bc_code init"

CHANGELOG.md

@@ -0,0 +1,46 @@
+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [0.7.0] - 2023-03-24
+
+### Added
+- [32](https://github.com/OSC/bc_osc_codeserver/pull/32) Codeserver 4.8 support
+
+### Removed
+- - [32](https://github.com/OSC/bc_osc_codeserver/pull/32) Codeserver 3.4 selection
+
+## [0.4.0] - 2021-08-16
+
+### Added
+
+- [20](https://github.com/OSC/bc_osc_codeserver/pull/20) add better support around
+  cpp extension, initializing a db on a local file system.
+
+### Changed
+
+- [19](https://github.com/OSC/bc_osc_codeserver/pull/19) changed the shebang of the
+  main script to `bash -l` so that modules and extra PATH settings get loaded from
+  a user's ~/.bashrc file.
+
+## [0.3.0] - 2021-08-16
+
+- entry missing!
+
+## [0.2.0] - 2021-08-16
+
+- entry missing!
+
+## 0.1.0 - 2020-10-07
+### Added
+- Initial release of OSC Code Server.
+
+[Unreleased]: https://github.com/OSC/bc_osc_codeserver/compare/v0.7.0...HEAD
+[0.7.0]: https://github.com/OSC/bc_osc_codeserver/compare/v0.6.0...v0.7.0
+[0.4.0]: https://github.com/OSC/bc_osc_codeserver/compare/v0.3.0...v0.4.0
+[0.3.0]: https://github.com/OSC/bc_osc_codeserver/compare/v0.2.0...v0.3.0
+[0.2.0]: https://github.com/OSC/bc_osc_codeserver/compare/v0.1.0...v0.2.0

README.md

@@ -1,8 +1,86 @@
-# Batch Connect - Jupyter
+# Batch Connect - OSC Code Server
 
-![GitHub Release](https://img.shields.io/github/release/osc/bc_osc_jupyter.svg)
+![GitHub Release](https://img.shields.io/github/release/osc/bc_osc_codeserver.svg)
 [![GitHub License](https://img.shields.io/badge/license-MIT-green.svg)](https://opensource.org/licenses/MIT)
 
-An interactive app template designed for the BioHive Portal that launches a Jupyter
-server.
+An improved file viewer / editor for OSC OnDemand that launches a
+Code Server within an Owens batch job. Code Server leverages VSCode as its
+editor.
 
+## Prerequisites
+
+This Batch Connect app requires the following software be installed on the
+**compute nodes** that the batch job is intended to run on (**NOT** the
+OnDemand node):
+
+- [Lmod] 6.0.1+ or any other `module purge` and `module load <modules>` based
+  CLI used to load appropriate environments within the batch job before
+  launching Code server.
+- [Code Server] 2.x+ available from Github: https://github.com/cdr/code-server/releases
+
+[Code Server]: https://coder.com/
+[Lmod]: https://www.tacc.utexas.edu/research-development/tacc-projects/lmod
+[VS Code]: https://code.visualstudio.com/
+
+## Install
+
+1. Use Git to clone this app and checkout the desired branch/version you want to
+use and place this wherever you store batch connect apps (`/var/www/ood/apps/sys` or `~/ondemand/dev`):
+
+    ```sh
+    scl enable git29 -- git clone <repo>
+    cd <dir>
+    scl enable git29 -- git checkout <tag/branch>
+    ```
+
+2. Deploy code-server on your systems.
+
+    ```sh
+    # replace URL with latest release from code-server
+    wget https://github.com/cdr/code-server/releases/download/3.2.0/code-server-3.2.0-linux-x86_64.tar.gz
+    tar -xzf code-server-3.2.0-linux-x86_64.tar.gz
+    ```
+
+3. You will notice code-server is an executable inside that directory and can get the full path: 
+
+    ```sh
+    $ readlink -f code-server-3.2.0-linux-x86_64.tar.gz
+    /users/PZS0562/efranz/code-server-3.2.0-linux-x86_64.tar.gz
+    ```
+
+4. Update the path to the code-server binary in the script https://github.com/OSC/bc_osc_codeserver/blob/3082790ee69c82fe6fe757074da7d8d18c7d7e3d/template/script.sh.erb#L27:
+
+    ```diff
+     # An arbitrary path...
+    - /fs/project/PZS0714/mrodgers/bin/code-server-2.1523-vsc1.38.1 \
+    + /users/PZS0562/efranz/code-server-3.2.0-linux-x86_64/code-server \
+     --auth=password \
+     --port="$port" \
+    ```
+
+5. Update form.yml to use the correct cluster, and any other changes as necessary to form.yml or submit.yml that is appropriate for your cluster.
+
+## Update
+
+To update the app you would:
+
+```sh
+cd <dir>
+scl enable git29 -- git fetch
+scl enable git29 -- git checkout <tag/branch>
+```
+
+Again, you do not need to restart the app as it isn't a Passenger app.
+
+## Known Issues
+
+- In-app installation of extensions does not work
+- The authentication provided by code-server is unencrypted
+
+## Contributing
+
+1. Fork it ( https://github.com/OSC/bc_osc_codeserver/fork )
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create a new Pull Request

