
|
||||
use of the trademark "Creative Commons" or any other trademark or logo
|
||||
of Creative Commons without its prior written consent including,
|
||||
without limitation, in connection with any unauthorized modifications
|
||||
to any of its public licenses or any other arrangements,
|
||||
understandings, or agreements concerning use of licensed material. For
|
||||
the avoidance of doubt, this paragraph does not form part of the
|
||||
public licenses.
|
||||
|
||||
Creative Commons may be contacted at creativecommons.org.
|
||||
@@ -1,8 +0,0 @@
|
||||
name = "XM_40017"
|
||||
uuid = "97f213cd-d64a-481d-bc9d-afa871b8c535"
|
||||
authors = ["Francesc Verdugo <f.verdugo.rojano@vu.nl>"]
|
||||
version = "0.1.0"
|
||||
|
||||
[deps]
|
||||
Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
|
||||
Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
|
||||
@@ -1,6 +0,0 @@
|
||||
# XM_40017
|
||||
Jupyter notebook scripts for the course Programming Large-Scale Parallel Systems (XM_40017) at Vrije Universiteit Amsterdam.
|
||||
|
||||
- [**Go to webpage**](https://fverdugo.github.io/XM_40017/dev)
|
||||
|
||||
NB: The `notebooks` folder contains material under construction. The material that is ready for study is the one accessible from the website. The material will be added incrementally to the website as the course advances.
|
||||
@@ -0,0 +1 @@
|
||||
{"documenter":{"julia_version":"1.11.7","generation_timestamp":"2025-09-24T05:37:55","documenter_version":"1.14.1"}}
|
||||
File diff suppressed because one or more lines are too long
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Load Diff
|
Before Width: | Height: | Size: 18 KiB After Width: | Height: | Size: 18 KiB |
|
Before Width: | Height: | Size: 96 KiB After Width: | Height: | Size: 96 KiB |
Vendored
|
Before Width: | Height: | Size: 4.0 KiB After Width: | Height: | Size: 4.0 KiB |
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@@ -0,0 +1,84 @@
|
||||
// Small function to quickly swap out themes. Gets put into the <head> tag..
|
||||
function set_theme_from_local_storage() {
|
||||
// Initialize the theme to null, which means default
|
||||
var theme = null;
|
||||
// If the browser supports the localstorage and is not disabled then try to get the
|
||||
// documenter theme
|
||||
if (window.localStorage != null) {
|
||||
// Get the user-picked theme from localStorage. May be `null`, which means the default
|
||||
// theme.
|
||||
theme = window.localStorage.getItem("documenter-theme");
|
||||
}
|
||||
// Check if the users preference is for dark color scheme
|
||||
var darkPreference =
|
||||
window.matchMedia("(prefers-color-scheme: dark)").matches === true;
|
||||
// Initialize a few variables for the loop:
|
||||
//
|
||||
// - active: will contain the index of the theme that should be active. Note that there
|
||||
// is no guarantee that localStorage contains sane values. If `active` stays `null`
|
||||
// we either could not find the theme or it is the default (primary) theme anyway.
|
||||
// Either way, we then need to stick to the primary theme.
|
||||
//
|
||||
// - disabled: style sheets that should be disabled (i.e. all the theme style sheets
|
||||
// that are not the currently active theme)
|
||||
var active = null;
|
||||
var disabled = [];
|
||||
var primaryLightTheme = null;
|
||||
var primaryDarkTheme = null;
|
||||
for (var i = 0; i < document.styleSheets.length; i++) {
|
||||
var ss = document.styleSheets[i];
|
||||
// The <link> tag of each style sheet is expected to have a data-theme-name attribute
|
||||
// which must contain the name of the theme. The names in localStorage much match this.
|
||||
var themename = ss.ownerNode.getAttribute("data-theme-name");
|
||||
// attribute not set => non-theme stylesheet => ignore
|
||||
if (themename === null) continue;
|
||||
// To distinguish the default (primary) theme, it needs to have the data-theme-primary
|
||||
// attribute set.
|
||||
if (ss.ownerNode.getAttribute("data-theme-primary") !== null) {
|
||||
primaryLightTheme = themename;
|
||||
}
|
||||
// Check if the theme is primary dark theme so that we could store its name in darkTheme
|
||||
if (ss.ownerNode.getAttribute("data-theme-primary-dark") !== null) {
|
||||
primaryDarkTheme = themename;
|
||||
}
|
||||
// If we find a matching theme (and it's not the default), we'll set active to non-null
|
||||
if (themename === theme) active = i;
|
||||
// Store the style sheets of inactive themes so that we could disable them
|
||||
if (themename !== theme) disabled.push(ss);
|
||||
}
|
||||
var activeTheme = null;
|
||||
if (active !== null) {
|
||||
// If we did find an active theme, we'll (1) add the theme--$(theme) class to <html>
|
||||
document.getElementsByTagName("html")[0].className = "theme--" + theme;
|
||||
activeTheme = theme;
|
||||
} else {
|
||||
// If we did _not_ find an active theme, then we need to fall back to the primary theme
|
||||
// which can either be dark or light, depending on the user's OS preference.
|
||||
var activeTheme = darkPreference ? primaryDarkTheme : primaryLightTheme;
|
||||
// In case it somehow happens that the relevant primary theme was not found in the
|
||||
// preceding loop, we abort without doing anything.
|
||||
if (activeTheme === null) {
|
||||
console.error("Unable to determine primary theme.");
|
||||
return;
|
||||
}
|
||||
// When switching to the primary light theme, then we must not have a class name
|
||||
// for the <html> tag. That's only for non-primary or the primary dark theme.
