adds some progress output to the generator script

.gitignore

@@ -6,3 +6,4 @@ Gemfile
 Gemfile.lock
 vendor/
 .bundle
+*.pyc

.markdownlint.json

@@ -0,0 +1,5 @@
+{
+  "MD013": false,
+  "MD024": { "siblings_only": true },
+  "MD033": false
+}

CHANGELOG.md

@@ -1,32 +1,87 @@
 # Changelog
 
+## [2.1.0] - 2026-06-01
+
+### Added
+
+#### My Templates
+
+- **"My Templates" section on the home page** — saved templates are shown as thumbnails in the same
+  grid style as regular apps, using the source app's own icon. Clicking a template opens its source
+  app form pre-filled with the saved values.
+- **Save as Template** button on any application form. Saves the current form values, the source
+  app path, and the app icon into a YAML file under `{data_dir}/templates/`.
+- **Save button** (replaces "Save as Template") when a template has been loaded into the form —
+  overwrites the stored values without prompting for a name again.
+- **Edit (pencil) button** on each template thumbnail — opens an inline modal to rename the
+  template or update its description without leaving the home page.
+- **Delete (×) button** on each template thumbnail — deletes the template after a confirmation prompt.
+- New routes: `POST /templates`, `POST /templates/:slug/overwrite`,
+  `POST /templates/:slug/rename`, `POST /templates/:slug/delete`.
+
+#### Nodes page
+
+- **Dynamic GRES columns** — the Nodes table automatically discovers every GRES type reported
+  by the scheduler (e.g. `gpu`, `nvme`) and creates one column per type. No static column
+  configuration is needed.
+- GRES columns are displayed in **alphabetical order**.
+- Each GRES cell shows **available / total** resource counts with the existing resource-bar style,
+  broken out by subtype (e.g. `A100`, `H100`).
+- Removed the **Type** and **Arch** filter checkboxes from the Nodes page.
+
+#### History page
+
+- **One-by-one job cancellation** — "Cancel Job" now issues one `scancel` call per selected job
+  instead of a single bulk call.
+- An **animated Bootstrap progress bar** (`X / N jobs`) is shown inside the cancel modal while
+  cancellation is running.
+- On full success the bar turns green and the page auto-reloads after one second. On partial
+  failure the bar turns yellow and each error is listed.
+- New route: `POST /history/cancel_one` — cancels a single job and returns JSON
+  `{ok: true}` / `{ok: false, error: "..."}`.
+
+### Fixed
+
+- Clicking "Save" to overwrite a template no longer discards content that was already entered in the
+  form. Previously, saving would clear fields the user had filled in; now the existing form values are
+  preserved correctly.
+
 ## [2.0.0] - 2026-05-11
+
 ### Add
+
 - Add side-by-side syntax highlighting overlays for the script and submit textareas.
 - Add configurable `highlight_theme` and `directive_color` settings for history/script highlighting.
 - Add advanced history search options for date range, AND/OR matching, and field selection.
 - Add history search elapsed-time output next to the entry count.
 
 ### Changed
+
 - Change history storage from PStore to SQLite with automatic migration from legacy `.db` files.
 - Expand history search to index all stored job values, including Job Details and Job Script contents.
 - Improve history search highlighting so it follows AND/OR search terms and the selected field.
 
-## Fix
+### Fix
+
 - Fix initialization error in Dynamic Form Widget
 
 ## [1.9.0] - 2026-03-20
+
 ### Add
+
 - A warning will be displayed before manual changes to the script and submit sections are deleted.
 - Support OC_ROUNDING_ROUND, OC_ROUNDING_FLOOR, and OC_ROUNDING_CEIL in calc().
 - Local Development is added in install manual.
 
 ### Changed
+
 - RACK is used for development.
 - Improve README to match Appverse documentation standard in [18](https://github.com/RIKEN-RCCS/OpenComposer/issues/28).
 
 ## [1.8.0] - 2025-12-26
+
 ### Add
+
 - Add the function to define multiple login_nodes and ssh_wrappers in conf.yml in [25](https://github.com/RIKEN-RCCS/OpenComposer/discussions/25).
 - Add calc function in [20](https://github.com/RIKEN-RCCS/OpenComposer/pull/20).
 - History page items can be freely changed in [19](https://github.com/RIKEN-RCCS/OpenComposer/pull/19).
@@ -35,58 +90,73 @@
 - Add a variable @OC_DIR_NAME.
 
 ### Changed
+
 - Change clusters from cluster in conf.yml (It is an incompatible change).
 - Change related_apps from related_apps in manifest.yml (It is an incompatible change).
 - Changed dirname and basename to work the same as linux commands.
 - Change a variable OC_SCRIPT_CONTENT from SCRIPT_CONTENT.
 
