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cluster:224 [2023/10/13 09:39]
hmeij07 a 		cluster:224 [2024/01/12 09:36] (current)
hmeij07
Line 7: Line 7:
  
 <code> <code>
 +
 +# first step
 +yum update -y  # get to the latest
 +reboot
  
 # IP ranges # IP ranges
Line 12: Line 16:
 10.10.102.48 n38-eth1 10.10.102.48 n38-eth1
 10.11.103.48 n38-ib0 10.11.103.48 n38-ib0
 +DEVROUTE=yes # others no
 +GATEWAY=192,168.102.251 # greentail52
  
 cd /etc/sysconfig/network-scripts/ cd /etc/sysconfig/network-scripts/
 vi ifcfg-eth0 # 192.168.102.x vi ifcfg-eth0 # 192.168.102.x
 vi ifcfg-eth1 # 10.10.102.x   # 'uuidgen eth1' to get uuid vi ifcfg-eth1 # 10.10.102.x   # 'uuidgen eth1' to get uuid
 +
 +# 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
  
 # root: sync cottontail's master and known_hosts (tails+stores) # root: sync cottontail's master and known_hosts (tails+stores)
 ssh-keygen -t rsa ssh-keygen -t rsa
-scp 10.10.102.253:/root/.ssh/authorized_keys /root/.ssh/+scp 10.10.102.250:/root/.ssh/authorized_keys /root/.ssh/ #ctt2
 /etc/ssh/sshd_config (PermitRootLogin) /etc/ssh/sshd_config (PermitRootLogin)
 vi /etc/selinux/config # disabled, do not mistype, kernel will not boot! vi /etc/selinux/config # disabled, do not mistype, kernel will not boot!
Line 35: Line 57:
 systemctl start iptables  systemctl start iptables 
  
-dnf install bind-utils+yum install bind-utils -y
 dig google.com dig google.com
 iptables -L # check! iptables -L # check!
  
  
-# Rocky8 ??? +# CentOS 7 
-dnf config-manager --set-enabled powertools -y +yum-complete-transaction --cleanup-only 
-dnf install epel-release -y +yum install epel-release -y 
-dnf install netcdf netcdf-devel -y +yum install netcdf netcdf-devel -y 
-dnf install yum-utils # yumdownloader -y +yum install yum-utils # yumdownloader -y 
-dnf install ddd grace gnuplot alpine -y # pico+yum install ddd grace gnuplot alpine -y # pico
  
-yum install munge munge-devel+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 # done via media
Line 66: Line 93:
 yum install libjpeg libjpeg-devel libjpeg-turbo-devel -y yum install libjpeg libjpeg-devel libjpeg-turbo-devel -y
  
-#easybuild +# check first 
-yum install libibverbs libibverbs-devel+systemctl status rdma # loaded/active 
 +rpm -qa | egrep  "libibverbs|libibverbs-devel" 
 +# no # yum groupinstall "Infiniband Support" # ib already working 
 +yum install libibverbs-devel ibutils infiniband-diags perftest qperf -y
  
 # amber20 cmake readline error fix needs # amber20 cmake readline error fix needs
-yum install ncurses-c++-libs-6.1-9.20180224.el8.x86_64.rpm \ +yum install ncurses-devel readline-devel -y
-            ncurses-devel-6.1-9.20180224.el8.x86_64.rpm \ +
-            readline-devel-7.0-10.el8.x86_64.rpm+
  
 # amber20 # amber20
Line 84: Line 112:
 # FINISH native vanilla installs # FINISH native vanilla installs
 # R version 4.1.2 (2021-11-01) -- "Bird Hippie" # R version 4.1.2 (2021-11-01) -- "Bird Hippie"
-yum install R R-devel+yum install R R-devel -y
 # openjdk version "1.8.0_322" # openjdk version "1.8.0_322"
-rpm -qa | grep ^java  # check+rpm -qa | grep ^java  # check, else
 yum install java-1.8.0-openjdk java-1.8.0-openjdk-devel \ yum install java-1.8.0-openjdk java-1.8.0-openjdk-devel \
-java-1.8.0-openjdk-headless javapackages-filesystem +java-1.8.0-openjdk-headless  -y  
-# python v 3.9 +# python v 2.7.5
-yum install python39 python39-devel +
-ln -s /usr/bin/python3.9 /usr/bin/python+
 # fftw 3.3.5-11.el8 # fftw 3.3.5-11.el8
-yum install fftw fftw-devel+yum install fftw fftw-devel -y 
 #gnu scientific libraries #gnu scientific libraries
-yum install gsl gsl-devel+yum install gsl gsl-devel -y 
 # ruby 2.5.9-109.module+el8.5.0 # ruby 2.5.9-109.module+el8.5.0
-yum install ruby ruby-devel+yum install ruby ruby-devel -y 
 # obabel chem file formats # obabel chem file formats
-yum install openbabel openbabel-devel+yum install openbabel openbabel-devel -y
  
 # compute nodes old level 3 # compute nodes old level 3
 systemctl set-default multi-user.target systemctl set-default multi-user.target
 +
 +### centos7 so not an OpenHPC environment
  
 # other configs # other configs
 +umount /home
 cd /; mv home /usr/local/ cd /; mv home /usr/local/
 mkdir /home mkdir /home
 ln -s /home /share ln -s /home /share
 vi /etc/passwd (/usr/local/home) vi /etc/passwd (/usr/local/home)
- +vi /etc/fstab  (same) 
- +mount -a
-# other configs +
-mv /home /usr/local/ +
-mkdir /home +
-ln -s /home /share +
-vi /etc/passwd (/usr/local/home)+
  
