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Use generated resource allocation options for veda hub #3566

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Jan 4, 2024
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Use generated resource allocation options for veda hub #3566

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0763ee8
Use generated resource allocation options for veda hub
yuvipanda Jan 3, 2024
0c64bb1
Fix missing resource allocation choice for custom image
yuvipanda Jan 3, 2024
c822e4d
Update capacities & regenerate veda choices
yuvipanda Jan 3, 2024
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357 changes: 141 additions & 216 deletions config/clusters/nasa-veda/common.values.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -59,31 +59,147 @@ basehub:
- wildintellect
singleuser:
defaultUrl: /lab
image:
name: public.ecr.aws/nasa-veda/nasa-veda-singleuser
# Based off pangeo/pangeo-notebook:2023.07.05 which uses JupyterLab <4, so jupyterlab-git and dask-dashboard work
# If updating this tag, also update it in the `profile_options.image.options.pangeo.kubespawner_override.image`below
tag: "5068290376e8c3151d97a36ae6485bb7ff79650b94aecc93ffb2ea1b42d76460"
profileList:
# NOTE: About node sharing
#
# CPU/Memory requests/limits are actively considered still. This
# profile list is setup to involve node sharing as considered in
# https://github.com/2i2c-org/infrastructure/issues/2121.
#
# - Memory requests are different from the description, based on:
# whats found to remain allocate in k8s, subtracting 1GiB
# overhead for misc system pods, and transitioning from GB in
# description to GiB in mem_guarantee.
# - CPU requests are lower than the description, with a factor of
# 10%.
#
- display_name: "Small: up to 4 CPU / 32 GB RAM"
description: &profile_list_description "Start a container with at least a chosen share of capacity on a node of this type"
slug: small
- display_name: "Modified Pangeo Notebook"
slug: modified-pangeo
description: Pangeo based notebook with a Python environment
default: true
kubespawner_override:
image: public.ecr.aws/nasa-veda/nasa-veda-singleuser:5068290376e8c3151d97a36ae6485bb7ff79650b94aecc93ffb2ea1b42d76460
init_containers:
# Need to explicitly fix ownership here, as otherwise these directories will be owned
# by root on most NFS filesystems - neither EFS nor Google Filestore support anonuid
- name: volume-mount-ownership-fix
image: busybox:1.36.1
command:
- sh
- -c
- id && chown 1000:1000 /home/jovyan /home/jovyan/shared && ls -lhd /home/jovyan
securityContext:
runAsUser: 0
volumeMounts:
- name: home
mountPath: /home/jovyan
subPath: "{username}"
# mounted without readonly attribute here,
# so we can chown it appropriately
- name: home
mountPath: /home/jovyan/shared
subPath: _shared
# this container uses nbgitpuller to mount https://github.com/NASA-IMPACT/veda-docs/ for user pods
# image source: https://github.com/NASA-IMPACT/veda-jh-environments/tree/main/docker-images/base/nasa-veda-singleuser-init
- name: nasa-veda-singleuser-init
image: public.ecr.aws/nasa-veda/nasa-veda-singleuser-init:38e8998f9be64b0a59ac6c4d6d152d3403121dfc4be6d49bdf52ddc92827af8a
command:
- "python3"
- "/opt/k8s-init-container-nb-docs.py"
- "/home/jovyan"
volumeMounts:
- name: home
mountPath: /home/jovyan
subPath: "{username}"
securityContext:
runAsUser: 1000
runAsGroup: 1000
profile_options: &profile_options
resource_allocation: &profile_options_resource_allocation
display_name: Resource Allocation
choices:
mem_1_9:
display_name: 1.9 GB RAM, upto 3.75 CPUs
kubespawner_override:
mem_guarantee: 1991341312
mem_limit: 1991341312
cpu_guarantee: 0.234375
cpu_limit: 3.75
node_selector:
node.kubernetes.io/instance-type: r5.xlarge
default: true
mem_3_7:
display_name: 3.7 GB RAM, upto 3.75 CPUs
kubespawner_override:
mem_guarantee: 3982682624
mem_limit: 3982682624
cpu_guarantee: 0.46875
cpu_limit: 3.75
node_selector:
node.kubernetes.io/instance-type: r5.xlarge
mem_7_4:
display_name: 7.4 GB RAM, upto 3.75 CPUs
