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26 changes: 11 additions & 15 deletions README.html
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</script>

<!-- Loaded before other Sphinx assets -->
<link href="_static/styles/theme.css?digest=bd9e20870c6007c4c509" rel="stylesheet" />
<link href="_static/styles/bootstrap.css?digest=bd9e20870c6007c4c509" rel="stylesheet" />
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<link href="_static/styles/bootstrap.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
<link href="_static/styles/pydata-sphinx-theme.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />


<link href="_static/vendor/fontawesome/6.5.1/css/all.min.css?digest=bd9e20870c6007c4c509" rel="stylesheet" />
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<link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.5.1/webfonts/fa-solid-900.woff2" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.5.1/webfonts/fa-brands-400.woff2" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.5.1/webfonts/fa-regular-400.woff2" />
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<link rel="stylesheet" type="text/css" href="_static/theme.css?v=ec48f040" />

<!-- Pre-loaded scripts that we'll load fully later -->
<link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=bd9e20870c6007c4c509" />
<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=bd9e20870c6007c4c509" />
<script src="_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=bd9e20870c6007c4c509"></script>
<link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=8d27b9dea8ad943066ae" />
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<script src="_static/documentation_options.js?v=c607423c"></script>
<script src="_static/doctools.js?v=888ff710"></script>
Expand All @@ -60,7 +60,6 @@
<a id="pst-skip-link" class="skip-link" href="#main-content">Skip to main content</a>

<div id="pst-scroll-pixel-helper"></div>


<button type="button" class="btn rounded-pill" id="pst-back-to-top">
<i class="fa-solid fa-arrow-up"></i>
Expand Down Expand Up @@ -100,13 +99,10 @@
<span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd>K</kbd></span>
</form></div>
</div>

<header>

<div class="bd-header navbar navbar-expand-lg bd-navbar">
</div>
<header class="bd-header navbar navbar-expand-lg bd-navbar">
</header>

</header>

<div class="bd-container">
<div class="bd-container__inner bd-page-width">
Expand Down Expand Up @@ -536,8 +532,8 @@ <h1><span>⚗️</span> Lab Manual<a class="headerlink" href="#lab-manual" title
</div>

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57 changes: 16 additions & 41 deletions _sources/computing-resources/neuropoly/README.md
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Expand Up @@ -6,19 +6,17 @@ cpus
gpus
```

## Poly-Grames
## GE

### Poly-Grames Network Account
A [**GE**](https://www.ge.polymtl.ca/compte-informatique/) network account is required to have access to internal computational resources.

A **Poly-Grames** network account is required to have access to various computation resources available in the laboratory.

In order to request a **Poly-Grames** network account you need to have your Polytechnique ID number, which you get during your [onboarding](https://github.com/neuropoly/onboarding/issues).
You will receive a GE account during your [onboarding](https://github.com/neuropoly/onboarding/issues).


```{note}
If you want to find out who is behind u/pXXXXXX Grames account, type this:
~~~
getent passwd <GRAMES_ACCOUNT>
getent passwd <ID>
~~~
To list all lab members:
~~~
Expand All @@ -32,27 +30,11 @@ getent group neuropoly | cut -f 4 -d : | tr , '\n' | xargs -n1 getent passwd | l
Once in a while, you are requested to change your password. To do so, log onto another machine (eg `bireli`, `joplin`) and use the command `passwd` to change your password.
```

### Groups

### Home folder

Every [GRAMES](#poly-grames) account has a school-wide personal home folder. It is backed-up nightly.

::::{tab-set}
:::{tab-item} macOS
1. Open Finder
2. CMD+K
3. for students:
1. `smb://hvclusterfs.grames.polymtl.ca/usagers/etudiants/USERNAME`
4. for personnel:
1. `smb://hvclusterfs.grames.polymtl.ca/usagers/personnels/USERNAME`
:::
::::

### Poly-Grames Groups

The list permissions for shared folders on `duke` are available [here](https://docs.google.com/document/d/1ZJUUBpiZPl0wxFsUPxkkR6vXZgfSAd3YBK5vlIpf_aA/edit).
The list of permissions for shared folders on `duke` are available [here](https://docs.google.com/document/d/1ZJUUBpiZPl0wxFsUPxkkR6vXZgfSAd3YBK5vlIpf_aA/edit).

