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  • 26-add-screenshots-for-newer-rdp-v10-client
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.DS_Store 0 → 100644
View file @ d1fc6a75
File added
.gitignore
View file @ d1fc6a75
public/
.cache/
__pycache__/
site/
.gitlab-ci.yml
View file @ d1fc6a75
variables:
BASE_URL: "//hcc.unl.edu/docs"
DEPLOY_ROOT: "/var/www/html/hcc-docs"
HUGO_TARBALL: "https://github.com/gohugoio/hugo/releases/download/v0.51/hugo_0.51_Linux-64bit.tar.gz"
GIT_SUBMODULE_STRATEGY: recursive
MKDOCS_PREFIX: /tmp/gitlab-${CI_JOB_ID}-${CI_COMMIT_SHORT_SHA}/mkdocs
MICROMAMBA_ROOT_PREFIX: /tmp/gitlab-${CI_JOB_ID}-${CI_COMMIT_SHORT_SHA}/micromamba
.fetch_external_files: &fetch_external_files
- curl -L https://raw.githubusercontent.com/unlhcc/singularity-dockerfiles/master/IMAGELIST.md > docs/static/markdown/singularity-images.md
- curl -L http://swan-head.unl.edu:8192/bio/data/json > docs/static/json/biodata.json
- curl -L http://swan-head.unl.edu:8192/lmod/spider/json > docs/static/json/lmod.json
- curl -L http://swan-head.unl.edu:8192/slurm/partitions/json > docs/static/json/swan_partitions.json
stages:
- test
......@@ -10,15 +16,19 @@ stages:
test:
stage: test
image: unlhcc/docker-glibc
image: python:3.11
except:
- master
tags:
- docker
before_script:
- curl -L -o - ${HUGO_TARBALL} | tar -zxv -C /usr/local/bin
- apt-get -q update
- apt-get -q -y install zip pandoc
- pip install -q -r requirements.txt
- *fetch_external_files
script:
- hugo --ignoreCache -v
- mkdocs build
- ./pandoc-build.sh
deploy:
stage: deploy
......@@ -29,8 +39,16 @@ deploy:
- master
tags:
- hcc-docs-prod
before_script:
- mkdir -p ${MICROMAMBA_ROOT_PREFIX} ${MKDOCS_PREFIX}
- *fetch_external_files
- micromamba create -y -q -p ${MKDOCS_PREFIX}/mkdocs python=3.11 pip cairo pandoc
- micromamba run -p ${MKDOCS_PREFIX}/mkdocs pip install -q -r requirements.txt
script:
- curl -L https://raw.githubusercontent.com/unlhcc/singularity-dockerfiles/master/IMAGELIST.md > static/markdown/singularity-images.md
- hugo --ignoreCache -b ${BASE_URL} -v
- pandoc -s content/facilities.md -o public/facilities.docx
- rsync -avz --delete public/ $DEPLOY_ROOT
- micromamba run -p ${MKDOCS_PREFIX}/mkdocs mkdocs build
- find site/ -type f -name "*.html" -exec sed -i -e 's/src="\//src="\/docs\//g' -e 's/href="\//href="\/docs\//g' {} +
- micromamba run -p ${MKDOCS_PREFIX}/mkdocs ./pandoc-build.sh
- rsync -avz --delete site/ ${DEPLOY_ROOT}
after_script:
- rm -rf /tmp/gitlab-${CI_JOB_ID}-${CI_COMMIT_SHORT_SHA}
CONTRIBUTING.md 0 → 100644
View file @ d1fc6a75
# Contributing
Our users have a wonderful perspective into our documentation that our staff do not.
It's easy for people who have been using it for a while
to forget how impenetrable some of this material can be. As such, we
greatly welcome feedback and contributions of all kinds:
suggested changes,
fixes to existing material,
and bug reports are all welcome.
## Contributor Agreement
By contributing,
you agree that we may redistribute your work under [our license](LICENSE).
## How to Contribute a Fix or Suggested Change
The easiest way to get started is to file an issue
to tell us about a spelling mistake,
some awkward wording,
or a factual error.
1. If you do not have access to [UNL's GitLab instance](http://git.unl.edu),
you can [send us comments by email](mailto:hcc-support@unl.edu).
However,
we will be able to respond more quickly if you use one of the other methods described below.
2. If you have access to [UNL's GitLab instance](http://git.unl.edu),
but do not know how to use Git,
you can report problems or suggest improvements by [creating an issue](https://git.unl.edu/hcc/hcc-docs/issues/new).
This allows us to assign the item to someone
and to respond to it in a threaded discussion. Detailed information on creating
issues can be found in the [GitLab Documentation](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html)
3. If you are comfortable with Git,
and would like to add or change material,
you can submit a pull request (PR).
Instructions for doing this are [included below](#using-gitlab).
## Where to Contribute
1. Checking for outstanding [issues](https://git.unl.edu/hcc/hcc-docs/issues) is a quick way to identify contribution areas. Additionally,
review an comments on existing merge requests are welcome.
