Compare revisions

Jeff Ohrstrom · Jeff Ohrstrom · Jeff Ohrstrom · Jeff Ohrstrom · Jeff Ohrstrom · Jeff Ohrstrom
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
 variables:
  # older versions of git have issues fetching.
  GIT_STRATEGY: clone
-
+  OOD_PACKAGING_DEBUG: 'true'
+  OOD_PACKAGING_GPG_PRIVATE_KEY: /systems/osc_certs/gpg/ondemand/ondemand.sec
+  OOD_PACKAGING_GPG_PASSPHRASE: /systems/osc_certs/gpg/ondemand/.gpgpass

 before_script:
  - docker info
  - '[ -d tmp ] || mkdir tmp'
-  - git clone https://github.com/OSC/ondemand-packaging.git tmp/ondemand-packaging
-  - cp /systems/osc_certs/gpg/ondemand/.gpgpass $CI_PROJECT_DIR/tmp/ondemand-packaging/
-  - cp /systems/osc_certs/gpg/ondemand/ondemand.sec $CI_PROJECT_DIR/tmp/ondemand-packaging/
+  - git clone --branch main https://github.com/OSC/ondemand-packaging.git tmp/ondemand-packaging
 stages:
  - build
  - deploy

 rpm-build:
  stage: build
-  only:
-    - tags
+  rules:
+    - if: $CI_COMMIT_TAG
+    - if: '$CI_PIPELINE_SOURCE == "external_pull_request_event"'
  script:
-    - ./tmp/ondemand-packaging/build.sh -w $CI_PROJECT_DIR/tmp/work -o $CI_PROJECT_DIR/tmp/output -V $CI_COMMIT_TAG -u -v $CI_PROJECT_DIR/packaging
+    - ./tmp/ondemand-packaging/bin/ood_packaging -w $CI_PROJECT_DIR/tmp/work -o $CI_PROJECT_DIR/tmp/output -V $CI_COMMIT_TAG -T $CI_PROJECT_DIR
+  parallel:
+    matrix:
+      - OOD_PACKAGING_DIST: [el7, el8]
  artifacts:
    paths:
      - tmp/output
    name: "$CI_PROJECT_NAME-$CI_COMMIT_TAG"

-
-rpm-deploy-ci:
-  stage: deploy
-  only:
-    - tags
-  script:
-    - ./tmp/ondemand-packaging/release.py --debug --pkey /systems/osc_certs/ssh/ondemand-packaging/id_rsa -c ci ./tmp/output/*
 rpm-deploy:
  stage: deploy
-  only:
-    - tags
-  except:
-    variables:
-      - $CI_COMMIT_TAG =~ /.*_.*/
+  rules:
+    - if: $CI_COMMIT_TAG
  script:
    - ./tmp/ondemand-packaging/release.py --debug --pkey /systems/osc_certs/ssh/ondemand-packaging/id_rsa -c main ./tmp/output/*
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,27 @@ 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]
+## [0.11.0] - 2022-04-04
+### Added
+- Adds a new Matlab default version of 2022a
+
+## [0.10.0] - 2021-12-10
+### Added
+- [15](https://github.com/OSC/bc_osc_matlab/pull/15)
+  - Enabled the Pitzer Cluster in Matlab along with the related selection configurations.
+  - Migrated all select functionality to the new Dynamic JS select functionality.
+
+## [0.9.0] - 2021-01-20
+### Added
+- [13](https://github.com/OSC/bc_osc_matlab/pull/13)
+  - removed owens-slurm and torque related configurations
+  - changed account to be a select widget with only valid groups as options
+
+## [0.8.0] - 2020-11-18
+### Added
+- Added owens-slurm cluster to being migrating Owens to Slurm in
+  [11](https://github.com/OSC/bc_osc_matlab/pull/11)
+
 ## [0.7.0] - 2019-12-10
 ### Added
 - Adds a new Matlab default version of 2019b
@@ -71,8 +92,13 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### Added
 - Initial release!

-[Unreleased]: https://github.com/OSC/bc_osc_matlab/compare/v0.7.0...HEAD
-[0.6.1]: https://github.com/OSC/bc_osc_matlab/compare/v0.6.1...v0.7.0
+[Unreleased]:
+https://github.com/OSC/bc_osc_matlab/compare/v0.11.0...HEAD
+[0.11.0]: https://github.com/OSC/bc_osc_matlab/compare/v0.10.0...v0.11.0
+[0.10.0]: https://github.com/OSC/bc_osc_matlab/compare/v0.9.0...v0.10.0
+[0.9.0]: https://github.com/OSC/bc_osc_matlab/compare/v0.8.0...v0.9.0
+[0.8.0]: https://github.com/OSC/bc_osc_matlab/compare/v0.7.0...v0.8.0
+[0.7.0]: https://github.com/OSC/bc_osc_matlab/compare/v0.6.1...v0.7.0
 [0.6.1]: https://github.com/OSC/bc_osc_matlab/compare/v0.6.0...v0.6.1
 [0.6.0]: https://github.com/OSC/bc_osc_matlab/compare/v0.5.1...v0.6.0
 [0.5.1]: https://github.com/OSC/bc_osc_matlab/compare/v0.5.0...v0.5.1

