initial commit

ATMOS5100/CHANGELOG.md

@@ -0,0 +1,125 @@
+# 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]
+
+## [0.6.2] - 2018-04-27
+### Changed
+- Namespace Conda environment kernel paths to avoid collision with module
+  environment kernels.
+- Only attempt to install package if it doesn't exist to speed up launch
+  process.
+
+### Fixed
+- *Hopefully* fixed race condition when downloading packages.
+
+## [0.6.1] - 2018-04-26
+### Changed
+- Added timing information in output logs and increased timeout to 10 minutes.
+
+### Fixed
+- Fixed issue with Conda environments not being loaded properly.
+
+## [0.6.0] - 2018-04-17
+### Added
+- Added debug queue as an option.
+- Users can now specify number of cores on the node.
+
+### Changed
+- Changed server timeout to 120 seconds to account for running on shared node.
+
+## [0.5.0] - 2018-03-28
+### Added
+- Added support for user-created Conda environments.
+
+### Changed
+- Use custom Jupyter Notebook module provided by SciApps.
+
+## [0.4.1] - 2018-03-06
+### Changed
+- Output more debug info.
+
+## [0.4.0] - 2018-03-06
+### Added
+- Added the various Python modules on OSC Owens as Jupyter kernels.
+- Added the Julia module on OSC Owens as a Jupyter kernel.
+
+### Changed
+- Updated date in `LICENSE.md`.
+- Renamed Account to Project.
+- Changed favicon to cogs.
+- Changed the way we launch Jupyter notebook by now pointing to a custom
+  location for the Jupyter notebook installation.
+- Stopped using login shells to speed up process start times.
+
+## [0.3.0] - 2017-12-07
+### Added
+- Added helpful links in the app description and node type description.
+  [#17](https://github.com/OSC/bc_osc_jupyter/issues/17)
+
+### Changed
+- Updated links in `README.md` to point to correct locations.
+  [#15](https://github.com/OSC/bc_osc_jupyter/issues/15)
+- Made log file more verbose.
+
+### Fixed
+- Fixed some text formatting issues.
+  [#16](https://github.com/OSC/bc_osc_jupyter/issues/16)
+- Removed references to RStudio.
+  [#14](https://github.com/OSC/bc_osc_jupyter/issues/14)
+
+## [0.2.1] - 2017-10-20
+### Changed
+- Moved the account input field to the top of the form.
+
+### Fixed
+- Removed need for message to user about waiting for server to start.
+  [#13](https://github.com/OSC/bc_osc_jupyter/issues/13)
+
+## [0.2.0] - 2017-10-11
+### Changed
+- Modified app to take advantage of ERB templates in updated Dashboard.
+- Changed the `CHANGELOG.md` formatting.
+
+## [0.1.0] - 2017-06-14
+### Changed
+- Refactored for the new Batch Connect app.
+
+## [0.0.5] - 2017-05-18
+### Fixed
+- Disable XSRF protection that broke VNCSim auto-login capabilities.
+
+## [0.0.4] - 2017-05-11
+### Added
+- Added CUDA support to Jupyter through a separate sub-app.
+
+## [0.0.3] - 2017-04-24
+### Removed
+- Versioning the assets removed need for `bin/setup`.
+
+## [0.0.2] - 2017-04-21
+### Added
+- Added `bin/setup` script for easier deployment.
+
+## 0.0.1 - 2017-04-04
+### Added
+- Initial release!
+
+[Unreleased]: https://github.com/OSC/bc_osc_jupyter/compare/v0.6.2...HEAD
+[0.6.2]: https://github.com/OSC/bc_osc_jupyter/compare/v0.6.1...v0.6.2
+[0.6.1]: https://github.com/OSC/bc_osc_jupyter/compare/v0.6.0...v0.6.1
+[0.6.0]: https://github.com/OSC/bc_osc_jupyter/compare/v0.5.0...v0.6.0
+[0.5.0]: https://github.com/OSC/bc_osc_jupyter/compare/v0.4.1...v0.5.0
+[0.4.1]: https://github.com/OSC/bc_osc_jupyter/compare/v0.4.0...v0.4.1
+[0.4.0]: https://github.com/OSC/bc_osc_jupyter/compare/v0.3.0...v0.4.0
+[0.3.0]: https://github.com/OSC/bc_osc_jupyter/compare/v0.2.1...v0.3.0
+[0.2.1]: https://github.com/OSC/bc_osc_jupyter/compare/v0.2.0...v0.2.1
+[0.2.0]: https://github.com/OSC/bc_osc_jupyter/compare/v0.1.0...v0.2.0
+[0.1.0]: https://github.com/OSC/bc_osc_jupyter/compare/v0.0.5...v0.1.0
+[0.0.5]: https://github.com/OSC/bc_osc_jupyter/compare/v0.0.4...v0.0.5
+[0.0.4]: https://github.com/OSC/bc_osc_jupyter/compare/v0.0.3...v0.0.4
+[0.0.3]: https://github.com/OSC/bc_osc_jupyter/compare/v0.0.2...v0.0.3
+[0.0.2]: https://github.com/OSC/bc_osc_jupyter/compare/v0.0.1...v0.0.2

