Migrate deeplabcut

bc_vt_deeplabcut/CHANGELOG.md

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+# 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).
+
+## 1.0.0 - 2022-02-06
+### Added
+- Initial release!
+

bc_vt_deeplabcut/DevGuide.md

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+
+# Batch Connect - DeepLabCut App 
+
+An example Batch Connect app that launches a DeepLabCut application within a
+batch job.
+
+## 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):
+
+- [OpenSSL](https://www.openssl.org/) 1.0.1+ (used to hash the Jupyter Notebook
+  server password)
+- [Lmod](https://www.tacc.utexas.edu/research-development/tacc-projects/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
+  the Jupyter Notebook server.
+- [Singularity](https://sylabs.io/guides/3.0/user-guide/installation.html) Singularity is a container platform. It allows you to create and run containers that package up pieces of software in a way that is portable and reproducible. ... Your container is a single file, and you don't have to worry about how to install all the software you need on each different operating system and system.
+
+### Development Installation
+
+```bash
+cd /home/<user>/ondemand/dev
+git clone [email protected]:AdvancedResearchComputing/OnDemandApps.git
+```
+
+### System Installation
+```bash
+cd /var/www/ood/apps/sys
+git clone [email protected]:AdvancedResearchComputing/OnDemandApps.git
+```
+> Make sure to give executable permissions for *image file*
+
+
+- Make necessary description changes to **[manifest.yml](./manifest.yml)**
+## Contributing
+
+1. Fork it 
+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
+
+---

bc_vt_deeplabcut/LICENSE.txt

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+Copyright (c) 2020 Virginia Tech
+
+Copyright (c) 2016-2018 Ohio Supercomputer Center
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

bc_vt_deeplabcut/README.md

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+![GitHub release (latest by date)](https://img.shields.io/github/v/release/rsettlage/ARC-ondemand-apps)
+[![GitHub License](https://img.shields.io/badge/license-MIT-green.svg)](https://opensource.org/licenses/MIT)
+
+# Batch Connect - VT Deeplabcut
+
+A Batch Connect app designed for [Advanced Research Computing]'s VT OnDemand that launches <APP NAME>
+within a <CLUSTER> batch job.  For other apps and assistance with Open OnDemand, see [Open OnDemand].
+
+## 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):
+
+<LIST DEPENDENCIES>
+- [COMSOL Multiphysics] 5.1+
+- [Xfce Desktop] 4+
+
+For VNC server support:
+
+- [TurboVNC] 2.1+
+- [websockify] 0.8.0+
+
+For hardware rendering support (coming soon ...):
+
+- [X server]
+- [VirtualGL] 2.3+
+
+**Optional** software:
+
+- [Lmod] 6.0.1+ or any other `module purge` and `module load <modules>` based
+  CLI used to load appropriate environments within the batch job
+
+[Open OnDemand] http://openondemand.org/  
+[Advanced Research Computing] https://arc.vt.edu/  
+[DeepLabCut]: https://github.com/DeepLabCut/DeepLabCut
+[Xfce Desktop]: https://xfce.org/  
+[TurboVNC]: http://www.turbovnc.org/  
+[websockify]: https://github.com/novnc/websockify  
+[X server]: https://www.x.org/  
+[VirtualGL]: http://www.virtualgl.org/  
+[Lmod]: https://www.tacc.utexas.edu/research-development/tacc-projects/lmod   
+
+## Install
+
+Use git to clone this app:
+
+```sh
+git clone <repo>
+cd <dir>
+```
+
+You will not need to do anything beyond this as all necessary assets are
+installed. You will also not need to restart this app as it isn't a Passenger
+app.
+
+Again, you do not need to restart the app as it isn't a Passenger app.
+
+## Contributing, see https://osc.github.io/ood-documentation/master/install-ihpc-apps.html for inspiration.
+1. Fork it 
+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

