init

c4978433 · Milan Jaros · ec53be3d · c4978433 · c4978433 · c4978433
Commit c4978433 authored 11 months ago by Milan Jaros
--- a/README.md
+++ b/README.md
-# bc_it4i_matlab
+# Batch Connect - IT4I - Matlab
+A Batch Connect app designed for IT4I OnDemand that launches Matlab (https://www.mathworks.com/) within an slurm batch job. Based on https://github.com/OSC/bc_osc_matlab.
-## Getting started
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
-## Add your files
- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
-```
-cd existing_repo
-git remote add origin https://code.it4i.cz/ood/bc_it4i_matlab.git
-git branch -M main
-git push -uf origin main
-```
-## Integrate with your tools
- [ ] [Set up project integrations](https://code.it4i.cz/ood/bc_it4i_matlab/-/settings/integrations)
-## Collaborate with your team
- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
- [ ] [Set auto-merge](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
-## Test and Deploy
-Use the built-in continuous integration in GitLab.
- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing (SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
-***
-# Editing this README
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thanks to [makeareadme.com](https://www.makeareadme.com/) for this template.
-## Suggestions for a good README
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
-## Name
-Choose a self-explaining name for your project.
-## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
-## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
-## Visuals
-Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
-## Installation
-Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
-## Usage
-Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
-## Support
-Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
-## Roadmap
-If you have ideas for releases in the future, it is a good idea to list them in the README.
-## Contributing
-State if you are open to contributions and what your requirements are for accepting them.
-For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
-You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
-## Authors and acknowledgment
-Show your appreciation to those who have contributed to the project.
-## License
-For open source projects, say how it is licensed.
-## Project status
-If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
--- a/form.yml
+++ b/form.yml
+---
+cluster:
+  - "owens"
+  - "pitzer"
+form:
+  - auto_modules_matlab
+  - auto_accounts
+  - bc_num_hours
+  - bc_num_slots
+  - num_cores
+  - node_type
+  - bc_vnc_resolution
+  - bc_email_on_started
+attributes:
+  num_cores:
+    widget: "number_field"
+    label: "Number of cores"
+    value: 1
+    help: |
+      Number of cores on node type (4 GB per core unless requesting whole
+      node). Leave blank if requesting full node.
+    min: 0
+    max: 28
+    step: 1
+  bc_num_slots: "1"
+  bc_vnc_resolution:
+    required: true
+  node_type:
+      widget: select
+      label: "Node type"
+      help: |
+        - **Standard Compute** <br>
+          These are standard HPC machines. Owens has 648 of these nodes with 40
+          cores and 128 GB of memory. Pitzer has 224 of these nodes with 40 cores and
+          340 of these nodes with 48 cores. All pitzer nodes have 192 GB of RAM. Chosing "any" as the node type will decrease
+          your wait time.
+        - **GPU Enabled** <br>
+          These are HPC machines with GPUs. Owens has 160 nodes with 1 [NVIDIA Tesla P100 GPU]
+          and Pitzer has 74 nodes with 2 [NVIDIA Tesla V100 GPUs]. They have the same
+          CPU and memory characteristics of standard compute. However, Pitzer's 40 core machines
+          have 2 GPUs with 16 GB of RAM; and Pitzer's 48 core machines have 2 GPUs with 32 GB of RAM.
+          Dense GPU types have 4 GPUs with 16 GB of RAM.
+        - **Large Memory** <br>
+          These are HPC machines with very large amounts of memory. Owens has 16 hugemem nodes
+          with 48 cores and 1.5 TB of RAM. Pitzer has 4 hugemem nodes with 3 TB of RAM and 80 cores.
+          Pitzer also has 12 Largmem nodes which have 48 cores with 768 GB of RAM.