2. All documentation content can be found within the `docs` folder. Subdirectories indicate menu items,
with the top level document called `index.md` within each subdirectory.
Note: please do not submit modifications to theme or CSS items unless they
adhere to [UNL style guidelines](https://wdn.unl.edu/unl-web-framework-5-standards-guide).
## What to Contribute
There are many ways to contribute,
from contributing additional documentation topics or submitting software specific job examples,
to updating or adding to existing documentation and submitting [bug reports](https://git.unl.edu/hcc/hcc-docs/issues)
about things that don't work, aren't clear, or are missing.
Comments on issues and reviews of pull requests are just as welcome:
we are smarter together than we are on our own.
Reviews from novices and newcomers are particularly valuable:
so fresh eyes are always welcome.
## Using GitLab
The best way to submit proposed changes is:
1. Create a fork of the HCC docs repository.
- [Documentation on how to fork a project](https://docs.gitlab.com/ee/gitlab-basics/fork-project.html)
2. Clone your forked repository and commit changes.
- [Details on setting up a Hugo environment on your personal machine](README.md)
3. Submit a merge request between your fork and the main HCC docs repository.
- [How to submit a merge request](https://docs.gitlab.com/ee/gitlab-basics/add-merge-request.html)
## Other Resources
If you have any questions or feedback, please contact us at hcc-support@unl.edu.
LICENSE 0 → 100644
View file @ d1fc6a75
GNU GENERAL PUBLIC LICENSE
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propagate the contents of its contributor version.
In the following three paragraphs, a "patent license" is any express
agreement or commitment, however denominated, not to enforce a patent
(such as an express permission to practice a patent or covenant not to
sue for patent infringement). To "grant" such a patent license to a
party means to make such an agreement or commitment not to enforce a
patent against the party.
If you convey a covered work, knowingly relying on a patent license,
and the Corresponding Source of the work is not available for anyone
to copy, free of charge and under the terms of this License, through a
publicly available network server or other readily accessible means,
then you must either (1) cause the Corresponding Source to be so
available, or (2) arrange to deprive yourself of the benefit of the
patent license for this particular work, or (3) arrange, in a manner
consistent with the requirements of this License, to extend the patent
license to downstream recipients. "Knowingly relying" means you have
actual knowledge that, but for the patent license, your conveying the
covered work in a country, or your recipient's use of the covered work
in a country, would infringe one or more identifiable patents in that
country that you have reason to believe are valid.
If, pursuant to or in connection with a single transaction or
arrangement, you convey, or propagate by procuring conveyance of, a
covered work, and grant a patent license to some of the parties
receiving the covered work authorizing them to use, propagate, modify
or convey a specific copy of the covered work, then the patent license
you grant is automatically extended to all recipients of the covered
work and works based on it.
A patent license is "discriminatory" if it does not include within
the scope of its coverage, prohibits the exercise of, or is
conditioned on the non-exercise of one or more of the rights that are
specifically granted under this License. You may not convey a covered
work if you are a party to an arrangement with a third party that is
in the business of distributing software, under which you make payment
to the third party based on the extent of your activity of conveying
the work, and under which the third party grants, to any of the
parties who would receive the covered work from you, a discriminatory
patent license (a) in connection with copies of the covered work
conveyed by you (or copies made from those copies), or (b) primarily
for and in connection with specific products or compilations that
contain the covered work, unless you entered into that arrangement,
or that patent license was granted, prior to 28 March 2007.
Nothing in this License shall be construed as excluding or limiting
any implied license or other defenses to infringement that may
otherwise be available to you under applicable patent law.
12. No Surrender of Others' Freedom.
If conditions are imposed on you (whether by court order, agreement or
otherwise) that contradict the conditions of this License, they do not
excuse you from the conditions of this License. If you cannot convey a
covered work so as to satisfy simultaneously your obligations under this
License and any other pertinent obligations, then as a consequence you may
not convey it at all. For example, if you agree to terms that obligate you
to collect a royalty for further conveying from those to whom you convey
the Program, the only way you could satisfy both those terms and this
License would be to refrain entirely from conveying the Program.
13. Use with the GNU Affero General Public License.
Notwithstanding any other provision of this License, you have
permission to link or combine any covered work with a work licensed
under version 3 of the GNU Affero General Public License into a single
combined work, and to convey the resulting work. The terms of this
License will continue to apply to the part which is the covered work,
but the special requirements of the GNU Affero General Public License,
section 13, concerning interaction through a network will apply to the
combination as such.
14. Revised Versions of this License.
The Free Software Foundation may publish revised and/or new versions of
the GNU General Public License from time to time. Such new versions will
be similar in spirit to the present version, but may differ in detail to
address new problems or concerns.
Each version is given a distinguishing version number. If the
Program specifies that a certain numbered version of the GNU General
Public License "or any later version" applies to it, you have the
option of following the terms and conditions either of that numbered
version or of any later version published by the Free Software
Foundation. If the Program does not specify a version number of the
GNU General Public License, you may choose any version ever published
by the Free Software Foundation.
