Slurm setup scripts

head-setup.sh

#!/bin/bash
# head-setup.sh
#
# Copies the configuration files and enables, but does not start the services.
# Use the services-start/stop.sh scripts to start and stop the munge and slurmd services.  

set -e

echo "Copying munge key"
cp ~/slurm/munge.key /tmp/
sudo chown munge: /tmp/munge.key 
sudo mv /tmp/munge.key /etc/munge

echo "Enabling munge service"
sudo systemctl enable munge.service

echo "Copying SLURM config"
if [ ! -d /etc/slurm ]; then
  sudo mkdir /etc/slurm
fi
sudo chown slurm: /etc/slurm
cp ~/slurm/slurm.conf /tmp/
sudo chown slurm: /tmp/slurm.conf 
sudo mv /tmp/slurm.conf /etc/slurm/

cp ~/slurm/cgroup.conf /tmp/
sudo chown slurm: /tmp/cgroup.conf 
sudo mv /tmp/cgroup.conf /etc/slurm/

cp ~/slurm/cgroup_allowed_devices_file.conf /tmp/
sudo chown slurm: /tmp/cgroup_allowed_devices_file.conf 
sudo mv /tmp/cgroup_allowed_devices_file.conf /etc/slurm/

echo "Enabling SLURM service"
sudo systemctl enable slurmctld.service

echo "Done"

head-start.sh

#!/bin/bash
# head-start.sh
#
# Start the munge and slurmctld services

set -e

echo "Starting munge"
sudo systemctl start munge.service

echo "Starting SLURM"
sudo systemctl start slurmctld.service

echo "Done"

head-stop.sh

#!/bin/bash
# head-stop.sh
#
# Stop the munge and slurmctld services

set -e

echo "Stoppinging munge"
sudo systemctl stop munge.service

echo "Stopping SLURM"
sudo systemctl stop slurmctld.service

echo "Done"

install-pulsar.sh

#!/bin/bash
#
# basic install for pulsar allowing slurm-drmaa support

mkdir /root/pulsar
cd /root/pulsar/
virtualenv venv
. venv/bin/activate
pip install --upgrade pip
pip install drmaa pulsar-app

services-setup.sh

#!/bin/bash
# services-setup.sh
#
# Copies the configuration files and enables, but does not start the services.
# Use the services-start/stop.sh scripts to start and stop the munge and slurmd services.  

set -e

echo "Copying munge key"
cp ~/slurm/munge.key /tmp/
sudo chown munge: /tmp/munge.key 
sudo mv /tmp/munge.key /etc/munge

echo "Starting munge"
sudo systemctl enable munge.service

echo "Copying SLURM config"
if [ ! -d /etc/slurm ]; then
  sudo mkdir /etc/slurm
fi
sudo chown slurm: /etc/slurm
cp ~/slurm/slurm.conf /tmp/
sudo chown slurm: /tmp/slurm.conf 
sudo mv /tmp/slurm.conf /etc/slurm/

cp ~/slurm/cgroup.conf /tmp/
sudo chown slurm: /tmp/cgroup.conf 
sudo mv /tmp/cgroup.conf /etc/slurm/

cp ~/slurm/cgroup_allowed_devices_file.conf /tmp/
sudo chown slurm: /tmp/cgroup_allowed_devices_file.conf 
sudo mv /tmp/cgroup_allowed_devices_file.conf /etc/slurm/

echo "Starting SLURM"
sudo systemctl enable slurmd.service

echo "Done"

services-start.sh

#!/bin/bash
# services-start.sh
#
# Start the munge and slurmd services

set -e

echo "Starting munge"
sudo systemctl start munge.service

echo "Starting SLURM"
sudo systemctl start slurmd.service

echo "Done"

services-stop.sh

#!/bin/bash
# services-stop.sh
#
# Stop the munge and slurmd services

set -e

echo "Stoppinging munge"
sudo systemctl stop munge.service

echo "Stopping SLURM"
sudo systemctl stop slurmd.service

echo "Done"

slurm+drmaa.sh

#!/bin/bash
#
# builds slurm and slurm-drmaa from source.
# both packges are installed.
# currently don't know how to build slurm-drmaa RPMs. see https://github.com/natefoo/slurm-drmaa/issues/25

cd /root

# install required packages
yum -y install epel-release
yum -y install wget gcc rpmbuild perl-ExtUtils-MakeMaker mariadb-server mariadb-devel rpm-build munge-devel munge-libs readline-devel openssl pam-devel python-pip python-virtualenv

# download slurm and slurm-drmaa
wget https://download.schedmd.com/slurm/slurm-18.08.5-2.tar.bz2
wget https://github.com/natefoo/slurm-drmaa/releases/download/1.1.0/slurm-drmaa-1.1.0.tar.gz

# build slurm
rpmbuild -ta slurm-18.08.5-2.tar.bz2
# install slurm
yum --nogpgcheck localinstall -y rpmbuild/RPMS/x86_64/slurm-*.rpm

# build slurm-drmaa
tar xvfz slurm-drmaa-1.1.0.tar.gz 
cd slurm-drmaa-1.1.0
./configure 
make
# install slurm-drmaa
make install

slurm-setup.sh

#!/bin/bash
# slurm-setup.sh

#
# This script sets up a base image for a slurm node by installing munge and slurm.
#
# It assumes you are using a base image that already has /home mounted from an nfs export from node nextflow-head-1.
#
# When the instance is fired up munge and slurm need configuring and starting. See the slurm-start.sh script for this.



# setup nextflow if not already done

#sudo yum -y install java-1.8.0-openjdk-headless procps

# setup users

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


# setup munge

sudo yum -y install epel-release
sudo yum -y install munge

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

# setup slurm

sudo yum -y install openssl numactl hwloc lua libibmad libibumad -y

cd ~/rpmbuild/RPMS/x86_64/
SLURM_VERSION=18.08.5-2
sudo yum --nogpgcheck localinstall -y slurm-$SLURM_VERSION.el7.x86_64.rpm slurm-perlapi-$SLURM_VERSION.el7.x86_64.rpm slurm-slurmd-$SLURM_VERSION.el7.x86_64.rpm

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