kubespawner_override:
mem_guarantee: 7965365248
mem_limit: 7965365248
cpu_guarantee: 0.9375
cpu_limit: 3.75
node_selector:
node.kubernetes.io/instance-type: r5.xlarge
mem_14_8:
display_name: 14.8 GB RAM, upto 3.75 CPUs
kubespawner_override:
mem_guarantee: 15930730496
mem_limit: 15930730496
cpu_guarantee: 1.875
cpu_limit: 3.75
node_selector:
node.kubernetes.io/instance-type: r5.xlarge
mem_29_7:
display_name: 29.7 GB RAM, upto 3.75 CPUs
kubespawner_override:
mem_guarantee: 31861460992
mem_limit: 31861460992
cpu_guarantee: 3.75
cpu_limit: 3.75
node_selector:
node.kubernetes.io/instance-type: r5.xlarge

mem_60_7:
display_name: 60.7 GB RAM, upto 15.725 CPUs
kubespawner_override:
mem_guarantee: 65147242496
mem_limit: 65147242496
cpu_guarantee: 7.8625
cpu_limit: 15.725
node_selector:
node.kubernetes.io/instance-type: r5.4xlarge
mem_121_3:
display_name: 121.3 GB RAM, upto 15.725 CPUs
kubespawner_override:
mem_guarantee: 130294484992
mem_limit: 130294484992
cpu_guarantee: 15.725
cpu_limit: 15.725
node_selector:
node.kubernetes.io/instance-type: r5.4xlarge
- display_name: "Rocker Geospatial with RStudio"
slug: rocker
description: R environment with many geospatial libraries pre-installed
kubespawner_override:
image: rocker/binder:4.3
# Launch RStudio after the user logs in
default_url: /rstudio
# Ensures container working dir is homedir
# https://github.com/2i2c-org/infrastructure/issues/2559
working_dir: /home/rstudio
profile_options: *profile_options
- display_name: "QGIS on Linux Desktop"
slug: qgis
description: Linux desktop in the browser, with qgis installed
kubespawner_override:
# Explicitly unset this - we set this to 'jupyterhub-singleuser'
# in basehub/values.yaml. We instead want to leave this unset,
# so the default command for the docker image is used instead.
# This is required for .desktop files to show up correctly.
cmd: null
# Launch people directly into the Linux desktop when they start
default_url: /desktop
# Built from https://github.com/jupyterhub/jupyter-remote-desktop-proxy/pull/51
image: "quay.io/jupyter-remote-desktop-proxy/qgis:2023-09-27"
profile_options: *profile_options
- display_name: "Bring your own image"
description: Specify your own docker image (must have python and jupyterhub installed in it)
slug: custom
profile_options:
image: &image_options
image:
display_name: Image
unlisted_choice:
enabled: True
Expand All @@ -92,200 +208,9 @@ basehub:
validation_message: "Must be a publicly available docker image, of form <image-name>:<tag>"
kubespawner_override:
image: "{value}"
choices:
pangeo:
display_name: Modified Pangeo Notebook
default: true
slug: pangeo
kubespawner_override:
image: public.ecr.aws/nasa-veda/nasa-veda-singleuser:5068290376e8c3151d97a36ae6485bb7ff79650b94aecc93ffb2ea1b42d76460
init_containers:
# Need to explicitly fix ownership here, as otherwise these directories will be owned
# by root on most NFS filesystems - neither EFS nor Google Filestore support anonuid
- name: volume-mount-ownership-fix
image: busybox:1.36.1
command:
- sh
- -c
- id && chown 1000:1000 /home/jovyan /home/jovyan/shared && ls -lhd /home/jovyan
securityContext:
runAsUser: 0
volumeMounts:
- name: home
mountPath: /home/jovyan
subPath: "{username}"
# mounted without readonly attribute here,
# so we can chown it appropriately
- name: home
mountPath: /home/jovyan/shared
subPath: _shared
# this container uses nbgitpuller to mount https://github.com/NASA-IMPACT/veda-docs/ for user pods
# image source: https://github.com/NASA-IMPACT/veda-jh-environments/tree/main/docker-images/base/nasa-veda-singleuser-init
- name: nasa-veda-singleuser-init
image: public.ecr.aws/nasa-veda/nasa-veda-singleuser-init:38e8998f9be64b0a59ac6c4d6d152d3403121dfc4be6d49bdf52ddc92827af8a
command:
- "python3"
- "/opt/k8s-init-container-nb-docs.py"
- "/home/jovyan"
volumeMounts:
- name: home
mountPath: /home/jovyan
subPath: "{username}"
securityContext:
runAsUser: 1000
runAsGroup: 1000
qgis:
display_name: QGIS on Linux Desktop
slug: qgis
kubespawner_override:
