diff --git a/assets/js/academic-search.js b/assets/js/academic-search.js new file mode 100644 index 00000000..de29e191 --- /dev/null +++ b/assets/js/academic-search.js @@ -0,0 +1,185 @@ +/************************************************* + * Academic + * https://github.com/gcushen/hugo-academic + * + * In-built Fuse based search algorithm. + **************************************************/ + +/* --------------------------------------------------------------------------- +* Configuration. +* --------------------------------------------------------------------------- */ + +// Configure Fuse. +let fuseOptions = { + shouldSort: true, + includeMatches: true, + tokenize: true, + threshold: search_config.threshold, // Set to ~0.3 for parsing diacritics and CJK languages. + location: 0, + distance: 100, + maxPatternLength: 32, + minMatchCharLength: search_config.minLength, // Set to 1 for parsing CJK languages. + keys: [ + {name:'title', weight:0.99}, /* 1.0 doesn't work o_O */ + {name:'summary', weight:0.6}, + {name:'authors', weight:0.5}, + {name:'content', weight:0.2}, + {name:'tags', weight:0.5}, + {name:'categories', weight:0.5} + ] +}; + +// Configure summary. +let summaryLength = 60; + +/* --------------------------------------------------------------------------- +* Functions. +* --------------------------------------------------------------------------- */ + +// Get query from URI. +function getSearchQuery(name) { + return decodeURIComponent((location.search.split(name + '=')[1] || '').split('&')[0]).replace(/\+/g, ' '); +} + +// Set query in URI without reloading the page. +function updateURL(url) { + if (history.replaceState) { + window.history.replaceState({path:url}, '', url); + } +} + +// Pre-process new search query. +function initSearch(force, fuse) { + let query = $("#search-query").val(); + + // If query deleted, clear results. + if ( query.length < 1) { + $('#search-hits').empty(); + } + + // Check for timer event (enter key not pressed) and query less than minimum length required. + if (!force && query.length < fuseOptions.minMatchCharLength) + return; + + // Do search. + $('#search-hits').empty(); + searchAcademic(query, fuse); + let newURL = window.location.protocol + "//" + window.location.host + window.location.pathname + '?q=' + encodeURIComponent(query) + window.location.hash; + updateURL(newURL); +} + +// Perform search. +function searchAcademic(query, fuse) { + let results = fuse.search(query); + // console.log({"results": results}); + + if (results.length > 0) { + $('#search-hits').append('
-
+
+
-
+
+
c. Go to `Analyze` > `Set Measurements...`. In the popup dialog specify the parameters as shown in this screenshot. Click `OK`.
d. Go to `Analyze` > `Analyze Particles` and set up the parameters as shown. Click `OK`.
-
-
+
+
e. These steps should create a `Results` and a `Summary` table.
diff --git a/content/courses/fiji-image-processing/introduction/index.md b/content/courses/fiji-image-processing/introduction/index.md
index 186c3091..1e4302a5 100644
--- a/content/courses/fiji-image-processing/introduction/index.md
+++ b/content/courses/fiji-image-processing/introduction/index.md
@@ -10,7 +10,7 @@ url_dataset: data/intro-fiji-images.zip
{{< figure src="/img/fiji.png" >}}
-{{% link-button href="/data/intro-fiji-images.zip" icon="fa fa-download" %}}Data{{% /link-button %}}
+{{% link-button href="/data/intro-fiji-images.zip" icon="fa fa-download" aria-label="Download Data" title="Download Data" %}}Data{{% /link-button %}}
## Fiji Installation
diff --git a/content/courses/fiji-image-processing/scripting/index.md b/content/courses/fiji-image-processing/scripting/index.md
index 5f4e91d4..5d49b0ad 100644
--- a/content/courses/fiji-image-processing/scripting/index.md
+++ b/content/courses/fiji-image-processing/scripting/index.md
@@ -9,7 +9,7 @@ url_code: /scripts/fiji/fiji-example-scripts.zip
{{< figure library="true" src="fiji.png" >}}
-{{% link-button href="/scripts/fiji/fiji-example-scripts.zip" icon="fa fa-download" %}}Scripts{{% /link-button %}}
+{{% link-button href="/scripts/fiji/fiji-example-scripts.zip" icon="fa fa-download" title="Download Scripts" aria-label="Download Scripts" %}}Scripts{{% /link-button %}}
This chapter is an introduction to the scripting interface of the [Fiji](https://fiji.sc) application, an open-source and enhanced version of the popular ImageJ program used for scientific image processing. Here you will learn how to write scripts for automated execution of image processing pipelines and batch processing of multiple image files in Fiji.