bc_vt_deeplabcut/form.js

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+'use strict'
+
+/**
+ * Fix num cores, allowing blanks to remain
+ */
+function fix_num_cores() {
+  let node_type_input = $('#batch_connect_session_context_node_type');
+  let node_type = node_type_input.val();
+  let num_cores_input = $('#num_cores');
+
+  if(num_cores_input.val() === '') {
+    return;
+  }
+
+  if(node_type === 'hugemem') {
+    set_ppn_owens_hugemem(num_cores_input);
+  } else {
+    set_ppn_owens_regular(num_cores_input);
+  }
+}
+
+/**
+ * Sets the PPN limits available for Owens hugemem nodes.
+ * 
+ * hugemem reservations are always assigned the full node
+ *
+ * @param      {element}  num_cores_input  The input for num_cores
+ */
+function set_ppn_owens_hugemem(num_cores_input) {
+  const NUM_CORES = 48;
+  num_cores_input.attr('max', NUM_CORES);
+  num_cores_input.attr('min', NUM_CORES);
+  num_cores_input.val(NUM_CORES);
+}
+
+/**
+ * Sets the PPN limits available for non hugemem Owens nodes.
+ *
+ * @param      {element}  num_cores_input  The input for num_cores
+ */
+function set_ppn_owens_regular(num_cores_input) {
+  const NUM_CORES = 28;
+  num_cores_input.attr('max', NUM_CORES);
+  num_cores_input.attr('min', 0);
+  num_cores_input.val(Math.min(NUM_CORES, num_cores_input.val()));
+}
+
+
+/**
+ * Change the maximum number of cores selected.
+ */
+function set_node_type_change_handler() {
+  let node_type_input = $('#batch_connect_session_context_node_type');
+  node_type_input.change(node_type_input, fix_num_cores);
+}
+
+$(document).ready(function() {
+  // Set the max value to be what was set in the last session
+  fix_num_cores();
+  set_node_type_change_handler();
+});

bc_vt_deeplabcut/form.yml.erb

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+# Batch Connect app configuration file
+#
+---
+cluster: 
+  - 'tinkercliffs'
+  - 'infer'
+
+# Define attribute values that aren't meant to be modified by the user within
+# the Dashboard form
+attributes:
+
+# specify widgets for user modifiable job settings
+  bc_queue:
+    help: |
+      - To request a GPU enabled queue, preface it with v100_. Example: v100_normal_q, t4_normal_q
+
+  bc_num_hours:
+    label: Number of hours (min-1, max-48)
+    required: true
+    value: 1
+    min: 1
+    max: 72
+    step: 1
+
+  bc_num_slots: 1
+#    label: Number of nodes (currently confined to 1)
+#    required: true
+#    value: 1
+#    min: 1
+#    max: 1
+#    step: 1
+
+  bc_account:
+    widget: text_field
+    label: Account
+    value: ""
+    help: |
+       - The allocation you would like to use for SLURM.
+
+  num_cores:
+    widget: number_field
+    label: Number of cores per node (min-1, max-128)
+    value: 1
+    min: 1
+    max: 128
+    step: 1
+
+  gpu_per_node:
+    widget: number_field
+    label: Number of GPUs per node (min-0, max-2)
+    value: 0
+    min: 0
+    max: 2
+    step: 1
+    help: |
+       - If requesting GPU nodes, you must enter a GPU-enabled Partition above or the job will fail.
+
+  Container: deeplabcut-24Sep2021-gui.sif
+#    widget: select
+#    label: "use container"
+#    help: "This defines the remote DeepLabCut version to run."
+#    options:
+#    <%- Dir.glob('/projects/arcsingularity/*deeplabcut*sif').each do |f| -%>
+#      <%- sif = f.sub('/projects/arcsingularity/','') -%>
+#      - [ "Container: <%= sif %>", "<%= sif %>" ]
+#    <%- end -%>
+
+  bc_vnc_resolution:
+    required: true
+
+# All of the attributes that make up the Dashboard form (in respective order),
+# and made available to the submit configuration file and the template ERB
+# files
+#
+form:
+  - cluster
+  - Container
+  - bc_account
+  - reservation
+  - bc_queue
+  - bc_num_hours
+  - bc_num_slots
+  - num_cores
+  - gpu_per_node
+  - bc_vnc_resolution
+  - bc_email_on_started

