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_config.yml
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_config.yml
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# LAMMPS on HPC Jekyll configuration
---
#------------------------------------------------------------
# SITE specific configuration
#------------------------------------------------------------
# Cluster host and scheduler options: the defaults come from
# Jureca at JSC, running SLURM. Other options can
# be found in the library of snippets_library,
# `_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
# PBS, we could replace the options below with those from
#
# _includes/snippets_library/EPCC_Cirrus_pbs/_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!
snippets: "/snippets_library/JSC_JURECA_SLURM"
local:
prompt: "[user@laptop ~]$"
remote:
name: "JURECA"
login: "jureca01.fz-juelich.de"
host: "jrl12"
node: "jrc0940"
location: "Juelich Supercomputing Centre"
homedir: "/p/home/jusers/yourUsername/jureca"
prompt: "[yourUsername@jrl12 ~]$"
sched:
name: "SLURM"
user: "yourUsername"
submit:
name: "sbatch"
# Use this to include account options etc. when submitting
options: ""
status: "squeue"
flag:
user: "-u yourUsername"
interactive: "--pty /bin/bash -i"
histdetail: "-l -j"
name: "-J"
time: "-t"
queue: "--partition"
node: "-N"
del: "scancel"
interactive: "srun"
info: "sinfo"
comment: "#SBATCH"
hist: "sacct -u yourUsername"
queue:
default: "batch"
lammps:
version: "3Mar2020"
exec: "lmp"
kokkos:
env:
- "module purge"
- "module use /usr/local/software/jureca/OtherStages"
- "module load Stages/Devel-2019a"
- "module load intel-para/2019a LAMMPS/9Jan2020-kokkos"
exec: "lmp"
gpu:
env:
- "module purge"
- "module use /usr/local/software/jureca/OtherStages"
- "module load Stages/Devel-2019a"
- "module load intel-para/2019a LAMMPS/9Jan2020-cuda"
exec: "lmp"
openmp:
env:
- "module purge"
- "module use /usr/local/software/jureca/OtherStages"
- "module load Stages/Devel-2019a"
- "module load intel-para/2019a LAMMPS/9Jan2020-cuda"
exec: "lmp"
mpi_runtime:
implementation: "ParaStation"
launcher: "srun"
# Interactive queue names, one or more as a list
workshop_interactive_queues:
- devel
- develgpus
#------------------------------------------------------------
# Values for this lesson.
#------------------------------------------------------------
# Which carpentry is this?
# "swc": Software Carpentry
# "dc": Data Carpentry
# "lc": Library Carpentry
# "cp": Carpentries (e.g., instructor training)
carpentry: "swc"
# Overall title for pages.
title: "Running LAMMPS on HPC systems"
# Email address, no mailto:
email: "[email protected]"
# Life cycle stage of the lesson
# possible values: "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/
- .docker-vendor/
# Turn on built-in syntax highlighting.
highlighter: rouge