--- a/form.js
+++ b/form.js
-'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');
+const table = {
+  "interactive": { "max_cpu": 48, "max_hour": 2, "max_gpu": 0 },
+  "express": { "max_cpu": 48, "max_hour": 2, "max_gpu": 0 },
+  "short": { "max_cpu": 48, "max_hour": 12, "max_gpu": 0 },
+  "pascalnodes": { "max_cpu": 28, "max_hour": 12, "max_gpu": 4 },
+  "pascalnodes-medium": { "max_cpu": 28, "max_hour": 48, "max_gpu": 4 },
+  "medium": { "max_cpu": 48, "max_hour": 50, "max_gpu": 0 },
+  "long": { "max_cpu": 48, "max_hour": 150, "max_gpu": 0 },
+  "intel-dcb": { "max_cpu": 24, "max_hour": 150, "max_gpu": 0 },
+  "amd-hdr100": { "max_cpu": 128, "max_hour": 150, "max_gpu": 0 },
+  "largemem": { "max_cpu": 24, "max_hour": 50, "max_gpu": 0 },
+  "largemem-long": { "max_cpu": 24, "max_hour": 150, "max_gpu": 0 },
+  "amperenodes": { "max_cpu": 128, "max_hour": 12, "max_gpu": 2 },
+  "amperenodes-medium": { "max_cpu": 128, "max_hour": 48, "max_gpu": 2 },
+}

-  if(num_cores_input.val() === '') {
-    return;
-  }
+const gpu_part_regex = /pascal|ampere/;

-  if(node_type === 'hugemem') {
-    set_ppn_owens_hugemem(num_cores_input);
-  } else {
-    set_ppn_owens_regular(num_cores_input);
-  }
+function set_max_value(form_id, value) {
+  const form_element = $(form_id);
+  form_element.attr({'max': value});
+  if (form_element.val() > value)
+    form_element.val(value)
 }

-/**
- * 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);
+function set_partition_change_handler() {
+  let partition_select = $("#batch_connect_session_context_bc_partition");
+  partition_select.change( function(e) {
+    toggle_gpu_visibility(e);
+  });
 }

-/**
- * 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', 1);
-  num_cores_input.val(Math.min(NUM_CORES, num_cores_input.val()));
+function toggle_gpu_visibility(event) {
+  const partition = event.target.value;
+  const cpu_selector = '#batch_connect_session_context_bc_num_slots';
+  const gpu_selector = '#batch_connect_session_context_bc_num_gpus';
+  const hour_selector = '#batch_connect_session_context_bc_num_hours';
+
+  toggle_visibilty_of_form_group(gpu_selector, gpu_part_regex.test(partition));
+  set_max_value(cpu_selector, table[partition]["max_cpu"]);
+  set_max_value(gpu_selector, table[partition]["max_gpu"]);
+  set_max_value(hour_selector, table[partition]["max_hour"]);
 }

+function toggle_visibilty_of_form_group(form_id, show) {
+  let form_element = $(form_id);
+  let parent = form_element;

-/**
- * 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);
+  while (
+    (! parent[0].classList.contains('form-group')) &&
+    (! parent.is('html')) // ensure that we don't loop infinitely
+  ) {
+    parent = parent.parent();
+  }
+
+  // If parent is HTML then something has gone wrong and visibility should not be changed
+  if ( parent.is('html') ) {
+    return;
+  }
+
+  if(show) {
+    parent.show();
+  } else {
+    parent.hide();
+  }
 }

