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cluster:213 [2022/03/16 13:27]
hmeij07 		cluster:213 [2023/02/08 14:31]
hmeij07
Line 42: Line 42:
 scp 10.10.102.253:/root/.ssh/authorized_keys /root/.ssh/ scp 10.10.102.253:/root/.ssh/authorized_keys /root/.ssh/
 /etc/ssh/sshd_config (PermitRootLogin) /etc/ssh/sshd_config (PermitRootLogin)
 +
 +# Put the warewulf cluster key in authorized_keys
 +# Put eth0 fingerprints in cottontail/greentail52 known hosts
 +# add to relevant known_hosts_servername file
  
 # configure private subnets and ping file server # configure private subnets and ping file server
Line 53: Line 57:
  
 # make internet connection for yum # make internet connection for yum
-# eth3 for ctt2 or eth1 for n100-101 
-dnf install bind-utils 
-dig google.com 
- 
-#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 
  
 # iptables # iptables
Line 76: Line 66:
 systemctl stop firewalld systemctl stop firewalld
 systemctl disable firewalld systemctl disable firewalld
 +
 +
 +# eth3 for ctt2 or eth1 for n100-101
 +dnf install bind-utils
 +dig google.com
 +iptables -L # check!
 +
 +
  
 # other configs # other configs
 vi /etc/selinux/config # disabled, do not mistype, kernel will not boot! vi /etc/selinux/config # disabled, do not mistype, kernel will not boot!
 mv /home /usr/local/ mv /home /usr/local/
 +cd /;ln -s /usr/local/home 
 +cd /; ln -s /home /share
 vi /etc/passwd (exx, dockeruser $HOME) vi /etc/passwd (exx, dockeruser $HOME)
  
-## edit passwd, shadow, group, hosts files ## 
-## make -orig backups and stage in /home/tmp/global 
-## cottontail2 = greentail52 sections 
  
 +#exx96
 mkdir /sanscratch /home/localscratch mkdir /sanscratch /home/localscratch
 chmod ugo+rwx /sanscratch /home/localscratch chmod ugo+rwx /sanscratch /home/localscratch
 chmod o+t /sanscratch /home/localscratch  chmod o+t /sanscratch /home/localscratch 
 +# exx96
 # link localscratch in 1.4T /home to / # link localscratch in 1.4T /home to /
-mkdir /home  + 
-cd /home # local dir+cd /home 
 ln -s /zfshomes/apps ln -s /zfshomes/apps
 ln -s /zfshomes/tmp ln -s /zfshomes/tmp
 ln -s /zfshomes/csmith06 ln -s /zfshomes/csmith06
-ln -s /zfshomes /share+ 
 +cat /sanscratch/tmp/fstab.tmp >> /etc/fstab; mkdir /astrostore; mount -a; df -h; cd /smithlab/;  ln -s /smithlab/home/opt/rhel08 opt; ls -l
  
 # fstab file mounts # fstab file mounts
 +mkdir -p /zfshomes /home66 /home33 /mindstore /opt/ohpc/pub /opt/intel
 # cottontail2 = greentail52 # cottontail2 = greentail52
 # n100-n101 = n79 # 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 192.168.0.0/16
 # compute nodes /etc/chronyc.conf # compute nodes /etc/chronyc.conf
 #pool 2.pool.ntp.org iburst #pool 2.pool.ntp.org iburst
 Server 192.168.102.250 Server 192.168.102.250
 Server 192.168.102.251 Server 192.168.102.251
 +# check
 +chronyc sources
 +
 +# 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
 +yum groupinstall "Server" # server for compute nodes "Server with GUI"
 +
 +
 +# on head node install from epel repo
 +### yum install slurm-openlava
 +# error on conflicting libs, too bad!
  