|
||||
if (darkPreference) {
|
||||
document.getElementsByTagName("html")[0].className =
|
||||
"theme--" + activeTheme;
|
||||
} else {
|
||||
document.getElementsByTagName("html")[0].className = "";
|
||||
}
|
||||
}
|
||||
for (var i = 0; i < document.styleSheets.length; i++) {
|
||||
var ss = document.styleSheets[i];
|
||||
// The <link> tag of each style sheet is expected to have a data-theme-name attribute
|
||||
// which must contain the name of the theme. The names in localStorage much match this.
|
||||
var themename = ss.ownerNode.getAttribute("data-theme-name");
|
||||
// attribute not set => non-theme stylesheet => ignore
|
||||
if (themename === null) continue;
|
||||
// we'll disable all the stylesheets, except for the active one
|
||||
ss.disabled = !(themename == activeTheme);
|
||||
}
|
||||
}
|
||||
set_theme_from_local_storage();
|
||||
@@ -0,0 +1,68 @@
|
||||
function maybeAddWarning() {
|
||||
// DOCUMENTER_NEWEST is defined in versions.js, DOCUMENTER_CURRENT_VERSION and DOCUMENTER_STABLE
|
||||
// in siteinfo.js. DOCUMENTER_IS_DEV_VERSION is optional and defined in siteinfo.js.
|
||||
// If the required variables are undefined something went horribly wrong, so we abort.
|
||||
if (
|
||||
window.DOCUMENTER_NEWEST === undefined ||
|
||||
window.DOCUMENTER_CURRENT_VERSION === undefined ||
|
||||
window.DOCUMENTER_STABLE === undefined
|
||||
) {
|
||||
return;
|
||||
}
|
||||
|
||||
// Current version is not a version number, so we can't tell if it's the newest version. Abort.
|
||||
if (!/v(\d+\.)*\d+/.test(window.DOCUMENTER_CURRENT_VERSION)) {
|
||||
return;
|
||||
}
|
||||
|
||||
// Current version is newest version, so no need to add a warning.
|
||||
if (window.DOCUMENTER_NEWEST === window.DOCUMENTER_CURRENT_VERSION) {
|
||||
return;
|
||||
}
|
||||
|
||||
// Add a noindex meta tag (unless one exists) so that search engines don't index this version of the docs.
|
||||
if (document.body.querySelector('meta[name="robots"]') === null) {
|
||||
const meta = document.createElement("meta");
|
||||
meta.name = "robots";
|
||||
meta.content = "noindex";
|
||||
|
||||
document.getElementsByTagName("head")[0].appendChild(meta);
|
||||
}
|
||||
|
||||
const div = document.createElement("div");
|
||||
// Base class is added by default
|
||||
div.classList.add("warning-overlay-base");
|
||||
const closer = document.createElement("button");
|
||||
closer.classList.add("outdated-warning-closer", "delete");
|
||||
closer.addEventListener("click", function () {
|
||||
document.body.removeChild(div);
|
||||
});
|
||||
const href = window.documenterBaseURL + "/../" + window.DOCUMENTER_STABLE;
|
||||
|
||||
// Determine if this is a development version or an older release
|
||||
let warningMessage = "";
|
||||
if (window.DOCUMENTER_IS_DEV_VERSION === true) {
|
||||
div.classList.add("dev-warning-overlay");
|
||||
warningMessage =
|
||||
"This documentation is for the <strong>development version</strong> and may contain unstable or unreleased features.<br>";
|
||||
} else {
|
||||
div.classList.add("outdated-warning-overlay");
|
||||
warningMessage =
|
||||
"This documentation is for an <strong>older version</strong> that may be missing recent changes.<br>";
|
||||
}
|
||||
|
||||
warningMessage +=
|
||||
'<a href="' +
|
||||
href +
|
||||
'">Click here to go to the documentation for the latest stable release.</a>';
|
||||
|
||||
div.innerHTML = warningMessage;
|
||||
div.appendChild(closer);
|
||||
document.body.appendChild(div);
|
||||
}
|
||||
|
||||
if (document.readyState === "loading") {
|
||||
document.addEventListener("DOMContentLoaded", maybeAddWarning);
|
||||
} else {
|
||||
maybeAddWarning();
|
||||
}
|
||||
File diff suppressed because one or more lines are too long
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Binary file not shown.
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@@ -0,0 +1,2 @@
|
||||
var DOCUMENTER_CURRENT_VERSION = "dev";
|
||||
var DOCUMENTER_IS_DEV_VERSION = true;
|
||||
File diff suppressed because one or more lines are too long
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@@ -1,8 +0,0 @@
|
||||
build/
|
||||
site/
|
||||
src/notebook-output/
|
||||
src/notebooks/
|
||||
Manifest.toml
|
||||
src/*.ipynb
|
||||
src/*/index.html
|
||||
src/*.md
|
||||
@@ -1,4 +0,0 @@
|
||||
[deps]
|
||||
Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
|
||||
Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
|
||||
XM_40017 = "97f213cd-d64a-481d-bc9d-afa871b8c535"
|
||||
-139
@@ -1,139 +0,0 @@
|
||||
using XM_40017
|
||||
using Documenter
|
||||
using Glob
|
||||
|
||||
const md_nb_template = """
|
||||
```@meta
|
||||
EditURL = "https://github.com/fverdugo/XM_40017/blob/main/notebooks/SCRIPT_NAME.ipynb"
|
||||
```
|
||||
|
||||
```@raw html
|
||||
<div class="admonition is-success">
|
||||
<header class="admonition-header">Tip</header>
|
||||
<div class="admonition-body">
|
||||
<ul>
|
||||
<li>
|
||||
Download this notebook and run it locally on your machine [highly recommended]. Click <a href="https://www.francescverdugo.com/XM_40017/dev/SCRIPT_NAME.ipynb" download>here</a>.