-$(document).ready(function() {
-  // Set the max value to be what was set in the last session
-  fix_num_cores();
-  set_node_type_change_handler();
-});
\ No newline at end of file
+toggle_gpu_visibility(
+  // Fake the event
+  { target: document.querySelector('#batch_connect_session_context_bc_partition') }
+);
+set_partition_change_handler();
--- a/form.yml
+++ b/form.yml
---
-cluster:
-  - "owens"
-  - "owens-slurm"
-form:
-  - version
-  - bc_account
-  - 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: 48
-    step: 1
-    id: 'num_cores'
-  bc_num_slots: "1"
-  bc_vnc_resolution:
-    required: true
-  bc_account:
-    label: "Project"
-    help: "You can leave this blank if **not** in multiple projects."
-  node_type:
-    widget: select
-    label: "Node type"
-    help: |
-      - **any** - (*1-28 cores*) Use any available Owens node. This reduces the
-        wait time as there are no node requirements.
-      - **hugemem** - (*48 cores*) Use an Owens node that has 1.5TB of
-        available RAM as well as 48 cores. There are 16 of these nodes on
-        Owens. Requesting hugemem nodes allocates entire nodes.
-      - **vis** - (*1-28 cores*) Use an Owens node that has an [NVIDIA Tesla P100
-        GPU](http://www.nvidia.com/object/tesla-p100.html) with an X server
-        running in the background. This utilizes the GPU for hardware
-        accelerated 3D visualization. There are 160 of these nodes on Owens.
-    options:
-      - "any"
-      - "hugemem"
-      - "vis"
-  version:
-    widget: select
-    label: "MATLAB version"
-    help: "This defines the version of MATLAB you want to load."
-    options:
-      - [ "R2019b", "matlab/r2019b" ]
-      - [ "R2018b", "matlab/r2018b" ]
-      - [ "R2018a", "matlab/r2018a" ]
-      - [ "R2017a", "matlab/r2017a" ]
-      - [ "R2016b", "matlab/r2016b" ]
-      - [ "R2015b", "matlab/r2015b" ]
--- a/form.yml.erb
+++ b/form.yml.erb
+<%-
+  partitions = OodAppkit.clusters[:SLURM_CLUSTER].custom_config[:partitions]
+-%>
+---
+cluster: "SLURM_CLUSTER"
+attributes:
+  custom_environment:
+    widget: text_area
+    label: Environment Setup
+    value: |
+      # If you would like to load other modules
+      # or add other things in your environment please list below
+      #
+      # format:
+      # module load example_module/VERSION example_module2
+      # export PATH=....
+
+  bc_num_hours:
+    value: 1
+
+  bc_num_slots:
+    widget: "number_field"
+    label: Number of CPU
+    value: 1
+    min: 1
+    max: 24
+    step: 1
+
+  bc_num_mems:
+    widget: "number_field"
+    label: Memory per CPU (GB)
+    value: 4
+    min: 1
+    max: 128
+    step: 1
+
+  bc_num_gpus:
+    widget: "number_field"
+    label: Number of GPUs
+    value: 1
+    min: 0
+    max: 4
+    step: 1
+
+  bc_partition:
+    widget: select
+    label: Partition
+    options:
+    <%- partitions.each do |p| -%>
+      - [ "<%= p %>", "<%= p %>" ]
+    <%- end -%>
+
+  version:
+    widget: select
+    label: "MATLAB version"
+    help: "This defines the version of MATLAB you want to load."
+    options:
+      - [ "R2023a", "rc/matlab/R2023a"]
+      - [ "R2022a", "rc/matlab/R2022a"]
+      - [ "R2021b", "rc/matlab/R2021b"]
+      - [ "R2021a", "rc/matlab/R2021a"]
+      - [ "R2020a", "rc/matlab/R2020a"]
+      - [ "R2019b", "rc/matlab/R2019b"]
+      - [ "R2019a", "rc/matlab/R2019a"]
+      - [ "R2018a", "rc/matlab/R2018a"]
+      - [ "R2017b", "rc/matlab/R2017b"]
+      - [ "R2017a", "rc/matlab/R2017a"]
+      - [ "R2016b", "rc/matlab/R2016b"]
+      - [ "R2016a", "rc/matlab/R2016a"]
+      - [ "R2015a", "rc/matlab/R2015a"]
+      - [ "R2013a", "rc/matlab/R2013a"]
+      - [ "R2012a", "rc/matlab/R2012a"]
+
+  cuda_toolkit: "cuda10.0/toolkit"
+
+form:
+  - custom_environment
+  - version
+  - bc_num_hours
+  - bc_partition
+  - bc_num_gpus
+  - bc_num_slots
+  - bc_num_mems
+  - bc_email_on_started
+  - cuda_toolkit
--- a/manifest.yml
+++ b/manifest.yml
@@ -4,8 +4,8 @@ category: Interactive Apps
 subcategory: GUIs
 role: batch_connect
 description: |
-  This app will launch a [MATLAB] GUI on the [Owens cluster]. You will be able
+  This app will launch a [MATLAB] GUI on the [Cheaha 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
+  [Cheaha cluster]: https://uabrc.github.io
--- a/packaging/ondemand-bc_osc_matlab.spec
+++ b/packaging/ondemand-bc_osc_matlab.spec
@@ -34,14 +34,9 @@ DESCRIPTION