ATMOS5100/LICENSE.txt

@@ -0,0 +1,22 @@
+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.

ATMOS5100/README.md

@@ -0,0 +1,2 @@
+# Batch Connect - CHPC Jupyter for ATMOS5100
+

ATMOS5100/README.md~

@@ -0,0 +1,80 @@
+# Batch Connect - CHPC Jupyter
+
+![GitHub Release](https://img.shields.io/github/release/osc/bc_osc_jupyter.svg)
+[![GitHub License](https://img.shields.io/badge/license-MIT-green.svg)](https://opensource.org/licenses/MIT)
+
+An interactive app designed for Open OnDemand that launches a Jupyter
+server on a CHPC infrastructure.
+
+CHPC modifications include local cluster and Linux host adapter settings and custom Python environment entry.
+
+Most content below is from the original [OSC app](https://github.com/OSC/bc_osc_jupyter).
+
+## 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 the Jupyter server.
+- [Jupyter] 4.2.3+ (earlier versions are untested but may work for
+  you)
+- [OpenSSL] 1.0.1+ (used to hash the Jupyter server password)
+
+[Jupyter]: https://jupyter.org/
+[OpenSSL]: https://www.openssl.org/
+[Lmod]: https://www.tacc.utexas.edu/research-development/tacc-projects/lmod
+
+## Install
+
+Use Git to clone this app and checkout the desired branch/version you want to
+use:
+
+```sh
+scl enable git19 -- git clone <repo>
+cd <dir>
+scl enable git19 -- git checkout <tag/branch>
+```
+
+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.
+
+To update the app you would:
+
+```sh
+cd <dir>
+scl enable git19 -- git fetch
+scl enable git19 -- git checkout <tag/branch>
+```
+
+Again, you do not need to restart the app as it isn't a Passenger app.
+
+## CHEN3603 changes
+
+- James installed Notebook Extensions, to figure out what extension is loaded in the notebook, in the terminal, source the Anaconda environment, in file ```/home/mcuma/.jupyter/jupyter_notebook_config.py```, modify ``` c.Application.show_config = True```, run ```jupyter notebook``` to see what is the config option, e.g.:
+```
+  .nbserver_extensions = {'jupyter_nbextensions_configurator': True}
+``` 
+This goes to template/before.sh as:
+```
+c.NotebookApp.nbserver_extensions = {"jupyter_nbextensions_configurator": True}
+```
+
+- then in template/script.sh, we load the environment as:
+```
+module use /uufs/chpc.utah.edu/common/home/u0033394/MyModules
+module load miniconda3/CHEN3603
+# to export to PDF, need xetex which is not part of the system:
+module load texlive/2019
+```
+
+## Contributing
+
+1. Fork it ( https://github.com/OSC/bc_osc_jupyter/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