 ### Fixed
+
 - Do nothing if expr returns an error.
 
 ## [1.7.0] - 2025-11-06
+
 ### Add
+
 - The function only saves job scripts.
 - The function allows users to view and edit preprocessing.
 
 ### Changed
+
 - Manual format changed from Markdown to HTML.
 
 ### Fixed
+
 - An error occurs when you first open the History page in [18](https://github.com/RIKEN-RCCS/OpenComposer/pull/18).
 - An issue where variables could not be referenced in the submit and check sections.
 - An error where the separator was not reflected when using an array as the second argument in the options of checkbox and multi_select widgets.
 - An error that disabled elements could not be referenced on the initial screen.
 
 ## [1.6.0] - 2025-10-19
+
 ### Add
+
 - The function for zeropadding.
 - The function to output log.
 - The custom PBS Pro scheduler for Miyabi.
 
 ### Changed
+
 - Change the manual format from Markdown to HTML.
 - Change "cancel job" from "delete job" in history page.
 - The name of the page from Top Page to Home Page.
 
 ### Fixed
+
 - The initial value was not set correctly when the value was a number.
 - Consolidate querying both running and history jobs in PBS Pro in [9](https://github.com/RIKEN-RCCS/OpenComposer/pull/9).
 - PBS Pro qstat bug in [8](https://github.com/RIKEN-RCCS/OpenComposer/pull/8).
 
 ## [1.5.0] - 2025-05-08
+
 ### Add
+
 - Add highlights to filtered results in history page.
 - Support multiple clusters.
 
 ### Changed
+
 - Filter in history page searches all job information.
 
 ### Fixed
+
 - Sanitization for XSS.
 
 ## [1.4.0] - 2025-04-08
 
 ### Added
+
 - Support to set a main label and a sub-label.
 - Support to hide job scripts.
 - Dynamic Form Widget is also enabled in the header.
@@ -95,6 +165,7 @@
 - Add a function oc_assert() which can be used in form.yml.
 
 ### Changed
+
 - For slurm, remove init_bash and added --export=NONE to the sbatch option.
 - For slurm, PBSpro and Fujitsu TCS, increase the amount of verbose output.
 - On the history page, when you hover the cursor over the image of a visualization app, the name of the application is displayed.
@@ -105,11 +176,13 @@
 - Display error messages more clearly in form.
 
 ### Fixed
+
 - A reference so that it works even if the destination of related_app in manuscript is a link.
 
 ## [1.3.0] - 2025-02-12
 
 ### Added
+
 - Support Grid Engine job scheduler.
 - It is possible to define headers for each application.
 - For pre-processing, submit section in form.yml is added. And delete submit.yml.
@@ -118,28 +191,33 @@
 - It is possible to define headers for each application.
 
 ### Changed
+
 - Change path selector modal overflow behavior in [1](https://github.com/RIKEN-RCCS/OpenComposer/pull/1)
 - To speed up the history page, update the status only for the job IDs that are displayed.
 - The separator option enables output without spaces.
 - To prevent elements that are initially hidden from appearing for just a moment, make them visible after all loading is complete.
 
 ### Fixed
+
 - Fixed behavior of the path widget with or without a slash at the end of a directory.
 
 ## [1.2.0] - 2025-01-20
 
 ### Added
+
 - Support PBS job scheduler.
 - Add bin_overrides in conf.yml.erb.
 - Add a utility misc/read_yml_erb.rb.
 
 ### Changed
+
 - login_node in conf.yml.erb has been made optional.
 - Simplify `ident` parameter.
 - When a job scheduler error occurs, output stdout as well as stderr.
 - Get the job submission date and time from a Ruby function, not from the scheduler.
 
 ### Fixed
+
 - Fixed a mistake in the application name link on the form.
 - Element with disabled is considered unchecked.
 - When the selected option in select widget becomes disabled by dynamic form widget, the non-disabled option is selected.
@@ -148,6 +226,7 @@
 ## [1.1.0] - 2025-01-09
 
 ### Added
+
 - Added `ident` parameter in the web form.
 - Enabled setting related applications.
 - Added support for Font Awesome icons.
@@ -156,6 +235,7 @@
 - Added an option to include the value of "Job Name" in the header as part of the job submission command.
 
 ### Changed
+
 - Divided the manual into sections for creating web forms and using Open Composer.
 - Extended the inquiry period for completed Fujitsu_TCS jobs to 365 days.
 - Improved error handling: when job submission fails, the same page reloads with the failed parameters pre-filled.
@@ -165,11 +245,14 @@
 - Ensured that changes in header values do not update `JOB_SCRIPT_CONTENTS`.
 