 %install
-export PASSENGER_APP_ENV=production
-export PASSENGER_BASE_URI=/pun/sys/%{app_name}
 mkdir -p %{buildroot}%{_localstatedir}/www/ood/apps/sys/%{app_name}
-if [ -x bin/setup ]; then
-    bin/setup
-fi
 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)

--- a/script.sh.erb
+++ b/script.sh.erb
+#!/usr/bin/env bash
+
+# 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)"
+  module reset
+  set -x
+  xfwm4 --compositor=off --daemon --sm-client-disable
+  xsetroot -solid "#D3D3D3"
+  xfsettingsd --sm-client-disable
+  xfce4-panel --sm-client-disable
+) &
+
+#
+# Start MATLAB
+#
+
+<%- if context.bc_partition == "pascalnodes" -%>
+# Load CUDA toolkit
+module load <%= context.cuda_toolkit %>
+<%- end -%>
+# Load the required environment
+module load <%= context.version %>
+# Launch MATLAB
+module list
+set -x
+matlab -desktop
--- a/submit.yml.erb
+++ b/submit.yml.erb
 <%-
-  ppn = num_cores.blank? ? 28 : num_cores.to_i
-  nodes = bc_num_slots.blank? ? 1 : bc_num_slots.to_i
-  torque_cluster = OodAppkit.clusters[cluster].job_config[:adapter] == 'torque'
-
-  case node_type
-  when "hugemem"
-    ppn = 48
-    partition = bc_num_slots.to_i > 1 ? "hugemem-parallel" : "hugemem"
-    slurm_args = [ "--nodes", "#{nodes}", "--ntasks-per-node", "#{ppn}", "--partition", partition ]
-    torque_args = "#{nodes}:ppn=#{ppn}:#{node_type}"
-  when "vis"
-    slurm_args = ["--nodes", "#{nodes}", "--ntasks-per-node", "#{ppn}", "--gpus-per-node", "1", "--gres", "vis" ]
-    torque_args = "#{nodes}:ppn=#{ppn}:#{node_type}:gpus=1"
-  else
-    slurm_args = ["--nodes", "#{nodes}", "--ntasks-per-node", "#{ppn}" ]
-    torque_args = "#{nodes}:ppn=#{ppn}"
+  email = ENV['USER']
+  if !email.include? '@'
+    email = email + '@uab.edu'
  end
-%>
+-%>
 ---
 batch_connect:
-  template: vnc
+  template: "vnc"
 script:
+  job_environment:
+    USER: "<%= ENV['USER'] %>"
  native:
-  <%- if torque_cluster %>
-    resources:
-      nodes: "<%= torque_args %>"
-  <%- else %>
-  <%- slurm_args.each do |arg| %>
-    - "<%= arg %>"
-  <%- end %>
-  <%- end %>
+    - "-N 1"
+    - "-n <%= bc_num_slots.blank? ? 1 : bc_num_slots.to_i %>"
+    - "--mem-per-cpu=<%= bc_num_mems.blank? ? 4 : bc_num_mems.to_i %>G"
+    - "--partition=<%= bc_partition %>"
+    - "--time=<%= bc_num_hours.blank? ? 1 : bc_num_hours.to_i %>:00:00"
+    - "--job-name=ood-matlab-<%= version.split("/")[-1] %>"
+<%- if bc_partition.include? "pascalnodes" or bc_partition.include? "amperenodes" -%>
+    - "--gres=gpu:<%= bc_num_gpus.blank? ? 1 : bc_num_gpus.to_i %>"
+<%- end -%>
+<%- if bc_email_on_started == "1" -%>
+    - "--mail-type=BEGIN"
+    - "--mail-user=<%= email %>"
+<%- end -%>
--- 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}"

@@ -17,7 +12,7 @@ cd "${HOME}"
  export XDG_CONFIG_HOME="<%= session.staged_root.join("config") %>"
  export XDG_DATA_HOME="<%= session.staged_root.join("share") %>"
  export XDG_CACHE_HOME="$(mktemp -d)"
-  module restore
+  module reset
  set -x
  xfwm4 --compositor=off --daemon --sm-client-disable
  xsetroot -solid "#D3D3D3"
@@ -29,17 +24,15 @@ cd "${HOME}"
 # Start MATLAB
 #

+<%- if context.bc_partition == "pascalnodes" -%>
+# Load CUDA toolkit
+module load <%= context.cuda_toolkit %>
+<%- end -%>
 # Load the required environment
-module load xalt/latest <%= context.version %>
+module load <%= context.version %>

+<%= context.custom_environment.gsub(/\r\n?/, "\n") %>
 # 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 -%>
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