diff --git a/content/landing/_index.md b/content/landing/_index.md
index 74176e63..8ec49902 100644
--- a/content/landing/_index.md
+++ b/content/landing/_index.md
@@ -5,9 +5,9 @@ subtitle = ""
## [Tutorials](/tutorials) are perfect for introducing yourself to a new topic.
-Some tutorials are offered as in-person and/or Zoom workshops regularly. Find the notes or slides and download materials [here](/tutorials).
+Some tutorials are offered as in-person and/or Zoom workshops regularly. Find the notes or slides and download materials [on the Tutorials page](/tutorials).
-For a list of upcoming workshops, please see our [page](https://www.rc.virginia.edu/education/workshops/) at the UVARC Website.
+For a list of upcoming workshops, please see [the Workshops page](https://www.rc.virginia.edu/education/workshops/) at the UVARC Website.
## [Short courses](/courses) are longer and more in-depth than tutorials or workshops.
diff --git a/content/notes/slurm-from-cli/_index.md b/content/notes/slurm-from-cli/_index.md
index 99183d94..ee2b5005 100644
--- a/content/notes/slurm-from-cli/_index.md
+++ b/content/notes/slurm-from-cli/_index.md
@@ -5,12 +5,13 @@ type: docs
weight: 1
menu:
slurm-from-cli:
+ name: The Slurm Resource Manager
---
-{{< figure src="/notes/slurm-from-cli/img/slurm_logo.png" width=30% >}}
+{{< figure src="/notes/slurm-from-cli/img/slurm_logo.png" width=30% alt="Slurm resource manager logo" >}}
-[Slurm](https://slurm.schedmd.com/) is a __resource manager__ (RM), also known as a _queueing system_.
+[Slurm](https://slurm.schedmd.com/ "The official Slurm website") is a __resource manager__ (RM), also known as a _queueing system_.
Resource managers are used to submit _jobs_ on a computing cluster to compute nodes from an access point generally called a login node.
diff --git a/content/notes/slurm-from-cli/img/slurm_logo.png b/content/notes/slurm-from-cli/img/slurm_logo.png
index f3e7acd7..b99e7459 100644
Binary files a/content/notes/slurm-from-cli/img/slurm_logo.png and b/content/notes/slurm-from-cli/img/slurm_logo.png differ
diff --git a/content/notes/slurm-from-cli/section1.md b/content/notes/slurm-from-cli/section1.md
index 4efa862b..9e2716d0 100644
--- a/content/notes/slurm-from-cli/section1.md
+++ b/content/notes/slurm-from-cli/section1.md
@@ -10,7 +10,7 @@ menu:
## Resources and Partitions
-An HPC **job** is a description of the resources required, any preparatory steps such as loading [modules](https://www.rc.virginia.edu/userinfo/rivanna/software/modules/) or otherwise setting up an environment, and the commands to run the software, along with any postprocessing that may be appropriate.
+An HPC **job** is a description of the resources required, any preparatory steps such as loading [modules](https://www.rc.virginia.edu/userinfo/rivanna/software/modules/ "The Research Computing website's modules page") or otherwise setting up an environment, and the commands to run the software, along with any postprocessing that may be appropriate.
The job is specified through a special form of script often called a _batch script_. Usually it is written in `bash`.
@@ -34,7 +34,7 @@ Slurm began when cpus had only one core each. Beginning around 2005, cpus began
**Memory** refers to _random-access memory_. It is not the same thing as storage. If a process reports running out of memory, it means RAM memory. Running out of disk space will result in a different error.
-For more details about the structure of a computational cluster, see our [introduction](https://learning.rc.virginia.edu/notes/hpc-intro/).