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
```
|
||||
|
||||
```@raw html
|
||||
<iframe id="notebook" src="../SCRIPT_NAME_src/" style="width:100%"></iframe>
|
||||
<script>
|
||||
document.addEventListener('DOMContentLoaded', function(){
|
||||
var myIframe = document.getElementById("notebook");
|
||||
iFrameResize({log:true}, myIframe);
|
||||
});
|
||||
</script>
|
||||
```
|
||||
"""
|
||||
|
||||
function convert_embedded_img_to_base64(notebook_path)
|
||||
doc = open(io->read(io, String), notebook_path)
|
||||
# Regex matching: extract filename and base64 code
|
||||
regex = r"attachments\\\":\s*\{\s*\\\"(?<filename>.*).png\\\":\s*\{\s*\\\"image/png\\\":\s*\\\"(?<base64code>.*)\\\""
|
||||
res = eachmatch(regex, doc)
|
||||
matches = collect(res)
|
||||
# Replace img src with base64 code
|
||||
for m in matches
|
||||
filename = m[:filename]
|
||||
base64 = m[:base64code]
|
||||
doc = replace(doc, "attachment:$filename.png" => "data:image/png;base64,$base64")
|
||||
end
|
||||
filename = splitpath(notebook_path)[end]
|
||||
open("docs/src/$filename","w") do f
|
||||
write(f, doc)
|
||||
end
|
||||
end
|
||||
|
||||
# Write markdown file that includes notebook html
|
||||
function create_md_nb_file( filename )
|
||||
global md_nb_template;
|
||||
content = replace(md_nb_template, "SCRIPT_NAME" => filename)
|
||||
md_path = joinpath(@__DIR__, "src", filename * ".md" )
|
||||
open(md_path, "w") do md_file
|
||||
write(md_file, content)
|
||||
end
|
||||
return md_path
|
||||
end
|
||||
|
||||
# Convert to html using nbconvert
|
||||
function convert_notebook_to_html(notebook_path; output_name,output_dir, theme = "light")
|
||||
command_jup = "jupyter"
|
||||
command_nbc = "nbconvert"
|
||||
output_format = "--to=html"
|
||||
theme = "--theme=$theme"
|
||||
output = "--output=$output_name"
|
||||
output_dir = "--output-dir=$output_dir"
|
||||
infile = notebook_path
|
||||
run(`$command_jup $command_nbc $output_format $output $output_dir $theme $infile`)
|
||||
end
|
||||
|
||||
# Modify html contents
|
||||
function modify_notebook_html( html_filepath )
|
||||
content = open( html_filepath, "r" ) do html_file
|
||||
read( html_file, String )
|
||||
end
|
||||
# Resize iframes using IframeResizer
|
||||
content = replace(content,
|
||||
r"(<script\b[^>]*>[\s\S]*?<\/script>\K)" =>
|
||||
s"\1\n\t<script src='../assets/iframeResizer.contentWindow.min.js'></script>\n";
|
||||
count = 1
|
||||
)
|
||||
open( html_filepath, "w" ) do html_file
|
||||
write( html_file, content )
|
||||
end
|
||||
return nothing
|
||||
end
|
||||
|
||||
|
||||
# Loop over notebooks and generate html and markdown
|
||||
repo_root = joinpath(@__DIR__,"..") |> normpath
|
||||
notebook_files = glob("*.ipynb", joinpath(repo_root,"notebooks/"))
|
||||
for filepath in notebook_files
|
||||
#continue
|
||||
convert_embedded_img_to_base64(filepath)
|
||||
filename_with_ext = splitpath(filepath)[end]
|
||||
filename = splitext(filename_with_ext)[1]
|
||||
pth = mkpath(joinpath(repo_root,"docs","src",filename*"_src"))
|
||||
create_md_nb_file(filename)
|
||||
convert_notebook_to_html("docs/src/$filename_with_ext", output_dir=pth, output_name = "index")
|
||||
modify_notebook_html("docs/src/$(filename)_src/index.html")
|
||||
end
|
||||
|
||||
makedocs(;
|
||||
modules=[XM_40017],
|
||||
authors="Francesc Verdugo <f.verdugo.rojano@vu.nl>",
|
||||
repo="https://github.com/fverdugo/XM_40017/blob/{commit}{path}#{line}",
|
||||
sitename="XM_40017",
|
||||
format=Documenter.HTML(;
|
||||
assets = ["assets/favicon.ico", "assets/iframeResizer.min.js", "assets/custom.css"],
|
||||
prettyurls=get(ENV, "CI", "false") == "true",
|
||||
canonical="https://fverdugo.github.io/XM_40017",
|
||||
edit_link="main",),
|
||||
pages=["Home" => "index.md","Getting started"=>"getting_started_with_julia.md",
|
||||
"Notebooks"=>[
|
||||
"Julia Basics" => "julia_basics.md",
|
||||
"Asynchronous programming in Julia" => "julia_async.md",
|
||||
"Distributed computing in Julia" => "julia_distributed.md",
|
||||
#"Distributed computing with MPI" => "mpi_tutorial.md",
|
||||
"Matrix-matrix multiplication"=>"matrix_matrix.md",
|
||||
"MPI (point-to-point)" => "julia_mpi.md",
|
||||
"MPI (collectives)" => "mpi_collectives.md",
|
||||
"Jacobi method" => "jacobi_method.md",
|
||||
"All pairs of shortest paths" => "asp.md",
|
||||
"Gaussian elimination" => "LEQ.md",
|
||||
"Traveling salesperson problem" => "tsp.md",
|
||||
#"Partial differential equations" => "pdes.md",
|
||||
],
|
||||
"Solutions" => "solutions_for_all_notebooks.md",
|
||||
],
|
||||
)
|
||||
|
||||
deploydocs(;
|
||||
repo="github.com/fverdugo/XM_40017",
|
||||
devbranch="main",
|
||||
)
|
||||
@@ -1,435 +0,0 @@
|
||||
# Getting started
|
||||
|
||||
|
||||
## Introduction
|
||||
|
||||
The programming of this course will be done using the [Julia programming language](https://julialang.org). Thus, we start by explaining how to get up and running with Julia. After studying 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](https://github.com/JuliaAcademy/JuliaTutorials/blob/724e15a350d150a9773afe51a3830709dbed422f/introductory-tutorials/intro-to-julia/09.%20Julia%20is%20fast.ipynb) 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.