If the Program specifies that a proxy can decide which future
versions of the GNU General Public License can be used, that proxy's
public statement of acceptance of a version permanently authorizes you
to choose that version for the Program.
Later license versions may give you additional or different
permissions. However, no additional obligations are imposed on any
author or copyright holder as a result of your choosing to follow a
later version.
15. Disclaimer of Warranty.
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
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IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
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IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.
17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided
above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:
<program> Copyright (C) <year> <name of author>
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
<https://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
<https://www.gnu.org/licenses/why-not-lgpl.html>.
README.md
View file @ d1fc6a75
......@@ -3,8 +3,8 @@ HCC-DOCS
This is the repository for HCC's user documentation. The documentation is a
combination of [Markdown](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet)
for the source and the [Hugo](https://gohugo.io) static site generator. Currently,
the theme used is [docDock](https://themes.gohugo.io/docdock/).
for the source and the [MkDocs](https://www.mkdocs.org/) static site generator. Currently,
the theme used is [Material for MkDocs](https://squidfunk.github.io/mkdocs-material/).
The website is viewable at https://hcc.unl.edu/docs.
......@@ -19,23 +19,16 @@ edit/create content, and preview your changes locally before creating the MR/PR.
#### Clone the repo (including submodules) and create a new branch
Clone the repo somewhere convenient. The DocDock theme is provided via a git submodule,
so after cloning, run `git submodule update --init --recursive` in the root of the repo.
Run `git checkout -b <mybranch>` to create a new branch for your changes.
Clone the repo somewhere convenient.
#### Download and install Hugo
#### Download and install MkDocs
Download the appropriate Hugo tarball from the Hugo [releases page](https://github.com/gohugoio/hugo/releases).
MkDocs, the Material for MkDocs theme, and all plugins are installable with pip.
(Direct links for [Linux](https://github.com/gohugoio/hugo/releases/download/v0.51/hugo_0.51_Linux-64bit.tar.gz), [Mac](https://github.com/gohugoio/hugo/releases/download/v0.51/hugo_0.51_macOS-64bit.tar.gz), and [Windows](https://github.com/gohugoio/hugo/releases/download/v0.51/hugo_0.51_Windows-64bit.zip))
The `hugo` program is a single binary with no dependencies and does not require root priviledges,
so just place it somewhere convenient in your `PATH` (i.e. `~/bin`).
Verify it works by running the command `hugo version`:
```
bash-4.4# hugo version
Hugo Static Site Generator v0.51 linux/amd64 BuildDate: 2018-11-07T10:10:13Z
```bash
pip install mkdocs mkdocs-material mkdocs-nav-weight \
mkdocs-material[imaging] mkdocs-awesome-nav mkdocs-macros-plugin \
mkdocs-table-reader-plugin mkdocs-include-markdown-plugin
```
### Previewing the site and adding content
......@@ -44,89 +37,129 @@ Hugo Static Site Generator v0.51 linux/amd64 BuildDate: 2018-11-07T10:10:13Z
The `hugo server` command will build the site and run a small webserver to allow you to
preview it. Depending whether you're working on your local machine or a VM on Anvil,
the option you pass needs to be slightly different. The `hugo server` command should be
run from the root of the repository (i.e. the same directory the `config.toml` file
the option you pass needs to be slightly different. The `mkdocs serve` command should be
run from the root of the repository (i.e. the same directory the `mkdocs.yml` file
resides in).
**If you're working on your local laptop/deskop:**
This will allow you to view the webiste by going to `http://localhost:8080` in your web browser.
Run the command:
```
hugo server -b http://127.0.0.1
```
Alternatively you can build the HTML files to view in a web browser using the `mkdocs build` command
from the root of the repository.
You should now be able to preview the website by going to `http://localhost:1313` in your web
browser.
**If you're working in a VM on Anvil:**
You'll first need to allow port 1313. If your VM is under the `swanson` project, there is
already an existing "Hugo" security group. Just add that group to your VM. Otherwise, first
create it and allow TCP port 1313 though. You may also need to allow port 1313 through your
You'll first need to allow port 8080. If your VM is under the `swanson` project, there is
already an existing "Port 8080" security group. Just add that group to your VM. Otherwise, first
create it and allow TCP port 8080 though. You may also need to allow port 8080 through your
instance's firewall.
Once that is done, run the command:
```
hugo server -b http://<instance IP> --bind <instance IP>
mkdocs serve
```
where *\<instance IP\>* is the 10.71.x.x address of your instance.
You should now be able to preview the website by going to `http://<instance IP>:1313` in your web
browser.
*Note: The hugo server command will watch the filesystem for changes and force an update in your browswer,
You should now be able to preview the website by going to `http://<instance IP>:8080` in your web
browser, where *\<instance IP\>* is the 10.71.x.x address of your instance.
*Note: The mkdocs serve command will watch the filesystem for changes and force an update in your browswer,
so you can simply leave the server running as you work.*
#### Adding content
The page content for the site is under the `content/` directory. The directory structure will determine
The page content for the site is under the `docs/` directory. The directory structure will determine
how the site itself is structured, so place content based on where in the site you would like it to be.