+For more details about the structure of a computational cluster, see our [introduction](/notes/hpc-intro/ "Intro to High Performance Computing notes").
## Processes and Tasks
A **process** can be envisioned an instance of an executable that is running on a particular computer. Most executables run only a single process. Some executables run _threads_ within the _root_ process.
@@ -44,7 +44,7 @@ Slurm refers to the root process as a **task**. By default, each task is assigne
## Slurm Resource Requests
-SLURM refers to queues as __partitions__ . We do not have a default partition; each job must request one explicitly.
+SLURM refers to queues as __partitions__. We do not have a default partition; each job must request one explicitly.
{{< table >}}
| Queue Name | Purpose | Job Time Limit | Max Memory / Node / Job | Max Cores / Node |
diff --git a/content/notes/slurm-from-cli/section2.md b/content/notes/slurm-from-cli/section2.md
index b8d0a6f0..22f1b137 100644
--- a/content/notes/slurm-from-cli/section2.md
+++ b/content/notes/slurm-from-cli/section2.md
@@ -16,13 +16,13 @@ Several options are available to prepare batch scripts.
### Graphical Editors
-You can log in to a [FastX](https://www.rc.virginia.edu/userinfo/rivanna/logintools/fastx/), which provides a [MATE](https://mate-desktop.org/) desktop environment. One of the tools is a graphical editor very similar to Notepad. It is called `pluma` by MATE, but we have made it available as `gedit` if started from a terminal. If you wish to start it from a menu, it is available from Applications→Accessories.
+You can log in to a [FastX](https://www.rc.virginia.edu/userinfo/rivanna/logintools/fastx/ "Research Computing's FastX info page"), which provides a [MATE](https://mate-desktop.org/ "The official MATE website") desktop environment. One of the tools is a graphical editor very similar to Notepad. It is called `pluma` by MATE, but we have made it available as `gedit` if started from a terminal. If you wish to start it from a menu, it is available from Applications→Accessories.
-You can also use [Open OnDemand's](https://www.rc.virginia.edu/userinfo/rivanna/ood/overview/) built-in file manager and editor. Create a new file from the Files menu. Select the file and choose `Edit` from the three-dot dropdown menu to the right of the file name. This will open a very basic text editor.
+You can also use [Open OnDemand's](https://www.rc.virginia.edu/userinfo/rivanna/ood/overview/ "Research Computing's Open OnDemand info page") built-in file manager and editor. Create a new file from the Files menu. Select the file and choose `Edit` from the three-dot dropdown menu to the right of the file name. This will open a very basic text editor.
### Command-Line Editors
-Editors available at the command line are [nano](https://www.nano-editor.org/), [vim](https://www.vim.org/), and [emacs](https://www.gnu.org/software/emacs/). Nano is a simple text-only editor. Vim is also available text-only from a command line, but a graphical version called `gvim` can be invoked from a MATE Desktop through the Applications→Accessories menu. Emacs can also be started from the Accessories menu but, if a graphical environment, will start a graphical user interface. If invoked within a text-only environment, it will fall back to a text interface.
+Editors available at the command line are [nano](https://www.nano-editor.org/ "The official nano website"), [vim](https://www.vim.org/ "The official vim website"), and [emacs](https://www.gnu.org/software/emacs/ "The official emacs website"). Nano is a simple text-only editor. Vim is also available text-only from a command line, but a graphical version called `gvim` can be invoked from a MATE Desktop through the Applications→Accessories menu. Emacs can also be started from the Accessories menu but, if a graphical environment, will start a graphical user interface. If invoked within a text-only environment, it will fall back to a text interface.
### Open OnDemand Tool
@@ -60,7 +60,7 @@ The lines starting with `#SBATCH` are the resource requests. They are called "p
```
Here we are requesting
* 1 node, 1 task, 1 core
- * 32GB of memory (measured in MB). Strictly speaking this will be "Gibibyes."
+ * 32GB of memory (measured in MB). Strictly speaking this will be "Gibibytes."
* 2 hours of running time.
* The interactive partition (queue). A partition must be specified.
* The account (allocation) group `hpc_training`
@@ -120,7 +120,7 @@ Angle brackets `< >` indicate a value to be specified, and are not typed.
| -t \