 ### Fixed
+
 - Fixed the issue with loading the bash environment when executing `pjsub`/`sbatch` commands.
 - Resolved the issue where `public/no_image_square.jpg` could not be displayed.
 
 ### Security
+
 - Applied URL encoding for special characters on the history page to enhance security.
 
 ## [1.0.0] - 12-11-2024
+
 First release.

README.md

@@ -1,3 +1,5 @@
+# Open Composer
+
 ## Overview
 
 Open Composer is a web application to generate batch job scripts and submit batch jobs for HPC clusters on [Open OnDemand](https://openondemand.org/).
@@ -8,31 +10,37 @@ interface for creating, previewing, editing, and submitting batch job scripts. I
 supports multiple job schedulers and can be configured for different HPC applications.
 
 - **App type:** Workflow Composer (Jobs category)
-- **Latest release:** [`v2.0.0`](https://github.com/RIKEN-RCCS/OpenComposer/releases/tag/v2.0.0) (see [Changelog](https://github.com/RIKEN-RCCS/OpenComposer/blob/main/CHANGELOG.md))
+- **Latest release:** [`v2.1.0`](https://github.com/RIKEN-RCCS/OpenComposer/releases/tag/v2.1.0) (see [Changelog](CHANGELOG.md))
 - **License:** MIT (see [LICENSE file](https://github.com/RIKEN-RCCS/OpenComposer/blob/main/LICENSE))
 - **Requirements:** Open OnDemand 3.0 or later.
 - **Supported job schedulers:** Slurm, PBS Pro, Grid Engine, Fujitsu TCS
 - **Features**
   - Graphical web interface for generating and submitting batch job scripts
   - Multi-scheduler and multi-cluster support
   - Job history page with filtering, status tracking, and job cancellation
+  - One-by-one job cancellation with an animated in-modal progress bar
   - Editable job script preview before submission
   - Configurable application forms via `form.yml`
   - Dynamic form widgets with conditional visibility and validation
   - Support for preprocessing steps via submit sections
   - Customizable per-application headers and labels
   - Path selector widget for file and directory selection
+  - My Templates — save, manage, and reuse form configurations
+  - Nodes page with dynamic GRES columns auto-discovered from the scheduler
   - Bilingual documentation (English and Japanese)
 
 ## Screenshots
 
 ### Home page
+
   <img width="600" style="border: 1px solid #333;" alt="Home" src="https://riken-rccs.github.io/OpenComposer/docs/img/home_page.png">
 
 ### Application page
+
   <img width="600" style="border: 1px solid #333;" alt="Application" src="https://riken-rccs.github.io/OpenComposer/docs/img/application_page.png">
 
 ### History page
+
   <img width="600" style="border: 1px solid #333;" alt="History" src="https://riken-rccs.github.io/OpenComposer/docs/img/history_page.png">
 
 ## Documents
@@ -63,21 +71,20 @@ The following steps assume you have administrator privileges.
 If you do not have administrator privileges, see [Section 4. "Installation by general user" in installation document](https://riken-rccs.github.io/OpenComposer/docs/install.html#general).
 
 ```sh
-$ cd /var/www/ood/apps/sys/
-$ sudo git clone https://github.com/RIKEN-RCCS/OpenComposer.git
-$ cd OpenComposer
-$ sudo cp conf.yml.erb.sample conf.yml.erb
+cd /var/www/ood/apps/sys/
+sudo git clone https://github.com/RIKEN-RCCS/OpenComposer.git
+cd OpenComposer
+sudo cp conf.yml.erb.sample conf.yml.erb
 ```
 
 You need to edit `conf.yml.erb`. For details, see [Section 2. "Setting" in installation manual](https://riken-rccs.github.io/OpenComposer/docs/install.html#setting).
 
 ## Testing
 
-| System      | Site        | Scheduler          | Repository |
-|-------------|-------------|--------------------|------------|
-| Fugaku      | RIKEN RCCS  | Fujitsu TCS, Slurm | https://github.com/RIKEN-RCCS/composer_fugaku     |
-| R-CCS Cloud | RIKEN RCCS  | Slurm              | https://github.com/RIKEN-RCCS/composer_rccs_cloud |
-
+| System      | Site       | Scheduler          | Repository                                                                               |
+|-------------|------------|--------------------|------------------------------------------------------------------------------------------|
+| Fugaku      | RIKEN RCCS | Fujitsu TCS, Slurm | [composer_fugaku](https://github.com/RIKEN-RCCS/composer_fugaku)                         |
+| R-CCS Cloud | RIKEN RCCS | Slurm              | [composer_rccs_cloud](https://github.com/RIKEN-RCCS/composer_rccs_cloud)                 |
 
 ## Contributing
 
@@ -88,11 +95,13 @@ For discussions, see the [GitHub Discussions](https://github.com/RIKEN-RCCS/Open
 For bugs or feature requests, [open an issue](https://github.com/RIKEN-RCCS/OpenComposer/issues) with detailed logs and reproduction steps.
 