 # postfix # postfix
-dnf install postfix +yum install postfix mailx 
-dnf install mailx+echo "relayhost = 192.168.102.251" >> /etc/postfix/main.cf
 systemctl enable postfix systemctl enable postfix
-echo "relayhost = 192.168.102.251" >> /etc/postfix/main.cf+systemctl restart postfix
  
 ### DONE ### DONE
-undo vlan52, down iptables, reboot, test you can it via privs+undo vlan52, down iptables, reboot,  
 +test you can to it via privaate networks
 ### REST AT HOME ### REST AT HOME
  
-# or via  rc.local? 
-vi ifcfg-ib0 
-DEVICE=ib0 
-ONBOOT=yes 
-MTU=65520 
-CONNECTED_MODE=yes 
-BOOTPROTO=none 
-IPADDR=10.11.103.48 
-PREFIX=16 
  
-mkdir /sanscratch /localscratch +# /etc/fstab 
-chmod ugo+rwx /sanscratch /home/localscratch +/dev/sdb /localscratch5tb        ext4    defaults        0 0 
-chmod o+t /sanscratch /home/localscratch  + 
-ln -s /localscratch /localscratch5tb+# if sdb present 
 +mkdir /sanscratch /localscratch5tb 
 +chmod ugo+rwx /sanscratch /localscratch5tb 
 +chmod o+t /sanscratch /localscratch5tb 
 +ln -s /localscratch5tb /localscratch
  
 cd /home  cd /home 
Line 148: Line 168:
 ls -l ls -l
  
-cat /sanscratch/tmp/fstab.tmp >> /etc/fstab; mkdir /astrostore; mount -a; df -h+# ADD all the NFS mounts see greentail52:/root/n45.fstab
  
 # fstab file mounts # fstab file mounts
-mkdir -p /zfshomes /home66 /home33 /mindstore /opt/ohpc/pub /opt/intel+mkdir -p /zfshomes /home66 /home33 /mindstore /astrostore
 mkdir -p /smithlab/home;cd /smithlab;ln -s /smithlab/home/opt/rhel07 opt; ls -l 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 # compute nodes /etc/chronyc.conf
Line 162: Line 182:
 systemctl restart chronyd systemctl restart chronyd
 chronyc sources chronyc sources
- 
-cat /sanscratch/tmp/fstab.tmp >> /etc/fstab; mkdir /astrostore; mount -a; df -h; cd /smithlab/;  ln -s /smithlab/home/opt/rhel08 opt; ls -l 
  
  
Line 169: Line 187:
 rocommunity public rocommunity public
 dontLogTCPWrappersConnects yes dontLogTCPWrappersConnects yes
-# enable, start, add to zenoss +# add to zenoss 
 +systemctl enable snmpd 
 +systemctl start snmpd 
  
  
 # compute nodes only # compute nodes only
-# scp fron n79:/usr/local/ +# scp from n79:/usr/local/ 
-amber16/  amber20/ fsl-5.0.10/ gromacs-2018/ lammps-22Aug18/+# 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-22.05.2 . 
 +ln -s /usr/local/slurm-22.05.2 /usr/local/slurm 
 + 
 + 
 +# backup and update passwd, shadow, group and hosts files 
 +# scp from n79 or n45 
 + 
 +# slurm config 
 +echo SLURMD_OPTIONS="--conf-server 192.168.102.250" > /etc/sysconfig/slurmd 
 +  mkdir /var/log/slurm  
 +  chown slurm:munge /var/log/slurm  
 +  mkdir /var/spool/slurm  
 +  chown slurm:munge /var/spool/slurm  
 +# check 
 +chown -R munge:munge /etc/munge /var/log/munge /var/lib/munge /var/run/munge 
 +chown -R slurm:munge /var/log/slurm /var/spool/slurm 
 +systemctl enable munge 
 +systemctl start munge 
 +# test unmunge 
 +/usr/local/slurm/sbin/slurmd 
 +# check log 
 + 
 +# /etc/bashrc (login node) 
 +export PATH=/usr/local/slurm/bin:$PATH 
 +export LD_LIBRARY_PATH=/usr/local/slurm/lib:$LD_LIBRARY_PATH 
 + 
 +# crontab 
 + 
 +# ionice gaussian 
 +0,15,30,45 * * * * /share/apps/scripts/ionice_lexes.sh  > /dev/null 2>&1 
 + 
 +# cpu temps 
 +40 * * * * /share/apps/scripts/lm_sensors.sh > /dev/null 2>&1 
 + 
 +on compute node /etc/security/limits.conf 
 +*                -       memlock         270039400 
 + 
 + 
 +/etc/rc.local 
 +#timing issue with munge 
 +#sleep 15 
 +#/usr/local/slurm/sbin/slurmd 
 +chmod +x /etc/rc.d/rc.local 
 + 
 +# important!! put private back in place 
 +systemctl disable iptables 
 +systemctl stop iptables 
 +reboot 
 + 
 +# file date_ctt2.sh 
 + 
 +# ctt /etc/pdsh 
 + 
 +# ctt:/root/scripts 
 + 
 +# ctt2:/usr/local/bin/rslurm2022.sh
  
-# Put the warewulf cluster key in authorized_keys 
 # Put eth0 fingerprints in cottontail/greentail52 known hosts # Put eth0 fingerprints in cottontail/greentail52 known hosts
-# add to relevant known_hosts_servername file+ 
 +# test slurm unmunge and update slurm.conf file
  
 </code> </code>
cluster/224.1697204347.txt.gz · Last modified: 2023/10/13 09:39 by hmeij07

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