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Introduction

Install Slurm on CentOS-7 Virtual Cluster.

Preparation

  1. Connect Virtual Machines

  2. Setup NFS Server

Cluster Server and Computing Nodes

List of master node and computing nodes within the cluster.

Hostname IP Addr
master 10.0.1.5
node1 10.0.1.6
node2 10.0.1.7

(Optional) Delete failed installation of Slurm

Remove database:

yum remove mariadb-server mariadb-devel -y

Remove Slurm and Munge:

yum remove slurm munge munge-libs munge-devel -y

Delete the users and corresponding folders:

userdel -r slurm
suerdel -r munge

Create the global users

Slurm and Munge require consistent UID and GID across every node in the cluster. For all the nodes, before you install Slurm or Munge:

export MUNGEUSER=991
groupadd -g $MUNGEUSER munge
useradd  -m -c "MUNGE Uid 'N' Gid Emporium" -d /var/lib/munge -u $MUNGEUSER -g munge  -s /sbin/nologin munge
export SLURMUSER=992
groupadd -g $SLURMUSER slurm
useradd  -m -c "SLURM workload manager" -d /var/lib/slurm -u $SLURMUSER -g slurm  -s /bin/bash slurm

Install Munge

Get the latest REPL repository:

yum install epel-release -y

Install Munge:

yum install munge munge-libs munge-devel -y

Create a secret key on master node. First install rig-tools to properly create the key:

yum install rng-tools -y
rngd -r /dev/urandom
/usr/sbin/create-munge-key -r
dd if=/dev/urandom bs=1 count=1024 > /etc/munge/munge.key
chown munge: /etc/munge/munge.key
chmod 400 /etc/munge/munge.key

Send this key to all of the compute nodes:

scp /etc/munge/munge.key [email protected]:/etc/munge
scp /etc/munge/munge.key [email protected]:/etc/munge

SSH into every node and correct the permissions as well as start the Munge service:

chown -R munge: /etc/munge/ /var/log/munge/
chmod 0700 /etc/munge/ /var/log/munge/

systemctl enable munge
systemctl start munge

To test Munge, try to access another node with Munge from master node:

munge -n
munge -n | munge
munge -n | ssh 10.0.1.6 unmunge
remunge

If you encounter no errors, then Munge is working as expected.

Install Slurm

Install a few dependencies:

yum install openssl openssl-devel pam-devel numactl numactl-devel hwloc hwloc-devel lua lua-devel readline-devel rrdtool-devel ncurses-devel man2html libibmad libibumad -y

Download the latest version of Slurm in the shared folder:

cd /nfsshare
wget https://download.schedmd.com/slurm/slurm-19.05.4.tar.bz2

If you don't have rpmbuild yet:

yum install rpm-build
rpmbuild -ta slurm-19.05.4.tar.bz2

Check the rpms created by rpmbuild:

cd /root/rpmbuild/RPMS/x86_64

Move the Slurm rpms for installation for all nodes:

mkdir /nfsshare/slurm-rpms
cp * /nfsshare/slurm-rpms

On every node, install these rpms:

yum --nogpgcheck localinstall * -y

On the master node:

vim /etc/slurm/slurm.conf

Paste the slurm.conf in Configs and paste it into slurm.conf.

Notice: we manually add lines under #COMPUTE NODES.

NodeName=node1 NodeAddr=10.0.1.6 CPUs=1 State=UNKNOWN
NodeName=node2 NodeAddr=10.0.1.7 CPUs=1 State=UNKNOWN

Now the master node has the slurm.conf correctly, we need to send this file to the other compute nodes:

scp /etc/slurm/slurm.conf [email protected]:/etc/slurm/
scp /etc/slurm/slurm.conf [email protected]:/etc/slurm/

On the master node, make sure that the master has all the right configurations and files:

mkdir /var/spool/slurm
chown slurm: /var/spool/slurm/
chmod 755 /var/spool/slurm/
touch /var/log/slurmctld.log
chown slurm: /var/log/slurmctld.log
touch /var/log/slurm_jobacct.log /var/log/slurm/slurm_jobcomp.log
chown slurm: /var/log/slurm_jobacct.log /var/log/slurm_jobcomp.log

