From 6d6d0de8e7128c0190a15c1d82ec1351ea193545 Mon Sep 17 00:00:00 2001 From: Jeff Ohrstrom Date: Thu, 16 Jan 2025 09:52:55 -0500 Subject: [PATCH] More misspelling updates (#1073) Fix these pages mispellings and add lots of spelling words to this list. --- source/glossary.rst | 2 +- .../how-tos/app-development/app-sharing.rst | 16 ++--- .../enabling-development-mode.rst | 28 ++++----- source/how-tos/debug/debug-apache.rst | 6 +- source/install-ihpc-apps.rst | 4 +- source/release-notes/v1.3-release-notes.rst | 38 ++++++------ source/release-notes/v1.4-release-notes.rst | 40 ++++++------- source/release-notes/v1.5-release-notes.rst | 34 +++++------ source/release-notes/v1.7-release-notes.rst | 34 +++++------ source/release-notes/v1.8-release-notes.rst | 40 ++++++------- source/release-notes/v2.0-release-notes.rst | 22 +++---- source/release-notes/v3.1-release-notes.rst | 42 +++++++------- source/release-notes/v4.0-release-notes.rst | 12 ++-- source/spelling_wordlist.txt | 58 +++++++++++++++++++ source/version-policy.rst | 4 +- 15 files changed, 219 insertions(+), 161 deletions(-) diff --git a/source/glossary.rst b/source/glossary.rst index 2a2180464..57f96da5f 100644 --- a/source/glossary.rst +++ b/source/glossary.rst @@ -14,7 +14,7 @@ Glossary Runs on the cluster but is not a compute-node. Web-node - A term used for when a site or institution has enough funds/personel to run the OOD login on a dedicated server and not on a login-node. + A term used for when a site or institution has enough funds/personnel to run the OOD login on a dedicated server and not on a login-node. PUN The Per User Nginx. An Nginx instance running as the user. diff --git a/source/how-tos/app-development/app-sharing.rst b/source/how-tos/app-development/app-sharing.rst index a82654a32..2ac176b7b 100644 --- a/source/how-tos/app-development/app-sharing.rst +++ b/source/how-tos/app-development/app-sharing.rst @@ -23,7 +23,7 @@ Apps may be shared via a variety of methods including: System Installed Apps --------------------- -Admins may install apps to the system by copying the application directory to ``/var/www/ood/apps/sys``. Default directory permissions (``755``) will allow all users with access to OnDemand to see and run that app. Apps may have their access restricted by changing the permissions on individual application directories. For example if a site does not wish to show licensed software to un-licensed users they might do the following: +Admins may install apps to the system by copying the application directory to ``/var/www/ood/apps/sys``. Default directory permissions (``755``) will allow all users with access to OnDemand to see and run that app. Apps may have their access restricted by changing the permissions on individual application directories. For example if a site does not wish to show licensed software to unlicensed users they might do the following: .. code-block:: sh @@ -95,7 +95,7 @@ These changes take effect immediately, although when a user is added or removed Code Sharing ------------ -Code sharing is when an application's source code is shared between two or more users who run it as a personal development application. Models for this sharing can include using a web-based file repository such as Github, emailing Zip'd app directories, or a group readable directory symlinked to each user's ``~/ondemand/dev/`` directory. +Code sharing is when an application's source code is shared between two or more users who run it as a personal development application. Models for this sharing can include using a web-based file repository such as Github, emailing zipped app directories, or a group readable directory symlinked to each user's ``~/ondemand/dev/`` directory. For an example of the later consider: @@ -138,7 +138,7 @@ Enabling The App Sharing Dashboard for finding an app. #. Set ``OOD_APP_CATALOG_URL=https://link.to.online/app/catalog`` to link externally to an advertised listing of apps available. -#. Pin usr apps to the dashboard and group them by category. +#. Pin user (``usr``) apps to the dashboard and group them by category. .. code:: yaml @@ -185,7 +185,7 @@ approach has these benefits (assuming users named ``efranz`` and ``an0047``: permissions on this directory. Thus by setting ``750`` on ``/var/www/ood/apps/usr/an0047`` this ensures that an0047 can only share apps with users in his primary group. At times