### Connect to Poly-Grames Server
### Connect to Windows Servers

Use Microsoft Remote Desktop Connection on creer51, creer52, creer53.

Expand Down Expand Up @@ -87,7 +69,7 @@ brew install openconnect

Open your Keychain program and click '+' to add a new item:
- Name: `poly-vpn`
- Account: your `YOUR_CAS_USERNAME` (corresponds to your GRAMES username)
- Account: your `YOUR_CAS_USERNAME`
- Password: enter your password here.

Note: the new item has to be added as an `application password` to your `login` Keychain (i.e., not to your `iCloud` Keychain).
Expand Down Expand Up @@ -157,7 +139,7 @@ In case the above links ever break, the steps are:

### Locally

To log into a local station at NeuroPoly use your GRAMES account.
To log into a desktop station while at NeuroPoly use your GE account.

### SSH (command line)

Expand All @@ -168,7 +150,7 @@ If working off-campus, start your [VPN](#vpn) first.
Connect via ssh using the `STATION` you want:

```bash
ssh <POLYGRAMES_USERNAME>@<STATION>.neuro.polymtl.ca
ssh <GE_USERNAME>@<STATION>.neuro.polymtl.ca
```

```{note}
Expand All @@ -183,7 +165,7 @@ Match Host abbey,betty,bireli,coltrane,davis,django,ella,ferguson,jarrett,joplin
HostName %h.neuro.polymtl.ca
Match host *.neuro.polymtl.ca
User <POLYGRAMES USERNAME> # fill in your username and remove this comment
User <GE USERNAME> # fill in your username and remove this comment
# passwords are required to access /mnt/duke: https://github.com/neuropoly/computers/issues/90:
PreferredAuthentications password
EOF
Expand Down Expand Up @@ -242,7 +224,7 @@ If you use `~` or nothing (as shown) after the `:`, the connection will be relat
sshfs <USERNAME>@<STATION>:~/project1/ cluster_folder
```