On the computing nodes node[1-2], make sure that all the computing nodes have the right configurations and files:

mkdir /var/spool/slurm
chown slurm: /var/spool/slurm
chmod 755 /var/spool/slurm
touch /var/log/slurm/slurmd.log
chown slurm: /var/log/slurm/slurmd.log

Use the following command to make sure that slurmd is configured properly:

slurmd -C

You should get something like this:

NodeName=node1 CPUs=4 Boards=1 SocketsPerBoard=1 CoresPerSocket=4 ThreadsPerCore=1 RealMemory=990 UpTime=0-07:45:41

Disable the firewall on the computing nodes node[1-2]:

systemctl stop firewalld
systemctl disable firewalld

On the master node, open the default ports that Slurm uses:

firewall-cmd --permanent --zone=public --add-port=6817/udp
firewall-cmd --permanent --zone=public --add-port=6817/tcp
firewall-cmd --permanent --zone=public --add-port=6818/udp
firewall-cmd --permanent --zone=public --add-port=6818/tcp
firewall-cmd --permanent --zone=public --add-port=6819/udp
firewall-cmd --permanent --zone=public --add-port=6819/tcp
firewall-cmd --reload

If the port freeing does not work, stop the firewall for testing.

Sync clocks on the cluster. On every node:

yum install ntp -y
chkconfig ntpd on
ntpdate pool.ntp.org
systemctl start ntpd

On the computing nodes node[1-2]:

systemctl enable slurmd.service
systemctl start slurmd.service
systemctl status slurmd.service

Setting up MariaDB database: master

Install MariaDB:

yum install mariadb-server mariadb-devel -y

Start the MariaDB service:

systemctl enable mariadb
systemctl start mariadb
systemctl status mariadb

Create the Slurm database user:

mysql

In mariaDB:

MariaDB[(none)]> GRANT ALL ON slurm_acct_db.* TO 'slurm'@'localhost' IDENTIFIED BY '1234' with grant option;
MariaDB[(none)]> SHOW VARIABLES LIKE 'have_innodb';
MariaDB[(none)]> FLUSH PRIVILEGES;
MariaDB[(none)]> CREATE DATABASE slurm_acct_db;
MariaDB[(none)]> quit;

Verify the databases grants for the slurm user:

mysql -p -u slurm

Tpye password for slurm: 1234. In mariaDB:

MariaDB[(none)]> show grants;
MariaDB[(none)]> quit;

Create a new file /etc/my.cnf.d/innodb.cnf containing:

[mysqld]
innodb_buffer_pool_size=1024M
innodb_log_file_size=64M
innodb_lock_wait_timeout=900

To implement this change you have to shut down the database and move/remove logfiles:

systemctl stop mariadb
mv /var/lib/mysql/ib_logfile? /tmp/
systemctl start mariadb

You can check the current setting in MySQL like so:

MariaDB[(none)]> SHOW VARIABLES LIKE 'innodb_buffer_pool_size';

Create slurmdbd configuration file:

vim /etc/slurm/slurmdbd.conf

Set up files and permissions:

chown slurm: /etc/slurm/slurmdbd.conf
chmod 600 /etc/slurm/slurmdbd.conf
touch /var/log/slurmdbd.log
chown slurm: /var/log/slurmdbd.log

Paste the slurmdbd.conf in Configs and paste it into slurmdbd.conf.

Some variables are:

DbdAddr=localhost
DbdHost=localhost
DbdPort=6819
StoragePass=1234
StorageLoc=slurm_acct_db

Try to run slurndbd manually to see the log:

slurmdbd -D -vvv

Terminate the process by Control+C when the testing is OK.

Start the slurmdbd service:

systemctl enable slurmdbd
systemctl start slurmdbd
systemctl status slurmdbd

On the master node:

systemctl enable slurmctld.service
systemctl start slurmctld.service
systemctl status slurmctld.service

Reference: slothparadise, Niflheim, gabrieleiannetti