we have created a \ - supplemental group (shinyusr) and chgrp the share directory to this group so + supplemental group (``shinyusr``) and chgrp the share directory to this group so that the developer can share apps with every user in this group. #. The developer who can share apps can modify permissions on the app directories themselves i.e. @@ -206,9 +206,9 @@ In summary, to enable a new user to create shared apps, run these commands: Example of Executable Sharing ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -This is with two users Eric (efranz) and Bob (an0047). +This is with two users Eric (``efranz``) and Bob (``an0047``). -Eric has a dev app "MATLAB", and interactive plugin app. Eric can +Eric has a development app "MATLAB", and interactive plugin app. Eric can 1. Launch MATLAB 2. View and Edit the code @@ -224,11 +224,11 @@ i.e. ``~efranz/ondemand/dev/matlab``: .. figure:: /images/app-sharing-2.png :align: center -If Eric shares the git repo path or URL with Bob, Bob can clone this into his +If Eric shares the git repository path or URL with Bob, Bob can clone this into his home directory if he is enabled as a developer. This is called "Source Code Sharing". Eric can share this app with Bob by selecting "My Shared Apps" and cloning the MATLAB -repo to deploy ``~efranz/ondemand/share/matlab`` +repository to deploy ``~efranz/ondemand/share/matlab`` .. figure:: /images/app-sharing-3.png :align: center diff --git a/source/how-tos/app-development/enabling-development-mode.rst b/source/how-tos/app-development/enabling-development-mode.rst index d5734b3c8..11af72ee2 100644 --- a/source/how-tos/app-development/enabling-development-mode.rst +++ b/source/how-tos/app-development/enabling-development-mode.rst @@ -6,9 +6,9 @@ Enabling App Development Enable in OnDemand v1.6+: ......................... -Here are example steps to enable a user "efranz", assuming efranz's home directory is at ``/home/efranz``: +Here are example steps to enable a user ``efranz``, assuming ``efranz``'s home directory is at ``/home/efranz``: -#. Create a symlink so OnDemand finds efranz's apps: +#. Create a symlink so OnDemand finds ``efranz``'s apps: .. code:: sh @@ -17,15 +17,15 @@ Here are example steps to enable a user "efranz", assuming efranz's home directo sudo ln -s /home/efranz/ondemand/dev gateway -#. Have efranz access the Dashboard, and efranz will see the Develop dropdown +#. Have ``efranz`` access the Dashboard, and they will see the Develop drop-down. Enable in OnDemand v1.4 & v1.5: ............................... -Here are example steps to enable a user "efranz", assuming efranz's home directory is at ``/home/efranz``: +Here are example steps to enable a user ``efranz``, assuming ``efranz``'s home directory is at ``/home/efranz``: -#. Create a symlink so OnDemand finds efranz's apps: +#. Create a symlink so OnDemand finds ``efranz``'s apps: .. code:: sh @@ -33,17 +33,17 @@ Here are example steps to enable a user "efranz", assuming efranz's home directo cd /var/www/ood/apps/dev/efranz sudo ln -s /home/efranz/ondemand/dev gateway -#. Create dev directory ``/home/efranz/ondemand/dev`` where efranz's dev apps will go (or ask efranz to do that) -#. Have efranz access the Dashboard, and efranz will see the Develop dropdown +#. Create ``dev`` directory ``/home/efranz/ondemand/dev`` where ``efranz``'s development apps will go (or ask ``efranz`` to do that). +#. Have ``efranz`` access the Dashboard, and they will see the Develop drop-down. Enable in OnDemand v1.3: ........................ -Here are example steps to enable a user "efranz", assuming efranz's home directory is at ``/home/efranz``: +Here are example steps to enable a user ``efranz``, assuming ``efranz``'s home directory is at ``/home/efranz``: -#. Create dev directory ``/home/efranz/ondemand/dev`` where efranz's dev apps will go (or ask efranz to do that) -#. Have efranz access the Dashboard, and efranz will see the Develop dropdown. (if this doesn't happen, ) +#. Create ``dev`` directory ``/home/efranz/ondemand/dev`` where ``efranz``'s development apps will go (or ask ``efranz`` to do that). +#. Have ``efranz`` access the Dashboard, and they will see the Develop drop-down. (if this doesn't happen, ) .. note:: @@ -55,13 +55,13 @@ Specify dedicated host for development (optional) The default host for the shell app is typically a login node. If this node