  
Line 125: Line 142:
 yum install cmake -y yum install cmake -y
 yum install libjpeg libjpeg-devel libjpeg-turbo-devel -y yum install libjpeg libjpeg-devel libjpeg-turbo-devel -y
-# amber+ 
 +#easybuild 
 +yum install libibverbs libibverbs-devel 
 + 
 +# amber20 cmake readline error fix needs 
 +yum install ncurses-c++-libs-6.1-9.20180224.el8.x86_64.rpm \ 
 +            ncurses-devel-6.1-9.20180224.el8.x86_64.rpm \ 
 +            readline-devel-7.0-10.el8.x86_64.rpm 
 + 
 +# amber20
 yum -y install tcsh make \ yum -y install tcsh make \
                gcc gcc-gfortran gcc-c++ \                gcc gcc-gfortran gcc-c++ \
Line 132: Line 158:
                perl perl-ExtUtils-MakeMaker util-linux wget \                perl perl-ExtUtils-MakeMaker util-linux wget \
                bzip2 bzip2-devel zlib-devel tar                 bzip2 bzip2-devel zlib-devel tar 
-yum update -y 
-yum clean all 
  
 # CENTOS7 pick the kernel vendor used for now # CENTOS7 pick the kernel vendor used for now
Line 144: Line 168:
 # compute nodes old level 3 # compute nodes old level 3
 systemctl set-default multi-user.target systemctl set-default multi-user.target
-# remove internet, bring private back up + 
-reboot+ 
 +# postfix 
 +dnf install postfix 
 +dnf install mailx 
 +systemctl enable postfix 
 +echo "relayhost = 192.168.102.251" >> /etc/postfix/main.cf 
 + 
 +yum install net-snmp-utils net-snmp-libs net-snmp net-snmp-agent-libs 
 + 
 +# edit /etc/snmp/snmpd.conf, enable and start 
 +rocommunity public 
 +dontLogTCPWrappersConnects yes 
 +# enable, start, add to zenoss  
  
 # compute nodes only # compute nodes only
Line 163: Line 200:
 # openjdk version "1.8.0_322" # openjdk version "1.8.0_322"
 rpm -qa | grep ^java  # check rpm -qa | grep ^java  # check
 +yum install java-1.8.0-openjdk java-1.8.0-openjdk-devel \
 +java-1.8.0-openjdk-headless javapackages-filesystem
 # python v 3.9 # python v 3.9
 yum install python39 python39-devel 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
Line 175: Line 215:
 # dmtcp # dmtcp
 yum install dmtcp dmtcp-devel yum install dmtcp dmtcp-devel
 +
 +
  
 yum clean all yum clean all
 +# eth3 onboot=no, private networks only
 +systemctl disable iptables
 reboot reboot
 +
 +# now make it an ohpc compute node
 +  yum repolist
 +  yum install singularity-ohpc
 +  yum  install ohpc-base-compute --nobest
 +  
 +  scp cottontail2:/etc/resolv.conf /etc/resolv.conf
 +  yum  install ohpc-slurm-client
 +  # check status of service munge
 +  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
 +  scp cottontail2:/etc/profile.d/lmod.sh /etc/profile.d/
 +  
 +# /etc/bashrc add
 +# ohpc lmod gcc mpicc
 +export PATH=/usr/local/slurm/bin:$PATH
 +export LD_LIBRARY_PATH=/usr/local/slurm/lib:$LD_LIBRARY_PATH
 +
 +  
 +# /var/[log|spool|run] need to be removed from
 +/usr/libexec/warewulf/wwmkchroot/gold-template
 +
 +#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
 +
 +
 +## edit passwd, shadow, group, hosts files ##
 +## make -orig backups and stage in /home/tmp/global
 +## cottontail2 = greentail52 sections
 +
 +  
 +# slurmd ???
 + libhwloc.so.15 => /opt/ohpc/pub/libs/hwloc/lib/libhwloc.so.15 (0x00007fd6e5684000)
 +
  
  
 </code> </code>
-==== Configure Recipe ==== 
  
-Steps. "Ala n37" ... so the RTX nodes are similar to the K20 nodes and we can put the local software in place. See [[cluster:172|K20 Redo]] page and [[cluster:192|exx96]] Recipe for CentOS 7+==== Pics ====
  
-New recipe for n100-n101 sporting Rocky 8.5 on ''cottontail2''\\ 
-Put node on internet...first though 
  
-  * ** Vanilla Backups** using Warewulf and plain rsync (--exclude=[proc/,sys/,run/]+My data center robot thingie and node n100's gpus\\ 
 + 
 +\\ 
 + 
 +{{:cluster:dcrobot.jpg?400|}} 
 +\\ 
 +{{:cluster:n100.jpg?400|}}\\ 
 +\\ 
 + 
 +==== Amber20 ==== 
 + 
 +OpenHPC
  