Each level in the tree will need to have an `_index.md` file to designate it as a new section. The content
itself is almost all standard markdown. However, there are a few things that are specific to Hugo that
Each level in the tree will need to have an `index.md` file to designate it as a new section. The content
itself is almost all standard markdown. However, there are a few things that are specific to MkDocs that
are used:
1. *Front matter*
[Front matter](https://gohugo.io/content-management/front-matter) is Hugo-specific metadata added
to the page. The format can be TOML, YAML, or JSON. The example here uses TOML, which is identified
by opening and closing `+++`. At minimum, each page should have a title and description:
1. *YAML Style Metadata*
[YAML Style Metadata](https://www.mkdocs.org/user-guide/writing-your-docs/#yaml-style-meta-data) is Hugo-specific metadata added
to the page. The format needs to be YAML. The example here is for our contact-us page, and is identified
by opening and closing `---` At minimum, each page should have a title and description:
```
+++
title = "Contact Us"
description = "Contact Information for HCC"
+++
---
title: "Contact Us"
description: "Contact Information for HCC"
---
```
Another useful parameter is the `weight` option. This will determine the order of display in the navigation tree;
lower numbers are displayed before higher numbers.
2. *Shortcodes*
[Shortcodes](https://gohugo.io/content-management/shortcodes) are "helper functions" to add content
that would otherwise require using raw HTML. Hugo provides some [built-in](https://gohugo.io/content-management/shortcodes/#use-hugo-s-built-in-shortcodes)
shortcodes. The DocDock theme also provides its own [shortcodes](http://docdock.netlify.com/shortcodes).
Shortcodes are added via a `{{% shortcodename parameters %}}` declaration. For example, to embed a YouTube
video with ID `-Vh7SyC-3mA`:
```
{{< youtube -Vh7SyC-3mA >}}
```
Other useful shortcodes include language-specific syntax highlighting, figures, and automatic listing
of page children for navgiation/summary pages.
3. *Using `relref` for link generation*
The `relref` shortcode should generally be used for linking to other pages within the site. This will
generate relative links that should work no matter what the base URL is. For example, assume you're
editing "my\_page.md" and want to link to the page "my\_other\_page.md" in the subdirectory "mystuff".
To do so, add the line
2. *Macros and variables*
[Macros](https://mkdocs-macros-plugin.readthedocs.io/en/latest/) are "helper functions" to add content
that would otherwise require using raw HTML.
Currently, a few custom ones are implemented.
- `{{ youtube('Emded_URL_OR_Share_Code') }}` - Embeds a youtube video into the docs
- `{{ md_table('path_or_url') }}` - Embeds a markdown table as a sortable table.
- `{{ json_table('path_or_url') }}` - Embeds a JSON table as a sortable table.
Variables allow for the use of defining shorthand codes for using the same value in multiple places in the documentation.
These are all defined in the `mkdocs.yml` file in the `extra:` section.
Variables are called using `{{ variable.path.to.value }}` where the path starts after the `extra:` block.
```yaml
extra:
hcc:
# Swan Cluster Specific Information
swan:
xfer: "swan-xfer.unl.edu"
ood:
name: "Swan Open OnDemand"
url: "https://swan-ood.unl.edu"
work:
block: "100 TiB"
```
[My other page]({{< relref "mystuff/my_other_page" >}})
Using a section of the YAML above we can get the following exampls:
- `{{ hcc.swan.xfer }}` would yield the URL for Swan's high speed transfer node
- `{{ hcc.swan.ood.url }}` would yield the block quota for Swan's $WORK filesystem
- `{{ hcc.swan.work.block }}` would yield the Open OnDemand URL for Swan
- ` {{ children('path_after_docs') }} ` - List child pages and Descriptions - do not add trailing `/`
A good file for examples of the use of these variables is `docs/handling_data/index.md` where many variables
are used to discuss the filesystems.
3. Code Blocks
Code blocks are able to use language specific formatting and use the standard markdown format for codeblocks.
```` markdown title="Example Code Block"
``` python
print('Hello World!')
```
````
4. Links
MkDocs uses standard markdown links, `[Text to Display](URL or path/to/file)`
Note that you can omit the `.md` suffix from the filename.
4. *Static content*
Hugo has special handling for static content (images, linked zip files, etc.). In the root of the repo,
there is a `static/` directory; all static content should go there. Subdirectories can be made to keep
things organized; there are existing directories for `images` and `attachments`. Feel free to create
additional directories if it makes sense. To link to static content, you can use an absolute path from
any page. For example, assuming there is an image in the repo at `static/images/my_image.png`,
you can link to it using the `figure` shortcode as `{{< figure src="/images/my_image.png" >}}`.
5. *Static content*
1. Images
Images are stored in `docs/images`.
Images can then be embeded in one of two methods. The path starts from the `images` directory.
Using markdown: `![Optional Image Title](/image/picture.png)`
Using HTML: `<img src="/images/picture.png">`
- HTML will also allow the use of standard `img` embedding and customization.