does not contain a similar environment as the host OnDemand is installed on, including access to Software Collection (SCL) packages, it may be useful to provide developers a dedicated development host they can SSH to. This could even be the OnDemand host itself. If you configure the OnDemand dashboard to know about the dedicated development host, the dashboard will present links to open the shell app to this host. -To specify a dedicated development host so OnDemand, set ``OOD_DEV_SSH_HOST`` environment variable for the dashboard in the file ``/etc/ood/config/apps/dashboard/env``. For example at OSC one of our OnDemand installs uses ondemand-test.osc.edu for the development host so we have this line: `OOD_DEV_SSH_HOST="ondemand-test.osc.edu" `_ +To specify a dedicated development host so OnDemand, set ``OOD_DEV_SSH_HOST`` environment variable for the dashboard in the file ``/etc/ood/config/apps/dashboard/env``. For example at OSC one of our OnDemand installs uses ``ondemand-test.osc.edu`` for the development host so we have this line: `OOD_DEV_SSH_HOST="ondemand-test.osc.edu" `_ Make everyone a developer by default (optional) ............................................... -To revert to the way developer enabling worked in OnDemand 1.3, change the nginx_stage app_root configuration for dev apps by modifying /etc/ood/config/nginx_stage.yml and replacing +To revert to the way developer enabling worked in OnDemand 1.3, change the ``nginx_stage`` app_root configuration for development apps by modifying ``/etc/ood/config/nginx_stage.yml`` and replacing .. code-block:: yaml :emphasize-lines: 2 @@ -83,11 +83,11 @@ with usr: '/var/www/ood/apps/usr/%{owner}/gateway/%{name}' sys: '/var/www/ood/apps/sys/%{name}' -Then users can just create the directory ``~/ondemand/dev`` and the Develop dropdown will appear. +Then users can just create the directory ``~/ondemand/dev`` and the Develop drop-down will appear. .. warning:: If you do this, it is recommended that you treat the node that OnDemand is running on as a login node, as you are effectively giving those users shell access by letting them run arbitrary code on the OnDemand node (of course the UID of the processes are still their regular unprivileged user UID). -If you do this, you still might want to restrict who sees the Develop dropdown in the Dashboard. To do that you can explicitly show or hide the dropdown in the Dashboard by setting ``Configuration.app_development_enabled`` to true based on one or more Ruby statements in the initializer ``/etc/ood/config/apps/dashboard/initializers/ood.rb``. Code in the initializer runs as the user. This code also has access to the `ood_support library `__ in which we provide some helper classes to work with User's and Groups. For example: +If you do this, you still might want to restrict who sees the Develop drop-down in the Dashboard. To do that you can explicitly show or hide the drop-down in the Dashboard by setting ``Configuration.app_development_enabled`` to true based on one or more Ruby statements in the initializer ``/etc/ood/config/apps/dashboard/initializers/ood.rb``. Code in the initializer runs as the user. This code also has access to the `ood_support library `__ in which we provide some helper classes to work with User's and Groups. For example: .. code-block:: ruby diff --git a/source/how-tos/debug/debug-apache.rst b/source/how-tos/debug/debug-apache.rst index fa1375647..6a1092564 100644 --- a/source/how-tos/debug/debug-apache.rst +++ b/source/how-tos/debug/debug-apache.rst @@ -47,7 +47,7 @@ and the ServerName you may have configured. Showing virtualhosts can help debug Apache request routing. The output from these commands will show you how Apache is routing based off of the ServerName in the VirtualHost. -If you're seeing the default Apache webpage you likely have to :ref:`configure the ServerName ` +If you're seeing the default Apache web-page you likely have to :ref:`configure the ServerName ` which corresponds directly to `Apache's ServerName configuration`_ (and restart Apache). Or you're using the wrong hostname in your browser. @@ -71,7 +71,7 @@ Performance Tuning If you're servicing many clients at time (more than 50) you will likely need to change the `Apache Httpd's MPM configuration`_. The default configuration may degrade service when -Httpd has to serve many clients (I.e., when you have a lot