bc_vt_deeplabcut/manifest.yml

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+---
+name: DeepLabCut
+category: Interactive Apps
+role: batch_connect
+description: |
+  This app will launch a [DeepLabCut] in a container on one node.  Currently works on [TinkerCliffs] and [Infer].  For issues or requests, please submit a github issue for the [desktop OOD app] or the [desktop container].<P>  **NOTE** this app does not work without installing DeepLabCut in your profile first, so the first time you use this app it will take ~5min to start!!
+
+  [TinkerCliffs]: https://www.arc.vt.edu/TinkerCliffs
+  [Infer]: https://www.arc.vt.edu/infer
+  [DragonsTooth]: https://www.arc.vt.edu/dragonstooth
+  [Cascades]: https://www.arc.vt.edu/cascades
+  [Huckleberry]: https://www.arc.vt.edu/huckleberry
+  [desktop OOD app]:https://github.com/AdvancedResearchComputing/ARC-ondemand-apps/tree/master/bc_vt_desktop
+  [DeepLabCut]: https://github.com/DeepLabCut/DeepLabCut

bc_vt_deeplabcut/submit.yml.erb

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+# Job submission configuration file
+#
+---
+
+#
+# Configure the content of the job script for the batch job here
+# @see http://www.rubydoc.info/gems/ood_core/OodCore/BatchConnect/Template
+#
+batch_connect:
+  template: "basic"
+  set_host: "host=$(hostname -s)"
+  conn_params:
+    - ondemand_host
+#
+# Configure the job script submission parameters for the batch job here
+# @see http://www.rubydoc.info/gems/ood_core/OodCore/Job/Script
+#
+script:
+  copy_environment: true      
+  native: 
+    - "--nodes=<%= bc_num_slots.blank? ? "1" : bc_num_slots.to_i %>"
+    - "--cpus-per-task=<%= num_cores.blank? ? "1" : num_cores %>"
+    - "--time=<%= bc_num_hours + ":0:0" %>"
+    - "--reservation=<%= reservation %>"
+    - "--account=<%= bc_account %>"
+    - "--gres=gpu:<%= gpu_per_node.blank? ? "0" : gpu_per_node.to_i %>"

bc_vt_deeplabcut/template/after.sh.erb

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+# Wait for the X server to start
+
+while [ ! -f ./connection.rc ]; do sleep 1; done
+source connection.rc
+
+echo "Waiting for VNC Server to open port ${host}:${port}..."
+if wait_until_port_used "${host}:${port}" 2400; then
+  echo "Discovered VNC Server listening on port ${port}!"
+else
+  echo "Timed out waiting for VNC Server to open port ${port}!"
+  clean_up 1
+fi
+sleep 2

bc_vt_deeplabcut/template/before.sh.erb

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+echo starting begin.sh
+if [ -z ${HOME+x} ];
+then
+    export HOME=$(echo ~)
+	source /etc/profile
+	source /etc/bashrc
+	source $HOME/.bashrc
+fi
+
+# Export the module function if it exists
+[[ $(type -t module) == "function" ]] && export -f module
+hostname
+pwd
+
+module reset
+module load containers/singularity
+
+singularity run --cleanenv --nv \
+    --bind `pwd`:/cwd,$TMPDIR:/TMPDIR,/projects,/work/$USER,/cm \
+    /projects/arcsingularity/ubuntu-xfce-v0.2.0.sif -d "Desktop-$(hostname)" &
+