will attach the remote `/home/GRAMES.POLYMTL.CA/$USER/project1/` to the local `./cluster_folder`, and
will attach the remote `/home/ge.polymtl.ca/$USER/project1/` to the local `./cluster_folder`, and

```
sshfs <USERNAME>@<STATION>:project1/ cluster_folder
Expand Down Expand Up @@ -375,7 +357,7 @@ _For system administrators_: Please log all the changes on the station by updati
| **VNC** | [NeuroPoly Internal Document: Bireli TeamViewer Credentials](https://docs.google.com/document/d/13iNhiBKYZWT9ytsvYeeYV4FJn6Wn00q9Ctka7toMV08/edit#heading=h.zc65h9q5641z) |

* Add event to the computer calendar
* Use your **Poly-Grames** account to connect on the machine
* Use your **GE** account to connect on the machine
* [How to use GPU Clusters at NeuroPoly](https://intranet.neuro.polymtl.ca/computing-resources/computing-resources-neuropoly/gpus)

### joplin
Expand All @@ -387,14 +369,7 @@ _For system administrators_: Please log all the changes on the station by updati
| **Hostname** | |
| **VNC** | |

The server is bound to the GRAMES domain.

Connect to the server via ssh using the **Poly-Grames** account.

To access the sct_testing_management development webpage use the username: sct_test_user; passwd: management.

For fast I/O, use the NVMe hard drive, which is automatically mounted on your home at: `~/data_nvme_XXX` (XXX being your GRAMES matricule). If there is no more space on this disk, use `/mnt/extrassd1/`.

The server is bound to the GRAMES which is linked to the GE domain.

### abbey

Expand Down Expand Up @@ -469,7 +444,7 @@ For SCT database interface use: [SCT annotations](http://tristano.neuro.polymtl.
| **Model** | PC, NVIDIA RTX A6000 (1x) |
| **OS** | Windows 10 (Connect with Microsoft Remote Desktop) |
| **Hostname** | `peterson.grames.polymtl.ca` |
| **Credentials** | <GRAMES_USERNAME>/<GRAMES_PASSWORD> |
| **Credentials** | <GE_USERNAME>/<GE_PASSWORD> |


### node006 (Poly-Grames)
Expand All @@ -480,7 +455,7 @@ For SCT database interface use: [SCT annotations](http://tristano.neuro.polymtl.
| **Model** | PC, NVIDIA Tesla V100S-PCIE-32GB (1x) |
| **OS** | Windows 10 (Connect with Microsoft Remote Desktop) |
| **Hostname** | `node006.grames.polymtl.ca` |
| **Credentials** | <GRAMES_USERNAME>/<GRAMES_PASSWORD> |
| **Credentials** | <GE_USERNAME>/<GE_PASSWORD> |


### node007 (Poly-Grames)
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18 changes: 9 additions & 9 deletions _static/webpack-macros.html
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-->
{# Load FontAwesome icons #}
{% macro head_pre_icons() %}
<link href="{{ pathto('_static/vendor/fontawesome/6.5.1/css/all.min.css', 1) }}?digest=bd9e20870c6007c4c509" rel="stylesheet" />
<link href="{{ pathto('_static/vendor/fontawesome/6.5.1/css/all.min.css', 1) }}?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="{{ pathto('_static/vendor/fontawesome/6.5.1/webfonts/fa-solid-900.woff2', 1) }}" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="{{ pathto('_static/vendor/fontawesome/6.5.1/webfonts/fa-brands-400.woff2', 1) }}" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="{{ pathto('_static/vendor/fontawesome/6.5.1/webfonts/fa-regular-400.woff2', 1) }}" />
{% endmacro %}

{% macro head_pre_assets() %}
<!-- Loaded before other Sphinx assets -->
<link href="{{ pathto('_static/styles/theme.css', 1) }}?digest=bd9e20870c6007c4c509" rel="stylesheet" />
<link href="{{ pathto('_static/styles/bootstrap.css', 1) }}?digest=bd9e20870c6007c4c509" rel="stylesheet" />
<link href="{{ pathto('_static/styles/pydata-sphinx-theme.css', 1) }}?digest=bd9e20870c6007c4c509" rel="stylesheet" />
<link href="{{ pathto('_static/styles/theme.css', 1) }}?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
<link href="{{ pathto('_static/styles/bootstrap.css', 1) }}?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
<link href="{{ pathto('_static/styles/pydata-sphinx-theme.css', 1) }}?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
{% endmacro %}

{% macro head_js_preload() %}
<!-- Pre-loaded scripts that we'll load fully later -->
<link rel="preload" as="script" href="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=bd9e20870c6007c4c509" />
<link rel="preload" as="script" href="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=bd9e20870c6007c4c509" />
<script src="{{ pathto('_static/vendor/fontawesome/6.5.1/js/all.min.js', 1) }}?digest=bd9e20870c6007c4c509"></script>
<link rel="preload" as="script" href="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=8d27b9dea8ad943066ae" />
<link rel="preload" as="script" href="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=8d27b9dea8ad943066ae" />
<script src="{{ pathto('_static/vendor/fontawesome/6.5.1/js/all.min.js', 1) }}?digest=8d27b9dea8ad943066ae"></script>
{% endmacro %}

{% macro body_post() %}
<!-- Scripts loaded after <body> so the DOM is not blocked -->
<script src="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=bd9e20870c6007c4c509"></script>
<script src="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=bd9e20870c6007c4c509"></script>