of customers using Open OnDemand). +httpd has to serve many clients (I.e., when you have a lot of customers using Open OnDemand). We suggest configurations similar to this. @@ -84,7 +84,7 @@ We suggest configurations similar to this. The example configuration below can handle about 256 simultaneous requests. Use this as an example and increase or decrease `MaxRequestWorkers` accordingly - (based on your resources, cpus & memory and how much traffic you anticipate) then recalculate + (based on your resources, CPUs & memory and how much traffic you anticipate) then recalculate `ServerLimit`, `ThreadsPerChild` and whatever else you may want to change. diff --git a/source/install-ihpc-apps.rst b/source/install-ihpc-apps.rst index a8641ce70..74db82e11 100644 --- a/source/install-ihpc-apps.rst +++ b/source/install-ihpc-apps.rst @@ -131,8 +131,8 @@ interactive apps that are currently deployed at OSC and other contributing insti - https://github.com/OSC/bc_osc_qgis - yes - noVNC - * - RELION (for REgularised LIkelihood OptimisatioN) - - Shanghai Jiao Tong University (SJTU) + * - RELION (for ``REgularised LIkelihood OptimisatioN``) + - Shanghai ``Jiao Tong University (SJTU)`` - https://github.com/SJTU-HPC/bc_relion - yes - diff --git a/source/release-notes/v1.3-release-notes.rst b/source/release-notes/v1.3-release-notes.rst index 96b5b3284..948d32370 100644 --- a/source/release-notes/v1.3-release-notes.rst +++ b/source/release-notes/v1.3-release-notes.rst @@ -7,9 +7,9 @@ Highlights in 1.3: - `RPM based installation`_ - `Store configuration under /etc instead of under app directories`_ -- `Config changes no longer require app rebuilds`_ -- `Xfce support Interactive Desktops`_ -- `Cluster config verification script`_ +- `Configuration changes no longer require app rebuilds`_ +- `XFCE support Interactive Desktops`_ +- `Cluster configuration verification script`_ - `Ignore apps if they have a period in directory name`_ - `Enable multiple Dashboard announcements with embedded HTML`_ - `Open "help" links in new window`_ @@ -235,7 +235,7 @@ RPM based installation This is the biggest change and constitutes the bulk of this release's work. RPM based installation will now be the default and documented way to install and -update OnDemand. The latest rpms that are in use at OSC can be accessed from +update OnDemand. The latest RPMs that are in use at OSC can be accessed from https://yum.osc.edu/ondemand/latest/ and the stable releases will be available in specific release version directories, such as https://yum.osc.edu/ondemand/1.3/. @@ -248,32 +248,32 @@ configuration for OnDemand: 1. All configuration can be moved to files under /etc/ood 2. Modifications to configuration only require Passenger app, Per User NINGX, - or Apache server restart (with the exception of the ood-portal-generater - config) + or Apache server restart (with the exception of the ood-portal-generator + configuration) Since all configuration is stored under /etc/ood this directory can be easily managed by Puppet or versioned in a git repository. -Config changes no longer require app rebuilds +Configuration changes no longer require app rebuilds .................................................................. It is now much faster to make and test configuration changes. For most configuration changes, you can make the change and then select "Restart Web -Server" from the "Help" or "Develop" dropdown to see the change. +Server" from the "Help" or "Develop" drop-down to see the change. -Xfce support Interactive Desktops +XFCE support Interactive Desktops .................................................................. -We now have documentation for enabling Xfce 4+ as the desktop environment for -OnDemand Interactive Desktops. Xfce is the desktop environment we now use +We now have documentation for enabling XFCE 4+ as the desktop environment for +OnDemand Interactive Desktops. XFCE is the desktop environment we now use internally at OSC. See :ref:`enable-desktops-modify-form-attributes` for -documentation on how to use Xfce in OnDemand. +documentation on how to use XFCE in OnDemand. -Cluster config verification script +Cluster configuration verification script .................................................................. A Rake task has been added to the Dashboard app that will submit and check the -status of jobs for each cluster specified in