ATMOS5100/aa

@@ -0,0 +1 @@
+download.file("http://home.chpc.utah.edu/~mcuma/index.html","index.html")

ATMOS5100/form.js

@@ -0,0 +1,108 @@
+'use strict'
+
+/**
+ * Clamp between two numbers
+ *
+ * @param      {number}  min     The minimum
+ * @param      {number}  max     The maximum
+ * @param      {number}  val     The value to clamp
+ */
+function clamp(min, max, val) {
+  return Math.min(max, Math.max(min, val));
+}
+
+/**
+ * Fix num cores, allowing blanks to remain
+ */
+function fix_num_cores() {
+  let node_type_input = $('#batch_connect_session_context_node_type');
+  let num_cores_input = $('#batch_connect_session_context_num_cores');
+
+  if(num_cores_input.val() === '') {
+    return;
+  }
+
+  set_ppn_by_node_type(node_type_input, num_cores_input);
+}
+
+/**
+ * Sets the ppn by node type.
+ *
+ * @param      {element}  node_type_input  The node type input
+ * @param      {element}  num_cores_input  The number cores input
+ */
+function set_ppn_by_node_type(node_type_input, num_cores_input) {
+  let data = node_type_input.find(':selected').data();
+
+  num_cores_input.attr('max', data.maxPpn);
+  num_cores_input.attr('min', data.minPpn);
+
+  // Clamp value between min and max
+  num_cores_input.val(
+    clamp(data.minPpn, data.maxPpn, num_cores_input.val())
+  );
+}
+
+/**
+ * Toggle the visibilty of a form group
+ *
+ * @param      {string}    form_id  The form identifier
+ * @param      {boolean}   show     Whether to show or hide
+ */
+function toggle_visibilty_of_form_group(form_id, show) {
+  let form_element = $(form_id);
+  let parent = form_element.parent();
+
+  if(show) {
+    parent.show();
+  } else {
+    form_element.val('');
+    parent.hide();
+  }
+}
+
+/**
+ * Toggle the visibilty of the CUDA select
+ *
+ * Looking for the value of data-can-show-cuda
+ */
+function toggle_cuda_version_visibility() {
+  let node_type_input = $('#batch_connect_session_context_node_type');
+
+  // Allow for cuda_version control not existing
+  if ( ! ($('#batch_connect_session_context_cuda_version').length > 0) ) {
+    return;
+  }
+
+  toggle_visibilty_of_form_group(
+    '#batch_connect_session_context_cuda_version',
+    node_type_input.find(':selected').data('can-show-cuda')
+  );
+}
+
+/**
+ * Sets the change handler for the node_type select.
+ */
+function set_node_type_change_handler() {
+  let node_type_input = $('#batch_connect_session_context_node_type');
+  node_type_input.change(node_type_change_hander);
+}
+
+/**
+ * Update UI when node_type changes
+ */
+function node_type_change_hander() {
+  fix_num_cores();
+  toggle_cuda_version_visibility();
+}
+
+/**
+ * Main
+ */
+
+// Set controls to align with the values of the last session context
+fix_num_cores();
+toggle_cuda_version_visibility();
+
+// Install event handlers
+set_node_type_change_handler();

ATMOS5100/form.yml

@@ -0,0 +1,30 @@
+---
+title: "ATMOS5100"
+attributes:
+  cluster: 
+    widget: "select"
+    options:
+      - "notchpeak"
+  bc_num_hours:
+    value: 1
+    min: 1
+    max: 8
+    step: 1
+    help: "Maximum wall time on notchpeak-shared-short is 8 hours."
+  my_account:
+    label: "Account"
+    widget: "select"
+    options:
+      - "notchpeak-shared-short"
+  my_queue:
+    label: "Partition"
+    widget: "select"
+    options:
+      - "notchpeak-shared-short"
+
+form:
+  - cluster
+  - bc_num_hours
+  - my_account
+  - my_queue
+  - bc_email_on_started