 <code> <code>
  
-# login as root check some things out... +# First **all the necessary packages ** (yum install...)
-free -g +
-nvidia-smi # if gpus +
-cat /proc/cpuinfo+
  
-# check and set local time zone + 988  tar xvfj ../AmberTools21.tar.bz2  
-mv /etc/localtime /etc/localtime.backup +  989  tar xvfj ../Amber20.tar.bz2  
-ln -s /usr/share/zoneinfo/America/New_York /etc/localtime+  993  cd amber20_src/ 
 +  994  cd build/ 
 +  996  vi run_cmake
  
-# change passwords for root and vendor account +#  Assume this is Linux:
-passwd +
-passwd microway +
-# set hostname +
-hostnamectl set-hostname cottontail2+
  
-# root: sync cottontail's master and known_hosts (tails+stores) +# serial, do on head node, with miniconda true, compile, install 
-ssh-keygen -t rsa +  cmake $AMBER_PREFIX/amber20_src \ 
-scp 10.10.102.253:/root/.ssh/authorized_keys /root/.ssh/ +    -DCMAKE_INSTALL_PREFIX=/share/apps/CENTOS8/ohpc/software/amber/20 \ 
-/etc/ssh/sshd_config (PermitRootLogin)+    -DCOMPILER=GNU  \ 
 +    -DMPI=FALSE -DCUDA=FALSE -DINSTALL_TESTS=TRUE \ 
 +    -DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE \ 
 +    2>&1 | tee  cmake.log
  
-# configure private subnets and ping file server +# Env
-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 +[hmeij@n100 ~]$ module load cuda/11.6
-# eth3 for ctt2 or eth1 for n100-101 +
-dnf install bind-utils +
-dig google.com+
  
-#rocky8 +[hmeij@n100 ~]$ echo $CUDA_HOME 
-# https://docs.fedoraproject.org/en-US/epel/#Quickstart +/usr/local/cuda
-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+
  
-# iptables +[hmeij@n100 ~]$ which nvcc mpicc gcc 
-dnf install -y iptables-services +/usr/local/cuda/bin/nvcc 
-vi /etc/sysconfig/iptables +/opt/ohpc/pub/mpi/openmpi4-gnu9/4.1.1/bin/mpicc 
-# add 'local allow' ports  --dport 0:65535 +/opt/ohpc/pub/compiler/gcc/9.4.0/bin/gcc
-systemctl start iptables # and enable +
-iptables -L +
-systemctl stop firewalld +
-systemctl disable firewalld+
  
-# other configs +# [FIXED} cmake error on conda install, set to FALSE 
-vi /etc/selinux/config # disabled, do not mistype, kernel will not boot! +# OS native python, install on n[100-101] 
-mv /home /usr/local/ +-- Python version 3.9 -- OK 
-vi /etc/passwd (exx, dockeruser $HOME)+-- Found PythonLibs: /usr/lib64/libpython3.9.so (found version "3.9.6")  
 +-- Checking for Python package numpy -- not found 
 +-- Checking for Python package scipy -- not found 
 +-- Checking for Python package matplotlib -- not found 
 +-- Checking for Python package setuptools -- found 
 +[END FIXED]
  
-## edit passwd, shadow, group, hosts files ## +# mpi & cuda FALSE builds serial 
-## make -orig backups and stage in /home/tmp/global +./run_cmake 
-## cottontail2 = greentail52 sections+make install 
 +# lots and lots of warnings
  
-mkdir /sanscratch /home/localscratch +# then 
-chmod ugo+rwx /sanscratch /home/localscratch +source /share/apps/CENTOS8/ohpc/software/amber/20/amber.sh
-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 +# on n100 now, parallel, set miniconda flags to FALSE 
-# cottontail2 = greentail52 +-MPI=TRUE 
-# n100-n101 = n79+./run_cmake 
 +make install
  
-# postfix +# on n100 just change cuda flag 
-dnf install postfix +-CUDA=TRUE 
-dnf install mailx +./run_cmake 
-systemctl enable postfix +make install
-echo "relayhost = 192.168.102.42" >> /etc/postfix/main.cf+
  