2. Markdown and HTML Files
Sometimes there are cases where information is stored statically elsewhere. These files are organized in `docs/static`
``` markdown
{%
include "relative/path/to/file.html"
%}
```
- **Special note for .png files**: In order to keep the repo size as small as possible, all images
should be png's if possible, and further processed using the [pngquant](https://pngquant.org) compression
tool. This will reduce the size by ~3-4x while keeping good quality. For example, to process and
......@@ -134,6 +167,20 @@ are used:
prior to committing the files to the repo, otherwise git will be forced to keep multiple copies as the files
are binary.*
6. Callouts
These are the callouts used to highlight information and have a few customization options.
Callout Template:
``` markdown
!!! type "Optional Title"
Content goes here. It is important to make sure to have space in the markdown file above and below the callout.
Content must also be indented
```
A full list of callout types and additional usage information is available in the [Material for MkDocs documentation page](https://squidfunk.github.io/mkdocs-material/reference/admonitions/#supported-types).
#### Adding your changes
Once you've got your set of changes, add and commit them to your branch. Push the branch and
......
archetypes/default.md deleted 100644 → 0
View file @ 2383ec36
---
title: "{{ replace .Name "-" " " | title }}"
date: {{ .Date }}
draft: true
---
config.toml deleted 100644 → 0
View file @ 2383ec36
#baseURL = "http://hcc-docs.unl.edu/"
languageCode = "en-us"
title = "HCC-DOCS"
theme = "docdock"
contentdir = "content"
layoutdir = "layouts"
publishdir = "public"
baseURL = "/"
canonifyURLs = "true"
relativeURLs = "true"
DefaultContentLanguage = "en"
pygmentsCodeFences = true
pygmentsStyle = "monokailight"
defaultContentLanguage = "en"
defaultContentLanguageInSubdir= false
enableMissingTranslationPlaceholders = false
[params]
editURL = "https://git.unl.edu/hcc/hcc-docs/edit/master/content/"
showVisitedLinks = true # default is false
themeStyle = "original" # "original" or "flex" # default "flex"
themeVariant = "blue" # choose theme variant "green", "gold" , "gray", "blue" (default)
ordersectionsby = "weight" # ordersectionsby = "title"
disableHomeIcon = false # default is false
disableSearch = false # default is false
disableNavChevron = false # set true to hide next/prev chevron, default is false
highlightClientSide = false # set true to use highlight.pack.js instead of the default hugo chroma highlighter
menushortcutsnewtab = true # set true to open shortcuts links to a new tab/window
enableGitInfo = true
[outputs]
home = [ "HTML", "RSS", "JSON"]
[[menu.shortcuts]]
name = "hcc.unl.edu"
identifier = "ds"
url = "https://hcc.unl.edu"
weight = 10
content/_footer.md deleted 100644 → 0
View file @ 2383ec36
+++
title = "Footer"
+++
{{< icon name="copyright-mark" >}} [Holland Computing Center] (https://hcc.unl.edu) | 118 Schorr Center, Lincoln NE 68588 | {{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu) | {{< icon name="phone-alt" >}}402-472-5041
content/_header.md deleted 100644 → 0
View file @ 2383ec36
+++
title = "Header"
+++
{{< figure src="/images/UNMasterwhite.gif" link="https://nebraska.edu" target="_blank" >}}
### [Holland Computing Center](https://hcc.unl.edu)
#### [HCC-DOCS]({{< relref "/" >}})
content/_index.md deleted 100644 → 0
View file @ 2383ec36
+++
title = "HCC Documentation"
description = "HCC Documentation Home"
weight = "1"
+++
HCC Documentation
============================
The Holland Computing Center supports a diverse collection of research
computing hardware. Anyone in the University of Nebraska system is
welcome to apply for an account on HCC machines.
Access to these resources is by default shared with the rest of the user
community via various job schedulers. These policies may be found on the
pages for the various resources. Alternatively, a user may buy into an
existing resource, acquiring 'priority access'. Finally, several
machines are available via Condor for opportunistic use. This will allow
users almost immediate access, but the job is subject to preemption.
#### [New Users Sign Up](http://hcc.unl.edu/new-user-request)
#### [Quick Start Guides](/quickstarts)
Which Cluster to Use?
---------------------
**Crane**: Crane is the newest and most powerful HCC resource . If you
are new to using HCC resources, Crane is the recommended cluster to use
initially. Limitations: Crane has only 2 CPU/16 cores and 64GB RAM per
node. CraneOPA has 2 CPU/36 cores with a maximum of 512GB RAM per node.
If your job requires more than 36 cores per node or you need more than
512GB of memory, consider using Tusker instead.
**Tusker**: Similar to Crane, Tusker is another cluster shared by all
campus users. It has 4 CPU/ 64 cores and 256GB RAM per node. Two nodes
have 1024GB RAM for very large memory jobs. So for jobs requiring more
than 36 cores per node or large memory, Tusker would be a better option.
