This is an old revision of the document!
We're embarking on a transition to a new head/login node name cottontail2
. This server will be running Rocky 8 operating system. Early design ideas can be found at Cottontail2, all pre-pandemic. We are staying with a 1G ethernet network as we could not find 10G switches. Maybe in the near term we can upgrade.
Two new compute nodes (n100, n101) will be set up in a test queue. They each have four RTX5000 gpus which have the same architecture as our other gpus so all compiled software should work. These gpus have 16G memory foot print (twice as large as other gpus we have).
OpenHPC will be deployed next and I'll make some notes. We will to Slurm scheduler. (Slurm Test Env for users and Slurm Test Env techie page). Any old hardware that can be reimaged with Rocky 8 will be migrated to Slurm using Warewulf. But that all will take some time.
Some pictures below.
Steps. “Ala n37” … so the RTX nodes are similar to the K20 nodes and we can put the local software in place. See K20 Redo page and exx96 Recipe for CentOS 7
New recipe for n100-n101 sporting Rocky 8.5 on cottontail2
Put node on internet…first though
# login as root check some things out... free -g nvidia-smi # if gpus cat /proc/cpuinfo # check and set local time zone mv /etc/localtime /etc/localtime.backup ln -s /usr/share/zoneinfo/America/New_York /etc/localtime # change passwords for root and vendor account passwd passwd microway # set hostname hostnamectl set-hostname cottontail2 # 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) # Put the warewulf cluster key in authorized_keys # configure private subnets and ping file server cd /etc/sysconfig/network-scripts/ vi ifcfg-eth0 # 192.168.102.x vi ifcfg-eth1 # 10.10.102.x vi ifcfg-eth3 # 129.133.52.x systemctl restart network ping -c 3 192.168.102.42 ping -c 3 10.10.102.42 # make internet connection for yum # iptables dnf install -y iptables-services vi /etc/sysconfig/iptables # add 'local allow' ports --dport 0:65535 systemctl start iptables # and enable iptables -L systemctl stop firewalld systemctl disable firewalld # eth3 for ctt2 or eth1 for n100-101 dnf install bind-utils dig google.com iptables -L # check! # Rocky8 # https://docs.fedoraproject.org/en-US/epel/#Quickstart dnf config-manager --set-enabled powertools dnf install epel-release dnf install netcdf netcdf-devel dnf install yum-utils # yumdownloader dnf install ddd dnf install grace dnf install gnuplot dnf install alpine # pico # other configs vi /etc/selinux/config # disabled, do not mistype, kernel will not boot! mv /home /usr/local/ vi /etc/passwd (exx, dockeruser $HOME) ## edit passwd, shadow, group, hosts files ## ## make -orig backups and stage in /home/tmp/global ## cottontail2 = greentail52 sections mkdir /sanscratch /home/localscratch chmod ugo+rwx /sanscratch /home/localscratch chmod o+t /sanscratch /home/localscratch # link localscratch in 1.4T /home to / mkdir /home cd /home # local dir ln -s /zfshomes/apps ln -s /zfshomes/tmp ln -s /zfshomes/csmith06 ln -s /zfshomes /share # fstab file mounts # cottontail2 = greentail52 # n100-n101 = n79 # postfix dnf install postfix dnf install mailx systemctl enable postfix echo "relayhost = 192.168.102.251" >> /etc/postfix/main.cf # on head node /etc/chronyc.conf allow 192.168.0.0/6 # compute nodes /etc/chronyc.conf #pool 2.pool.ntp.org iburst Server 192.168.102.250 Server 192.168.102.251 # check chronyc sources # on head node install from epel repo yum install slurm-openlava # error on conflicting libs, too bad! # add packages and update yum install epel-release -y yum install flex bison -y yum install tcl tcl-devel dmtcp -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 # amber 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 # CENTOS7 pick the kernel vendor used for now grep ^menuentry /etc/grub2.cfg grub2-set-default 1 ls -d /sys/firmware/efi && echo "EFI" || echo "Legacy" #grub2-mkconfig -o /boot/grub2/grub.cfg # legacy #grub2-mkconfig -o /boot/efi/EFI/centos/grub.cfg # efi # compute nodes old level 3 systemctl set-default multi-user.target # compute nodes only # leave old cuda versions behind (9.2 | 10.2) cd usr/local/ # scp fron n79:/usr/local/ amber16/ amber20/ fsl-5.0.10/ gromacs-2018/ lammps-22Aug18/ # compute nodes only /usr/local/bin/ # copy scripts: gpu-free, gpu-info, gpu-process # copy 10.10.102.89:/usr/local/bin/n37.openmpi.wrapper /usr/local/bin/ # done # FINISH native vanilla installs # R version 4.1.2 (2021-11-01) -- "Bird Hippie" yum install R R-devel # openjdk version "1.8.0_322" rpm -qa | grep ^java # check # python v 3.9 yum install python39 python39-devel # fftw 3.3.5-11.el8 yum install fftw fftw-devel #gnu scientific libraries yum install gsl gsl-devel # ruby 2.5.9-109.module+el8.5.0 yum install ruby ruby-devel # obabel chem file formats yum install openbabel openbabel-devel # dmtcp yum install dmtcp dmtcp-devel yum clean all # eth3 onboot=no, private networks only systemctl disable iptables reboot # now make it an ohpc compute node yum repolist yum install ohpc-base-compute scp cottontail2:/etc/resolv.conf /etc/resolv.conf yum install ohpc-slurm-client systemctl enable munge systemctl start munge scp cottontail2:/etc/munge/munge.key /etc/munge/munge.key echo SLURMD_OPTIONS="--conf-server 192.168.102.250" > /etc/sysconfig/slurmd yum install --allowerasing lmod-ohpc grep '/var' /etc/slurm/slurm.conf mkdir /var/log/slurm chown slurm:munge /var/log/slurm mkdir /var/spool/slurm chown slurm:munge /var/spool/slurm scp cottontail2:/etc/slurm/slurm.conf /etc/slurm/slurm.conf scp cottontail2:/etc/slurm/gres.conf /etc/slurm/gres.conf #test /usr/sbin/slurmd -D # start via rc.local chmod +x /etc/rc.d/rc.local #timing issue with munge sleep 15 /usr/sbin/slurmd # slurmd ??? libhwloc.so.15 => /opt/ohpc/pub/libs/hwloc/lib/libhwloc.so.15 (0x00007fd6e5684000) # add to zenoss edit /etc/snmp/snmpd.conf, enable and start rocommunity public dontLogTCPWrappersConnects yes