|
||||
|
||||
- Download and install Julia from [julialang.org](https://julialang.org);
|
||||
- Follow the specific instructions for your operating system: [Windows](https://julialang.org/downloads/platform/#windows), [MacOS](https://julialang.org/downloads/platform/#macos), or [Linux](https://julialang.org/downloads/platform/#linux_and_freebsd)
|
||||
- Download and install [VSCode and its Julia extension](https://www.julia-vscode.org/docs/dev/gettingstarted/);
|
||||
|
||||
|
||||
## 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
|
||||
julia> 1 + 1
|
||||
```
|
||||
|
||||
A "Hello world" example looks like this in Julia
|
||||
|
||||
```julia
|
||||
julia> println("Hello, world!")
|
||||
```
|
||||
|
||||
Try to run it in the REPL.
|
||||
|
||||
### Help mode
|
||||
|
||||
Curious about what the function `println` does? Enter into *help* mode to look into the documentation. This is done by typing a question mark (`?`) into the input field:
|
||||
|
||||
```julia
|
||||
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.
|
||||
|
||||
```julia
|
||||
help?> println
|
||||
```
|
||||
|
||||
### Package and shell modes
|
||||
|
||||
The REPL comes with two more modes, namely *package* and *shell* modes. To enter package mode type
|
||||
|
||||
```julia
|
||||
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
|
||||
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,
|
||||
|
||||
```julia
|
||||
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
|
||||
julia> include("hello.jl")
|
||||
```
|
||||
|
||||
!!! warning
|
||||
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 by the path to the file containing the code you want to execute.
|
||||
|
||||
```
|
||||
$ julia hello.jl
|
||||
```
|
||||
|
||||
The previous line assumes that you have Julia properly installed in the system and that it's 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!
|
||||
|
||||
You can also run julia code from the terminal using the `-e` flag:
|
||||
|
||||
```
|
||||
$ julia -e 'println("Hello, world!")'
|
||||
```
|
||||
|
||||
!!! 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. Visit this link ([Julia workflow tips](https://docs.julialang.org/en/v1/manual/workflow-tips/))
|
||||
from the official Julia documentation for further information about how to develop Julia code effectivelly.
|
||||
|
||||
### 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
|
||||
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 probably only see output from 1 process. We need to add more processes to run the example in parallel. This is done with the `addprocs` function.
|
||||
|
||||
```julia
|
||||
julia> addprocs(3)
|
||||
```
|
||||
We have added 3 new processes. Plus the old one, we have 4 processes. Run the code again.
|
||||
|
||||
```julia
|
||||
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
|
||||
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"`
|
||||
|
||||
```julia
|
||||
# file hello_mpi.jl
|
||||
using MPI
|
||||
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
|
||||
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
|
||||
julia> ]
|
||||
```
|
||||
At this point, the prompt should have changed to `(@v1.11) 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 1.11 in this example, but it can be another version in your case).
|
||||
|
||||
To install the MPI package, type
|
||||
```julia
|
||||
(@v1.11) 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 installed the `MPI.jl` package even though we have only typed `MPI` in the REPL.
|
||||
|
||||
!!! note
|
||||
The package you have installed is the Julia interface to MPI, called `MPI.jl`. Note that it is not an 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 an MPI library for you, but it is also possible to use an MPI library already available in your system. This is useful, e.g., when running on HPC clusters. See the [documentation](https://juliaparallel.org/MPI.jl/stable/configuration/) 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
|
||||
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. 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
|
||||
julia> using MPI
|
||||
julia> run(`$(mpiexec()) -np 4 julia hello_mpi.jl`);
|
||||
```
|
||||
|
||||
Now, you should see output from 4 ranks.
|
||||
|
||||
## Package manager
|
||||
|
||||
### Installing packages locally
|
||||
|
||||
We have installed the `MPI` package globally and it will be available in all Julia sessions. However, in some situations, we want to work with different versions of the same package or to install packages in an isolated way to avoid potential conflicts with other packages. This can be done by using local projects.
|
||||
|
||||
A project is simply a folder in your file system. To use a particular folder as your project, you need to *activate* it. This is done by entering package mode and using the `activate` command followed by the path to the folder you want to activate.
|
||||
```julia
|
||||
(@v1.11) pkg> activate .
|
||||
```
|
||||
The previous command will activate the current working directory. Note that the dot `.` is indeed the path to the current folder.
|
||||
|
||||
The prompt has changed to `(lessons) pkg>` indicating that we are in the project within the `lessons` folder. The particular folder name can be different in your case.
|
||||
|
||||
!!! tip
|
||||
You can activate a project directly when opening Julia from the terminal using the `--project` flag. The command `$ 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, `(@v1.11) 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.
|
||||
|
||||
```julia
|
||||
(lessons) pkg> add DataFrames
|
||||
```
|
||||
Use the package to check that it is installed
|
||||
|
||||
```julia
|
||||
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.
|
||||
|
||||
```julia
|
||||
(lessons) pkg> activate
|
||||
```
|
||||
The prompt is again `(@v1.11) pkg>`
|
||||
|
||||
Now, try to use `DataFrames`.
|
||||
|
||||
```julia
|
||||
julia> using DataFrames
|
||||
julia> DataFrame(a=[1,2],b=[3,4])
|
||||
```
|
||||
You should get an error or a warning unless you already had `DataFrames` installed globally.
