Merge branch 'master' into…

Merge branch 'master' into 5-add-a-question-and-answer-to-the-faq-regarding-root-access-on-the-cluster

Gemfile

 source "https://rubygems.org"
 
-gem "jekyll-rtd-theme", "~> 2.0.10"
+gem "jekyll-rtd-theme", git: "https://github.com/StarHPC/jekyll-rtd-theme"
 
 gem "github-pages", group: :jekyll_plugins
 

README.md

@@ -17,12 +17,18 @@ code examples are provided under the [MIT](https://opensource.org/licenses/MIT)
 
 ### Install build tools and dependencies.
 
+<details> 
+	<summary>Liquid 4.0.3</summary>
+
 > [!WARNING]
-> Due to Liquid not being updated to work with Ruby 3.2.x, **make sure you have Ruby 3.1.x or older installed**.
+> If you have the latest dependencies installed, the following does not apply anymore.
+> 
+> The original `jekyll-rtd-theme` 2.0.10 required `github-pages` 209, which effectively capped the version of Liquid to 4.0.3.
+> Due to Liquid 4.0.3 and older not being updated to work with Ruby 3.2.x, Ruby 3.1.x or older was required for Liquid 4.0.3.
 > https://talk.jekyllrb.com/t/liquid-4-0-3-tainted/7946/18
 > 
 > #### With Cygwin
-> As of this writing (8/8/2024), Cygwin provides Ruby versions 2.6.4-1 and 3.2.2-2. Make sure to install the former. Additionally, the version of bundler supplied with Ruby 2.6 is too old and the version of RubyGems is too new. *After installing the following dependencies*, you must then install the correct versions of RubyGems and bundler manually:
+> As of 8/8/2024, Cygwin provided Ruby versions 2.6.4-1 and 3.2.2-2. You would need to make sure to install the former. As the version of bundler supplied with Ruby 2.6 is too old and the version of RubyGems is too new, the correct versions of RubyGems and bundler would need to be installed manually after installing all the other dependencies:
 > ```
 > gem update --system 3.2.3
 > gem install bundler -v 2.1.4
@@ -31,6 +37,8 @@ code examples are provided under the [MIT](https://opensource.org/licenses/MIT)
 > bundler -v
 > ```
 
+</details>
+
 To allow building of native extensions, install `ruby-devel`, `gcc`, and `make`.
 