+        [NVIDIA Tesla P100 GPU]: http://www.nvidia.com/object/tesla-p100.html
+        [NVIDIA Tesla V100 GPUs]: https://www.nvidia.com/en-us/data-center/v100/
+      options:
+        - [
+            "any",     "any",
+            data-max-num-cores-for-cluster-owens: 28,
+            data-max-num-cores-for-cluster-pitzer: 48,
+          ]
+        - [
+            "48 core",     "any-48core",
+            data-max-num-cores-for-cluster-pitzer: 48,
+            data-option-for-cluster-owens: false,
+          ]
+        - [
+            "40 core",     "any-40core",
+            data-max-num-cores-for-cluster-pitzer: 40,
+            data-option-for-cluster-owens: false,
+          ]
+        - [
+            "any gpu",     "gpu",
+            data-max-num-cores-for-cluster-owens: 28,
+            data-max-num-cores-for-cluster-pitzer: 48,
+          ]
+        - [
+            "40 core gpu",     "gpu-40core",
+          data-max-num-cores-for-cluster-pitzer: 40,
+          data-option-for-cluster-owens: false,
+          ]
+        - [
+            "48 core gpu",     "gpu-48core",
+            data-max-num-cores-for-cluster-pitzer: 48,
+            data-option-for-cluster-owens: false,
+          ]
+        - [
+            "largemem", "largemem",
+            data-min-num-cores-for-cluster-pitzer: 24,
+            data-max-num-cores-for-cluster-pitzer: 48,
+            data-option-for-cluster-owens: false,
+          ]
+        - [
+            "hugemem", "hugemem",
+            data-min-num-cores-for-cluster-owens: 4,
+            data-max-num-cores-for-cluster-owens: 48,
+            data-min-num-cores-for-cluster-pitzer: 20,
+            data-max-num-cores-for-cluster-pitzer: 80,
+          ]
+        - [
+            "debug",   "debug",
+            data-max-num-cores-for-cluster-owens: 28,
+            data-max-num-cores-for-cluster-pitzer: 48,
+            data-option-for-cluster-owens: false,
+            data-option-for-cluster-pitzer: false,
+          ]
--- a/icon.png
+++ b/icon.png
--- a/manifest.yml
+++ b/manifest.yml
+---
+name: MATLAB
+category: Interactive Apps
+subcategory: GUIs
+role: batch_connect
+description: |
+  This app will launch a [MATLAB] GUI on the [Owens cluster]. You will be able
+  to interact with the MATLAB GUI through a VNC session.
+  [MATLAB]: https://www.mathworks.com/products/matlab.html
+  [Owens cluster]: https://www.osc.edu/resources/technical_support/supercomputers/owens
--- a/submit.yml.erb
+++ b/submit.yml.erb
+<%-
+  err_msg = "You are not a member of the matlab group. Please email oschelp@osc.edu to request access to MATLAB."
+  raise(StandardError, err_msg) unless CurrentUser.group_names.include?('matlab')
+  nodes = bc_num_slots.blank? ? 1 : bc_num_slots.to_i
+  cores_lookup = {
+      "hugemem" => {"pitzer" => "80", "owens" => "48"},
+      "largemem" => {"pitzer" => "48", "owens" => "28"},
+      "any" => {"pitzer" => "40", "owens" => "28"},
+      "gpu" => {"pitzer" => "48", "owens" => "28"},
+      "any-48core" => {"pitzer" => "48", "owens" => "28"},
+      "gpu-48core" => {"pitzer" => "48", "owens" => "28"},
+      "any-40core" => {"pitzer" => "40", "owens" => "28"},
+      "gpu-40core" => {"pitzer" => "40", "owens" => "28"},
+  }
+  max_cores = cores_lookup[node_type][cluster]
+  ppn = num_cores.blank? ? max_cores : num_cores.to_i
+  case node_type
+  when "hugemem"
+    partition = bc_num_slots.to_i > 1 ? "hugemem-parallel" : "hugemem"
+    slurm_args = [ "--nodes", "#{nodes}", "--ntasks-per-node", "#{ppn}", "--partition", partition ]
+  when "gpu"
+    slurm_args = [ "--nodes", "#{nodes}", "--ntasks-per-node", "#{ppn}", "--gpus-per-node", "1" ]
+  when "any40-core"
+    slurm_args = [ "--nodes", "#{nodes}", "--ntasks-per-node", "#{ppn}", "--contstraint", "48core" ]
+  when "any48-core"
+    slurm_args = [ "--nodes", "#{nodes}", "--ntasks-per-node", "#{ppn}", "--contstraint", "48core" ]
+  when "gpu-48core"
+    slurm_args = [ "--nodes", "#{nodes}", "--ntasks-per-node", "#{ppn}", "--gpus-per-node", "1", "--constraint", "48core" ]
+  when "gpu-40core"
+    slurm_args = [ "--nodes", "#{nodes}", "--ntasks-per-node", "#{ppn}", "--gpus-per-node", "1", "--constraint", "40core" ]
+  else