-# compute nodes /etc/chronyc.conf +#tests 
-#pool 2.pool.ntp.org iburst +cd $AMBERHOME 
-Server 192.168.102.250 +make test.serial 
-Server 192.168.102.251+export DO_PARALLEL="mpirun -np 6" 
 +make test.parallel 
 +export CUDA_VISIBLE_DEVICES=0 
 +make test.cuda.serial 
 +make test.cuda.parallel
  
 +</code>
  
-# add packages and update +==== Amber22 ====
-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  +
-yum update -y +
-yum clean all+
  
-# CENTOS7 pick the kernel vendor used for now +OpenHPC
-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 +<code>
-systemctl set-default multi-user.target +
-# remove internet, bring private back up +
-reboot+
  
-# compute nodes only +# First **all the necessary packages ** (yum install...)
-# 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/ + 988  tar xvfj ../AmberTools22.tar.bz2  
-# copy scripts: gpu-free, gpu-info, gpu-process +  989  tar xvfj ../Amber22.tar.bz2  
-# copy 10.10.102.89:/usr/local/bin/n37.openmpi.wrapper /usr/local/bin/ +  993  cd amber20_src/ 
-# done+  994  cd build/ 
 +  996  vi run_cmake
  
-# FINISH native vanilla installs +#  Assume this is Linux:
-# 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 +# serial, do on head node, with miniconda true, compile, install 
-reboot+  cmake $AMBER_PREFIX/amber22_src \ 
 +    -DCMAKE_INSTALL_PREFIX=/share/apps/CENTOS8/ohpc/software/amber/22 \ 
 +    -DCOMPILER=GNU  \ 
 +    -DMPI=FALSE -DCUDA=FALSE -DINSTALL_TESTS=TRUE \ 
 +    -DDOWNLOAD_MINICONDA=TRUE \ 
 +    2>&1 | tee  cmake.log 
 +./run_cmake 
 +make install
  
 +
 +# Note !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 +The OpenMPI and MPICH system installations provided by CentOS 
 +(i.e., through yum install) 
 +are known to be somehow incompatible with Amber22.
 +# OUCH !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 +
 +
 +# GO TO node n100
 +
 +# copy head node's amber22_src/ to n100:/usr/local/src/tmp/
 +
 +
 +source /share/apps/CENTOS8/ohpc/software/amber/22/amber.sh
 +echo $AMBERHOME
 +
 +# install latest openmpi version
 +cd amber_src/Ambertools/src
 +tar xvfj ../../../../openmpi-4.1.4.tar.bz2 
 +
 +./configure_openmpi gnu # openhpc gcc/gfortran 
 +
 +
 +# on n100 now, parallel, set 
 +-MPI=TRUE
 +-DDOWNLOAD_MINICONDA=FALSE
 +./run_cmake
 +make install
 +
 +# on n100 just change cuda flag
 +
 +[hmeij@n100 build]$ module load cuda/11.6
 +[hmeij@n100 build]$ which gcc mpicc nvcc
 +/opt/ohpc/pub/compiler/gcc/9.4.0/bin/gcc
 +/share/apps/CENTOS8/ohpc/software/amber/22/bin/mpicc
 +/usr/local/cuda/bin/nvcc
 +[hmeij@n100 ~]$ echo $CUDA_HOME
 +/usr/local/cuda
 +
 +-MPI=TRUE
 +-CUDA=TRUE
 +-DDOWNLOAD_MINICONDA=FALSE
 +./run_cmake
 +make install
 +
 +
 +[hmeij@n100 ~]$ which nvcc mpicc gcc
 +/usr/local/cuda/bin/nvcc
 +/opt/ohpc/pub/mpi/openmpi4-gnu9/4.1.1/bin/mpicc
 +/opt/ohpc/pub/compiler/gcc/9.4.0/bin/gcc
 +
 +#tests
 +cd $AMBERHOME
 +make test.serial
 +export DO_PARALLEL="mpirun -np 6"
 +make test.parallel
 +export CUDA_VISIBLE_DEVICES=0
 +make test.cuda.serial
 +make test.cuda.parallel
  
 </code> </code>
  
-==== Pics ==== 
  
- 
-\\ 
 **[[cluster:0|Back]]** **[[cluster:0|Back]]**
  
cluster/213.txt · Last modified: 2024/01/12 15:09 by hmeij07

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