 Install `libxml2`, `libxml2-devel`, `libxslt`, `libxslt-devel`, `libiconv`,
@@ -58,6 +66,10 @@ want to try running `bundle update` or removing `Gemfile.lock` and then running
 git clone https://github.com/starhpc/docs.git star-docs
 cd star-docs
 gem install bundler
+bundle config set --local path ~/.bundler  # Optionally specify where to install gems (SO Q&A #8257833).
+                                           # Otherwise, bundler may attempt to install gems system-wide,
+                                           # e.g. /usr/share/gems, depending on your GEM_HOME
+                                           # (see SO Q&A #11635042 and #3408868).
 bundle install
 bundle exec jekyll serve
 ```

_config.yml

@@ -16,4 +16,4 @@ exclude:
 plugins:
   - jemoji
   - jekyll-avatar
-  - jekyll-mentions
+  - jekyll-mentions
\ No newline at end of file

help/faq.md

@@ -63,14 +63,37 @@ Yes. Please see `/software/python_r_perl`.
 
 ### How can I check my disk quota and disk usage?
 
-repquota prints a summary of the disc usage and quotas for the specified file systems.
+To check the disk quota of your home directory ( /home/username ), you can use the repquota command which prints a summary of the disc usage and quotas for the specified file systems.
 
     $ /usr/sbin/repquota -a -s
     $                    Block limits                 File limits
     $ User              used    soft    hard  grace    used   soft  hard  grace
     $ cchave6    --     116M   1024M   1280M           1922      0     0
 
-If you want to see the quota on the home directory where the file system is ext4, the quota information is stored in files named aquota.user and aquota.group at the root of filesystem.
+Here,
+
+Soft Limit -> This is a warning threshold. A user can exceed this limit temporarily, but they must reduce usage back under this limit within a "grace period."
+
+Hard Limit -> This is the absolute maximum disk space or number of files a user can use. The user cannot exceed this limit at all.
+
+Grace Period -> The amount of time a user is allowed to exceed the soft limit before they are required to get back under it. If this period expires, the soft limit becomes enforced like a hard limit.
+
+File limits (inodes) -> These limit the number of files a user can create, regardless of their size.
+
+
+
+To check the quota of the main project storage (parallel file system - /fs1/proj/<project>), you can use this command:
+
+    $ mmlsquota -j <fileset_name> <filesystem_name>
+
+The -j option specifies that you are querying a fileset. Filesets in GPFS are similar to directories that can have independent quota limits.
+
+fileset_name -> This is the name of the fileset whose quota you want to check.
+
+filesystem_name -> The name of the GPFS filesystem in which the fileset resides.
+
+example: mmlsquota -j project_fileset gpfs1
+
 
 ### How many CPU hours have I spent?
 

index.md

@@ -9,4 +9,4 @@ Please see the [Quick Start Guide]({{site.baseurl}}{% link quickstart/quickstart
 
 ## Getting help
 
-First, please read [how to write good support requests]({{site.baseurl}}{% link help/writing-support-requests.md %}). Then shoot us an email.
+First, please read [how to write good support requests]({{site.baseurl}}{% link help/writing-support-requests.md %}). Then [contact us]({{site.baseurl}}{% link help/contact.md %}).

quickstart/quickstart.md

@@ -87,5 +87,5 @@ Project-specific directories may be created upon request for shared storage amon
 
 To make proper use of the cluster, please familiarize yourself with the basics of using Slurm, fundamental HPC concepts, and the cluster's architecture.
 
-You may be familiar with the `.bashrc`, `.bash_profile`, or `.cshrc` files for environment customization. To support different environments needed for different software packages, environment modules are used. Modules allow you to load and unload various software environments tailored to your computational tasks.
+You may be familiar with the `.bashrc`, `.bash_profile`, or `.cshrc` files for environment customization. To support different environments needed for different software packages, [environment modules]({{site.baseurl}}{% link software/env-modules.md %}) are used. Modules allow you to load and unload various software environments tailored to your computational tasks.
 

storage/file_transfer.md

@@ -48,6 +48,20 @@ Rsync is a particularly useful tool and is recommended for transferring files to
 
 When transferring very large files or datasets, it is advised to use rsync and to calculate and confirm checksums to ensure data integrity.
 
+## Cyberduck
+
+Cyberduck is a file transfer application with an intuitive graphical interface for transfering files to or from a remote machine. Cyberduck is available for both Windows and Mac. Download it from [cyberduck.io](https://cyberduck.io/).
+
+Click "Open Connection" and a new window will be displayed like below. Select "SFTP (SSH File Transfer Protocol)" from the top dropdown menu. Enter the server, port number, your username, and Linux Lab password. Then click "Connect".
+
+   ![3-connection.png]({{ site.baseurl }}/images/cyberduck_setup_images/3-connection.png "3-connection.png")
+
+If you see a window asking about an "Unknown fingerprint", click "Always" and then "Allow".
+
+   ![4-fingerprint.png]({{ site.baseurl }}/images/cyberduck_setup_images/4-fingerprint.png "4-fingerprint.png")
+
+You should now be able to see your user's home directory on the cluster. You can transfer files to and from it by dragging and dropping files between this window and your "Finder" windows.
+
 ## Network Interfaces and Bandwidth
 
 All file transfer access to the Star HPC Cluster is currently through the login node's 1GbE interface. Users should be aware of potential bandwidth limitations, especially when transferring large amounts of data.
@@ -55,3 +69,4 @@ All file transfer access to the Star HPC Cluster is currently through the login
 ## User Authentication and Permissions
 
 File transfers are authenticated in the same way as SSH access. SSH keys are the preferred method for secure authentication, although password authentication is currently allowed. Plans for implementing Multi-Factor Authentication (MFA) are being considered for future security enhancements.
+