Sunrise.fjfi.cvut.cz

From NMS
Revision as of 23:31, 30 October 2017 by Vokacpet (Talk | contribs) (User software)

Jump to: navigation, search
Servery / Služby
Přístupné komukoliv
windows
srk
linux / unix
kmlinux
Omezený/individuální účet
linux / unix
bimbo · buon(KF) · km(KM) · lenochod(KJR) · linux · node(KM) · sunrise(KF) · unixlab(KFE) · vkstat(KM)
Služby
backup · DHCP · DNS · doména FJFI · eduroam · fileserver · IdM · forum · gitlab · lists · moodle · indico · mailgw · K4 · mailserver · NMS · openvpn · skolniftp · ssh · videokonference · VoIP · video · VPN · wififjfi · wiki · www
Učebny
e-sklipek · KFE unixlab · KFE pclab · PD1 · KM 105 · KM 115
Ostatní
Network · Blokované porty
[edit] · [view]

Základní informace (sunrise)

Správce 
Radek Novotný
HW 
~ 300 core cluster, 20TB storage
OS 
SLC6 (Scientific Linux CERN)
Využití 
cluster KF
Konto 
domluvit se správcem

Basic info & links

  • monitoring
  • services
    • NAT + DNS (for worker nodes)
    • Squid cache (CVMFS)
    • Apache (kickstart, yum repository, monitoring interfaces)
    • puppet (configuration management)
    • PBSPro server

(Re)Instalace worker nodů

Instalace

  • použít oficiální boot image SLC6 a nahrát na CD nebo flash
wget http://linuxsoft.cern.ch/cern/slc6X/x86_64/images/boot.iso
livecd-iso-to-disk boot.iso /dev/sd?1
# nahradit "?" písmenem zařízení odpovídající flash
  • nabootovat z CDROM/USB (na sunrise11-24 lze zobrazit boot menu po klávese F11)
  • přidat bootovací parametry pro instalaci, po stisku klávesy TAB doplnit (XX je číslo sunriseXX)
ks=http://192.168.20.1/ks.php?id=XX ksdevice=eth0 ip=192.168.20.1XX gateway=192.168.20.1 netmask=255.255.255.0 dns=147.32.9.4 ssh vnc
  • u worker nodů sunrise01-10 se při bootovaní z flash přehodí pořadí disků a je potřeba instalovat na sdb místo standardního prvního disku sda
ks=http://192.168.20.1/ks.php?id=XX&dev=sdb ...

Reinstall

  • před instalací (ale po zastavení puppetu) je potřeba odstranit aktuální certifikát z puppet serveru
puppet cert clean sunsetXX.kfcluster
  • z boot.iso vykopírovat vmlinuz a initramfs do /boot
  • do konfigurace grubu v /boot/grub/menu.lst přidat další záznam s výše uvedenými soubory
  • přidat parametry odpovídající bootovacím parametrům uvedeným v sekci Instalace
  • v principu by mělo stačit spustit níže uvedený skript (01 je potřeba nahradit číslem sunrise stroje):
XX=01
cd /boot
wget -O vmlinuz http://linuxsoft.cern.ch/cern/slc6X/x86_64/isolinux/vmlinuz
wget -O initrd.img http://linuxsoft.cern.ch/cern/slc6X/x86_64/isolinux/initrd.img
wget -O ks.cfg "http://192.168.20.1/ks.php?id=${XX}"

cat >> /boot/grub/menu.lst <<EOF
title Install
        root (hd0,0)
        kernel /vmlinuz ks=hd:/dev/sda1:/ks.cfg ksdevice=eth0 ip=192.168.20.1${XX} gateway=192.168.20.1 netmask=255.255.255.0 dns=147.32.9.4 ssh vnc
        initrd /initrd.img
EOF
  • pokud na puppet serveru nefunguje autosign, tak je potreba podepsat novy puppet certifikat
# vypsání nepodepsaných certifikátů (parametr --all vypíše všechny)
puppet cert list
# podepsání certifikátu
puppet cert sign sunsetXX.kfcluster

Konfigurace

Konfigurace worker nodů se provádí pomocí puppetu z ashley.fjfi.cvut.cz.

Creating puppet.git repository

# source scl_source enable git19
cd
git init --bare puppet.git
git clone ssh://root@ashley.fjfi.cvut.cz:/root/puppet.git
cd puppet
cp -a /etc/puppetlabs/code/environments/production/* 
rm -rf .git
git commit -m "Initial commit with basic configuration for puppet 4.10.1"
git branch -m master production
git push origin production
# create puppet.git/hooks/post-receive using code from
# https://puppet.com/blog/git-workflow-and-puppet-environments
# modify code to skip post-receive hook for branches with "tmp" prefix

Puppet configuration workflow

The layout of production directory is inspired by common profiles/roles/nodes abstraction layers described e.g. here.