User Login
----------
For Windows users, please refer to this link [For Windows Users]({{< relref "for_windows_users" >}}).
For Mac or Linux users, please refer to this link [For Mac/Linux Users]({{< relref "for_maclinux_users">}}).
**Logging into Crane or Tusker**
{{< highlight bash >}}
ssh <username>@crane.unl.edu
or
ssh <username>@tusker.unl.edu
{{< /highlight >}}
Duo Security
------------
Duo two-factor authentication is **required** for access to HCC
resources. Registration and usage of Duo security can be found in this
section: [Setting up and using Duo]({{< relref "setting_up_and_using_duo">}})
**Important Notes**
- The Crane and Tusker clusters are separate. But, they are
similar enough that submission scripts on whichever one will work on
another, and vice versa.
- The worker nodes cannot write to the `/home` directories. You must
use your `/work` directory for processing in your job. You may
access your work directory by using the command:
{{< highlight bash >}}
$ cd $WORK
{{< /highlight >}}
Resources
---------
- ##### Crane - HCC's newest machine, Crane has 7232 Intel Xeon cores in 452 nodes with 64GB RAM per node.
- ##### Tusker - consists of 106 AMD Interlagos-based nodes (6784 cores) interconnected with Mellanox QDR Infiniband.
- ##### Red - This cluster is the resource for UNL's US CMS Tier-2 site.
- [CMS](http://www.uscms.org/)
- [Open Science Grid](http://www.opensciencegrid.org)
- [MyOSG](https://myosg.grid.iu.edu/)
- ##### Anvil - HCC's cloud computing cluster based on Openstack
- ##### Glidein - A gateway to running jobs on the OSG, a collection of computing resources across the US.
Resource Capabilities
---------------------
| Cluster | Overview | Processors | RAM | Connection | Storage
| ------- | ---------| ---------- | --- | ---------- | ------
| **Crane** | 548 node Production-mode LINUX cluster | 452 Intel Xeon E5-2670 2.60GHz 2 CPU/16 cores per node<br> <br>116 Intel Xeon E5-2697 v4 2.3GHz, 2 CPU/36 cores per node<br><br>("CraneOPA") | 452 nodes @ \*64GB<br><br>79 nodes @ \*\*256GB<br><br>37 nodes @ \*\*\*512GB | QDR Infiniband<br><br>EDR Omni-Path Architecture | ~1.8 TB local scratch per node<br><br>~4 TB local scratch per node<br><br>~1452 TB shared Lustre storage
| **Tusker** | 82 node Production-mode LINUX cluster | Opteron 6272 2.1GHz, 4 CPU/64 cores per node | \*\*256 GB RAM per node<br>\*\*\*2 Nodes with 512GB per node<br>\*\*\*\*2 Nodes with 1024GB per node | QDR Infiniband | ~500 TB shared Lustre storage<br>~500GB local scratch |
| **Red** | 344 node Production-mode LINUX cluster | Various Xeon and Opteron processors 7,280 cores maximum, actual number of job slots depends on RAM usage | 1.5-4GB RAM per job slot | 1Gb, 10Gb, and 40Gb Ethernet | ~6.67PB of raw storage space |
| **Anvil** | 76 Compute nodes (Partially used for cloud, the rest used for general computing), 12 Storage nodes, 2 Network nodes Openstack cloud | 76 Intel Xeon E5-2650 v3 2.30GHz 2 CPU/20 cores per node | 76 nodes @ 256GB | 10Gb Ethernet | 528 TB Ceph shared storage (349TB available now) |
You may only request the following amount of RAM: <br>
\*62.5GB <br>
\*\*250GB <br>
\*\*\*500GB <br>
\*\*\*\*1000GB
content/events/2012/_index.md deleted 100644 → 0
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+++
title = "2012"
description = "Historical listing of various HCC events for the year 2012."
weight = "30"
+++
Historical listing of HCC Events
----------
{{% children %}}
content/events/2013/HCC_Supercomputing_Symposium_2013.md deleted 100644 → 0
View file @ 2383ec36
+++
title = "HCC Supercomputing Symposium 2013"
description = "HCC Supercomputing Symposium 2013"
+++
<strong>Location: Wick Alumni Center, Dana Board Room</strong><br>
The morning sessions will be interactive – attendees should bring a laptop if at all possible! The first sessions will be primarily planned tutorial format, while the “Open Lab” will involve more individualized help of those in attendance as desired.