# Explicitly unset this - we set this to 'jupyterhub-singleuser'
# in basehub/values.yaml. We instead want to leave this unset,
# so the default command for the docker image is used instead.
# This is required for .desktop files to show up correctly.
cmd: null
# Launch people directly into the Linux desktop when they start
default_url: /desktop
# Built from https://github.com/jupyterhub/jupyter-remote-desktop-proxy/pull/51
image: "quay.io/jupyter-remote-desktop-proxy/qgis:2023-09-27"
rocker:
display_name: Rocker Geospatial with RStudio
slug: rocker
kubespawner_override:
image: rocker/binder:4.3
# Launch RStudio after the user logs in
default_url: /rstudio
# Ensures container working dir is homedir
# https://github.com/2i2c-org/infrastructure/issues/2559
working_dir: /home/rstudio
init_containers:
# Need to explicitly fix ownership here, as otherwise these directories will be owned
# by root on most NFS filesystems - neither EFS nor Google Filestore support anonuid
- name: volume-mount-ownership-fix
image: busybox:1.36.1
command:
[
"sh",
"-c",
"id && chown 1000:1000 /home/rstudio && ls -lhd /home/rstudio ",
]
securityContext:
runAsUser: 0
volumeMounts:
- name: home
mountPath: /home/rstudio
subPath: "{username}"
# this container uses nbgitpuller to mount https://github.com/NASA-IMPACT/veda-docs/ for user pods
# image source: https://github.com/NASA-IMPACT/veda-jh-environments/tree/main/docker-images/base/nasa-veda-singleuser-init
- name: nasa-veda-singleuser-init
image: public.ecr.aws/nasa-veda/nasa-veda-singleuser-init:38e8998f9be64b0a59ac6c4d6d152d3403121dfc4be6d49bdf52ddc92827af8a
command:
- "python3"
- "/opt/k8s-init-container-nb-docs.py"
- "/home/rstudio"
volumeMounts:
- name: home
mountPath: /home/rstudio
subPath: "{username}"
securityContext:
runAsUser: 1000
runAsGroup: 1000
requests:
# NOTE: Node share choices are in active development, see comment
# next to profileList: above.
display_name: Node share
choices:
mem_1:
default: true
display_name: ~1 GB, ~0.125 CPU
kubespawner_override:
mem_guarantee: 0.904G
cpu_guarantee: 0.013
mem_2:
display_name: ~2 GB, ~0.25 CPU
kubespawner_override:
mem_guarantee: 1.809G
cpu_guarantee: 0.025
mem_4:
display_name: ~4 GB, ~0.5 CPU
kubespawner_override:
mem_guarantee: 3.617G
cpu_guarantee: 0.05
mem_8:
display_name: ~8 GB, ~1.0 CPU
kubespawner_override:
mem_guarantee: 7.234G
cpu_guarantee: 0.1
mem_16:
display_name: ~16 GB, ~2.0 CPU
kubespawner_override:
mem_guarantee: 14.469G
cpu_guarantee: 0.2
mem_32:
display_name: ~32 GB, ~4.0 CPU
kubespawner_override:
mem_guarantee: 28.937G
cpu_guarantee: 0.4
kubespawner_override:
cpu_limit: null
mem_limit: null
node_selector:
node.kubernetes.io/instance-type: r5.xlarge
- display_name: "Medium: up to 16 CPU / 128 GB RAM"
description: *profile_list_description
slug: medium
profile_options:
image: *image_options
requests:
# NOTE: Node share choices are in active development, see comment
# next to profileList: above.
display_name: Node share
choices:
mem_1:
display_name: ~1 GB, ~0.125 CPU
kubespawner_override:
mem_guarantee: 0.942G
cpu_guarantee: 0.013
mem_2:
display_name: ~2 GB, ~0.25 CPU
kubespawner_override:
mem_guarantee: 1.883G
cpu_guarantee: 0.025
mem_4:
default: true
display_name: ~4 GB, ~0.5 CPU
kubespawner_override:
mem_guarantee: 3.766G
cpu_guarantee: 0.05
mem_8:
display_name: ~8 GB, ~1.0 CPU
kubespawner_override:
mem_guarantee: 7.532G
cpu_guarantee: 0.1
mem_16:
display_name: ~16 GB, ~2.0 CPU
kubespawner_override:
mem_guarantee: 15.064G
cpu_guarantee: 0.2
mem_32:
display_name: ~32 GB, ~4.0 CPU
kubespawner_override:
mem_guarantee: 30.128G
cpu_guarantee: 0.4
mem_64:
display_name: ~64 GB, ~8.0 CPU
kubespawner_override:
mem_guarantee: 60.257G
cpu_guarantee: 0.8
mem_128:
display_name: ~128 GB, ~16.0 CPU
kubespawner_override:
mem_guarantee: 120.513G
cpu_guarantee: 1.6
kubespawner_override:
cpu_limit: null
mem_limit: null
node_selector:
node.kubernetes.io/instance-type: r5.4xlarge
choices: {}
resource_allocation: *profile_options_resource_allocation

scheduling:
userScheduler:
enabled: true
4 changes: 2 additions & 2 deletions deployer/commands/generate/resource_allocation/instance_capacities.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -131,9 +131,9 @@ r5.4xlarge:
cpu_capacity_high: 16.0
cpu_allocatable_low: 15.89
cpu_allocatable_high: 15.89
mem_capacity_low: 124.364Gi
mem_capacity_low: 124.353Gi
mem_capacity_high: 124.364Gi
mem_allocatable_low: 121.504Gi
mem_allocatable_low: 121.492Gi
mem_allocatable_high: 121.504Gi
m5.large:
cpu_capacity_low: 2.0
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