cluster:224
This is an old revision of the document!
Recipe for n38-n45 conversion of openlava/centos6 to slurm/centos7.
First install “server with GUI” via USB installation media. Enter BIOS (delete key). Set Date&Time and boot order (Removable, USB, Cd&DVD, Hdd). Reclaim disk space.. Kdump disabled.
# IP ranges
192.168.102.48 n38 n38-eth0
10.10.102.48 n38-eth1
10.11.103.48 n38-ib0
cd /etc/sysconfig/network-scripts/
vi ifcfg-eth0 # 192.168.102.x
vi ifcfg-eth1 # 10.10.102.x # 'uuidgen eth1' to get uuid
# root: sync cottontail's master and known_hosts (tails+stores)
ssh-keygen -t rsa
scp 10.10.102.253:/root/.ssh/authorized_keys /root/.ssh/
/etc/ssh/sshd_config (PermitRootLogin)
vi /etc/selinux/config # disabled, do not mistype, kernel will not boot!
# make internet connection for yum
# iptables
systemctl stop firewalld
systemctl disable firewalld
dnf install -y iptables-services
# port 22 wesleyan only
-A INPUT -i eth1 -m state --state NEW -m tcp -p tcp -s 129.133.0.0/17 -d 129.133.52.222 --dport 22 -j ACCEPT
-A INPUT -i eth1 -m state --state NEW -m tcp -p tcp -s 129.133.128.0/18 -d 129.133.52.222 --dport 22 -j ACCEPT
systemctl start iptables
yum install bind-utils -y
dig google.com
iptables -L # check!
# CentOS 7
yum-complete-transaction --cleanup-only
yum install epel-release -y
yum install netcdf netcdf-devel -y
yum install yum-utils # yumdownloader -y
yum install ddd grace gnuplot alpine -y # pico
yum install munge munge-devel -y
scp -rp cottontail2.wesleyan.edu:/etc/munge /etc/
ls -ld /etc/munge # check
chown munge:munge /etc/munge/munge.key
ls -l /etc/munge/munge.key # check
# test unmunge both ways when before starting slurmd
# done via media
#yum groupinstall "Server"
# server for compute nodes "Server with GUI"
# add packages and update
yum install epel-release -y
yum install flex bison -y
yum install tcl tcl-devel dmtcp dmtcp-devel -y
yum install net-snmp net-snmp-libs net-tools net-snmp-utils -y
yum install freeglut-devel libXi-devel libXmu-devel -y
yum install blas blas-devel lapack lapack-devel boost boost-devel -y
yum install lm_sensors lm_sensors-libs -y
yum install zlib-devel bzip2-devel -y
yum install openmpi openmpi-devel perl-ExtUtils-MakeMaker -y
yum install cmake -y
yum install libjpeg libjpeg-devel libjpeg-turbo-devel -y
# check first
systemctl status rdma # loaded/active
rpm -qa | egrep "libibverbs|libibverbs-devel"
# no # yum groupinstall "Infiniband Support" # ib already working
yum install libibvers-devel ibutils infiniband-diags perftest qperf
# amber20 cmake readline error fix needs
yum install ncurses-devel readline-devel -y
# amber20
yum -y install tcsh make \
gcc gcc-gfortran gcc-c++ \
which flex bison patch bc \
libXt-devel libXext-devel \
perl perl-ExtUtils-MakeMaker util-linux wget \
bzip2 bzip2-devel zlib-devel tar
# FINISH native vanilla installs
# R version 4.1.2 (2021-11-01) -- "Bird Hippie"
yum install R R-devel -y
# openjdk version "1.8.0_322"
rpm -qa | grep ^java # check, else
yum install java-1.8.0-openjdk java-1.8.0-openjdk-devel \
java-1.8.0-openjdk-headless -y
# python v 2.7.5
# fftw 3.3.5-11.el8
yum install fftw fftw-devel -y
#gnu scientific libraries
yum install gsl gsl-devel -y
# ruby 2.5.9-109.module+el8.5.0
yum install ruby ruby-devel -y
# obabel chem file formats
yum install openbabel openbabel-devel -y
# compute nodes old level 3
systemctl set-default multi-user.target
# other configs
umount /home
cd /; mv home /usr/local/
mkdir /home
ln -s /home /share
vi /etc/passwd (/usr/local/home)
vi /etc/fstab (same)
mount -a
# postfix
yum install postfix mailx
echo "relayhost = 192.168.102.251" >> /etc/postfix/main.cf
systemctl enable postfix
systemctl restart postfix
### DONE
undo vlan52, down iptables, reboot,
test you can to it via privaate networks
### REST AT HOME
# or via rc.local? see n102
vi ifcfg-ib0
DEVICE=ib0
ONBOOT=yes
MTU=65520
CONNECTED_MODE=yes
BOOTPROTO=none
IPADDR=10.11.103.48
PREFIX=16
# check with ibstat
Port 1:
State: Active
Physical state: LinkUp
# check with ethtool ib0
Speed: 40000Mb/s
# /etc/fstab
/dev/sdb /localscratch5tb ext4 defaults 0 0
# if sdb present
mkdir /sanscratch /localscratch5tb
chmod ugo+rwx /sanscratch /localscratch5tb
chmod o+t /sanscratch /localscratch5tb
ln -s /localscratch5tb /localscratch
cd /home
ln -s /zfshomes/apps
ln -s /zfshomes/tmp
ln -s /zfshomes/csmith06
ls -l
# ADD all the NFS mounts see greentail52:/root/n45.fstab
# fstab file mounts
mkdir -p /zfshomes /home66 /home33 /mindstore /astrostore
mkdir -p /smithlab/home;cd /smithlab;ln -s /smithlab/home/opt/rhel07 opt; ls -l
mount -a # via 10.10
# compute nodes /etc/chronyc.conf
#pool 2.pool.ntp.org iburst
Server 192.168.102.250
Server 192.168.102.251
# check
systemctl restart chronyd
chronyc sources
# edit /etc/snmp/snmpd.conf, enable and start
rocommunity public
dontLogTCPWrappersConnects yes
# enable, start, add to zenoss
# compute nodes only
# scp from n79:/usr/local/
# amber16/ amber20/ fsl-5.0.10/ gromacs-2018/ lammps-22Aug18/
scp -rp 10.10.102.89:/usr/local/amber16 .
# copy slurm from n79
scp -rp 10.10.102.89:/usr/local/slurm-??? .
ln -s
# Put the warewulf cluster key in authorized_keys
# Put eth0 fingerprints in cottontail/greentail52 known hosts
# add to relevant known_hosts_servername file
cluster/224.1697210439.txt.gz · Last modified: by hmeij07