|
||||
|
||||
### Project and Manifest files
|
||||
|
||||
The information about a project is stored in two files `Project.toml` and `Manifest.toml`.
|
||||
|
||||
- `Project.toml` contains the packages explicitly installed (the direct dependencies)
|
||||
|
||||
- `Manifest.toml` contains direct and indirect dependencies along with the concrete version of each package.
|
||||
|
||||
|
||||
In other words, `Project.toml` contains the packages relevant for the user, whereas `Manifest.toml` is the detailed snapshot of all dependencies. The `Manifest.toml` can be used to reproduce the same environment in another machine.
|
||||
|
||||
You can see the path to the current `Project.toml` file by using the `status` operator (or `st` in its short form) while in package mode
|
||||
|
||||
```julia
|
||||
(@v1.11) pkg> status
|
||||
```
|
||||
|
||||
The information about the `Manifest.toml` can be inspected by passing the `-m` flag.
|
||||
|
||||
```julia
|
||||
(@v1.11) pkg> status -m
|
||||
```
|
||||
|
||||
### Installing packages from a project file
|
||||
|
||||
Project files can be used to install lists of packages defined by others. E.g., to install all the dependencies of a Julia application.
|
||||
|
||||
Assume that a colleague has sent to you a `Project.toml` file with this content:
|
||||
|
||||
```
|
||||
[deps]
|
||||
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
|
||||
julia> mkdir("newproject")
|
||||
```
|
||||
|
||||
To install all the packages registered in this file you need to activate the folder containing your `Project.toml` file
|
||||
```julia
|
||||
(@v1.11) pkg> activate newproject
|
||||
```
|
||||
and then *instantiating* it
|
||||
```julia
|
||||
(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
|
||||
|
||||
```julia
|
||||
(@v1.11) pkg> help activate
|
||||
```
|
||||
|
||||
You can get an overview of all package commands by typing `help` alone
|
||||
```julia
|
||||
(@v1.11) 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
|
||||
julia> using Pkg
|
||||
julia> Pkg.status()
|
||||
```
|
||||
is equivalent to calling `status` in package mode.
|
||||
```julia
|
||||
(@v1.11) pkg> status
|
||||
```
|
||||
|
||||
### Creating you own package
|
||||
|
||||
In many situations, it is useful to create your own package, for instance, when working with a large code base, when you want to reduce compilation latency using [`Revise.jl`](https://github.com/timholy/Revise.jl),
|
||||
or if you want to eventually [register your package](https://github.com/JuliaRegistries/Registrator.jl) and share it with others.
|
||||
|
||||
The simplest way of generating a package (called `MyPackage`) is as follows. Open Julia, go to package mode, and type
|
||||
|
||||
```julia
|
||||
(@v1.11) pkg> generate MyPackage
|
||||
```
|
||||
|
||||
This will crate a minimal package consisting of a new folder `MyPackage` with two files:
|
||||
|
||||
* `MyPackage/Project.toml`: Project file defining the direct dependencies of your package.
|
||||
* `MyPackage/src/MyPackage.jl`: Main source file of your package. You can split your code in several files if needed, and include them in the package main file using function `include`.
|
||||
|
||||
!!! tip
|
||||
This approach only generates a very minimal package. To create a more sophisticated package skeleton (including unit testing, code coverage, readme file, licence, etc.) use
|
||||
[`PkgTemplates.jl`](https://github.com/JuliaCI/PkgTemplates.jl) or [`BestieTemplate.jl`](https://github.com/JuliaBesties/BestieTemplate.jl). The later one is developed in Amsterdam at the
|
||||
[Netherlands eScience Center](https://www.esciencecenter.nl/).
|
||||
|
||||
You can add dependencies to the package by activating the `MyPackage` folder in package mode and adding new dependencies as always:
|
||||
|
||||
```julia
|
||||
(@v1.11) pkg> activate MyPackage
|
||||
(MyPackage) pkg> add MPI
|
||||
```
|
||||
|
||||
This will add MPI to your package dependencies.
|
||||
|
||||
### Using your own package
|
||||
|
||||
To use your package you first need to add it to a package environment of your choice. This is done by changing to package mode and typing `develop ` followed by the path to the folder containing the package. For instance:
|
||||
|
||||
```julia
|
||||
(@v1.11) pkg> develop MyPackage
|
||||
```
|
||||
|
||||
!!! note
|
||||
You do not need to "develop" your package if you activated the package folder `MyPackage`.
|
||||
|
||||
Now, we can go back to standard Julia mode and use it as any other package:
|
||||
|
||||
```julia
|
||||
using MyPackage
|
||||
MyPackage.greet()
|
||||
```
|
||||
|
||||
Here, we just called the example function defined in `MyPackage/src/MyPackage.jl`.
|
||||
|
||||
|
||||
## Conclusion
|
||||
|
||||
We have learned the basics of how to work with Julia, including how to run serial and parallel code, and how to manage, create, and use Julia packages.
|
||||
This knowledge will allow you to follow the course effectively!
|
||||
If you want to further dig into the topics we have covered here, you can take a look at the following links:
|
||||
|
||||
- [Julia Manual](https://docs.julialang.org/en/v1/manual/getting-started/)
|
||||
- [Package manager](https://pkgdocs.julialang.org/v1/getting-started/)
|
||||
|
||||
|
||||
@@ -1,57 +0,0 @@
|
||||
```@meta
|
||||
CurrentModule = XM_40017
|
||||
```
|
||||
# Programming Large-Scale Parallel Systems (XM_40017)
|
||||
|
||||
Welcome to the interactive lecture notes of the [Programming Large-Scale Parallel Systems course](https://studiegids.vu.nl/EN/courses/2023-2024/XM_40017#/) at [VU Amsterdam](https://vu.nl)!