<script src="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=8d27b9dea8ad943066ae"></script>
<script src="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=8d27b9dea8ad943066ae"></script>
{% endmacro %}
28 changes: 11 additions & 17 deletions agenda-and-calendar.html
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</script>

<!-- Loaded before other Sphinx assets -->
<link href="_static/styles/theme.css?digest=bd9e20870c6007c4c509" rel="stylesheet" />
<link href="_static/styles/bootstrap.css?digest=bd9e20870c6007c4c509" rel="stylesheet" />
<link href="_static/styles/pydata-sphinx-theme.css?digest=bd9e20870c6007c4c509" rel="stylesheet" />
<link href="_static/styles/theme.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
<link href="_static/styles/bootstrap.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
<link href="_static/styles/pydata-sphinx-theme.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />


<link href="_static/vendor/fontawesome/6.5.1/css/all.min.css?digest=bd9e20870c6007c4c509" rel="stylesheet" />
<link href="_static/vendor/fontawesome/6.5.1/css/all.min.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.5.1/webfonts/fa-solid-900.woff2" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.5.1/webfonts/fa-brands-400.woff2" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.5.1/webfonts/fa-regular-400.woff2" />
Expand All @@ -34,9 +34,9 @@
<link rel="stylesheet" type="text/css" href="_static/theme.css?v=ec48f040" />

<!-- Pre-loaded scripts that we'll load fully later -->
<link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=bd9e20870c6007c4c509" />
<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=bd9e20870c6007c4c509" />
<script src="_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=bd9e20870c6007c4c509"></script>
<link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=8d27b9dea8ad943066ae" />
<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=8d27b9dea8ad943066ae" />
<script src="_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>

<script src="_static/documentation_options.js?v=c607423c"></script>
<script src="_static/doctools.js?v=888ff710"></script>
Expand All @@ -61,7 +61,6 @@
<a id="pst-skip-link" class="skip-link" href="#main-content">Skip to main content</a>

<div id="pst-scroll-pixel-helper"></div>


<button type="button" class="btn rounded-pill" id="pst-back-to-top">
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Expand Down Expand Up @@ -101,21 +100,16 @@
<span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd>K</kbd></span>
</form></div>
</div>

<header>

<div class="bd-header navbar navbar-expand-lg bd-navbar">
</div>
<header class="bd-header navbar navbar-expand-lg bd-navbar">
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Expand Down Expand Up @@ -759,8 +753,8 @@ <h2>Book a room<a class="headerlink" href="#book-a-room" title="Link to this hea
</div>

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<link href="../_static/styles/theme.css?digest=bd9e20870c6007c4c509" rel="stylesheet" />
<link href="../_static/styles/bootstrap.css?digest=bd9e20870c6007c4c509" rel="stylesheet" />
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<link href="../_static/styles/bootstrap.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
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<link href="../_static/vendor/fontawesome/6.5.1/css/all.min.css?digest=bd9e20870c6007c4c509" rel="stylesheet" />
<link href="../_static/vendor/fontawesome/6.5.1/css/all.min.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.1/webfonts/fa-solid-900.woff2" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.1/webfonts/fa-brands-400.woff2" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.1/webfonts/fa-regular-400.woff2" />
Expand All @@ -34,9 +34,9 @@
<link rel="stylesheet" type="text/css" href="../_static/theme.css?v=ec48f040" />

<!-- Pre-loaded scripts that we'll load fully later -->
<link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=bd9e20870c6007c4c509" />
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<script src="../_static/documentation_options.js?v=c607423c"></script>
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Expand All @@ -61,7 +61,6 @@
<a id="pst-skip-link" class="skip-link" href="#main-content">Skip to main content</a>

<div id="pst-scroll-pixel-helper"></div>


<button type="button" class="btn rounded-pill" id="pst-back-to-top">
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Expand Down Expand Up @@ -101,21 +100,16 @@
<span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd>K</kbd></span>
</form></div>
</div>

<header>

<div class="bd-header navbar navbar-expand-lg bd-navbar">
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<div class="bd-sidebar-primary bd-sidebar">


Expand Down Expand Up @@ -540,8 +534,8 @@ <h1><span>📚</span> Bibliography<a class="headerlink" href="#bibliography" tit
</div>

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<script src="../_static/scripts/bootstrap.js?digest=bd9e20870c6007c4c509"></script>
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