slurm-docker-scaleout

Docker compose cluster for testing Slurm

Prerequisites

• docker 2019-10-04+
  • IPv6 must be configured in docker: https://docs.docker.com/config/daemon/ipv6/
• docker-compose-plugin v2.18.1+
• ssh (client)
• jq

Changes needed in sysctl.conf:

net.ipv4.tcp_max_syn_backlog=4096
net.core.netdev_max_backlog=1000
net.core.somaxconn=15000
fs.file-max=992832

# Force gc to clean-up quickly
net.ipv4.neigh.default.gc_interval = 3600

# Set ARP cache entry timeout
net.ipv4.neigh.default.gc_stale_time = 3600

# Setup DNS threshold for arp
net.ipv4.neigh.default.gc_thresh3 = 8096
net.ipv4.neigh.default.gc_thresh2 = 4048
net.ipv4.neigh.default.gc_thresh1 = 1024

# Increase map count for elasticsearch
vm.max_map_count=262144

# Avoid running out of file descriptors
fs.file-max=10000000
fs.inotify.max_user_instances=65535
fs.inotify.max_user_watches=1048576

Docker configuration required with cgroupsv2

Make sure the host machine is running CgroupV2 and not hybrid mode: https://slurm.schedmd.com/faq.html#cgroupv2

Add these settings to the docker configuration: /etc/docker/daemon.json

{
  "exec-opts": [
    "native.cgroupdriver=systemd"
  ],
  "features": {
    "buildkit": true
  },
  "experimental": true,
  "cgroup-parent": "docker.slice",
  "default-cgroupns-mode": "host",
  "storage-driver": "overlay2"
}

Configure systemd to allow docker to run in it's own slice to avoid systemd conflicting with it:

/etc/systemd/system/docker.slice:

[Unit]
Description=docker slice
Before=slices.target
[Slice]
CPUAccounting=true
MemoryAccounting=true
Delegate=yes

/usr/lib/systemd/system/docker.service.d/local.conf:

[Service]
LimitNOFILE=infinity
LimitNPROC=infinity
LimitCORE=infinity
TasksMax=infinity
Delegate=yes

Activate the changes:

systemctl daemon-reload
systemctl restart docker.slice docker

Basic Architecture

Maria Database Node:

• db

Slurm Management Nodes:

• mgmtnode
• mgmtnode2
• slurmdbd

Compute Nodes:

• node[00-09]

Login Nodes:

• login

Nginx Proxy node:

• proxy

Rest API Nodes:

• rest

Kibana:

• View http://localhost:5601/

Elasticsearch:

• View http://localhost:9200/

Grafana:

• View http://localhost:3000/
• User: admin
• Password: admin

Open On-Demand:

• View http://localhost:8081/
• User: {user name - "fred" or "wilma"}
• Password: password

Open XDMoD:

• View http://localhost:8082/

Proxy:

• Auth REST API http://localhost:8080/auth
• Query REST API http://localhost:8080/slurm/

Multiple Instances

Each cluster must have a unique class B subnet.

Default IPv4 is SUBNET="10.11". Default IPv6 is SUBNET6="2001:db8:1:1::".

Custom Nodes

Custom node lists may be provided by setting NODELIST to point to a file containing list of nodes for the cluster or modifing the default generated "nodelist" file in the scaleout directory.

The node list follows the following format with one node per line:

${HOSTNAME} ${CLUSTERNAME} ${IPv4} ${IPv6}

Example line:

node00 scaleout 10.11.5.0 2001:db8:1:1::5:0

Note that the service nodes can not be changed and will always be placed into the following subnets:

${SUBNET}.1.0/24 ${SUBNET6}1:0/122

Custom Slurm version

To specify an explicit version of Slurm to be compiled and installed:

export SLURM_RELEASE=slurm-$version

Make sure to call make clean after to invalidate all the caches with the prior release.

To build images

git submodule update --init --force --remote --recursive
make build

To run:

make

To build and run in Cloud mode:

make cloud

Note: cloud mode will run in the foreground.

To build without caching:

make nocache

To stop:

make stop

To reverse all changes:

make clean

To remove all images:

make uninstall

To control:

make bash
make HOST=node1 bash

To login via ssh

ssh-keygen -f "/home/$(whoami)/.ssh/known_hosts" -R "10.11.1.5" 2>/dev/null
ssh -o StrictHostKeyChecking=no -l fred 10.11.1.5 -X #use 'password'

Federation Mode

Federation mode will create multiple Slurm clusters with nodes and slurmctld daemons. Other nodes will be shared, such as login and slurmdbd.

To create multiple federation clusters:

export FEDERATION="taco burrito quesadilla"
echo "FederationParameters=fed_display" >> scaleout/slurm/slurm.conf
truncate -s0 scaleout/nodelist
make clean
make build
make

Activate Federation mode in Slurm

Notify slurmdbd to use federation after building cluster:

export FEDERATION="taco burrito quesadilla"
make HOST=taco-mgmtnode bash
sacctmgr add federation scaleout cluster=taco,burrito,quesadilla

Deactivate to Federation mode

export FEDERATION="taco burrito quesadilla"
make uninstall
truncate -s0 scaleout/nodelist

Caveats

The number of CPU threads on the host are multiplied by the number of nodes. Do not attempt to use computationally intensive applications.

Docker work-arounds:

ERROR: Pool overlaps with other one on this address space

or

failed to prepare ${HASH}: max depth exceeded
ERROR: Service 'slurmdbd' failed to build : Build failed

Call this:

make clean
docker network prune -f
sudo systemctl restart docker

To save all images to ./scaleout.tar

make save

To load saved copy of all images

make load

How to trigger manual xdmod data dump:

make HOST=scaleout_mgmtnode_1 bash
bash /etc/cron.hourly/dump_xdmod.sh
exit
make bash
exec bash /etc/cron.hourly/dump_xdmod.sh
make HOST=xdmod bash
sudo -u xdmod -- /usr/bin/xdmod-shredder -r scaleout -f slurm -i /xdmod/data.csv
sudo -u xdmod -- /usr/bin/xdmod-ingestor
exit

How to disable buidling xdmod container

This is will only disable attempts to build and start the container.

export DISABLE_XDMOD=1