+    slurm_args = [ "--nodes", "#{nodes}", "--ntasks-per-node", "#{ppn}" ]
+  end
+%>
+---
+batch_connect:
+  template: vnc
+script:
+  native:
+  <%- slurm_args.each do |arg| %>
+    - "<%= arg %>"
+  <%- end %>
--- a/template/before.sh.erb
+++ b/template/before.sh.erb
+# Export the module function if it exists
+[[ $(type -t module) == "function" ]] && export -f module
--- a/template/config/menus/xfce-applications.menu
+++ b/template/config/menus/xfce-applications.menu
+<!DOCTYPE Menu PUBLIC "-//freedesktop//DTD Menu 1.0//EN"
+  "http://www.freedesktop.org/standards/menu-spec/1.0/menu.dtd">
+<Menu>
+    <Name>Xfce</Name>
+    <DefaultAppDirs/>
+    <DefaultDirectoryDirs/>
+    <DefaultMergeDirs/>
+    <Include>
+        <All/>
+    </Include>
+    <Layout>
+        <Filename>firefox.desktop</Filename>
+        <Filename>xfce4-terminal.desktop</Filename>
+        <Filename>Thunar.desktop</Filename>
+    </Layout>
+</Menu>
--- a/template/config/xfce4/terminal/terminalrc
+++ b/template/config/xfce4/terminal/terminalrc
+[Configuration]
+CommandLoginShell=TRUE
+FontName=DejaVu Sans Mono 11
--- a/template/config/xfce4/xfconf/xfce-perchannel-xml/xfce4-panel.xml
+++ b/template/config/xfce4/xfconf/xfce-perchannel-xml/xfce4-panel.xml
+<?xml version="1.0" encoding="UTF-8"?>
+<channel name="xfce4-panel" version="1.0">
+  <property name="configver" type="int" value="2"/>
+  <property name="panels" type="array">
+    <value type="int" value="1"/>
+    <property name="panel-1" type="empty">
+      <property name="position" type="string" value="p=6;x=99;y=24"/>
+      <property name="position-locked" type="bool" value="true"/>
+      <property name="size" type="uint" value="48"/>
+      <property name="length" type="uint" value="100"/>
+      <property name="length-adjust" type="bool" value="false"/>
+      <property name="plugin-ids" type="array">
+        <value type="int" value="1"/>
+        <value type="int" value="3"/>
+        <value type="int" value="8"/>
+        <value type="int" value="4"/>
+        <value type="int" value="5"/>
+      </property>
+      <property name="mode" type="uint" value="0"/>
+    </property>
+  </property>
+  <property name="plugins" type="empty">
+    <property name="plugin-3" type="string" value="tasklist">
+      <property name="flat-buttons" type="bool" value="false"/>
+      <property name="show-handle" type="bool" value="true"/>
+    </property>
+    <property name="plugin-4" type="string" value="pager"/>
+    <property name="plugin-5" type="string" value="clock">
+      <property name="digital-format" type="string" value="%r"/>
+      <property name="mode" type="uint" value="2"/>
+    </property>
+    <property name="plugin-8" type="string" value="separator">
+      <property name="expand" type="bool" value="true"/>
+      <property name="style" type="uint" value="2"/>
+    </property>
+    <property name="plugin-1" type="string" value="applicationsmenu">
+      <property name="show-generic-names" type="bool" value="true"/>
+      <property name="show-menu-icons" type="bool" value="true"/>
+      <property name="button-icon" type="string" value="fedora-logo-icon"/>
+      <property name="show-tooltips" type="bool" value="true"/>
+    </property>
+  </property>
+</channel>
--- a/template/script.sh.erb
+++ b/template/script.sh.erb
+#!/usr/bin/env bash
+<%- gpu = context.node_type.include?("vis") -%>
+# Clean the environment
+module purge
+# Set working directory to home directory
+cd "${HOME}"
+#
+# Launch Xfce Window Manager and Panel
+#
+(
+  export SEND_256_COLORS_TO_REMOTE=1
+  export XDG_CONFIG_HOME="<%= session.staged_root.join("config") %>"
+  export XDG_DATA_HOME="<%= session.staged_root.join("share") %>"
+  export XDG_CACHE_HOME="$(mktemp -d)"
+  export $(dbus-launch)
+  module restore
+  set -x
+  xfwm4 --compositor=off --daemon --sm-client-disable
+  xsetroot -solid "#D3D3D3"
+  xfsettingsd --sm-client-disable
+  xfce4-panel --sm-client-disable
+) &
+#
+# Start MATLAB
+#
+# Load the required environment
+module load xalt/latest <%= context.auto_modules_matlab %>
+# Launch MATLAB
+<%- if gpu -%>
+module load intel/16.0.3 virtualgl
+module list
+set -x
+vglrun matlab -desktop -nosoftwareopengl
+<%- else -%>
+module list
+set -x
+matlab -desktop
+<%- end -%>