|
||||
|
||||
## 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](https://studiegids.vu.nl/en/vakken/2025-2026/XM_40017#/)) 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](@ref).
|
||||
- Download the notebook.
|
||||
- Launch Julia. More information in [Getting started](@ref).
|
||||
- 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](https://github.com/fverdugo/) with the help of [Gelieza Kötterheinrich](https://www.linkedin.com/in/gelieza-k/). Part of the notebooks are based on the course slides by [Henri Bal](https://www.vuhpdc.net/henri-bal/).
|
||||
|
||||
|
||||
## License
|
||||
|
||||
All material on this page that is original to this course may be used under a [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) license.
|
||||
|
||||
|
||||
## Acknowledgment
|
||||
|
||||
This page was created with the support of the Faculty of Science of [Vrije Universiteit Amsterdam](https://vu.nl) 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".
|
||||
@@ -1,445 +0,0 @@
|
||||
# Solutions
|
||||
|
||||
## Julia Basics
|
||||
|
||||
### Exercise 1
|
||||
|
||||
```julia
|
||||
function ex1(a)
|
||||
j = 1
|
||||
m = a[j]
|
||||
for (i,ai) in enumerate(a)
|
||||
if m < ai
|
||||
m = ai
|
||||
j = i
|
||||
end
|
||||
end
|
||||
(m,j)
|
||||
end
|
||||
```
|
||||
|
||||
### Exercise 2
|
||||
|
||||
```julia
|
||||
ex2(f,g) = x -> f(x) + g(x)
|
||||
```
|
||||
|
||||
### Exercise 3
|
||||
|
||||
```julia
|
||||
n = 1000
|
||||
x = LinRange(-1.7,0.7,n)
|
||||
y = LinRange(-1.2,1.2,n)
|
||||
values = zeros(n,n)
|
||||
for j in 1:n
|
||||
for i in 1:n
|
||||
values[i,j] = surprise(x[i],y[j])
|
||||
end
|
||||
end
|
||||
using GLMakie
|
||||
heatmap(x,y,values)
|
||||
```
|
||||
|
||||
## Asynchronous programming in Julia
|
||||
|
||||
## Distributed computing in Julia
|
||||
|
||||
### Exercise 1
|
||||
|
||||
```julia
|
||||
f = () -> Channel{Int}(1)
|
||||
worker_ids = workers()
|
||||
chnls = [ RemoteChannel(f,w) for w in worker_ids ]
|
||||
@sync for (iw,w) in enumerate(worker_ids)
|
||||
@spawnat w begin
|
||||
chnl_snd = chnls[iw]
|
||||
if iw == 1
|
||||
chnl_rcv = chnls[end]
|
||||
msg = 2
|
||||
println("msg = $msg")
|
||||
put!(chnl_snd,msg)
|
||||
msg = take!(chnl_rcv)
|
||||
println("msg = $msg")
|
||||
else
|
||||
chnl_rcv = chnls[iw-1]
|
||||
msg = take!(chnl_rcv)
|
||||
msg += 1
|
||||
println("msg = $msg")
|
||||
put!(chnl_snd,msg)
|
||||
end
|
||||
end
|
||||
end
|
||||
```
|
||||
|
||||
This is another possible solution that does not use remote channels.
|
||||
|
||||
```julia
|
||||
@everywhere function work(msg,iw,worker_ids)
|
||||
println("msg = $msg")
|
||||
if iw < length(worker_ids)
|
||||
inext = iw+1
|
||||
next = worker_ids[iw+1]
|
||||
@fetchfrom next work(msg+1,inext,worker_ids)
|
||||
else
|
||||
@fetchfrom worker_ids[1] println("msg = $msg")
|
||||
end
|
||||
return nothing
|
||||
end
|
||||
msg = 2
|
||||
iw = 1
|
||||
worker_ids = workers()
|
||||
@fetchfrom worker_ids[iw] work(msg,iw,worker_ids)
|
||||
```
|
||||
|
||||
## Matrix-matrix multiplication
|
||||
|
||||
### Exercise 1
|
||||
|
||||
```julia
|
||||
function matmul_dist_3!(C,A,B)
|
||||
m = size(C,1)
|
||||
n = size(C,2)
|
||||
l = size(A,2)
|
||||
@assert size(A,1) == m
|
||||
@assert size(B,2) == n
|
||||
@assert size(B,1) == l
|
||||
@assert mod(m,nworkers()) == 0
|
||||
nrows_w = div(m,nworkers())
|
||||
@sync for (iw,w) in enumerate(workers())
|
||||
lb = 1 + (iw-1)*nrows_w
|
||||
ub = iw*nrows_w
|
||||
A_w = A[lb:ub,:]
|
||||
ftr = @spawnat w begin
|
||||
C_w = similar(A_w)
|
||||
matmul_seq!(C_w,A_w,B)