the cluster config. This provides +status of jobs for each cluster specified in the cluster configuration. This provides a quick way to verify that OnDemand has been properly configured for a new cluster and should speed up installation. See :ref:`resource-manager-test` in the cluster configuration documentation for more details. @@ -289,13 +289,13 @@ directory in the app deployment directory, e.g., :file:`../.hidden-app/`. Enable multiple Dashboard announcements with embedded HTML .................................................................. -Site-wide dashboard announcement support in OnDemand has been expanded. Orinally we supported a file ``/etc/ood/config/announcement.md`` but now a YAML file ``/etc/ood/config/announcement.yml`` can be used. A collection of markdown and yaml announcements in ``/etc/ood/config/announcements.d/`` can be added. The yaml file provides extra benefits: +Site-wide dashboard announcement support in OnDemand has been expanded. Originally we supported a file ``/etc/ood/config/announcement.md`` but now a YAML file ``/etc/ood/config/announcement.yml`` can be used. A collection of markdown and YAML announcements in ``/etc/ood/config/announcements.d/`` can be added. The YAML file provides extra benefits: -#. Pre process file using ERB so that ERB tags can provide per-request dynamic modification of the announcement +#. Preprocess file using ERB so that ERB tags can provide per-request dynamic modification of the announcement #. Control the color of announcement with ``:type`` which is the Bootstrap alert name (``warning``, ``info``, ``success``, or ``danger``) #. Control whether announcement appears or not by setting ``:msg`` to a string or ``nil`` -The ability to use ERB means we can set the msg to nil after a certain time period. For example: +The ability to use ERB means we can set the ``msg`` to nil after a certain time period. For example: .. code-block:: erb @@ -333,7 +333,7 @@ Better debugging of Interactive Apps by logging shell commands .................................................................. Whenever an Interactive Session is started from the Dashboard, the shell -command used to submit the job is logged to the user's NGINX config to help +command used to submit the job is logged to the user's NGINX configuration to help with debugging Interactive Apps. Job Composer: Optionally hide Account field in Job Options @@ -345,7 +345,7 @@ resource manager (whether it is ``-A`` or ``-P`` or ``--account``, etc.). Howeve sites do not use this, and others use different mechanisms for accounting. Long term we want to support flexible configuration of this web form, but for now we have added the ability to hide this Account field from the web form. This field -is hidden by adding to the Job Composer's env file: +is hidden by adding to the Job Composer's ``env`` file: ``OOD_SHOW_JOB_OPTIONS_ACCOUNT_FIELD=0`` Active Jobs: display list of nodes that a job is running on diff --git a/source/release-notes/v1.4-release-notes.rst b/source/release-notes/v1.4-release-notes.rst index 5f2cbc1e8..8db609bce 100644 --- a/source/release-notes/v1.4-release-notes.rst +++ b/source/release-notes/v1.4-release-notes.rst @@ -6,13 +6,13 @@ v1.4 Release Notes Highlights in 1.4: - `Upgrade to Ruby 2.4, NodeJS 6, Passenger 5`_ -- `Security Enhancement - PUN autogenerates secret key base if none is set`_ +- `Security Enhancement - PUN auto-generates secret key base if none is set`_ - `Security Enhancement: App development mode is disabled by default`_ - `Security Enhancement: Enable whitelisting of directories in several core apps`_ - `Security Enhancement: Require SSH for all hosts in Shell app`_ -- `Add ability to include Javascript in Batch Connect apps`_ +- `Add ability to include JavaScript in Batch Connect apps`_ - `Better environment setting`_ -- `Customizable error pages for missing home dirs`_ +- `Customizable error pages for missing home directories`_ - `Experimental SGE/UGE support`_ - `Fixed copy and paste issues in the Shell app for Firefox`_ - `Improve default discoverability of apps in the Dashboard's navbar`_ @@ -48,9 +48,9 @@ Upgrading from v1.3 .. warning:: - The nginx RPM used by ondemand will upgrade the nginx RPMs provided by EPEL, if they are installed. + The Nginx RPM used by ondemand will upgrade the Nginx RPMs provided by EPEL, if they are installed. -#. Rebuild any