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Simple Slurm configuration in Debian based systems

Slurm Configuration Debian based Cluster

Here I will describe a simple configuration of the slurm management tool for launching jobs in a really simplistic cluster. I will assume the following configuration: a main node (for me it is an Arch Linux distribution) and 3 compute nodes (for me compute nodes are Debian VMs). I also assume there is ping access between the nodes and some sort of mechanism for you to know the IP of each node at all times (most basic should be a local NAT with static IPs)

Basic Structure

Slurm management tool work on a set of nodes, one of which is considered the master node, and has the slurmctld daemon running; all other compute nodes have the slurmd daemon. All communications are authenticated via the munge service and all nodes need to share the same authentication key. Slurm by default holds a journal of activities in a directory configured in the slurm.conf file, however a Database management system can be set. All in all what we will try to do is:

  • Install munge in all nodes and configure the same authentication key in each of them
  • Configure the slurmctld service in the master node
  • Configure the slurmd service in the compute nodes
  • Create a basic file structure for storing jobs and jobs result that is equal in all the nodes of the cluster
  • Manipulate the state of the nodes, and learn to resume them if they are down
  • Run some simple jobs as test
  • Set up a database for slurm
  • Set up a user based job submission protocol
  • Set up MPI task on the cluster

Install Packages

Munge

Lets start installing munge authentication tool using the system package manager, for all nodes in the network:

sudo apt-get install -y libmunge-dev libmunge2 munge

munge requires that we generate a key file for testing authentication, for this we use the dd utility, with the fast pseudo-random device /dev/urandom. At master node do:

sudo dd if=/dev/urandom bs=1 count=1024 > /etc/munge/munge.key

Upon installing munge previously, a munge user should have been created, if it was not simply create it. Now we need to give full permissions to this user on the file munge.key:

chown munge:munge /etc/munge/munge.key
chmod 400 /etc/munge/munge.key

Now copy this key to each node via ssh:

scp /etc/munge/munge.key <node-user>@<node-ip>:/etc/munge/munge.key

We restrict login access to the munge account, for all nodes in the network:

vi  /etc/passwd

Edit the file as follows:

munge:x:501:501::/var/run/munge;/sbin/nologin

This much is enough configuration, lets enable and start the service in each node (including master) with the commands:

sudo systemctl enable munge
sudo systemctl start munge

Test communication with, locally and remotely with these commands respectively:

munge -n | unmunge
munge -n | ssh <some-host-node-of-the-network> unmunge

Slurm

Install the slurm packages from the distribution repositories, for all nodes in the network:

sudo apt-get install -y slurm-llnl

This will do the following things (among many others):

  • Create a slurm user
  • Create a configuration directory at /etc/slurm-llnl
  • Create a log directory at /var/log/slurm-llnl
  • Create two systemd files for configuring slurmd.service and slurmctld.service at /lib/systemd/system
  • Create a directory for saving the state of the service at /var/spool/slurm

First edit the configuration file in the master node, to make it suitable for our network. Take a look at the file provided, along with this instructions.md named slurm.conf and edit the values in the form <value> with the appropiate content. Do not override the default file given to you, rename it and then copy the provided (I have deleted various commented lines for sake of brevity). Notice that if you change the cluster name in the configuration file you should also modify the file /var/spool/slurm/ctld/clustername accordingly. Also, create as many compute nodes as you need.

Now we need to clean the file structure for slurm, check if all the directories mentioned before exists, if they don't, create them. All the directories mentioned should belong to the slurm user and the slurm group, to any file or directory in this directories that do not follow this criteria, change the permissions accordingly:

sudo chown slurm:slurm <file-or-directory>

Also we need to create a PID file for slurm, as it does not create it for us. Do:

# For master node
sudo touch /var/slurmctld.pid
sudo chown slurm:slurm /var/slurmctld.pid

# For compute nodes
sudo touch /var/slurmd.pid
sudo chown slurm:slurm /var/slurmd.pid

We are almost ready to activate the services, previous to that, we need to tell, in the .service files the user in which each script will run as. Under the [SERVICE] section add the following line (for the respective node types):

User=slurm  # Master node
User=root   # Slave node

Now enable and start the services:

# For master node
sudo systemctl enable slurmctld
sudo systemctl start slurmctld

# For compute nodes
sudo systemctl enable slurmd
sudo systemctl start slurmd
ClusterName=<cluster-name> # By default ClusterName=linux
ControlMachine=<name-of-the-master-node-machine>
ControlAddr=<ip-address-of-the-master-node-machine>
#
SlurmUser=slurm
SlurmdUser=slurm
SlurmctldPort=6817
SlurmdPort=6818
AuthType=auth/munge
StateSaveLocation=/var/spool/slurm/ctld
SlurmdSpoolDir=/var/spool/slurm/d
SwitchType=switch/none
MpiDefault=none
SlurmctldPidFile=/var/run/slurmctld.pid
SlurmdPidFile=/var/run/slurmd.pid
ProctrackType=proctrack/pgid
ReturnToService=0
# TIMERS
SlurmctldTimeout=300
SlurmdTimeout=300
InactiveLimit=0
MinJobAge=300
KillWait=30
Waittime=0
#
DebugFlags=NO_CONF_HASH
# LOGGING
SlurmctldDebug=3
SlurmctldLogFile=/var/log/slurm-llnl/slurmctld.log
SlurmdDebug=3
SlurmdLogFile=/var/log/slurmd.log
JobCompType=jobcomp/none
#
# COMPUTE NODES
NodeName=<node-name> NodeAddr=<node-ip-address> Port=<port-enabled-for-node> Procs=1 State=UNKNOWN # By default Port=17000
PartitionName=debug Nodes=ALL Default=YES MaxTime=INFINITE State=UP
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@luciandf luciandf commented Feb 5, 2020

do you mind adding a small instruction on how to test if the slurm install is correct? I have done what you said here but I have no clue if it works or not. Also, slurm.conf where is this file supporsed to be created?

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