 ## Reference
+
 If you use this software in your research or development work, please cite the following publication:
 
-> Masahiro Nakao and Keiji Yamamoto. 2025. ``Open Composer: A Web-Based Application for Generating and Managing Batch Jobs on HPC Clusters''. In Proceedings of the SC '25 Workshops of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC Workshops '25). Association for Computing Machinery, New York, NY, USA, 697-704. https://doi.org/10.1145/3731599.3767428
+> Masahiro Nakao and Keiji Yamamoto. 2025. "Open Composer: A Web-Based Application for Generating and Managing Batch Jobs on HPC Clusters". In Proceedings of the SC '25 Workshops of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC Workshops '25). ACM, New York, NY, USA, 697-704. [https://doi.org/10.1145/3731599.3767428](https://doi.org/10.1145/3731599.3767428)
 
 ## Presentation
+
 - [HUST: International Workshop on HPC User Support Tools](https://hust-workshop.github.io), St. Louis, USA, Nov. 2025 [[Paper](https://doi.org/10.1145/3731599.3767428)] [[Slide](https://www.mnakao.net/data/2025/HUST2025.pdf)]
 - [SupercomputingAsia 2025](https://sca25.sc-asia.org/), Singapore, Mar. 2025 [[Poster](https://mnakao.net/data/2025/sca.pdf)]
 - [The 197th HPC Research Symposium](https://www.ipsj.or.jp/kenkyukai/event/arc251hpc197.html), Fukuoka, Japan, Dec. 2024 [[Paper](https://mnakao.net/data/2024/HPC197.pdf)] [[Slide](https://mnakao.net/data/2024/HPC197-slide.pdf)] (Japanese)

apps/ABAQUS/form.yml.erb

@@ -0,0 +1,45 @@
+<%# AI generated %>
+<%
+base_path = File.join(File.dirname(yml_path), '../SlurmGPU/form.yml')
+base = YAML.load_file(base_path)
+
+new_form = {}
+base['form'].each do |k, v|
+  if k == 'time_days_hours_minutes'
+    new_form['abaqus_module'] = {
+      'widget' => 'module_load',
+      'module' => "ABAQUS",
+      'label'  => "ABAQUS Module"
+    }
+    new_form['abaqus_input'] = {
+      'widget' => 'text_field',
+      'label'  => "Input File",
+      'help'   => "Full path to your ABAQUS input file (.inp), e.g. /nesi/project/nesi99999/my_model.inp"
+    }
+  end
+  new_form[k] = v
+end
+
+base['form'] = new_form
+
+ntasks = cores_advanced_1.to_i > 1 ? cores_advanced_1.to_i : cores_simple.to_i
+cpus = cores_advanced_2.to_i > 1 ? cores_advanced_2.to_i : 1
+has_gpu = [gpu_any, gpu_genoa, gpu_milan].any? { |g| g.to_s != '' && g.to_s != 'None' }
+job_name = File.basename(abaqus_input.to_s, '.inp')
+if has_gpu
+  app_cmd = "abaqus input=#{abaqus_input} job=#{job_name} cpus=${SLURM_CPUS_PER_TASK} gpus=${SLURM_GPUS_PER_NODE} mp_mode=threads verbose=2 interactive"
+elsif ntasks > 1
+  app_cmd = "abaqus input=#{abaqus_input} job=#{job_name} cpus=${SLURM_NTASKS} mp_mode=mpi verbose=2 interactive"
+elsif cpus > 1
+  app_cmd = "abaqus input=#{abaqus_input} job=#{job_name} cpus=${SLURM_CPUS_PER_TASK} mp_mode=threads verbose=2 interactive"
+else
+  app_cmd = "abaqus input=#{abaqus_input} job=#{job_name} verbose=2 interactive"
+end
+
+base['script'] = base['script'].rstrip + "\n\n" + [
+  "module -q purge",
+  "module load #{abaqus_module}",
+  app_cmd
+].join("\n") + "\n"
+%>
+<%= base.to_yaml -%>