custom Node.js or Ruby apps +#. Rebuild any custom NodeJs or Ruby apps Since we upgraded to Ruby 2.4 from 2.2 and NodeJS 0.10 to NodeJS 6 any custom Passenger apps in Ruby or NodeJS that have their dependencies installed in @@ -79,7 +79,7 @@ Upgrading from v1.3 #. Verify Navbar contains all the apps you want. The behavior changed from 1.3 to 1.4 so by default all categories of any sys - app found appear as dropdown menus without the need for configuration changes. + app found appear as drop-down menus without the need for configuration changes. As a result menus may appear that you do not expect, if previously you were relying @@ -158,16 +158,16 @@ This upgrade updates our dependencies to Software Collections Ruby 2.4 and NodeJ .. warning:: - The Per User NGINX temporary directory has been moved from ``/var/lib/nginx`` to ``/var/tmp/nginx`` due to an issue with more restrictive permissions with NGINX 1.14. + The Per User Nginx temporary directory has been moved from ``/var/lib/nginx`` to ``/var/tmp/nginx`` due to an issue with more restrictive permissions with Nginx 1.14. - A consequence of this NGINX 1.14 upgrade is that NGINX directories like - ``/var/log/nginx`` have become more restrictive - owned by the nginx user and set by + A consequence of this Nginx 1.14 upgrade is that Nginx directories like + ``/var/log/nginx`` have become more restrictive - owned by the ``nginx`` user and set by default to 700. -Security Enhancement - PUN autogenerates secret key base if none is set -....................................................................... +Security Enhancement - PUN auto-generates secret key base if none is set +........................................................................ -The PUN will autogenerate its own unique per-user secret key base string which is generated at first launch if it doesn't exist. This is used by Rails apps to encrypt cookies and overrides the default one set in `env.production `__. +The PUN will auto-generate its own unique per-user secret key base string which is generated at first launch if it doesn't exist. This is used by Rails apps to encrypt cookies and overrides the default one set in `env.production `__. Security Enhancement: App development mode is disabled by default ................................................................. @@ -177,23 +177,23 @@ Development mode disabled by default: application development gives increased ac Security Enhancement: Enable whitelisting of directories in several core apps ............................................................................. -The file editor, file browser and job composer now support an optional whitelist of browseable/editable directories. Directories and files not in the whitelist will never be forbidden to users. The whitelist is controlled by the environment variable ``WHITELIST_PATH``, which is best be defined by editing ``/etc/ood/config/nginx_stage.yml`` under the ``pun_custom_env`` map. +The file editor, file browser and job composer now support an optional whitelist of browse-able/editable directories. Directories and files not in the whitelist will never be forbidden to users. The whitelist is controlled by the environment variable ``WHITELIST_PATH``, which is best be defined by editing ``/etc/ood/config/nginx_stage.yml`` under the ``pun_custom_env`` map. Security Enhancement: Require SSH for all hosts in Shell app ............................................................. Prior to this release it was possible for OOD users to change the URL in the shell application and connect directly to the web node by starting a Bash shell on localhost. Given that this ability for arbitrary user access is counter intuitive to how web servers are typically managed, the exemption for localhost has been removed; users will always use SSH to connect to any host, allowing SSH access controls to work. -Add ability to include Javascript in Batch Connect apps +Add ability to include JavaScript in Batch Connect apps ....................................................... -Batch Connect applications may now define a Javascript file to add interactive frontend functionality. `Github OSC/ood-dashboard#426 `_. +Batch Connect applications may now define a JavaScript file to add interactive frontend functionality. `Github OSC/ood-dashboard#426 `_. The contents of this JavaScript file will be embedded in ``