|
||||
C_w
|
||||
end
|
||||
@async C[lb:ub,:] = fetch(ftr)
|
||||
end
|
||||
C
|
||||
end
|
||||
|
||||
@everywhere function matmul_seq!(C,A,B)
|
||||
m = size(C,1)
|
||||
n = size(C,2)
|
||||
l = size(A,2)
|
||||
@assert size(A,1) == m
|
||||
@assert size(B,2) == n
|
||||
@assert size(B,1) == l
|
||||
z = zero(eltype(C))
|
||||
for j in 1:n
|
||||
for i in 1:m
|
||||
Cij = z
|
||||
for k in 1:l
|
||||
@inbounds Cij = Cij + A[i,k]*B[k,j]
|
||||
end
|
||||
C[i,j] = Cij
|
||||
end
|
||||
end
|
||||
C
|
||||
end
|
||||
```
|
||||
|
||||
## MPI (Point-to-point)
|
||||
|
||||
### Exercise 1
|
||||
|
||||
```julia
|
||||
function matmul_mpi_3!(C,A,B)
|
||||
comm = MPI.COMM_WORLD
|
||||
rank = MPI.Comm_rank(comm)
|
||||
P = MPI.Comm_size(comm)
|
||||
if rank == 0
|
||||
N = size(A,1)
|
||||
myB = B
|
||||
for dest in 1:(P-1)
|
||||
MPI.Send(B,comm;dest)
|
||||
end
|
||||
else
|
||||
source = 0
|
||||
status = MPI.Probe(comm,MPI.Status;source)
|
||||
count = MPI.Get_count(status,eltype(B))
|
||||
N = Int(sqrt(count))
|
||||
myB = zeros(N,N)
|
||||
MPI.Recv!(myB,comm;source)
|
||||
end
|
||||
L = div(N,P)
|
||||
myA = zeros(L,N)
|
||||
if rank == 0
|
||||
lb = L*rank+1
|
||||
ub = L*(rank+1)
|
||||
myA[:,:] = view(A,lb:ub,:)
|
||||
for dest in 1:(P-1)
|
||||
lb = L*dest+1
|
||||
ub = L*(dest+1)
|
||||
MPI.Send(view(A,lb:ub,:),comm;dest)
|
||||
end
|
||||
else
|
||||
source = 0
|
||||
MPI.Recv!(myA,comm;source)
|
||||
end
|
||||
myC = myA*myB
|
||||
if rank == 0
|
||||
lb = L*rank+1
|
||||
ub = L*(rank+1)
|
||||
C[lb:ub,:] = myC
|
||||
for source in 1:(P-1)
|
||||
lb = L*source+1
|
||||
ub = L*(source+1)
|
||||
MPI.Recv!(view(C,lb:ub,:),comm;source)
|
||||
end
|
||||
else
|
||||
dest = 0
|
||||
MPI.Send(myC,comm;dest)
|
||||
end
|
||||
C
|
||||
end
|
||||
```
|
||||
|
||||
### Exercise 2
|
||||
|
||||
```julia
|
||||
using MPI
|
||||
MPI.Init()
|
||||
comm = MPI.COMM_WORLD
|
||||
rank = MPI.Comm_rank(comm)
|
||||
nranks = MPI.Comm_size(comm)
|
||||
buffer = Ref(0)
|
||||
if rank == 0
|
||||
msg = 2
|
||||
buffer[] = msg
|
||||
println("msg = $(buffer[])")
|
||||
MPI.Send(buffer,comm;dest=rank+1,tag=0)
|
||||
MPI.Recv!(buffer,comm;source=nranks-1,tag=0)
|
||||
println("msg = $(buffer[])")
|
||||
else
|
||||
dest = if (rank != nranks-1)
|
||||
rank+1
|
||||
else
|
||||
0
|
||||
end
|
||||
MPI.Recv!(buffer,comm;source=rank-1,tag=0)
|
||||
buffer[] += 1
|
||||
println("msg = $(buffer[])")
|
||||
MPI.Send(buffer,comm;dest,tag=0)
|
||||
end
|
||||
```
|
||||
## MPI (collectives)
|
||||
|
||||
### Exercise 1
|
||||
|
||||
```julia
|
||||
function matmul_mpi_3!(C,A,B)
|
||||
comm = MPI.COMM_WORLD
|
||||
rank = MPI.Comm_rank(comm)
|
||||
P = MPI.Comm_size(comm)
|
||||
root = 0
|
||||
if rank == root
|
||||
N = size(A,1)
|
||||
Nref = Ref(N)
|
||||
else
|
||||
Nref = Ref(0)
|
||||
end
|
||||
MPI.Bcast!(Nref,comm;root)
|
||||
N = Nref[]
|
||||
if rank == root
|
||||
myB = B
|
||||
else
|
||||
myB = zeros(N,N)
|
||||
end
|
||||
MPI.Bcast!(myB,comm;root)
|
||||
L = div(N,P)
|
||||
# Tricky part
|
||||
# Julia works "col major"
|
||||
myAt = zeros(N,L)
|
||||
At = collect(transpose(A))
|
||||
MPI.Scatter!(At,myAt,comm;root)
|
||||
myCt = transpose(myB)*myAt
|
||||
Ct = similar(C)
|
||||
MPI.Gather!(myCt,Ct,comm;root)
|
||||
C .= transpose(Ct)
|
||||
C
|
||||
end
|
||||
```
|
||||
|
||||
This other solution uses a column partition instead of a row partition.
|
||||
It is more natural to work with column partitions in Julia if possible since matrices are
|
||||
in "col major" format. Note that we do not need all the auxiliary transposes anymore.