Our puppet configuration is stored in GIT repository and automatically applied on puppet server after successful GIT push in main puppet.git repository. Don't directly modify files in `puppet config print environmentpath` subdirectories. You can create your own test environment directly on puppet server only if its name starts with "tmp" or "work" prefix. Branches from puppet.git with "tmp" prefix are excluded from automatic post-receive commit hook and they are not cloned in the puppet configuration environment.

  • on RHEL6 it is necessary to use SCL version of git 1.9
source scl_source enable git19
  • checkout current data from remote production branch
git clone -b production ssh://root@ashley.fjfi.cvut.cz:/root/puppet.git work_user
cd work_user
git checkout -b work_user
git config user.name "First Surename"
git config user.email "first.surename@fjfi.cvut.cz"
  • modify files in "work_user" directory and if you cloned these files in puppet environment directory /etc/puppetlabs/code/environments you can test updated configuration
puppet apply --environment=work_user --test --debug
  • when you are happy with updated configuration merge modification in "production" branch and commit to master repository
git commit -m "summary info for modifications" file1 file2 ...
git checkout production
git pull
git checkout work_user
git rebase production
git checkout production
git merge work_user
git push

Monitoring puppet

Monitoring web interfaces listen only on localhost, you have to tunnel local ports from ashley.fjfi.cvut.cz to you machine before you are able to see provided data

ssh -L 1080:127.0.0.1:1080 -L 8080:127.0.0.1:8080 ashley.fjfi.cvut.cz

Batch

Currently this cluster is using PBSPro as a batch system.

  • show queue configuration
qstat -Q -f
qmgr -c 'p s'
  • set worker node online/offline
pbsnodes -o sunriseXX-0
pbsnodes -r sunriseXX-0

Squid (CVMFS)

Machines located at FNSPE should used for CVMFS our local squid proxy and as a backup it is also possible (allowed) to utilize FZU proxy. CVMFS configuration in /etc/cvmfs/default.local should contain:

CVMFS_HTTP_PROXY="http://squid.fjfi.cvut.cz:3128;http://squid.farm.particle.cz:3128;DIRECT"

For KF cluster worker nodes it is now better to use Squid cache directly from headnode

CVMFS_HTTP_PROXY="http://ashley.fjfi.cvut.cz:3128;http://squid.farm.particle.cz:3128;DIRECT"

User software

Intel compiler

# setup environment for Intel compiler
source /fjfi/apps/intel/Compiler/11.0/074/bin/ifortvars.sh intel64
# Hello World příklad kompilovaný pomocí Intel Fortran Compileru
cat > hello.f <<EOF
        program hello
           print *, "Hello World!"
        end program hello
EOF
ifortbin hello.f
./a.out

LCG Software Elements

One can also use software provided by LCG. To list availabe software you can use:

export LCGENV_PATH=/cvmfs/sft.cern.ch/lcg/releases
export PATH=/cvmfs/sft.cern.ch/lcg/releases/lcgenv/latest:${PATH}
lcgenv
lcgenv x86_64-slc6-gcc62-opt
lcgenv -p LCG_latest
lcgenv -p LCG_latest x86_64-slc6-gcc62-opt

E.g. if you need ROOT 6.08.06 with all dependencies (Boost, python, ...) use

export LCGENV_PATH=/cvmfs/sft.cern.ch/lcg/releases
export PATH=/cvmfs/sft.cern.ch/lcg/releases/lcgenv/latest:${PATH}
eval "`lcgenv -p LCG_88 x86_64-slc6-gcc49-opt ROOT`"

For most recent version use

export LCGENV_PATH=/cvmfs/sft.cern.ch/lcg/releases
export PATH=/cvmfs/sft.cern.ch/lcg/releases/lcgenv/latest:${PATH}
eval "`lcgenv x86_64-slc6-gcc62-opt all`"
eval "`lcgenv -p LCG_latest x86_64-slc6-gcc62-opt ROOT`"

Singularity containers

To run application in a completely different environment for your application you can use singularity containers. Use official documentation for information how to use singularity containers. Running shell from different distribution can be as simple as

# preview of official ATLAS SLC6 image
singularity shell --bind /cvmfs /cvmfs/atlas.cern.ch/repo/images/singularity/x86_64-slc6.img
# preview of official ATLAS CC7 image
singularity shell --bind /cvmfs /cvmfs/atlas.cern.ch/repo/images/singularity/x86_64-centos7.img

# test SL6 OSG image
singularity shell --bind /cvmfs /cvmfs/singularity.opensciencegrid.org/opensciencegrid/osg-3.3-wn-el6:latest
# test SL7 OSG image
singularity shell --bind /cvmfs /cvmfs/singularity.opensciencegrid.org/opensciencegrid/osg-3.3-wn-el7:latest