| Time | Title | Description |
|---------|-------------------------------------------------------|------------------------------------------------------------------|
| 9 - 10am| Getting started at HCC | HCC 101 (Linux Primer, Job submission) [Quick Start Guides](https://hcc.unl.edu/docs/quickstarts/) |
| 10 - 11am | Job management | Creating and deploying parallel jobs at HCC, OSG [Submitting Jobs](https://hcc.unl.edu/docs/guides/submitting_jobs/) |
| 11 - 11:45am | HCC Open Lab | Presentations and help from HCC staff |
| 12 - 1pm | LUNCH lecture with UNIT | Carl Lundstedt: How Big Data Allows Us to Investigate the Smallest Things |
|1:15 – 2pm | New User Spotlight – Steve Kolbe, Theatre | Media Arts Film Rendering @ HCC |
| 2 - 3pm | State of HCC; Crane Announcement | David Swanson |
1. <span style="line-height: 1.4285715;">Getting Started at HCC (9-10am</span>
1. [Getting an account at HCC](https://hcc.unl.edu/new-user-request)
2. Logging into HCC resources for [windows](https://hcc.unl.edu/docs/quickstarts/connecting/for_windows_users/) or [Mac/Linux Users](https://hcc.unl.edu/docs/quickstarts/connecting/for_maclinux_users/)
3. Basic Linux commands
4. [Transferring files to HCC](https://hcc.unl.edu/docs/guides/handling_data/)
2. Job Management (10-11am)
1. [End to End MPI](https://hcc.unl.edu/docs/guides/running_applications/mpi_jobs_on_hcc/) example. Including how to transfer source code and compile an MPI application on Tusker.
2. [Compiling](https://hcc.unl.edu/docs/guides/running_applications/compiling_source_code/compiling_an_openmp_application/) and [submitting](https://hcc.unl.edu/docs/guides/submitting_jobs/submitting_an_openmp_job/) multi-thread and OpenMP applications.
3. Using scheduler features such as [Arrays](https://hcc.unl.edu/docs/guides/submitting_jobs/submitting_a_job_array/
) and [Dependencies](https://hcc.unl.edu/docs/guides/submitting_jobs/job_dependencies/
).
4. Debugging on Tusker by using [interactive submission](https://hcc.unl.edu/docs/guides/submitting_jobs/submitting_an_interactive_job/).
<span style="line-height: 1.4285715;">&lt;lunch&gt;</span>
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title = "2013"
description = "Historical listing of various HCC events for the year 2013."
weight = "30"
+++
Historical listing of HCC Events
----------
{{% children %}}
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title = "HCC Condor Workshop 2013"
description = "HCC Condor Workshop 2013."
+++
Condor
============
Workshop presentation slides
&lt;[condor\_workshop.pdf](https://unl.box.com/s/ou8tf62bqkbrh7yx0cl4me1zbp3z0j08)&gt;
| Time | Title | Description |
|---------|-------------------------|------------------------------------------------|
| 1pm-2pm | Demo/Hand-On Practice | Executing Condor jobs on HCC supertcomputers |
| 2pm-3pm | Individual Consultation | Bring your research code on HCC supercomputers |
Password for all demo accounts is **HCC\_condor2013**.
Replace `<group name>` with `demo` and `<username>` with `demoXX` (e.g. `demo01`).
- Get started with [For Windows Users](https://hcc.unl.edu/docs/quickstarts/connecting/for_windows_users/)
or [For Mac/Linux Users](https://hcc.unl.edu/docs/quickstarts/connecting/for_maclinux_users/).
- Sample code for Fortran/C on HCC:
&lt;[serial\_dir.zip](https://unl.box.com/s/khkpt68pe3k0lu2ythn9kzjeva40itdd)&gt;
- Sample code for Condor on HCC:
&lt;[condor\_dir.zip](https://unl.box.com/s/qpvgnqr9ukjcmt0d2trde4qcp5e5ez17)&gt;
- For more details of this demonstration, see [Condor Jobs on
HCC](https://hcc.unl.edu/docs/guides/submitting_jobs/condor_jobs_on_hcc/).
MATLAB
============
Workshop presentation slides
&lt;[matlab\_workshop.pdf](https://unl.box.com/s/ou8tf62bqkbrh7yx0cl4me1zbp3z0j08)&gt;
| Time | Title | Description |
|---------|-------------------------|---------------------------------------------------|
| 1pm-2pm | Demo/Hand-On Practice | Implementing a MATLAB code on HCC supertcomputers |
| 2pm-3pm | Individual Consultation | Bring your MATLAB code on HCC supercomputers |
Password for all demo accounts is **HCC\_matlab2013**.
Replace `<group name>` with `demo` and `<username>` with `demoXX` (e.g. `demo01`).
- Get started with [For Windows Users](https://hcc.unl.edu/docs/quickstarts/connecting/for_windows_users/)
or [For Mac/Linux Users](https://hcc.unl.edu/docs/quickstarts/connecting/for_maclinux_users/).
- Hands On: [MATLAB on HCC](https://hcc.unl.edu/docs/guides/submitting_jobs/submitting_matlab_jobs/)
- Sample code for MATLAB on HCC:
&lt;[matlab\_dir.zip](https://unl.box.com/s/u19fy7cjeswfl1wi7h1nkeeie8gl3z90)&gt;
- Sample code for Parallel MATLAB Job:
&lt;[parallel\_matlab\_dir.zip](https://unl.box.com/s/fhl3kf6hg8dmtozkphq3u2r58yexrppe)&gt;
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title = "HCC Matlab Workshop 2013"
description = "HCC Matlab Workshop 2013."
