_config.yml

# HPC-Intro Jekyll configuration
---

#------------------------------------------------------------
# SITE specific configuration
#------------------------------------------------------------

# Cluster host and scheduler options: the defaults come from
# the HPC Carpentry tutorial cluster, running Slurm. Other
# options can be found in the library of snippets,
# `_includes/snippets_library`. To use one, replace options
# below with those in `_config_options.yml` from the
# library. E.g, to customise for Cirrus at EPCC, running
# Slurm, we could replace the options below with those from
# 
# _includes/snippets_library/EPCC_Cirrus_slurm/_config_options.yml
# 
# If your cluster is not represented in the library, please
# copy an existing folder, rename it, and customize for your
# installation. Remember to keep the leading slash on the
# `snippets` variable below!

# UCL, University College London: Myriad + SGE
snippets: "/snippets_library/UCL_Myriad_sge"

local:
  prompt: "[you@laptop:~]$"
  bash_shebang: "#!/usr/bin/env bash"

remote:
  name: "Myriad"
  login: "myriad.rc.ucl.ac.uk"
  host: "login12.myriad.ucl.ac.uk"
  node: node-d00a-005
  location: "University College London"
  homedir: "/home"
  user: "yourUsername"
  prompt: "[yourUsername@login12 ~]$ "
  module_python3: "python3"
  bash_shebang: "#!/bin/bash -l"

sched:
  name: "SGE"
  submit:
    name: "qsub"
    options: ""
    iopt: "" # TODO what does this mean?
  queue:
    debug: "debug"
    testing: "testing"
  status: "qstat"
  flag:
    user: "-u yourUsername"
    interactive: "-l mem=512M,h_rt=2:00:00"
    histdetail: "-j"
    name: "-N"
    time: "-l h_rt="
    queue: "-p" # TODO check for Myriad
    nodes: "-N" # TODO check for Myriad
    tasks: "-n" # TODO check for Myriad
  del: "qdel"
  interactive: "qrsh"
  info: "nodetypes"
  hosts: "qhost"
  comment: "#$"
  hist: "jobhist"

episode_order:
  - 10-hpc-intro
  - 11-connecting
  - 12-cluster
  - 13-scheduler
  - 14-environment-variables
  - 15-modules
  - 16-transferring-files
  - 17-parallel
  - 18-resources
  - 19-responsibility

#------------------------------------------------------------
# Values for this lesson
#------------------------------------------------------------

# Which carpentry is this?
# "swc": Software Carpentry
# "dc":  Data Carpentry
# "lc":  Library Carpentry
# "cp":  Carpentries (e.g., instructor training)
carpentry: "incubator"

# Overall title for pages.
title: "Introduction to High-Performance Computing"

# Email address, no mailto:
email: "team@carpentries.org"

# Life cycle stage of the lesson ("pre-alpha", "alpha", "beta", "stable")?
life_cycle: "alpha"

#------------------------------------------------------------
# Generic settings (should not need to change).
#------------------------------------------------------------

# What kind of thing is this ("workshop" or "lesson")?
kind: "lesson"

# Start time in minutes (0 to be clock-independent, 540 to show a start at 09:00 am).
start_time: 0

# Magic to make URLs resolve both locally and on GitHub. Please don't change.
repository: <USERNAME>/<PROJECT>

# Invoke the Carpentries theme rather than copying into our repository.
remote_theme: carpentries/carpentries-theme

# Sites.
amy_site: "https://amy.carpentries.org/"
carpentries_github: "https://github.com/carpentries"
carpentries_pages: "https://carpentries.github.io"
carpentries_site: "https://carpentries.org/"
dc_site: "https://datacarpentry.org"
example_repo: "https://github.com/carpentries/lesson-example"
example_site: "https://carpentries.github.io/lesson-example"
lc_site: "https://librarycarpentry.org/"
swc_github: "https://github.com/swcarpentry"
swc_pages: "https://swcarpentry.github.io"
swc_site: "https://software-carpentry.org"
template_repo: "https://github.com/carpentries/styles"
training_site: "https://carpentries.github.io/instructor-training"
workshop_repo: "https://github.com/carpentries/workshop-template"
workshop_site: "https://carpentries.github.io/workshop-template"
cc_by_human: "https://creativecommons.org/licenses/by/4.0/"

# Specify that things in the Episodes and Extras collections should be output.
collections:
  episodes:
    output: true
    permalink: /:path/index.html
  extras:
    output: true
    permalink: /:path/index.html

# Set the default layout for things in the episodes collection.
defaults:
  - values:
      root: .
      layout: page
  - scope:
      path: ""
      type: episodes
    values:
      root: ..
      layout: episode
  - scope:
      path: ""
      type: extras
    values:
      root: ..
      layout: page

# Files and directories that are not to be copied.
exclude:
  - Makefile
  - bin/
  - .Rproj.user/
  - .vendor/
  - vendor/
  - .docker-vendor/

# Turn on built-in syntax highlighting.
highlighter: rouge

plugins:
  - jekyll-redirect-from
  - jekyll-paginate