|
||||
|
||||
```julia
|
||||
function matmul_mpi_3!(C,A,B)
|
||||
comm = MPI.COMM_WORLD
|
||||
rank = MPI.Comm_rank(comm)
|
||||
P = MPI.Comm_size(comm)
|
||||
root = 0
|
||||
if rank == root
|
||||
N = size(A,1)
|
||||
Nref = Ref(N)
|
||||
else
|
||||
Nref = Ref(0)
|
||||
end
|
||||
MPI.Bcast!(Nref,comm;root)
|
||||
N = Nref[]
|
||||
if rank == root
|
||||
myA = A
|
||||
else
|
||||
myA = zeros(N,N)
|
||||
end
|
||||
MPI.Bcast!(myA,comm;root)
|
||||
L = div(N,P)
|
||||
myB = zeros(N,L)
|
||||
MPI.Scatter!(B,myB,comm;root)
|
||||
myC = myA*myB
|
||||
MPI.Gather!(myC,C,comm;root)
|
||||
C
|
||||
end
|
||||
```
|
||||
|
||||
## Jacobi method
|
||||
|
||||
### Exercise 1
|
||||
|
||||
```julia
|
||||
function jacobi_mpi(n,niters)
|
||||
u, u_new = init(n,comm)
|
||||
load = length(u)-2
|
||||
rank = MPI.Comm_rank(comm)
|
||||
nranks = MPI.Comm_size(comm)
|
||||
nreqs = 2*((rank != 0) + (rank != (nranks-1)))
|
||||
reqs = MPI.MultiRequest(nreqs)
|
||||
for t in 1:niters
|
||||
ireq = 0
|
||||
if rank != 0
|
||||
neig_rank = rank-1
|
||||
u_snd = view(u,2:2)
|
||||
u_rcv = view(u,1:1)
|
||||
dest = neig_rank
|
||||
source = neig_rank
|
||||
ireq += 1
|
||||
MPI.Isend(u_snd,comm,reqs[ireq];dest)
|
||||
ireq += 1
|
||||
MPI.Irecv!(u_rcv,comm,reqs[ireq];source)
|
||||
end
|
||||
if rank != (nranks-1)
|
||||
neig_rank = rank+1
|
||||
u_snd = view(u,(load+1):(load+1))
|
||||
u_rcv = view(u,(load+2):(load+2))
|
||||
dest = neig_rank
|
||||
source = neig_rank
|
||||
ireq += 1
|
||||
MPI.Isend(u_snd,comm,reqs[ireq];dest)
|
||||
ireq += 1
|
||||
MPI.Irecv!(u_rcv,comm,reqs[ireq];source)
|
||||
end
|
||||
# Upload interior cells
|
||||
for i in 3:load
|
||||
u_new[i] = 0.5*(u[i-1]+u[i+1])
|
||||
end
|
||||
# Wait for the communications to finish
|
||||
MPI.Waitall(reqs)
|
||||
# Update boundaries
|
||||
for i in (2,load+1)
|
||||
u_new[i] = 0.5*(u[i-1]+u[i+1])
|
||||
end
|
||||
u, u_new = u_new, u
|
||||
end
|
||||
return u
|
||||
end
|
||||
```
|
||||
|
||||
### Exercise 2
|
||||
|
||||
```julia
|
||||
function jacobi_mpi(n,niters,tol,comm) # new tol arg
|
||||
u, u_new = init(n,comm)
|
||||
load = length(u)-2
|
||||
rank = MPI.Comm_rank(comm)
|
||||
nranks = MPI.Comm_size(comm)
|
||||
nreqs = 2*((rank != 0) + (rank != (nranks-1)))
|
||||
reqs = MPI.MultiRequest(nreqs)
|
||||
for t in 1:niters
|
||||
ireq = 0
|
||||
if rank != 0
|
||||
neig_rank = rank-1
|
||||
u_snd = view(u,2:2)
|
||||
u_rcv = view(u,1:1)
|
||||
dest = neig_rank
|
||||
source = neig_rank
|
||||
ireq += 1
|
||||
MPI.Isend(u_snd,comm,reqs[ireq];dest)
|
||||
ireq += 1
|
||||
MPI.Irecv!(u_rcv,comm,reqs[ireq];source)
|
||||
end
|
||||
if rank != (nranks-1)
|
||||
neig_rank = rank+1
|
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u_snd = view(u,(load+1):(load+1))
|
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u_rcv = view(u,(load+2):(load+2))
|
||||
dest = neig_rank
|
||||
source = neig_rank
|
||||
ireq += 1
|
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MPI.Isend(u_snd,comm,reqs[ireq];dest)
|
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ireq += 1
|
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MPI.Irecv!(u_rcv,comm,reqs[ireq];source)
|
||||
end
|
||||
MPI.Waitall(reqs)
|
||||
# Compute the max diff in the current
|
||||
# rank while doing the local update
|
||||
mydiff = 0.0
|
||||
for i in 2:load+1
|
||||
u_new[i] = 0.5*(u[i-1]+u[i+1])
|
||||
diff_i = abs(u_new[i] - u[i])
|
||||
mydiff = max(mydiff,diff_i)
|
||||
end
|
||||
# Now we need to find the global diff
|
||||
diff_ref = Ref(mydiff)
|
||||
MPI.Allreduce!(diff_ref,max,comm)
|
||||
diff = diff_ref[]
|
||||
# If global diff below tol, stop!
|
||||
if diff < tol
|
||||
return u_new
|
||||
end
|
||||
u, u_new = u_new, u
|
||||
end
|
||||
return u
|
||||
end
|
||||
```
|
||||
|
||||
## All pairs of shortest paths
|
||||
|
||||
### Exercise 1
|
||||
|
||||
```julia
|
||||
function floyd_iterations!(myC,comm)
|
||||
L = size(myC,1)
|
||||
N = size(myC,2)
|
||||
rank = MPI.Comm_rank(comm)
|
||||
P = MPI.Comm_size(comm)
|
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lb = L*rank+1
|
||||
ub = L*(rank+1)
|
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C_k = similar(myC,N)
|
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for k in 1:N
|
||||
if (lb<=k) && (k<=ub)
|
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# If I have the row, fill in the buffer
|
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myk = (k-lb)+1
|
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C_k[:] = view(myC,myk,:)
|
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end
|
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# We need to find out the owner of row k.
|
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# Easy since N is a multiple of P
|
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root = div(k-1,L)
|
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MPI.Bcast!(C_k,comm;root)
|
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# Now, we have the data dependencies and
|
||||
# we can do the updates locally
|
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for j in 1:N
|
||||
for i in 1:L
|
||||
myC[i,j] = min(myC[i,j],myC[i,k]+C_k[j])
|
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end
|
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end
|
||||
end
|
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myC
|
||||
end
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```
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Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user