+++
Workshop presentation slides
&lt;[matlab\_workshop.pdf](https://unl.box.com/s/lulbnbrnr7xqwufrx5s20gxnyxpykn7j)&gt;
| Time | Title | Description |
|-------------|-------------------------|--------------------------------------------------|
| UNMC | | |
| 10am - 11am | Demo/Hand-On Practice | Implementing a MATLAB code on HCC supercomputers |
| 11am - 12pm | Individual Consultation | Bring your MATLAB code on HCC supercomputers |
| UNO | | |
| 2pm - 3pm | Demo/Hand-On Practice | Implementing a MATLAB code on HCC supercomputers |
| 3pm - 4pm | Individual Consultation | Bring your MATLAB code on HCC supercomputers |
Password for all demo accounts is **HCC\_matlab2013**.
Replace `<group name>` with `demo` and `<username>` with `demoXX`
(e.g. `demo01`).
- Get started with [For Windows Users](https://hcc.unl.edu/docs/quickstarts/connecting/for_windows_users/)
or [For Mac/Linux Users](https://hcc.unl.edu/docs/quickstarts/connecting/for_maclinux_users/).
- Hands On: [MATLAB on HCC](https://hcc.unl.edu/docs/guides/submitting_jobs/submitting_matlab_jobs/)
- Sample code for MATLAB on HCC:
&lt;[matlab\_dir.zip](https://unl.box.com/s/u19fy7cjeswfl1wi7h1nkeeie8gl3z90)&gt;
- Sample code for Parallel MATLAB Job:
&lt;[parallel\_matlab\_dir.zip](https://unl.box.com/s/fhl3kf6hg8dmtozkphq3u2r58yexrppe)&gt;
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title = "HCC MPI Workshop 2013"
description = "HCC MPI Workshop 2013."
+++
Workshop presentation slides &lt;[mpi\_workshop.pdf](https://unl.box.com/s/7rufq2a39n2vektg19ko9fjcbios4kqp)&gt;
| Time | Title | Description |
|---------|-------------------------|------------------------------------------------|
| 1pm-2pm | Demo/Hand-On Practice | Implementing a MPI code on HCC supertcomputers |
| 2pm-3pm | Individual Consultation | Bring your research code on HCC supercomputers |
Password for all demo accounts is **HCC\_mpi2013**.
Replace `<group name>` with `demo` and `<username>` with `demoXX` (e.g. `demo01`).
- Get started with [For Windows Users](https://hcc.unl.edu/docs/quickstarts/connecting/for_windows_users/)
or [For Mac/Linux Users](https://hcc.unl.edu/docs/quickstarts/connecting/for_maclinux_users/).
- Sample code for Fortran/C on HCC:
&lt;[serial\_dir.zip](https://unl.box.com/s/khkpt68pe3k0lu2ythn9kzjeva40itdd)&gt;
- Sample code for MPI on HCC:
&lt;[mpi\_dir.zip](https://unl.box.com/s/fekjdxx82gxp3x75nbsrqmrri52d4zlp)&gt;
- For more details of this demonstration, see [MPI Jobs on
HCC](https://hcc.unl.edu/docs/guides/submitting_jobs/submitting_an_mpi_job/).
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title = "2014"
description = "Historical listing of various HCC events for the year 2014."
weight = "30"
+++
Historical listing of HCC Events
----------
{{% children %}}
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title = "August 2014 UNO Workshop"
description = "August 2014 UNO Workshop."
+++
When: August 29, 2014
Where: UNO Criss Library room 232
<a href="http://hcc.unl.edu/fall-workshop-august-29-uno" class="external-link">Registration</a>
Please bring a laptop.
Download Slides: [ppt](attachments/8192949/8127063.pptx)
[ ](attachments/8192949/8127064.pdf)[PDF](attachments/8192949/8127064.pdf)
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[HCC\_UNO\_Workshop\_Aug\_2014.pptx](attachments/8192949/8127063.pptx)
(application/vnd.openxmlformats-officedocument.presentationml.presentation)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[HCC\_UNO\_Workshop\_Aug\_2014.pdf](attachments/8192949/8127065.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[HCC\_UNO\_Workshop\_Aug\_2014.pdf](attachments/8192949/8127064.pdf)
(application/pdf)
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title = "July 2014 Bioinformatics Workshop"
description = "July 2014 Bioinformatics Workshop"
+++
Quick
link: <a href="http://cse.unl.edu/~bioinfo/workshop/" class="external-link">http://cse.unl.edu/~bioinfo/workshop/</a>
Monday - Wednesday, July 28 -30 (lunch will be provided)
[Download Workshop Schedule](attachments/8192294/8126551.pdf)
[Download Galaxy101 PowerPoint](attachments/8192294/8126550.pptx)
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[Bioinfo2014\_Galaxy101.pptx](attachments/8192294/8126550.pptx)
(application/vnd.openxmlformats-officedocument.presentationml.presentation)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[Workshop\_schedule.pdf](attachments/8192294/8126551.pdf)
(application/pdf)