form.yml.erb

@@ -4,37 +4,41 @@
   }.map(&:name).grep(/^P./)
 -%>
 ---
-cluster:
-  - "slurm"
+cluster: "slurm"
 form:
   - bc_queue
-  - mode
-  - cuda_version
-  - version
   - bc_num_hours
   - num_cores
+  - gpu_type
+  - num_gpus
   - memory
-  - modules
-  - extra_jupyter_args
-  - bc_account
-  - bc_num_slots
-  - classroom 
+  - account
+  - working_dir
+  - version
 attributes:
-  cluster: "slurm"   
-  modules: "python"
-  cuda_version: "cuda11.8/toolkit/11.8.0"
-  classroom: 0
-  version: "3.1"
-  bc_account: null
-  bc_num_slots: null
+  gpu_type:
+    label: GPU Type
+    widget: select
+    options:
+      - ["none", "none"]
+      - ["a100", "a100"]
+      - ["1080ti", "1080ti"] 
+      - ["v100", "v100"]
+    class: "gpu-selection"
+  num_gpus:
+    widget: "number_field"
+    label: "Number of GPUS"
+    value: 0
+    required: true
+    help: "Specify the number of gpus for the job"
+    class: "gpu-count-field"
   bc_queue:
     label: Slurm Partition
     widget: select
     options:
       - ["batch", "batch"]
       - ["interactive", "interactive"]
       - ["mem", "mem"]
-  extra_jupyter_args: ""
   bc_num_hours:
     widget: "number_field"
     label: "Number of Hours"
@@ -58,11 +62,7 @@ attributes:
     min: 1
     max: 32
     required: true
-    help: "Specify the amount of memory in MB. Min: 1GB - Max: 32GB"
-  mode:
-    widget: "radio"
-    value: "1"
-    options:
-      - ["Jupyter Lab", "1"]
-      - ["Jupyter Notebook", "0"]
-
+    help: "Specify the amount of memory in MB. Min: 2GB, Max: 32GB"
+  account: null
+  version: "4.9.1"
+  working_dir: null

manifest.yml

@@ -1,9 +1,7 @@
 ---
-name: Jupyter Sandbox
+name: Code Server
 category: Interactive Apps
-subcategory: Servers
+subcategory: BioHive Applications
 role: batch_connect
 description: |
-  This app will launch a [Jupyter] server on the BioHive cluster.
-
-  [Jupyter]: https://jupyter.org/
+  This app will launch a VS Code server using Code Server on the BioHive cluster.

packaging/ondemand-bc_osc_codeserver.spec

@@ -0,0 +1,49 @@
+# Disable debuginfo as it causes issues with bundled gems that build libraries
+%global debug_package %{nil}
+%global repo_name bc_osc_codeserver
+%global app_name bc_osc_codeserver
+%{!?package_version: %define package_version %{major}.%{minor}.%{patch}}
+%{!?package_release: %define package_release 1}
+%{!?git_tag: %define git_tag v%{package_version}}
+%define git_tag_minus_v %(echo %{git_tag} | sed -r 's/^v//')
+
+Name:     ondemand-%{app_name}
+Version:  %{package_version}
+Release:  %{package_release}%{?dist}
+Summary:  Batch Connect - OSC Code Server
+
+Group:    System Environment/Daemons
+License:  MIT
+URL:      https://github.com/OSC/%{repo_name}
+Source0:  https://github.com/OSC/%{repo_name}/archive/%{git_tag}.tar.gz
+
+Requires: ondemand
+
+# Disable automatic dependencies as it causes issues with bundled gems and
+# node.js packages used in the apps
+AutoReqProv: no
+
+%description
+An interactive app designed for OSC OnDemand that launches a Code Server within an Owens batch job.
+
+
+%prep
+%setup -q -n %{repo_name}-%{git_tag_minus_v}
+
+
+%build
+
+
+%install
+%__mkdir_p %{buildroot}%{_localstatedir}/www/ood/apps/sys/%{app_name}
+%__cp -a ./. %{buildroot}%{_localstatedir}/www/ood/apps/sys/%{app_name}/
+echo v%{version} > %{buildroot}%{_localstatedir}/www/ood/apps/sys/%{app_name}/VERSION
+
+
+%files
+%defattr(-,root,root)
+%{_localstatedir}/www/ood/apps/sys/%{app_name}
+%{_localstatedir}/www/ood/apps/sys/%{app_name}/manifest.yml
+
+
+%changelog

submit.yml.erb

@@ -3,6 +3,9 @@ script:
   native:
   - "--mem=<%= memory.blank? ? 2 : memory.to_i %>G"
   - "--cpus-per-task=<%= num_cores.blank? ? 1 : num_cores.to_i %>"
+  - "<% if gpu_type == 'none' %>--gpus-per-node=<%= num_gpus.blank? ? 1 : num_gpus.to_i %><% else %>--gpus-per-node=<%= gpu_type %>:<%= num_gpus.blank? ? 1 : num_gpus.to_i %><% end %>"
 
 batch_connect:
-  template: "basic"
+template: "basic"
+conn_params:
+  - code_server_version

template/after.sh.erb

@@ -1,11 +1,11 @@
-<% if context.cluster !~ /kubernetes/ -%>
-# Wait for the Jupyter server to start
-echo "Waiting for Jupyter server to open port ${port}..."
+# Wait for the Code Server to start
+echo "$(date): Waiting for Code Server to open port ${port}..."
+
 if wait_until_port_used "${host}:${port}" 600; then
-  echo "Discovered Jupyter server listening on port ${port}!"
+  echo "$(date): Discovered code-server listening on port ${port}!"
 else
-  echo "Timed out waiting for Jupyter server to open port ${port}!"
+  echo "$(date): Timed out waiting for Code Server to open port ${port}!"
   clean_up 1
 fi
+
 sleep 2
-<% end -%>